Game over for antievolutionary No Free Lunch argument

Posted 4 December 2015 by

This has been obvious from the start, but as far as I know it has taken 10 years for the ID guys to finally admit it. Winston Ewert writes at the Discovery Institute blog:
However, Felsenstein and English note that a more realistic model of evolution wouldn't have a random fitness landscape. Felsenstein, in particular, argues that "the ordinary laws of physics, with their weakness of long-range interactions, lead to fitness surfaces much smoother than white-noise fitness surfaces." I agree that weak long-range interactions should produce a fitness landscape somewhat smoother than random chance and this fitness landscape would thus be a source of some active information.
GAME OVER, MAN. GAME OVER! The whole point of Dembski et al. invoking "No Free Lunch" theorems was to argue that, if evolutionary searches worked, it meant the fitness function must be designed, because (logical jump herein) the No Free Lunch theorems showed that evolutionary searches worked no better than chance, when averaged over all possible fitness landscapes. Emergency backup arguments to avoid admitting complete bankruptcy below the fold, just so I'm not accused of leaving out the context.
We disagree in that I do not think that is going to be a sufficient source of active information to account for biology. I do not have a proof of this. But neither does Felsenstein have a demonstration that it will produce sufficient active information. What I do have is the observation of existing models of evolution. The smoothness present in those models does not derive from some notion of weak long-range physics, but rather from telelogy as explored in my various papers on them.
As always, the ID objections to evolution, when stripped of pseudo-technical camouflage, boil down to "I just don't buy it because (gut feeling)." See also: recent PT posts and Jason Rosenhouse at EvolutionBlog.

254 Comments

Mike Elzinga · 5 December 2015

Ewert says:

"The smoothness present in those models does not derive from some notion of weak long-range physics, but rather from telelogy as explored in my various papers on them."

Total bunk. Go back to high school and learn some chemistry and physics for Pete's sake. Teleology is an anthropomorphic metaphor. There is no real teleology in chemistry and physics; and they still get the job done.

DS · 5 December 2015

Well, considering all of the evidence that evolution has indeed occurred and the complete lack of evidence for any intelligent designer, the burden of proof is on those who would claim that evolution is impossible. And having failed to demonstrate this, they cannot now decline the burden, simply because of pig headedness. As usual, they probably don't even realize just how devastating this latest admission is. Man, no wonder Dembski decided to call it quits. Even he must now realize that he never had anything at all convincing. Way to go Joe!

Kevin · 5 December 2015

You know this comment is very interesting
The smoothness present in those models does not derive from some notion of weak long-range physics, but rather from telelogy as explored in my various papers on them.
Thus is easily shown. There are many experiments that one could look at, determine the smoothness of the fitness landscape of the reality rather than the model. Lenski's work comes to mind as an example. Joyce's Darwinian evolution on a chip could be used too. Especially since the latter is beyond, I think, what Behe would consider possible (4 mutation families, with multiple mutations in each family... in 72 hours). So why doesn't one of the experts at ID Central take this on? Oh yeah, they don't do science...I forget... carry on.

TomS · 5 December 2015

DS said: Well, considering all of the evidence that evolution has indeed occurred and the complete lack of evidence for any intelligent designer, the burden of proof is on those who would claim that evolution is impossible. And having failed to demonstrate this, they cannot now decline the burden, simply because of pig headedness. As usual, they probably don't even realize just how devastating this latest admission is. Man, no wonder Dembski decided to call it quits. Even he must now realize that he never had anything at all convincing. Way to go Joe!
It's worse than that. They have, from the beginning, declined the burden of describing an alternative. "Intelligent Design" are empty words. All they have to offer is, there has to be a better explanation than one involving natural processes like evolution. Political revolutions can proceed without offering an alternative to the present condition, but has there ever been a scientific development like that? What they have been offering is, at best, a demonstration that a particular mathematical model does not describe the physical reality. However convincing one may think that model may be, the rational response ought to be that there is something wrong with the model. It reminds one of the "urban legend" of the engineer who demonstrated that bees can't fly.

stevaroni · 5 December 2015

Kevin said: Thus is easily shown. There are many experiments that one could look at, determine the smoothness of the fitness landscape of the reality rather than the model.
This is, of course, the nub of the thing. ID insists on arguing mathematical model of the fitness landscape, and, of course, there are various issues that muddy the theoretical waters and make getting a precise number difficult, which is exactly what they want. But in reality this is not something you need to rely on theoretically models for. You can step outside and actually measure it. It's like the old tale about how all the aerodynamic models show that bumblebees can't fly. Reasonable people would look at that and understand that the models are wrong because all the evidence shows that bumblebees are, in fact, airworthy. The DI looks at the model and argues that bumblebees don't exist.

Mike Elzinga · 5 December 2015

stevaroni said: Reasonable people would look at that and understand that the models are wrong because all the evidence shows that bumblebees are, in fact, airworthy. The DI looks at the model and argues that bumblebees don't exist.
Well, ID/creationism is, at its core, sectarian presuppositional apologetics; dogma first, all else bent and broken to fit. If the scientific facts don't fit the "model," the science is wrong. They actually say this in so many, many, many words; and the words are meant to cover up the rather obvious inadequacies of the "mathematical model."

Just Bob · 5 December 2015

stevaroni said: The DI looks at the model and argues that bumblebees don't exist.
It's more like they argue that FLIGHT itself can't happen.

Joe Felsenstein · 5 December 2015

Thanks, Nick (and thanks, DS). I hope to post a more specific reply to Ewert's recent ENV posts here in the next few days.

The whole point of Dembski's Complex Specified Information argument, and his No Free Lunch argument, and the more recent Search For a Search argument, was to present some math that showed that evolution could not lead to the good adaptations that we see, or that it could only if there was a Design Intervention. And the whole point of our refutations was that the math did not work to establish that there is some such barrier.

It was they who were presenting an impossibility proof (or an extreme improbability proof).

Now suddenly, in Winston Ewert's hands, the argument is about something else. It seems that the burden was on us. It was not good enough to show that evolutionary forces such as natural selection were in principle capable of doing the job. It was not good enough to show that there was no mathematical argument preventing that.

No, apparently, according to Ewert, we have to demonstrate that all these adaptations, in all these species, can actually be achieved.

A brief reading of anything by Dembski or Ewert will make it clear that they did in fact intend to present an impossibility-or-extreme-improbability proof. And they just haven't got one.

DS · 5 December 2015

Well that's pretty typical. They didn't really understand their argument and so, inadvertently destroyed it. And they did this without realizing that they had in fact given up the one critical point. So to review, all Dembski has proven is that evolution will not work given completely unrealistic assumptions about fitness landscapes. What he has not provided is:

1) Evidence that evolution cannot work in the real world

2) Evidence that evolution has not worked in the real world

3) Any alternative explanation for how all of the adaptations occurred (except some vague mumbo jumbo about how god is somehow still required don't ya just know it)

And this after twenty years of mathematical obfuscation.

It's a little late to be shifting the burden of proof now guys. Why should we have to show that something is theoretically possible when we have evidence that it did in fact already occur? Why should we have to explain anything, unless and until they address all of the available evidence first? I say, stick Dembski's face in the chromosome data. Make him come up with an explanation that is better than descent with modification. Make him admit to common descent of humans. Then even die hard dead heads like Floyd won't have a leg left to stand on.

Patrick · 5 December 2015

Won't they just now claim this proves the physics is designed?

Ravi · 5 December 2015

Joe Felsenstein said: A brief reading of anything by Dembski or Ewert will make it clear that they did in fact intend to present an impossibility-or-extreme-improbability proof. And they just haven't got one.
Neither you, nor Dembski, have a background in either physics or biochemistry so why are you pretending to claim something for which you have no knowledge of whatsoever?
"Felsenstein, in particular, argues that the ordinary laws of physics, with their weakness of long-range interactions, lead to fitness surfaces much smoother than white-noise fitness surfaces.”
Really? And what experimental evidence do you have to make such an assertion?

Ravi · 5 December 2015

From the blog: http://www.evolutionnews.org/2015/12/the_guc_bug101391.html
"Darwinian evolution has to account for finding rare protein folds and complex functional systems."
What do Felsenstein and English have to say about natural selection, by way of random exploration, finding extremely improbable protein folds (out of a near infinite number of amino acid sequence combinations)? Obfuscating the subject with math can't overcome the formidable biophysical/chemical problem at hand.

Doc Bill · 5 December 2015

I figured I might as well correct Ewert's statement:

"The smoothness present in those models does not derive from some notion of weak long-range physics, but rather from magic as explored in my various papers on them."

-W. Ewert, Baylor aka Texas Hogwarts

Mike Elzinga · 5 December 2015

Ravi said: From the blog: http://www.evolutionnews.org/2015/12/the_guc_bug101391.html
"Darwinian evolution has to account for finding rare protein folds and complex functional systems."
What do Felsenstein and English have to say about natural selection, by way of random exploration, finding extremely improbable protein folds (out of a near infinite number of amino acid sequence combinations)? Obfuscating the subject with math can't overcome the formidable biophysical/chemical problem at hand.
Where did you get the idea that the laws of physics and chemistry have to proceed according to the dictates of ID/creationism? ID/creationism is a pseudoscience that gets everything about the universe dead wrong; so of course ID/creationists can only see an insurmountable problem of their own making. Real scientists know otherwise because they have learned things that ID/creationists skipped over or distorted to comport with their presuppositional sectarian dogma. Why don't you check out the 2013 Nobel Prize in chemistry and explain to us why Dembski, Ewert, and Marks didn't win the Nobel instead of those real scientists who actually know what they are doing?

Nick Matzke · 5 December 2015

Ravi said: From the blog: http://www.evolutionnews.org/2015/12/the_guc_bug101391.html
"Darwinian evolution has to account for finding rare protein folds and complex functional systems."
What do Felsenstein and English have to say about natural selection, by way of random exploration, finding extremely improbable protein folds (out of a near infinite number of amino acid sequence combinations)? Obfuscating the subject with math can't overcome the formidable biophysical/chemical problem at hand.
Protein folds are the emergency backup-backup-backup argument after claims about specified complexity, "evolution can't produce new information", "evolution can't produce new genes", etc., have been debunked and tacitly abandoned. Most protein folds are very widespread (shared not just among animals but across eukaryotes and often prokaryotes also) so their origins must be very ancient -- the argument that Meyer, Luskin etc. have been making lately, which is that a whole bunch of new protein folds had to originate in the Cambrian Explosion, is just ignorant crazypants. So the origin of protein folds will typically be rarer and more ancient than almost anything short of the origin of life itself, and thus harder to study. But all that said, there is nevertheless a lot that can be said. In fact, there are known cases where tiny amounts of mutation can convert one protein fold into another one. Look up: Nick Grishin. https://scholar.google.com.au/scholar?q=Nick+Grishin%2C+protein+folds&btnG=&hl=en&as_sdt=0%2C5 Michael Buratovich (2015). Leaving the Fold. "Darwin's Doubt and the Evolution of Protein Folds." Reports of the National Center for Science Education Vol 35, No 5 (2015) http://reports.ncse.com/index.php/rncse/article/view/379/751

Scott F · 5 December 2015

I don't understand why protein folds are considered "hard".

See P.Z.Myer's recent post on the subject.

Sure, proteins can fold in an almost infinite number of ways. Sure, figuring out the sequence for a given folding pattern (shall we say, a "specified" pattern) is an NP-hard problem, computationally. But, the proteins aren't "computing" anything, and there is no specific "target". Proteins are going to fold in some way, no matter what. Once you have a mechanism that folds a protein, if that folded configuration is useful, and if the "mechanism" is heritable, then "Evolution".

My mental image is that sequences of amino acids are like building blocks; strange shaped building blocks to be sure: some curlicues, some funny ribbons, and the like, but building blocks none the less. The mechanism of the cell takes these building blocks and builds interesting three-dimensional objects out of them (i.e. folded proteins). If the blocks don't fit together, or if the resulting three-dimensional object isn't "useful" (in some sense), then the cell (over time or over generations) will stop making those proteins, and will make something else.

Sure, the protein-folding "space" that can be "explored" is huge, but there are lots of bacteria doing the "exploring". Wiki has an estimate of the number of bacteria in the world of 6x1030. If each cell folds one protein every second, in 3 billion years that's ~1046 operations, where each operation could be considered a "computation".

Yeah, the DI folks keep talking about really big scary probabilities. Even if you ignore contingency and take their simplistic probabilities at face value, they keep ignoring the really, really big numbers of cells cranking away on these "problems" in parallel, making the probability of finding something that is "useful" to be almost a certainty in very short order.

Why is this "search" considered "hard"?

Scott F · 5 December 2015

Oh, and "building blocks". Once the cell has "learned" how to fold a particular set of amino acids into a curlicue (for example), it doesn't have to figure out that whole sequence again for the next protein, or the next. In fact, once it's figured out how to fold a sequence of amino acids into a single helical loop (like a locking washer), the cell doesn't have to figure it out again, just to make the curlicue longer. It just repeats the pattern "X" times. That's the "contingency" part, which the DI completely ignores when it uses the simplistic probability computations of "random" events.

(In the following, I'm totally mangling the words, particularly of "probability", but I'm no expert, no biologist, chemist, or mathematician. So sue me. I'm just trying to get the gist right, using those "big number" that the DI is so fond of)

Let's say (for example) that a single coil in a curlicue requires 10 amino acids. (I have no idea what a "curlicue" is, but such a pattern keeps showing in the simple stick pictures that I see of folded proteins. It looks like a corkscrew or "curlicue", so that's what I'm calling it. Given how common it seems to be, I'm sure there's a name for it.) Let's say you have a coil that is 10 loops long, for a total length of 100 amino acids. If the raw probability of combining each amino acid is "X", then the probability of randomly combining those 100 amino acids together would be X100, which is prohibitively large, no matter what the base "X" is. It's a big, scary, Intelligently Designed number.

But building the curlicue isn't "random" at all. Let's say that the first loop of ten amino acids was built "randomly", requiring X10 "steps" of some sort. (Even that's not very big. 210 is just 1,024, which isn't that big.) But the next loop isn't random at all. It's just repeating the first loop, giving X10*X, or X11. For the total 100 amino acid chain, the total "probability" reduces from X100 down to just X19, which is a much more manageable number.

Building blocks simply aren't "random". Any kid with a set of Lego bricks can tell you that.

Ravi · 6 December 2015

Nick Matzke said: Protein folds are the emergency backup-backup-backup argument after claims about specified complexity, "evolution can't produce new information", "evolution can't produce new genes", etc., have been debunked and tacitly abandoned. Most protein folds are very widespread (shared not just among animals but across eukaryotes and often prokaryotes also) so their origins must be very ancient -- the argument that Meyer, Luskin etc. have been making lately, which is that a whole bunch of new protein folds had to originate in the Cambrian Explosion, is just ignorant crazypants.
The issue of how biologically useful protein folds arise is absolutely fundamental. And it is Douglas Axe and Mike Behe, not Stephen Meyer and Casey Luskin, who have the most to say about protein folds because they have written extensively about the enigma: Estimating the prevalence of protein sequences adopting functional enzyme folds:http://www.ncbi.nlm.nih.gov/pubmed/15321723
"Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences."
So the origin of protein folds will typically be rarer and more ancient than almost anything short of the origin of life itself, and thus harder to study. But all that said, there is nevertheless a lot that can be said. In fact, there are known cases where tiny amounts of mutation can convert one protein fold into another one.
According to evolutionary theory, many important genes, like hox genes with the distinctive helix-turn-helix homeodomain, did arise close to the Cambrian period. So Meyer is right to point this out. But let me ask, again, how is Felsenstein - a theoretical population geneticist and bioinformatician - capable of commenting on the biophysics of protein function and structure? Has he published any research on the subject?

Ravi · 6 December 2015

Scott F said: Why is this "search" considered "hard"?
Because it is blind. The independently foliding homeodomain, for example, contains 60 amino acid residues. The number of possible amino acid combinations for a sequence of that length is 1.153 * 10^78. That is roughly the number of electrons in the entire universe! Now, the homeodomain sequence is variable, of course, but only up to a point. The chance of a random search finding such a sequence is effectively zero. Natural selection only works if there is something useful to select. Assuming a smooth fitness landscape, with incremental steps along the way, is just nonsense.

Tom English · 6 December 2015

Ewert writes:
We disagree in that I do not think that is going to be a sufficient source of active information to account for biology. I do not have a proof of this. But neither does Felsenstein have a demonstration that it will produce sufficient active information.
Proof? He's reduced to using "active information" as a rhetorical device, invoking the notion nebulously when it suits him, and deep-sixing measurements that explode his dogma. In the first of his ENV responses, "These Critics of Intelligent Design Agree with Us More Than They Seem to Realize," to the PT post by Joe Felsenstein and me, he entirely ignored the GUC Bug model. I called him down for that in "The Law of Conservation of Information Is Defunct." So now he addresses the GUC Bug ad hoc, and ignores the highlight of our post, a lower bound on the active information of the evolutionary process with respect to the fittest genotype. He abandons not only active information in a little calculation meant to squash the scary bug, but also the Dembski, Ewert, and Marks (DEM) model of "search." To appreciate the irony fully, you have to recall that our post was motivated by Dembski's complaint that Joe had neglected the work of DEM. Winston Ewert wants nothing to do with our formal calculation of the bias ("active information"), due entirely to selection, in a simple evolutionary process. That word proof comes from a part of him that knows he as at a complete loss for a technical response. Like Joe, I am preparing a post. Mine will appear at The Skeptical Zone.

Ravi · 6 December 2015

Tom English said: The Law of Conservation of Information Is Defunct.
And, yet, all of the empirical evidence suggests that genetic/biochemical information is pervasively conserved by natural selection, so why do you want to show otherwise? Makes no sense.

DS · 6 December 2015

Ravi said: But let me ask, again, how is Felsenstein - a theoretical population geneticist and bioinformatician - capable of commenting on the biophysics of protein function and structure? Has he published any research on the subject?
But let me ask, again, how is Ravi - who probably isn't even a biologist of any kind - capable of commenting on the biophysics of protein function and structure? Has he published any research on the subject? If you want to play the authority game, creationists always lose. Why they go there I don't know.

Ravi · 6 December 2015

DS said: But let me ask, again, how is Ravi - who probably isn't even a biologist of any kind - capable of commenting on the biophysics of protein function and structure? Has he published any research on the subject? If you want to play the authority game, creationists always lose. Why they go there I don't know.
It isn't about authority. It is about knowledge. Felsenstein and English, and also Dembski for that matter, are talking about algortithmic searches that don't have anything of consequence to say about the biophysics of protein folding. Hence, whatever they come up with, may well by biologically meaningless. Felsenstein can't make sweeping claims about the physics of the fitness landscape of protein evolution without actually doing some experimental research of his own.

eric · 6 December 2015

I do not think that is going to be a sufficient source of active information to account for biology. I do not have a proof of this. But neither does Felsenstein have a demonstration that it will produce sufficient active information.
So, basically, they've gone back to raw argument from incredulity. 'Nobody can calculate the fitness landscape's exact smoothness. Therefore Jesus."

Nick Matzke · 6 December 2015

Ravi,

This thread is about the No Free Lunch theorem and how the ID guys have tried to use it, not the origin of protein folds. C'mon, let's have it, do you agree that it was correct for the ID guys to say that the No Free Lunch theorem had implications for evolution, given that the No Free Lunch theorem is a statement about searches averaged over all possible fitness functions (most of which will be totally random and thus ridiculously rough), when biological evolution is functioning in a world with laws of physics that specify all sorts of smooth and smooth-ish gradients everywhere (temperature, precipitation, nutrient levels, etc.).

Re: origin of protein folds. Have you read Nick Grishin? Have you bothered to Google Scholar the origin of hox genes? Do you think there is any chance that hox domains are part of a larger class of protein structures with a wider distribution? You obviously didn't bother to check -- why not? Are you lazy? Do you think being an ID proponent gives you the right to just say stuff and accidentally be right about it without bothering to do the bare minimum of due diligence on the topic? Why do you think anyone working in real science should take you ID guys seriously when we do have Google Scholar abilities and can clearly see you aren't doing the basic background research to even get to the starting point of an informed discussion on the matter?

Jon Fleming · 6 December 2015

Ravi said:
Scott F said: Why is this "search" considered "hard"?
Because it is blind. The independently foliding homeodomain, for example, contains 60 amino acid residues. The number of possible amino acid combinations for a sequence of that length is 1.153 * 10^78. That is roughly the number of electrons in the entire universe! Now, the homeodomain sequence is variable, of course, but only up to a point. The chance of a random search finding such a sequence is effectively zero.
Yup. That's why nobody in the mainstream is proposing any such idiotic idea.
Natural selection only works if there is something useful to select.
Yup. Are you familiar with Behe's Blunder as to how often something selectable will arise?
Assuming a smooth fitness landscape, with incremental steps along the way, is just nonsense.
Ah, the old argument from incredulity. Your ignorance is showing. Don't feel bad, that's all of what all ID arguments boil down to.

Mike Elzinga · 6 December 2015

Ravi said:
Scott F said: Why is this "search" considered "hard"?
Because it is blind. The independently foliding homeodomain, for example, contains 60 amino acid residues. The number of possible amino acid combinations for a sequence of that length is 1.153 * 10^78. That is roughly the number of electrons in the entire universe! Now, the homeodomain sequence is variable, of course, but only up to a point. The chance of a random search finding such a sequence is effectively zero. Natural selection only works if there is something useful to select. Assuming a smooth fitness landscape, with incremental steps along the way, is just nonsense.
Here is a basic ID/creationist puzzle for Ravi to do some ID/creationist critical thinking about. What are the odds of finding a nugget of copper that has a mass in the vicinity of, say, 64 grams? Here is the ID/creationist answer almost verbatim.

Oooh, oooh, oooh, pick me; I can do this one! This is almost exactly like the problem of finding 500 flips of a coin coming up all heads! There are 118 chemical elements. The number of repeated atoms of exactly copper in 64 grams is 6x10^23. (I looked up moles in a dictionary) Therefore the odds of finding an assembly of atoms that came up all copper atoms 6x10^23 times in a row is one out of 118^(6x10^23). Conclusion: You will never find such and arrangement of copper atoms in the lifetime of the universe unless it was intelligently designed.

DS · 6 December 2015

Ravi said:
DS said: But let me ask, again, how is Ravi - who probably isn't even a biologist of any kind - capable of commenting on the biophysics of protein function and structure? Has he published any research on the subject? If you want to play the authority game, creationists always lose. Why they go there I don't know.
It isn't about authority. It is about knowledge. Felsenstein and English, and also Dembski for that matter, are talking about algortithmic searches that don't have anything of consequence to say about the biophysics of protein folding. Hence, whatever they come up with, may well by biologically meaningless. Felsenstein can't make sweeping claims about the physics of the fitness landscape of protein evolution without actually doing some experimental research of his own.
So it's about knowledge. Well, you certainly haven't proven that you are qualified Joe Felsenstein is a real biologist, so am I for that matter. And while we are on the subject, no real biologist, you know the guys with all of the knowledge about real biology,. have concluded that evolution could not happen. None. So, according to your own logic. all of the people with the knowledge agree and Bill has no right to even question that conclusion, because he has absolutely no knowledge or understanding of biology. Therefore, Joe's qualifications a are irrelevant, since no real response to a fake challenge was ever needed. Glad we got that straight.

Ravi · 6 December 2015

Nick Matzke said:This thread is about the No Free Lunch theorem and how the ID guys have tried to use it, not the origin of protein folds. C'mon, let's have it, do you agree that it was correct for the ID guys to say that the No Free Lunch theorem had implications for evolution, given that the No Free Lunch theorem is a statement about searches averaged over all possible fitness functions (most of which will be totally random and thus ridiculously rough), when biological evolution is functioning in a world with laws of physics that specify all sorts of smooth and smooth-ish gradients everywhere (temperature, precipitation, nutrient levels, etc.).
Biological evolution does, indeed, encounter the problem of rough fitness landscapes. That is why it is proposed that stochastic "tunnelling" rather than selective "traversing" may be the appropriate course: http://www.nature.com/nrg/journal/v15/n7/full/nrg3744.html Yes, many adaptations may require just a few mutations, but these are mostly minor adjustments/tweaks to function (many degradatory) even if they have a larger effect on fitness.
Re: origin of protein folds. Have you read Nick Grishin? Have you bothered to Google Scholar the origin of hox genes? Do you think there is any chance that hox domains are part of a larger class of protein structures with a wider distribution? You obviously didn't bother to check -- why not? Are you lazy? Do you think being an ID proponent gives you the right to just say stuff and accidentally be right about it without bothering to do the bare minimum of due diligence on the topic? Why do you think anyone working in real science should take you ID guys seriously when we do have Google Scholar abilities and can clearly see you aren't doing the basic background research to even get to the starting point of an informed discussion on the matter?
The homeodomain is a DNA-binding domain. We know that 10 of the 60 residues are absolutely essential to its function: 6 bind to the major groove of the DNA molecule and 4 to the minor groove. If you delete one or two of these critical residues, you have a non-functioning hox protein: irreducible complexity! You didn't know that, did you? Game over, pal!

Ravi · 6 December 2015

DS said: So it's about knowledge. Well, you certainly haven't proven that you are qualified Joe Felsenstein is a real biologist, so am I for that matter. And while we are on the subject, no real biologist, you know the guys with all of the knowledge about real biology,. have concluded that evolution could not happen. None. So, according to your own logic. all of the people with the knowledge agree and Bill has no right to even question that conclusion, because he has absolutely no knowledge or understanding of biology. Therefore, Joe's qualifications a are irrelevant, since no real response to a fake challenge was ever needed. Glad we got that straight.
Felsenstein is not a biophysicist and has published no research in biophysics. His expertise is in phylogenetics, mathematics and bioinformatics. He has not shown how evolution can overcome extremely rough fitness landscapes that separate potentially functional sequences.

Yardbird · 6 December 2015

Ravi said: Biological evolution does, indeed, encounter the problem of rough fitness landscapes.
Describe just one.

Ravi · 6 December 2015

Yardbird said:
Ravi said: Biological evolution does, indeed, encounter the problem of rough fitness landscapes.
Describe just one.
Experimental Rugged Fitness Landscape in Protein Sequence Space http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000096
"Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region."

stevaroni · 6 December 2015

Yardbird said:
Ravi said: Biological evolution does, indeed, encounter the problem of rough fitness landscapes.
Describe just one.
Krakatoa. A lush, tropical Indonesian island one day, and a wasteland the next. Aside from all the critters outright killed, any (tiny) survivors would have to struggle in an environment that was suddenly dramatically different from anything they had been adapted to. Some did struggle back, of course, but many did not. (Much of the current Krakatoa biome came in from other islands) Likewise, the K-T extinction event. Once upon a time there were likely large predatory theropods disturbingly close to wherever you're reading this. Then, not. Mammals and the smaller proto-birds, which were more adaptable and could live through the bigger discontinuities in the definition of "fitness" survived, big lizards dependent on a very specific ecosystem, not so much. In a less dramatic vein, how about the recession of the last ice age? A fairly gradual and (on a global scale) not terribly dramatic shift in the environment, and many, many kinds of animals were easily able to ride it through, but the specialized and slow-breeding woolly mammoths were unable to adapt quickly enough and died. Or the introduction of the rabbit and cane toad to Australia? A truly tiny change in most environments that would quickly be absorbed on to the local lunch menu, but still disastrous to the native fauna down under who were highly specialized in their tiny niches and consequently didn't have time to adapt to even a small shift.

Joe Felsenstein · 6 December 2015

Ravi said:
DS said: So it's about knowledge. Well, you certainly haven't proven that you are qualified Joe Felsenstein is a real biologist, so am I for that matter. And while we are on the subject, no real biologist, you know the guys with all of the knowledge about real biology,. have concluded that evolution could not happen. None. So, according to your own logic. all of the people with the knowledge agree and Bill has no right to even question that conclusion, because he has absolutely no knowledge or understanding of biology. Therefore, Joe's qualifications a are irrelevant, since no real response to a fake challenge was ever needed. Glad we got that straight.
Felsenstein is not a biophysicist and has published no research in biophysics. His expertise is in phylogenetics, mathematics and bioinformatics. He has not shown how evolution can overcome extremely rough fitness landscapes that separate potentially functional sequences.
No, this is not a discussion of protein folding etc. I documented that Dembski, Ewert, and Marks interpreted their Active Information calculation as showing that when evolution successfully results in higher fitness, that this can only be because a Designer has shaped the fitness surface. I argued that the mere presence of genotypes that have phenotypes, and considerations of physical laws would bring about a considerable amount of Active Information. Ravi objected that I was not a physicist. So we await Ravi's counterargument -- can Ravi show that when there is a smoother-than-white-noise fitness surface, that this must result from Design? We await Ravi's explanation of how a superior knowledge of physics shows this. But in the meantime Ravi has tried to drag to the discussion off to Ravi's favorite example of Something Ravi Doesn't Think Evolution Can Do. Will not play. Will be happy to hear Ravi's insights on the topic actually under discussion.

Yardbird · 6 December 2015

stevaroni said:
Yardbird said:
Ravi said: Biological evolution does, indeed, encounter the problem of rough fitness landscapes.
Describe just one.
Krakatoa. A lush, tropical Indonesian island one day, and a wasteland the next. Aside from all the critters outright killed, any (tiny) survivors would have to struggle in an environment that was suddenly dramatically different from anything they had been adapted to. Some did struggle back, of course, but many did not. (Much of the current Krakatoa biome came in from other islands) Likewise, the K-T extinction event. Once upon a time there were likely large predatory theropods disturbingly close to wherever you're reading this. Then, not. Mammals and the smaller proto-birds, which were more adaptable and could live through the bigger discontinuities in the definition of "fitness" survived, big lizards dependent on a very specific ecosystem, not so much. In a less dramatic vein, how about the recession of the last ice age? A fairly gradual and (on a global scale) not terribly dramatic shift in the environment, and many, many kinds of animals were easily able to ride it through, but the specialized and slow-breeding woolly mammoths were unable to adapt quickly enough and died. Or the introduction of the rabbit and cane toad to Australia? A truly tiny change in most environments that would quickly be absorbed on to the local lunch menu, but still disastrous to the native fauna down under who were highly specialized in their tiny niches and consequently didn't have time to adapt to even a small shift.
Thanks. Most helpful. I could infer from these examples that a landscape is (are?) the changes in an organism's environmental conditions over time. Would it be reasonable to also say that a landscape is the changes in conditions that an organism encounters as it moves or attempts to move from one physical location to another?

eric · 6 December 2015

Ravi said:
Tom English said: The Law of Conservation of Information Is Defunct.
And, yet, all of the empirical evidence suggests that genetic/biochemical information is pervasively conserved by natural selection,
It depends on how you define 'information,' of course, but if you're using -log(P) or some form of Shannon entropy, then it is trivial to show that this is false. Every mutational duplication that adds to string length increases information, while every mutational change that reduces string length reduces it. OTOH if you want to define information in a way that relates to some sort of phenotypic function, then it should also be trivial to think of counter-examples where its not conserved. Any gain or loss of function would be non-conservation. The only way I can see 'information is conserved' to be true is if you make it functionally equivalent to energy, and you consider not just the organism's genetic code but all the uptake and waste streams too. Yes its true the energy inherent in the atoms and bonds that make up DNA "go somewhere" when there's a change, but that has little to do with what DNA codes or doesn't code for. But I could always be wrong. So wow me Ravi. Explain to me the definition of genotypic information under which copy increases and decreases conserve information.

DS · 6 December 2015

Ravi said:
DS said: So it's about knowledge. Well, you certainly haven't proven that you are qualified Joe Felsenstein is a real biologist, so am I for that matter. And while we are on the subject, no real biologist, you know the guys with all of the knowledge about real biology,. have concluded that evolution could not happen. None. So, according to your own logic. all of the people with the knowledge agree and Bill has no right to even question that conclusion, because he has absolutely no knowledge or understanding of biology. Therefore, Joe's qualifications a are irrelevant, since no real response to a fake challenge was ever needed. Glad we got that straight.
Felsenstein is not a biophysicist and has published no research in biophysics. His expertise is in phylogenetics, mathematics and bioinformatics. He has not shown how evolution can overcome extremely rough fitness landscapes that separate potentially functional sequences.
And neither are you. As Joe points out, you are merely trying to change the subject. This thread is not about protein folding. Dembski got his butt kicked and you can't come up with any counter argument. Deal with it.

Ravi · 6 December 2015

Joe Felsenstein said: No, this is not a discussion of protein folding etc.
Then what you argue is biologically meaningless. The theory of evolution purports to show how new protein functions and folds can arise from the natural selection of random variations. If it cannot demonstrate this, it is essentially a great package devoid of any real content.
I documented that Dembski, Ewert, and Marks interpreted their Active Information calculation as showing that when evolution successfully results in higher fitness, that this can only be because a Designer has shaped the fitness surface. I argued that the mere presence of genotypes that have phenotypes, and considerations of physical laws would bring about a considerable amount of Active Information.
But fitness can indeed increase whilst function decreases. Nobody in the ID movement denies that some mutations through random exploration (which degrade function) can increase reproductive fitness in some environments. If you are going to speak about physical laws, then you need to be apply this to such matters as protein folding because if a protein fails to fold properly, as would be the case in the vast majority of sequence combinations, it cannot function. Without addressing this issue, you have nothing.
Ravi objected that I was not a physicist. So we await Ravi's counterargument -- can Ravi show that when there is a smoother-than-white-noise fitness surface, that this must result from Design? We await Ravi's explanation of how a superior knowledge of physics shows this.
Nobody claims that some adaptations are possible by purely random changes. The Design argument is that there are formidable fitness barriers, evident in the biochemistry and biophysics of proteins,that prevent evolution from progressing beyond a limited scope for adaptive change.

Ravi · 6 December 2015

eric said: But I could always be wrong. So wow me Ravi. Explain to me the definition of genotypic information under which copy increases and decreases conserve information.
I am not using any particular definition of information. I am merely stating that natural selection tends to conserve DNA sequences to much more of an extent than it does to alter them. If this were not the case, the field of comparative genomics would be extremely difficult.

Rolf · 6 December 2015

Ravi said:
Nobody claims that some adaptations are possible by purely random changes. The Design argument is that there are formidable fitness barriers, evident in the biochemistry and biophysics of proteins,that prevent evolution from progressing beyond a limited scope for adaptive change.
I would like to know more about the barriers that prevent evolution to progress beyond a limited scope. Looking at the broader picture of evolution, where can we detec or observe the limited scope in action? From what you wrote, it appears like you see limits that prevent a species from adapting (beyond a limited scope)to the environment, meaning it is doomed to extinction. Is that it? Extinction instead of survival, unless the designer intervene. I would like to know more about supernatural intervention in biology. But in order to keep life going, the designer is busy all the time? What I see is life "slowly" adapting, establishing a shift in the distribution of alleles in a population. What exactly is it that prevents that from continuing?

Nick Matzke · 6 December 2015

Mike Elzinga said:
Ravi said:
Scott F said: Why is this "search" considered "hard"?
Because it is blind. The independently foliding homeodomain, for example, contains 60 amino acid residues. The number of possible amino acid combinations for a sequence of that length is 1.153 * 10^78. That is roughly the number of electrons in the entire universe! Now, the homeodomain sequence is variable, of course, but only up to a point. The chance of a random search finding such a sequence is effectively zero. Natural selection only works if there is something useful to select. Assuming a smooth fitness landscape, with incremental steps along the way, is just nonsense.
Here is a basic ID/creationist puzzle for Ravi to do some ID/creationist critical thinking about. What are the odds of finding a nugget of copper that has a mass in the vicinity of, say, 64 grams? Here is the ID/creationist answer almost verbatim.

Oooh, oooh, oooh, pick me; I can do this one! This is almost exactly like the problem of finding 500 flips of a coin coming up all heads! There are 118 chemical elements. The number of repeated atoms of exactly copper in 64 grams is 6x10^23. (I looked up moles in a dictionary) Therefore the odds of finding an assembly of atoms that came up all copper atoms 6x10^23 times in a row is one out of 118^(6x10^23). Conclusion: You will never find such and arrangement of copper atoms in the lifetime of the universe unless it was intelligently designed.

Genius!!

Nick Matzke · 6 December 2015

Ravi said:
eric said: But I could always be wrong. So wow me Ravi. Explain to me the definition of genotypic information under which copy increases and decreases conserve information.
I am not using any particular definition of information. I am merely stating that natural selection tends to conserve DNA sequences to much more of an extent than it does to alter them. If this were not the case, the field of comparative genomics would be extremely difficult.
"Tends" does not equal "conservation law". It means "sometimes". Please admit, then, that the claim that there is a "law of conservation of information" is incorrect.

Mike Elzinga · 6 December 2015

Ravi said: Nobody claims that some adaptations are possible by purely random changes. The Design argument is that there are formidable fitness barriers, evident in the biochemistry and biophysics of proteins,that prevent evolution from progressing beyond a limited scope for adaptive change.
Are "formidable fitness barriers" anything like "entropy barriers?" Explain what a "formidable fitness barrier" is.

Joe Felsenstein · 6 December 2015

Ravi said:
Joe Felsenstein said: ... Ravi objected that I was not a physicist. So we await Ravi's counterargument -- can Ravi show that when there is a smoother-than-white-noise fitness surface, that this must result from Design? We await Ravi's explanation of how a superior knowledge of physics shows this.
Nobody claims that some adaptations are possible by purely random changes. The Design argument is that there are formidable fitness barriers, evident in the biochemistry and biophysics of proteins,that prevent evolution from progressing beyond a limited scope for adaptive change.
Can you explain how this relates to the Dembski-Ewert-Marks argument that if there is a smooth fitness surface then Design is implicated in setting that up? I can't see the connection.

stevaroni · 6 December 2015

Yardbird said: I could infer from these examples that a landscape is (are?) the changes in an organism's environmental conditions over time. Would it be reasonable to also say that a landscape is the changes in conditions that an organism encounters as it moves or attempts to move from one physical location to another?
It's not a perfect metaphor, but "fitness landscape" is a sort of a map of the range of survival challenges an organism faces in its environment. An organism has some inherent adaptability, which allows it to move out across this landscape over bumps and valleys in an attempt to find an optimal habitat. An adaptable organism can move over large bumps and discontinuities, there are still cliffs and peaks where it cannot go. Humans and cockroaches, for example are supremely adaptable, and can overcome environmental challenges that other animals would have no chance at adapting to. Still, there are fitness barriers that we cannot go beyond, for example, drop a human and a tuna into the middle of the Pacific and see what happens. The converse is true, sometimes there is a local peak or valley that develops slowly enough that a species can adapt there, but then the pit becomes so deep the species can never climb back out. For example thermal vent tube worms live happily in one of the weirdest environments known, but they can only live there, it's difficult to see how they could ever adapt their way out of their niche because there's nothing mostly like a thermal vent to act as the next stepping stone. The tricky thing is that "fitness" is a moving target because the fitness landscape keeps changing, both because of physical events (climate, volcanoes, meteors) and because of the other players in the biome. A strategy that works today might be useless tomorrow with the arrival of new competition or a better predator. For example, take the megafauna that developed in North America after the last ice age. They had a pretty good angle for survival, which was they grew very big and lived in herds, which helped with the cold and deterred the predators. And then paleolilthic hunters (and later the white buffalo hunters) showed up and being big just served as a long-distance signal that here was enough meat in one place to make for a really valuable target.

Scott F · 6 December 2015

stevaroni said: The tricky thing is that "fitness" is a moving target because the fitness landscape keeps changing, both because of physical events (climate, volcanoes, meteors) and because of the other players in the biome. A strategy that works today might be useless tomorrow with the arrival of new competition or a better predator.
Yes, exactly this. Dembski (et al) seem to believe that once a fitness landscape is chosen, that it remains constant. Even if one considers a "random" fitness landscape, what was once a neutral adaptation might prove very useful in the next season. If the fitness landscape is constantly changing, the organism itself doesn't even have to "explore" as much. Just "standing still", your local fitness can increase or decrease, depending on changes in the environment.

Scott F · 6 December 2015

Ravi said:
Scott F said: Why is this "search" considered "hard"?
Because it is blind.
So? There is no "goal" in this search. There is no need to be able to "see" the top of the next mountain, or the one after that. Even a random walk is sufficient to explore the fitness landscape in some direction. Combine a bunch of amino acids randomly, and you're going to form some kind of protein. If it isn't useful, it will be replaced. If it is useful, it will tend to be conserved. I repeat, why is this considered to be "hard"?

Scott F · 6 December 2015

Ravi said:
Scott F said: Why is this "search" considered "hard"?
Because it is blind. The independently foliding homeodomain, for example, contains 60 amino acid residues. The number of possible amino acid combinations for a sequence of that length is 1.153 * 10^78. That is roughly the number of electrons in the entire universe! Now, the homeodomain sequence is variable, of course, but only up to a point. The chance of a random search finding such a sequence is effectively zero. Natural selection only works if there is something useful to select. Assuming a smooth fitness landscape, with incremental steps along the way, is just nonsense.
So? If I deal you five cards, what is the probability of coming up with a royal flush in spades? Pretty small. Wiki tells me it is about 0.0000385%. But I dealt you five cards. What is the probability that you have exactly the five cards that I dealt to you? It would be exactly the same odds as a specific royal flush, or 0.0000385%. Yet, despite those incredible odds, there you are holding those exact cards in your hand. Imagine that. Given the incredible odds against holding the cards that you do, you must admit that I cheated, that I "intelligently designed" the sequence of cards that you hold. According to your "logic", such as it is, it would be impossible to hold *any* 5 card sequence unless someone intentionally, intelligently, "designed" that exact 5 card sequence for you from an infinite selection of cards. Come on. I'm no mathematician, physicist, biologist, chemist, or any combination of those, or even a poker player. Yet it's obvious even to me that your so-called "argument" from "really big scary numbers" is totally bogus, contrived, and has no relationship to the real world. I don't care what your credentials are. I care about your "ideas", and your "ideas" (such as they are) aren't convincing. If you can't convince me, how can you hope to convince the real scientists who post here, who know what they're talking about? BTW, did I fail to mention "building blocks"? Which reduce the "odds" considerably, compared to a "random" sequence of amino acids? A point which you totally ignored, and again presented really, really big scary numbers? Numbers which are totally meaningless in the real world? Yeah, that's what I thought.

Ravi · 6 December 2015

Joe Felsenstein said: Can you explain how this relates to the Dembski-Ewert-Marks argument that if there is a smooth fitness surface then Design is implicated in setting that up? I can't see the connection.
A fitness landscape could be "smoothed out" by artifical means. This is what Dembski may mean by a "finely crafted assemblage." In some ways, those who practice the "directed" evolution of novel proteins do just that in the lab. But natural evolution is always undirected and unaided. Dembski also appears to be responding in his books to Kauffman's idea that Nature has inherent self-organizing properties that provide the fitness functions that make Darwinian evolution possible. Anyway, this is all very nebulous and arcane if taken out of the context of the quantum mechanics of biophysics.

Ravi · 6 December 2015

Nick Matzke said: "Tends" does not equal "conservation law". It means "sometimes". Please admit, then, that the claim that there is a "law of conservation of information" is incorrect.
Well, the really important regions of the genome - about 5% - are stringently conserved. But Dembski has a different concept of information. He links it with the environment. His idea of the conservation of information has more to do with the way in which information is transformed into different states just as energy is. So, an intelligent designer can transfer his/her information to an organism by imposing certain conditions and making it respond to them.

Ravi · 6 December 2015

Mike Elzinga said: Explain what a "formidable fitness barrier" is.
One which would require multiple, simultaneous changes in the right places to occur for any fitness to be gained.

Ravi · 6 December 2015

Scott F said: So? There is no "goal" in this search. There is no need to be able to "see" the top of the next mountain, or the one after that. Even a random walk is sufficient to explore the fitness landscape in some direction. Combine a bunch of amino acids randomly, and you're going to form some kind of protein. If it isn't useful, it will be replaced. If it is useful, it will tend to be conserved. I repeat, why is this considered to be "hard"?
Well, a random walk can involve taking one step forward and two steps back. A blind man will never find his way to the top of the Eiffel Tower, according to Mike Behe. There is plenty of evidence that random mutations can have beneficial effects. But nearly always this involves tweaking an existing protein, with its own functionality and fold. What you have in Darwinian evolution is a mechanism that allows living organisms to make minor adjustments in response to environmental changes without the need for any external intervention. Dembski sees this as good design.

DS · 6 December 2015

Ravi said:
Nick Matzke said: "Tends" does not equal "conservation law". It means "sometimes". Please admit, then, that the claim that there is a "law of conservation of information" is incorrect.
Well, the really important regions of the genome - about 5% - are stringently conserved. But Dembski has a different concept of information. He links it with the environment. His idea of the conservation of information has more to do with the way in which information is transformed into different states just as energy is. So, an intelligent designer can transfer his/her information to an organism by imposing certain conditions and making it respond to them.
So that would be a no. There is absolutely no "conservation of information". Got it.

Ravi · 6 December 2015

Rolf said: I would like to know more about the barriers that prevent evolution to progress beyond a limited scope. Looking at the broader picture of evolution, where can we detec or observe the limited scope in action?
What limits natural selection are rugged fitness landscapes. If the landscape isn't paved with adaptive paths, then evolution won't have any where to traverse. It won't go there.
From what you wrote, it appears like you see limits that prevent a species from adapting (beyond a limited scope)to the environment, meaning it is doomed to extinction. Is that it? Extinction instead of survival, unless the designer intervene. I would like to know more about supernatural intervention in biology.
No. I think most species can adapt to most changes in the environment. Obviously, many cannot and they go extinct. But adaptation is not the same thing as innovation which most likely requires design.
But in order to keep life going, the designer is busy all the time? What I see is life "slowly" adapting, establishing a shift in the distribution of alleles in a population. What exactly is it that prevents that from continuing?
No. Darwinian evolution ensures that life remains robust and versatile. But the limit of this mechanism, "the edge of evolution" as Behe describes it, is such that design interventions are necessary, such as for the creation of a new protein domain and fold or a new body plan.

stevaroni · 6 December 2015

Ravi said: Well, a random walk can involve taking one step forward and two steps back.

So? You've still moved one step away from where you started. You're still hung up on "forward". There is no "forward" because there is no goal past "survive long enough to get laid". There forward or back or left or right, there is only "around here somewhere". Sometimes surviving well involves what seems like moving backwards. Whales and snakes lost perfectly good legs, blind cave fish lost their eyes, both for the same reason. At one time they were useful structures but at the moment, on this part of the survival landscape, they don't help as much as using that energy and material elsewhere. Solutions tend to spread out from their point of origin, some of them will fall into holes. some of them will pass right next. to some local sweet spot but just miss it. Some, however, will find a nice sheltered cove where the tumult passes them by. Such is life. Literally.

A blind man will never find his way to the top of the Eiffel Tower, according to Mike Behe.

So what? There's probably an enormous pinnacle in every mammals survival landscape for the solution of direct photosynthesis, it's the holy grail of never being without food again, and plants manage it all the time. But the walls are too damn steep to climb in one go, and there's no gradual path, so no mammal can take that particular brass ring. A blind man will probably never climb Everest, either. You'll fall off. The landscape is too rough. Thing is, if you do enough random walks through a smooth enough landscape, one that at least doesn't kill you all the time, say, like the rolling hills of the Russian steppe, some of those walks will get to enormous heights. Especially since it's an iterative process and any individual only has to contribute one step.

What you have in Darwinian evolution is a mechanism that allows living organisms to make minor adjustments in response to environmental changes without the need for any external intervention. Dembski sees this as good design.

Well, Dembski can call it whatever he likes. The important thing is that Darwinian evolution exists, even Dembski can't deny this. Where Dembski fails is that he cannot demonstrate that design is necessary to make Darwinian evolution work. All the evidence seems to show the opposite, that evolution is the antithesis of design, a process that produces a similar result without requiring planning and forethought. Whereas design starts with a goal in mind an proceeds forward toward that goal, evolution simply tries a whole bunch of different solutions and then after the fact picks out the ones that worked. Evolution is not particularly elegant of efficient, but it has numbers going for it and that's really all you need to cover any reasonably smooth area. If I were covering a floor I could design a strategy to quickly and efficiently roll some paint on it and be done in an hour, or, I could allow a bunch of cats to step in paint and track it all over. That's not efficient or elegant, but after days or weeks there would be few spots on the floor more than a couple of inches away from a paw print. There'd probably even be paint in places I never expected.

Yardbird · 6 December 2015

Ravi said: So, an intelligent designer can transfer his/her information to an organism by imposing certain conditions and making it respond to them.
What is the mechanism by which those conditions are imposed?

Scott F · 6 December 2015

Ravi said: What limits natural selection are rugged fitness landscapes. If the landscape isn't paved with adaptive paths, then evolution won't have any where to traverse. It won't go there. …. No. I think most species can adapt to most changes in the environment. Obviously, many cannot and they go extinct. But adaptation is not the same thing as innovation which most likely requires design.
These two statements appear to contradict each other. Rugged fitness landscapes limit natural selection, yet most species can adapt to most changes in the environment. One of these things is not like the other.

Yardbird · 6 December 2015

stevaroni said: If I were covering a floor I could design a strategy to quickly and efficiently roll some paint on it and be done in an hour, or, I could allow a bunch of cats to step in paint and track it all over. That's not efficient or elegant, but after days or weeks there would be few spots on the floor more than a couple of inches away from a paw print. There'd probably even be paint in places I never expected.
Hmm. That's a use for cats I'd not considered. Maybe they have a purpose after all. But I digress.

Scott F · 6 December 2015

Ravi said: There is plenty of evidence that random mutations can have beneficial effects.
Perhaps you would care to argue this point with our resident creationists, who maintain that all mutations are detrimental, by the definition of "mutation".

Ravi · 6 December 2015

Yardbird said: What is the mechanism by which those conditions are imposed?
I believe it is called artificial selection.

Ravi · 6 December 2015

Scott F said: Perhaps you would care to argue this point with our resident creationists, who maintain that all mutations are detrimental, by the definition of "mutation".
Creationists dispute the idea of wholly beneficial mutations, without any cost, which confer not just an increase in reproductive fitness but also in function. This remains controversial.

Scott F · 6 December 2015

Ravi said:
Mike Elzinga said: Explain what a "formidable fitness barrier" is.
One which would require multiple, simultaneous changes in the right places to occur for any fitness to be gained.
Fortunately for Evolution, multiple, simultaneous changes are not required. Nor are the changes required to be in "the right places". There you go again, thinking that Evolution has a "goal" "in mind". The changes only have to be in some place. Many places are possible, most will be neutral, and some will be adequate for fitness to be gained at a later time. Not every step has to be forward or backward, up or down the fitness landscape. Some changes can be sideways. Some mutations can even add new dimensions to the fitness landscape that didn't exist before, because the genome itself can change the fitness landscape that it is exploring. Think nylonase.

Ravi · 6 December 2015

Scott F said:
Ravi said: What limits natural selection are rugged fitness landscapes. If the landscape isn't paved with adaptive paths, then evolution won't have any where to traverse. It won't go there. …. No. I think most species can adapt to most changes in the environment. Obviously, many cannot and they go extinct. But adaptation is not the same thing as innovation which most likely requires design.
These two statements appear to contradict each other. Rugged fitness landscapes limit natural selection, yet most species can adapt to most changes in the environment. One of these things is not like the other.
You misunderstood me. Species can adapt, but there are natural limits to how much they can change by. Mike Behe explains this in his book, "Edge of Evolution". It is a good read.

Ravi · 6 December 2015

Scott F said: Some mutations can even add new dimensions to the fitness landscape that didn't exist before, because the genome itself can change the fitness landscape that it is exploring. Think nylonase.
The latest research shows that "nylonase" is not a new enzyme, but rather a pre-existing hydrolase that was tinkered with and only involved two mutations. Generating a new enzyme, with its own distinctive domain and fold, is beyond the scope of natural evolution.

Scott F · 6 December 2015

Ravi said:
Yardbird said: What is the mechanism by which those conditions are imposed?
I believe it is called artificial selection.
What is the difference between "artificial" selection, and "natural" selection? How does "artificial" selection overcome the "barriers" that you say are imposed by your rugged fitness landscape? Remember, "artificial" selection can only work with "natural" mutations, the same as "natural" selection does. The only difference between "artificial" and "natural" selection, is that "artificial" selection has a goal "in mind", and we've already established that a goal is not needed for evolution to occur.

Scott F · 6 December 2015

Ravi said:
Scott F said: Some mutations can even add new dimensions to the fitness landscape that didn't exist before, because the genome itself can change the fitness landscape that it is exploring. Think nylonase.
The latest research shows that "nylonase" is not a new enzyme, but rather a pre-existing hydrolase that was tinkered with and only involved two mutations. Generating a new enzyme, with its own distinctive domain and fold, is beyond the scope of natural evolution.
You have just described Evolution. Taking what already exists and tinkering with it until it is useful.

Mike Elzinga · 6 December 2015

Ravi said:
Joe Felsenstein said: Can you explain how this relates to the Dembski-Ewert-Marks argument that if there is a smooth fitness surface then Design is implicated in setting that up? I can't see the connection.
A fitness landscape could be "smoothed out" by artifical means. This is what Dembski may mean by a "finely crafted assemblage." In some ways, those who practice the "directed" evolution of novel proteins do just that in the lab. But natural evolution is always undirected and unaided. Dembski also appears to be responding in his books to Kauffman's idea that Nature has inherent self-organizing properties that provide the fitness functions that make Darwinian evolution possible. Anyway, this is all very nebulous and arcane if taken out of the context of the quantum mechanics of biophysics.
So why don't you "put it in context" by explaining to us the quantum mechanics of biophysics? And I ask again why Dembski, Ewert, and Marks didn't win the 2013 Nobel Prize in chemistry? Do you have any clue about atomic and molecular interactions and what that 2013 Nobelk Prize in chemistry was all about? Even a high school chemistry and physics student knows about atomic and molecular interactions. I suspect you are just blowing smoke and haven't a clue of what you are talking about.

Yardbird · 6 December 2015

Ravi said:
Yardbird said: What is the mechanism by which those conditions are imposed?
I believe it is called artificial selection.
You misunderstand me. How does the designer effect the external intervention? X-rays? Magnetic fields? Spooky action at a distance?

Ravi · 6 December 2015

Yardbird said: You misunderstand me. How does the designer effect the external intervention? X-rays? Magnetic fields? Spooky action at a distance?
According to Ken Miller in his book, "Finding Darwin's God", the creator could make some mutations more likely to occur than others by availing of the indeterminancy principle of quantum theory.

Ravi · 6 December 2015

Scott F said: You have just described Evolution. Taking what already exists and tinkering with it until it is useful.
But tweaking and tinkering, .e. making small adjustments and modifications, has its natural limits. If you continue to tweak then you run up against a fitness abyss.

Ravi · 6 December 2015

Scott F said: What is the difference between "artificial" selection, and "natural" selection? How does "artificial" selection overcome the "barriers" that you say are imposed by your rugged fitness landscape? Remember, "artificial" selection can only work with "natural" mutations, the same as "natural" selection does.
Artificial selection is not impaired in the same way that natural selection is. It can choose something which is not useful itself, or even harmful, but which could provide a means by which to get to something useful upon further changes. Natural selection can only choose what is of immediate benefit to the organism. That is a major limitation.

Yardbird · 6 December 2015

Ravi said:
Yardbird said: You misunderstand me. How does the designer effect the external intervention? X-rays? Magnetic fields? Spooky action at a distance?
According to Ken Miller in his book, "Finding Darwin's God", the creator could make some mutations more likely to occur than others by availing of the indeterminancy principle of quantum theory.
And how would the creator avail of the indeterminancy principle?

Mike Elzinga · 6 December 2015

Ravi said:
Mike Elzinga said: Explain what a "formidable fitness barrier" is.
One which would require multiple, simultaneous changes in the right places to occur for any fitness to be gained.
That's a pretty glib "answer" that carefully avoids saying anything of substance. There is no goal in evolution for which "mutiple simultaneous changes in the right places" is required. Evolution goes where whatever the changes that occur take it; and those changes are constrained by physics and chemistry. Have you ever taken a minimum of high school physics, chemistry, and biology? If you did, did you fall asleep in your classes? Did you pass? I don't see any evidence that you have any knowledge in these areas; only ID/creationist talking points.

Mike Elzinga · 6 December 2015

Ravi said:
Scott F said: You have just described Evolution. Taking what already exists and tinkering with it until it is useful.
But tweaking and tinkering, .e. making small adjustments and modifications, has its natural limits. If you continue to tweak then you run up against a fitness abyss.
"Fitness abyss?" You are making up crap again.

fnxtr · 6 December 2015

Yardbird said:
Ravi said:
Yardbird said: You misunderstand me. How does the designer effect the external intervention? X-rays? Magnetic fields? Spooky action at a distance?
According to Ken Miller in his book, "Finding Darwin's God", the creator could make some mutations more likely to occur than others by availing of the indeterminancy principle of quantum theory.
And how would the creator avail of the indeterminancy principle?
Magic.

DS · 6 December 2015

Ravi, you wrote lots of incorrect nonsense, such as:

"No. Darwinian evolution ensures that life remains robust and versatile. But the limit of this mechanism, “the edge of evolution” as Behe describes it, is such that design interventions are necessary, such as for the creation of a new protein domain and fold or a new body plan."

RIght, he claims this, he just hasn't demonstrated it. You do know that new body plans can be produced without the need for new proteins domains, right? You do know that the hox genes are conserved throughout the entire animal kingdom, right? Or is evo devo another field that you have no knowledge of?

"Creationists dispute the idea of wholly beneficial mutations, without any cost, which confer not just an increase in reproductive fitness but also in function. This remains controversial."

The fact that creationist dispute something does not make it controversial. The fact that they are beneficial mutations is indisputable. Why on earth would thy have to have no cost? You are just making up nonsense.

"One which would require multiple, simultaneous changes in the right places to occur for any fitness to be gained."

No, you have fallen for creationist propaganda once again. Why on earth would the changes have to be simultaneous? Why on earth would they have to all be selected on? Why on earth couldn't they just happen and stick around until the other mutations arose? The answer is that they obviously can and that they do just that.

"The latest research shows that “nylonase” is not a new enzyme, but rather a pre-existing hydrolase that was tinkered with and only involved two mutations. Generating a new enzyme, with its own distinctive domain and fold, is beyond the scope of natural evolution."

RIght. That;s the way evolution works. The bacteria doesn't care if it is new enzyme or not. It evolved a new function.

"Natural selection can only choose what is of immediate benefit to the organism. That is a major limitation."

Yes it certainly is. But it does not prevent neutral variation for arising, persisting and even spreading. This represents the raw material on which selection can act if the environment changes. It's almost as if you have no knowledge of population genetics whatsoever.

You seem to have fallen for every creationist ploy in the play book. You also seem to lack the knowledge that all of these things are just a scam. You seem to think that the Gish gallop is going to work here. You seem to have forgotten what the topic of the thread is. So far you have completely failed to make any relevant point whatsoever. When trolls like you show up and try to disrupt conversations with piles of nonsense, they are usually dumped to the bathroom wall. All further responses by me to you will be there. Drop in if you dare, but we don't have to be so polite there.

Scott F · 6 December 2015

Ravi said:
Scott F said:
Ravi said: What limits natural selection are rugged fitness landscapes. If the landscape isn't paved with adaptive paths, then evolution won't have any where to traverse. It won't go there. …. No. I think most species can adapt to most changes in the environment. Obviously, many cannot and they go extinct. But adaptation is not the same thing as innovation which most likely requires design.
These two statements appear to contradict each other. Rugged fitness landscapes limit natural selection, yet most species can adapt to most changes in the environment. One of these things is not like the other.
You misunderstood me. Species can adapt, but there are natural limits to how much they can change by. Mike Behe explains this in his book, "Edge of Evolution". It is a good read.
I don't believe that Behe ever identified what those limits are, or what the physical barriers might be. He simply asserted this with no evidence, except "really really big scary numbers", which isn't evidence. Perhaps you would care to explain what you think you understand about what Behe said? For example, the one barrier that you have so far identified is that multiple simultaneous mutations are required for any (for some?) "beneficial" mutations. So far, this is a bald assertion, with no evidence to back it up. Even Behe has not presented any evidence that this assertion has any basis in reality. In fact, all evidence points in the exact opposite direction, that simultaneity is most definitely not required. (BTW, simply repeating that there are such barriers doesn't explain what those barriers are, or how these barriers physically act to stop "adaptation" in its tracks.) Are you saying, for example, that there is some barrier which, in a sequence of 1, 2, 3, … M mutations, that physically prevents mutation (N + 1) from occurring and thus preventing mutation "M" from happening? Even in principle?

eric · 6 December 2015

Ravi said: I am not using any particular definition of information. I am merely stating that natural selection tends to conserve DNA sequences to much more of an extent than it does to alter them. If this were not the case, the field of comparative genomics would be extremely difficult.
So then, you don't think there's a conservation law for information the way there is one for energy or momentum. Is that correct? There is no physical law that prevents mutation from increasing the amount of information in a genome?

eric · 6 December 2015

Ravi said: Well, the really important regions of the genome - about 5% - are stringently conserved. But Dembski has a different concept of information. He links it with the environment. His idea of the conservation of information has more to do with the way in which information is transformed into different states just as energy is. So, an intelligent designer can transfer his/her information to an organism by imposing certain conditions and making it respond to them.
This would happen regardless of the presence of a designer, correct? You've got an environment containing information, a genome, and via physicochemical processes one can cause the other to change, increase, or decrease ("just as energy is") . Correct?

eric · 6 December 2015

Mike Elzinga said:
Ravi said: But tweaking and tinkering, .e. making small adjustments and modifications, has its natural limits. If you continue to tweak then you run up against a fitness abyss.
"Fitness abyss?" You are making up crap again.
Yes I agree...he is asserting one of the key concepts of ID rather than giving evidence or argument for it.

Scott F · 6 December 2015

Ravi said:
Yardbird said: You misunderstand me. How does the designer effect the external intervention? X-rays? Magnetic fields? Spooky action at a distance?
According to Ken Miller in his book, "Finding Darwin's God", the creator could make some mutations more likely to occur than others by availing of the indeterminancy principle of quantum theory.
That's not "artificial" selection. That's called "magic". Unless you can explain the physics of changing the probabilities of atomic interactions?

Doc Bill · 6 December 2015

Ravi says: "But adaptation is not the same thing as innovation which most likely requires design."

Most likely? So, you just said that adaptation "could" provide innovation since design is only "most likely" and not "definitely."

Is that correct?

Second, how does artificial selection, animal breeding I suppose, differ from intelligent design? It seems to me there's no difference between breeding long legged sheep to get longer legged sheep, using only nature and sheep reproduction to do the job, than it would be for nature to produce longer legged sheep because to sheep they're more sexy.

What's the difference?

Scott F · 6 December 2015

Ravi said:
Scott F said: Some mutations can even add new dimensions to the fitness landscape that didn't exist before, because the genome itself can change the fitness landscape that it is exploring. Think nylonase.
The latest research shows that "nylonase" is not a new enzyme, but rather a pre-existing hydrolase that was tinkered with and only involved two mutations. Generating a new enzyme, with its own distinctive domain and fold, is beyond the scope of natural evolution.
That's called, "Moving the Goal Posts". Wiki describes an enzyme as:

Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions.

If it is catalyzing a new reaction with a novel material that didn't exist before, performing a new function that didn't exist before, then it is a "new" enzyme that didn't exist before. From an evolutionary view point, *every* protein (enzymes are themselves proteins) is simply a pre-existing protein that has been "tinkered with" by random mutations and natural selection. You now say that a new protein isn't "new" because two mutations aren't "big enough" to be considered "new". Yet just a few comments ago you said that it was "impossible" for a new function to develop that required two mutations, without intelligent intervention. You claimed that two mutations was one of those invisible "barriers" to evolution. Are you now saying that "research" has demonstrated that there was intelligent intervention in the creation of this not-new enzyme? Have scientists now shown incontrovertible "proof" of an intelligent agent in the creation of nylonase? Have, perhaps, those Intelligent Design "researchers" demonstrated this?

Rumraket · 7 December 2015

Ravi said:
Scott F said: Some mutations can even add new dimensions to the fitness landscape that didn't exist before, because the genome itself can change the fitness landscape that it is exploring. Think nylonase.
The latest research shows that "nylonase" is not a new enzyme, but rather a pre-existing hydrolase that was tinkered with and only involved two mutations. Generating a new enzyme, with its own distinctive domain and fold, is beyond the scope of natural evolution.
What an absurd reply. Are you even aware of how diverse the hydrolase class of enzymatic catalysts is? The mere fact that it is "still a hydrolase" is functionally equivalent to saying "but it is still just an animal" after seeing a terrestrial mammal evolve into a whale. You've just decided on some arbitrary system of classification and latched onto a category in order to deny that something "new" evolved because it still belongs to the same arbitrarily defined category. What's next, you're going to say "but it's still an enzyme" if a hydrolase evolves into a phosphatase? You can always come back after the fact and arbitrarily decide that the next level of classification is the "real" limit between "new" and "same"

RWard · 7 December 2015

What Ravi, and all the rest of the creationists who claim evolutionary change is too improbable to happen, fail to understand is that the alternative hypothesis - God employed magic to accomplish the change - is infinitely less probable. That's why it's called magic.

DS · 7 December 2015

Rumraket said: What an absurd reply. Are you even aware of how diverse the hydrolase class of enzymatic catalysts is? The mere fact that it is "still a hydrolase" is functionally equivalent to saying "but it is still just an animal" after seeing a terrestrial mammal evolve into a whale. You've just decided on some arbitrary system of classification and latched onto a category in order to deny that something "new" evolved because it still belongs to the same arbitrarily defined category. What's next, you're going to say "but it's still an enzyme" if a hydrolase evolves into a phosphatase? You can always come back after the fact and arbitrarily decide that the next level of classification is the "real" limit between "new" and "same"
Of course the Lenski experiments put the lie to this line of reasoning. A novel metabolic function, imparting a fitness advantage, did indeed evolve with no intelligent intervention whatsoever. Multiple mutations were involved, some of which were neutral and spread by drift for many generations before becoming selectively advantageous. Playing word games or redefining terms such as "new" isn't going to change this. The evidence is clear, not only is evolution capable of producing the living things around us, it actually has done so. To deny this is to deny the evidence. I once again note that the troll has provided none.

Michael Fugate · 7 December 2015

And a gene can arise "de novo" by a point mutation leading to a start codon in a noncoding region of the genome - it's as simple as that.
Links to Carl Zimmer - http://phenomena.nationalgeographic.com/2014/04/29/where-genes-come-from/

Michael Fugate · 7 December 2015

Let me ask Ravi, why would the Evolutionary Informatics lab where Ewert works have a section in its publications for "Christian Apologetics", if it were doing science? Seems it knows the answer before doing any "research".

As Bertrand Russell opined, "What is wanted is not the will-to-believe, but the wish to find out, which is the exact opposite."

This is ID's problem - they don't want to find anything out; they already "know" there is an agent god who does something - the problem is they have no idea what it does nor do they have the means for finding out. I think quixotic is the appropriate term.

harold · 7 December 2015

Michael Fugate said: Let me ask Ravi, why would the Evolutionary Informatics lab where Ewert works have a section in its publications for "Christian Apologetics", if it were doing science? Seems it knows the answer before doing any "research". As Bertrand Russell opined, "What is wanted is not the will-to-believe, but the wish to find out, which is the exact opposite." This is ID's problem - they don't want to find anything out; they already "know" there is an agent god who does something - the problem is they have no idea what it does nor do they have the means for finding out. I think quixotic is the appropriate term.
The underlying illogical and illegal assumption behind ID is that post-civil rights era fundamentalist Christianity, as endorsed by the Fox/Limbaugh/Tea Party "conservative" movement, is the unspoken default. The other presumption is that any attack on any isolated bit of scientific evidence invalidates all other evixence, which would be wrong even if they had one rational argument. Actually this was already true of "creation science", but because ID is a failed legal strategy, ID can't even admit its motivation. Hence such seeming paradoxes as YEC advocates being in favor of blathering about the Cambrian. Implied -"if I say something is wrong with any scientific field whatsoever, the entire Liberty University version of science wins by default and must be made the sole content of public school science class".

Ravi · 7 December 2015

Doc Bill said: Ravi says: "But adaptation is not the same thing as innovation which most likely requires design." Most likely? So, you just said that adaptation "could" provide innovation since design is only "most likely" and not "definitely."Is that correct?
I am saying that adaptation is more often than not a "quick-fix" to solve an immediate problem in response to an environmental change. Innovation, on the other hand, is something which requires genuine novelty to be introduced, not just a minor adjustment or tweak.
Second, how does artificial selection, animal breeding I suppose, differ from intelligent design? It seems to me there's no difference between breeding long legged sheep to get longer legged sheep, using only nature and sheep reproduction to do the job, than it would be for nature to produce longer legged sheep because to sheep they're more sexy. What's the difference?
Yes, both natural and artificial selection can converge on the same objective. However, as we can see with certain breeds of dog which would never survive in the wild, artificial selection isn't bound my same "fitness criteria" as natural selection is.

Yardbird · 7 December 2015

Ravi said:
Doc Bill said: Ravi says: "But adaptation is not the same thing as innovation which most likely requires design." Most likely? So, you just said that adaptation "could" provide innovation since design is only "most likely" and not "definitely."Is that correct?
I am saying that adaptation is more often than not a "quick-fix" to solve an immediate problem in response to an environmental change. Innovation, on the other hand, is something which requires genuine novelty to be introduced, not just a minor adjustment or tweak.
Second, how does artificial selection, animal breeding I suppose, differ from intelligent design? It seems to me there's no difference between breeding long legged sheep to get longer legged sheep, using only nature and sheep reproduction to do the job, than it would be for nature to produce longer legged sheep because to sheep they're more sexy. What's the difference?
Yes, both natural and artificial selection can converge on the same objective. However, as we can see with certain breeds of dog which would never survive in the wild, artificial selection isn't bound my same "fitness criteria" as natural selection is.
You keep waving your hands that fast and you're liable to end up flying out the window.

Michael Fugate · 7 December 2015

Ravi said:
Doc Bill said: Ravi says: "But adaptation is not the same thing as innovation which most likely requires design." Most likely? So, you just said that adaptation "could" provide innovation since design is only "most likely" and not "definitely."Is that correct?
I am saying that adaptation is more often than not a "quick-fix" to solve an immediate problem in response to an environmental change. Innovation, on the other hand, is something which requires genuine novelty to be introduced, not just a minor adjustment or tweak.
Second, how does artificial selection, animal breeding I suppose, differ from intelligent design? It seems to me there's no difference between breeding long legged sheep to get longer legged sheep, using only nature and sheep reproduction to do the job, than it would be for nature to produce longer legged sheep because to sheep they're more sexy. What's the difference?
Yes, both natural and artificial selection can converge on the same objective. However, as we can see with certain breeds of dog which would never survive in the wild, artificial selection isn't bound my same "fitness criteria" as natural selection is.
In typical ID/creationist fashion, words are thrown out without operational definitions. Genuine Novelty - wow that must be hard to come by - if we only knew what it referred to....

eric · 7 December 2015

Ravi said: I am saying that adaptation is more often than not a "quick-fix" to solve an immediate problem in response to an environmental change. Innovation, on the other hand, is something which requires genuine novelty to be introduced, not just a minor adjustment or tweak.
So, the fact that the immense variety of life seen on Earth is a result of replacements, rearrangements and copy/pastes of C, T, G, and A units is a pretty good indication of no "innovation" the way you're describing it, right? Its all adaptation. If genuine novelty is your proxy for design, then the fact that every single living thing shares the same DNA system and things like hox genes are conserved through loads of different organisms is a pretty clear empirical observation that phenotypic changes arise from minor adjustment overlaid on minor adjustment ad nauseum, with no novel genetic system anywhere in sight. Right? True novelty is nowhere to be found; every single organism uses a carbon backbone polymer with the same four units, just rearranged. Where is the novelty of other bases used? Where is the novelty of an alpha helix or quadruple helix?
Yes, both natural and artificial selection can converge on the same objective. However, as we can see with certain breeds of dog which would never survive in the wild, artificial selection isn't bound my same "fitness criteria" as natural selection is.
LOL this is the second time in a couple of weeks I've heard this; the "design inferred from crappy fit" argument must be becoming popular. Evidently where we see an organism which isn't adapted to its environment very well, we are to infer Jesus, because evolution wouldn't have done such a crappy job as Jesus obviously did (or so the argument goes). Is that really the argument you want to go with? Talk about your pyrrhic victories.

Ravi · 7 December 2015

Scott F said: If it is catalyzing a new reaction with a novel material that didn't exist before, performing a new function that didn't exist before, then it is a "new" enzyme that didn't exist before. From an evolutionary view point, *every* protein (enzymes are themselves proteins) is simply a pre-existing protein that has been "tinkered with" by random mutations and natural selection.
No. "Nylonase" simply is an esterase with enhanced hydrolytic capability, albeit with some cost too, that already could degrade oligomers associated with the production of nylon: http://www.ncbi.nlm.nih.gov/pubmed/17512009
You now say that a new protein isn't "new" because two mutations aren't "big enough" to be considered "new". Yet just a few comments ago you said that it was "impossible" for a new function to develop that required two mutations, without intelligent intervention. You claimed that two mutations was one of those invisible "barriers" to evolution.
That's because it isn't a new function. It is merely an altered/adjusted preexisting function.
Are you now saying that "research" has demonstrated that there was intelligent intervention in the creation of this not-new enzyme? Have scientists now shown incontrovertible "proof" of an intelligent agent in the creation of nylonase? Have, perhaps, those Intelligent Design "researchers" demonstrated this?
You just don't understand biochemistry well enough to see that "nylonase" is not a new enzyme.

Michael Fugate · 7 December 2015

ravi,
so? new proteins with new functions arise often (see my earlier ink) - going to comment on something relevant or just nitpick on something that doesn't matter?

Mike Elzinga · 7 December 2015

LOL! This is hilarious.

Man; these poor followers of ID/creationism think they have the art of faking knowledge down pat.

They are completely unaware of the fact that their continuous display of the shibboleths of complete ignorance of science is a dead giveaway.

But, if their PhD leaders can't fake it in their socio/political hunger games of clawing their way to the top of the social heap, there is certainly no reason to think that their followers will do any better.

Michael Fugate · 7 December 2015

I still haven't figured out why they believe that their god's existence is contingent on evolution being false. Given that god belief has weathered all kinds of challenges over the millennia, why would evolution lead to its demise? Wouldn't be easier just to accept science and move on?

Ravi · 7 December 2015

Michael Fugate said: ravi, so? new proteins with new functions arise often (see my earlier ink) - going to comment on something relevant or just nitpick on something that doesn't matter?
No. Protein can acquire slightly modified functions which can have a large effect.

Ravi · 7 December 2015

eric said: So, the fact that the immense variety of life seen on Earth is a result of replacements, rearrangements and copy/pastes of C, T, G, and A units is a pretty good indication of no "innovation" the way you're describing it, right? Its all adaptation. If genuine novelty is your proxy for design, then the fact that every single living thing shares the same DNA system and things like hox genes are conserved through loads of different organisms is a pretty clear empirical observation that phenotypic changes arise from minor adjustment overlaid on minor adjustment ad nauseum, with no novel genetic system anywhere in sight. Right? True novelty is nowhere to be found; every single organism uses a carbon backbone polymer with the same four units, just rearranged. Where is the novelty of other bases used? Where is the novelty of an alpha helix or quadruple helix?
All that Darwinian evolution can do is blindly tweak and twinker the product of intelligent design and innovation. This self-adjusting capabiluty of organisms is, nonetheless, essential to their survival as environmental pressures are subject to constant change.
LOL this is the second time in a couple of weeks I've heard this; the "design inferred from crappy fit" argument must be becoming popular. Evidently where we see an organism which isn't adapted to its environment very well, we are to infer Jesus, because evolution wouldn't have done such a crappy job as Jesus obviously did (or so the argument goes). Is that really the argument you want to go with? Talk about your pyrrhic victories.
Natural selection does a pretty good job at keeping a population reproductively fit.

Ravi · 7 December 2015

Michael Fugate said: And a gene can arise "de novo" by a point mutation leading to a start codon in a noncoding region of the genome - it's as simple as that. Links to Carl Zimmer - http://phenomena.nationalgeographic.com/2014/04/29/where-genes-come-from/
This is a controversial claim. The non-coding sequence was already functional and may some transcripts may code for both RNAs and proteins alike.

Scott F · 7 December 2015

Ravi said:
Scott F said: If it is catalyzing a new reaction with a novel material that didn't exist before, performing a new function that didn't exist before, then it is a "new" enzyme that didn't exist before. From an evolutionary view point, *every* protein (enzymes are themselves proteins) is simply a pre-existing protein that has been "tinkered with" by random mutations and natural selection.
No. "Nylonase" simply is an esterase with enhanced hydrolytic capability, albeit with some cost too, that already could degrade oligomers associated with the production of nylon: http://www.ncbi.nlm.nih.gov/pubmed/17512009
You now say that a new protein isn't "new" because two mutations aren't "big enough" to be considered "new". Yet just a few comments ago you said that it was "impossible" for a new function to develop that required two mutations, without intelligent intervention. You claimed that two mutations was one of those invisible "barriers" to evolution.
That's because it isn't a new function. It is merely an altered/adjusted preexisting function.
Are you now saying that "research" has demonstrated that there was intelligent intervention in the creation of this not-new enzyme? Have scientists now shown incontrovertible "proof" of an intelligent agent in the creation of nylonase? Have, perhaps, those Intelligent Design "researchers" demonstrated this?
You just don't understand biochemistry well enough to see that "nylonase" is not a new enzyme.
Now you're just dancing around. Stand still. Define your terms. How do you define a "new" enzyme, in contrast to one that is merely "altered" or adjusted" enzyme? What quantifiable differences make an enzyme "new"? If you give me two enzymes, what do I measure to determine if one is "new" relative to the other? How do you define "new" function? Again, a specific quantifiable definition please. No hand-wavy stuff. I'm sure with your expertise in biology, you can certainly bowl me over. Is "propane" a "new" hydrocarbon relative to "ethane"? How about "butane"? "Pentane"? How many carbon atoms must be added before the molecule is "new"? Or, are they all just "variations" within the same "kind" called "hydrocarbon"? What if I replaced one of the hydrogen atoms with a different kind of atom? Say, for example, an oxygen atom? That's just a simple "alteration" of the molecule, right? Just one simple little change. After all, it's still just a "molecule". It isn't "new". Right? How do you continue to move those goal posts? Now you're getting into the realm of defining "irreducible complexity", which has proven to be nothing more than a set of moving goal posts masquerading as an "argument". But perhaps you'll be better able to do that than Behe was at trial?

eric · 7 December 2015

Ravi said: All that Darwinian evolution can do is blindly tweak and twinker the product of intelligent design and innovation. This self-adjusting capabiluty of organisms is, nonetheless, essential to their survival as environmental pressures are subject to constant change.
This is not a refutation or counter-argument to anything I said. YOU said (paraphrasing) that novelty is the hallmark of design. I pointed out there isn't much novelty in Earth life; it all uses the same basic system, same basic polymer, same subunits. Only genetic arrangement differs. So why should we infer design if the novelty you claim signals it is entirely missing?
Natural selection does a pretty good job at keeping a population reproductively fit.
Yes, but you contrasted it with artificial selection, which you see as relevant to design, and you said that artificial selection doesn't have this fitness constraint. So you're basically arguing that one hallmark of design is the inability of an organism to survive in an environment absent its handlers/designers. Which is, as I said, is basically 'crappy fit, ergo Jesus.' So, 0 for 2 on this response Ravi. You didn't actually address either of my points. Instead you just threw out some non-sequiturs.

Doc Bill · 7 December 2015

I never get a good answer when I pose the question, "What's the difference between natural selection, artificial selection and intelligent design creationism?"

ID creationists are forever touting artificial selection as an example of design, but it isn't. One is simply replacing nature with the breeder to provide selection pressure. The breeder isn't designing anything, rather, hoping for the best. Even supposedly pure bred black poodles will occasionally produce spotted pups.

ID creationism, on the other hand, requires the direct, conscious, knowing, designing, blueprinting manipulation of the gene or genes at the molecular level. How is that done? When is that done? Did the Intelligent Designer (blessed be he) sneak into Lenski's lab and mess with Strain 8 (or whichever)? How could one tell?

Take Darwin's famous orchid, for example. Did the Designer create the orchid first, then the moth with a long tongue, or was it the other way around, or was it simultaneously? Answers, please, inquiring minds want to know.

Just Bob · 7 December 2015

Ravi, could you give us an example of something -- some part of the natural world -- which is NOT designed?

Daniel · 8 December 2015

Doc Bill said: ID creationists are forever touting artificial selection as an example of design, but it isn't. One is simply replacing nature with the breeder to provide selection pressure.
It's even worse, in my opinion. What is the physical difference between humans breeding cows for more milk yield, and ants that very literally farm fungus and herd aphids? I would say none, because the aphids, like our sheep, now depend on the ants for protection and the perpetuation of their species. Perhaps you can say the difference is in Intention (or Purpose), but we can't be sure of that either... perhaps its a gene, perhaps not. Or what is the difference between humans breeding cows knowingly, and cheetahs "breeding" faster/more elusive gazelles unknowingly? Not a single physical difference, merely one of intention. So is it the abstract concept of Intention the difference between natural and artificial selection? If not, then how can we identify the intentional selection humans make with cows with, for example, the selection farmer ants make? If it is Intention, then we cannot call the domestication of the dog and of crops artificial selection, because the prehistoric humans had absolutely no idea they were domesticating them. Ravi called artificial selection "design", claiming that his fitness abyss no longer applies there, but this abyss is present in natural selection, therefore evolution is wrong. Since we know for sure that the only difference between them is the abstract concept of Intention, and we know for sure that prehistoric humans most certainly did not have intention in mind when domesticating both dogs and crops, then it is obvious that his fitness abyss does not exist.

Rolf · 8 December 2015

Ravi said:
So, an intelligent designer can transfer his/her information to an organism by imposing certain conditions and making it respond to them.
How then, well adapted to his habitat, his fitness landscape, is the postualated designer? Is he a grey blob of matter with no discernible features, or is he only a figment of the pious creationist's brain? (My money is on the latter). Where is the evidence, what does he do, where, when and hod does he do it? From all the creationism I've ever seen there is only option left: He is the ultimate magician, making a joke out of all the natural sciences (and 99.9 of all scientists) as required to make ID fly. No science or arguments required, ID is the ultimate trump card. See a problem? ID is the antidote.

Rolf · 8 December 2015

Daniel said:
we know for sure that prehistoric humans most certainly did not have intention in mind when domesticating both dogs and crops, then it is obvious that his fitness abyss does not exist.
Well then, maybe it is time we added more intention to our efforts at modifying flora and fauna to suit our needs? Let us design Chicken Little

Rolf · 8 December 2015

Ravi said
You misunderstood me. Species can adapt, but there are natural limits to how much they can change by. Mike Behe explains this in his book, “Edge of Evolution”. It is a good read.
Yeah, his eloge to science at page 233 is a masterpiece.

harold · 8 December 2015

Michael Fugate said: I still haven't figured out why they believe that their god's existence is contingent on evolution being false. Given that god belief has weathered all kinds of challenges over the millennia, why would evolution lead to its demise? Wouldn't be easier just to accept science and move on?
Because, and this is important to understand, it's a social and political phenomenon. To understand them you have to understand this. Understanding this allows you to predict their behavior. Modeling them as if they were like, say, sincere believers in astrology or UFO abductions, does not. Everyone is free to send their children to private school, home school them, or tell them "In this family we don't accept what those science teachers say", and millions of law abiding if ignorant Americans do just that. But politically aggressive right authoritarian people reject those methods and demand that public schools teach the official religion of their political movement, instead of science. ID is just disguised creation science. Creation science took off in the late sixties, as part of a largely successful right wing reaction to social changes and scientific advances of the time. Creation science was intended to replace teaching of real science in public schools with narrow sectarian science denial. NOT ecumenical, koombaya, "we can still have spiritual meaning" stuff, replace it with claims that science shows that Noah's ark is a literal historical story and therefore latter day harsh authoritarian fundamentalist Protestant Christianity, and NOT other religions, is "scientifically" proven to be "true". Since creation science was about as blatantly unconstitutional as any partly successful education movement in the US, it was eventually shut down by the supreme court, although as you surely know, a much younger Antonin Scalia dissented and argued that right wing "literal Genesis" BS should be favored by the government and taught at taxpayer expense as science. Immediately after Edwards v Aguillard, the case that made officially sanctioned teaching of creation science illegal, ID was born, and the creationist textbook Of Pandas and People suddenly incorporated hilarious and well known language and typos reflecting the "change". ID is just disguised creationism. As I explained above, the presumption is that if "evolution" can be attacked, right wing science denial wins by default. The goal of ID is to push evolution denial and implications that if "evolution" is untrue then Fox News/Limbaugh/Tea Party science denial must be correct into public schools. To drive home the point, let's contrast ID with astrology. Is astrology 100% associated with one political stance? No, while ID advocates are all right wing, and 99% white male conservative Christians, none openly gay, astrology has a diverse fan base. Is astrology associated with a strong movement to replace teaching of science with teaching of astrology in public schools? No again. Do all astrology fans deny human contribution to climate change? No. Do they all oppose legal same gender marriage? No. In fact astrology doesn't even deny major scientific theories, it merely goes beyond them and makes additional claims that cannot be scientifically supported. We see quite a contrast. While belief in astrology is surely correlated with certain types of social biases, it is also a rather "sincere" and "spontaneous" superstition. People don't necessarily start with a political ax to grind and then take up astrology because it seems to rationalize and justify their unpopular political stance. On the other hand, essentially everyone who supports ID was already a right wing authoritarian tuned in to the right wing "conservative" movement before they decided that they support ID. To the best of my knowledge, there are no "converts" due to the quality of ID. (However low you or I may consider the quality of astrology, this is another contrast.) ID in the form being discussed here failed its legal and political mission at Dover. Since then, for ten years now, it has been in sharp decline. Discovery Institute/Behe/Dembski brand ID is just another outdated fashion from turn of the century. However, the underlying sentiment continues to be expressed, and leads to things like cutting funding for scientific research, cutting funding for scientific education, constant efforts to come up with new forms of science denial for public schools, pandering to science denial by all Republican candidates, even some who obviously don't share the belief privately, and so on. If someone wants to bother to understand this stuff they need to understand where it is coming from.

harold · 8 December 2015

harold said:
Michael Fugate said: I still haven't figured out why they believe that their god's existence is contingent on evolution being false. Given that god belief has weathered all kinds of challenges over the millennia, why would evolution lead to its demise? Wouldn't be easier just to accept science and move on?
Because, and this is important to understand, it's a social and political phenomenon. To understand them you have to understand this. Understanding this allows you to predict their behavior. Modeling them as if they were like, say, sincere believers in astrology or UFO abductions, does not. Everyone is free to send their children to private school, home school them, or tell them "In this family we don't accept what those science teachers say", and millions of law abiding if ignorant Americans do just that. But politically aggressive right authoritarian people reject those methods and demand that public schools teach the official religion of their political movement, instead of science. ID is just disguised creation science. Creation science took off in the late sixties, as part of a largely successful right wing reaction to social changes and scientific advances of the time. Creation science was intended to replace teaching of real science in public schools with narrow sectarian science denial. NOT ecumenical, koombaya, "we can still have spiritual meaning" stuff, replace it with claims that science shows that Noah's ark is a literal historical story and therefore latter day harsh authoritarian fundamentalist Protestant Christianity, and NOT other religions, is "scientifically" proven to be "true". Since creation science was about as blatantly unconstitutional as any partly successful education movement in the US, it was eventually shut down by the supreme court, although as you surely know, a much younger Antonin Scalia dissented and argued that right wing "literal Genesis" BS should be favored by the government and taught at taxpayer expense as science. Immediately after Edwards v Aguillard, the case that made officially sanctioned teaching of creation science illegal, ID was born, and the creationist textbook Of Pandas and People suddenly incorporated hilarious and well known language and typos reflecting the "change". ID is just disguised creationism. As I explained above, the presumption is that if "evolution" can be attacked, right wing science denial wins by default. The goal of ID is to push evolution denial and implications that if "evolution" is untrue then Fox News/Limbaugh/Tea Party science denial must be correct into public schools. To drive home the point, let's contrast ID with astrology. Is astrology 100% associated with one political stance? No, while ID advocates are all right wing, and 99% white male conservative Christians, none openly gay, astrology has a diverse fan base. Is astrology associated with a strong movement to replace teaching of science with teaching of astrology in public schools? No again. Do all astrology fans deny human contribution to climate change? No. Do they all oppose legal same gender marriage? No. In fact astrology doesn't even deny major scientific theories, it merely goes beyond them and makes additional claims that cannot be scientifically supported. We see quite a contrast. While belief in astrology is surely correlated with certain types of social biases, it is also a rather "sincere" and "spontaneous" superstition. People don't necessarily start with a political ax to grind and then take up astrology because it seems to rationalize and justify their unpopular political stance. On the other hand, essentially everyone who supports ID was already a right wing authoritarian tuned in to the right wing "conservative" movement before they decided that they support ID. To the best of my knowledge, there are no "converts" due to the quality of ID. (However low you or I may consider the quality of astrology, this is another contrast.) ID in the form being discussed here failed its legal and political mission at Dover. Since then, for ten years now, it has been in sharp decline. Discovery Institute/Behe/Dembski brand ID is just another outdated fashion from turn of the century. However, the underlying sentiment continues to be expressed, and leads to things like cutting funding for scientific research, cutting funding for scientific education, constant efforts to come up with new forms of science denial for public schools, pandering to science denial by all Republican candidates, even some who obviously don't share the belief privately, and so on. If someone wants to bother to understand this stuff they need to understand where it is coming from.
A final important and obvious point. It is important for me to note in advance that I am not religious, nor recommending the Bible as a source of ethics. Nevertheless... If the Bible isn't "literally true" then many parts of it can be "interpreted". The Bible is often condemned for the injustice and violence that it contains and implicitly condones, but its actual commands to contemporary humans slant toward the humane side. The Bible says that God forced Abraham to be about to kill his son as a sacrifice, and then said "just kidding, I was only testing you" at the last minute. But it doesn't say modern people should sacrifice their sons. It does say "do unto others as you would have others do unto you". The Bible has been used to justify slavery, torture, invasions, etc, but it has also been used successfully to argue against that type of thing. Clearly, if you allow the Bible to be "interpreted", you can't claim that it always supports the contemporary American right wing side of things. An extreme example of this was the civil rights movement - Dr. Martin Luther King was a seminary trained theologian and mainstream denominations mainly supported that movement. Technically, the Liberty University version doesn't really make use of a "literal" interpretation. They only "literally" interpret the parts that support their ideology. A lot of the New Testament, in particular, is ignored. Nevertheless, pretty much the only way to tell people "US society must be governed as I say and the harshest obscure passages of the Old Testament, 'interpreted' in various ways even by the most Orthodox rabbinical scholars, must be 'taken literally' in their KJV translation, and when we do this, my demands are justified. And also, they must be ethical, because I claim I got them from the Bible". This is all it's about. ID just denies evolution in a dissembling way because it's implied in their minds that evolution challenged their version of "literal interpretation", so if they can find something wrong with "evolution", they win again, by default, and they have to disguise the religion to get the evolution denial into public schools legally. It may be stupid, but it isn't complicated. Again, to emphasize, I'm not claiming here that the Bible argues for humane policy. I'm just pointing out that those who wish to claim that the most inhumane policy is commanded by the Bible use the ruse, in the contemporary context, of claiming to "interpret the (King James version of) the Bible literally".

eric · 8 December 2015

Doc Bill said: I never get a good answer when I pose the question, "What's the difference between natural selection, artificial selection and intelligent design creationism?"
Darwin specifically contrasted natural vs. artificial selection in OOS to make the point that nature without humans can do the same thing humans can do. He was making a teaching point rather than a philosophical point, and wasn't using 'natural' in the broad physical sense of 'anything that's possible under what we know of as scientific laws of nature.' Obviously if we use that definition, artificial selection by humans *is* natural selection. His definition is probably still pretty good as long as we don't confusingly insist that 'artificial' be contrasted with the big broad usage of 'natural', because that contrast makes no sense. Artificial is the selection humans (or other, yet-to-be-discovered sentient species) do, natural is the selection other (non-sentient) species and things in the environment do.
ID creationists are forever touting artificial selection as an example of design, but it isn't. One is simply replacing nature with the breeder to provide selection pressure. The breeder isn't designing anything, rather, hoping for the best. Even supposedly pure bred black poodles will occasionally produce spotted pups.
If you're going with 'direct genetic replacement/substitution/insertion' as a signal of design, then possibly some viruses would count as designers. Assuming you aren't hung up on requiring a designer to be sentient or have intention.

TomS · 8 December 2015

eric said:
Doc Bill said: I never get a good answer when I pose the question, "What's the difference between natural selection, artificial selection and intelligent design creationism?"
Darwin specifically contrasted natural vs. artificial selection in OOS to make the point that nature without humans can do the same thing humans can do. He was making a teaching point rather than a philosophical point, and wasn't using 'natural' in the broad physical sense of 'anything that's possible under what we know of as scientific laws of nature.' Obviously if we use that definition, artificial selection by humans *is* natural selection. His definition is probably still pretty good as long as we don't confusingly insist that 'artificial' be contrasted with the big broad usage of 'natural', because that contrast makes no sense. Artificial is the selection humans (or other, yet-to-be-discovered sentient species) do, natural is the selection other (non-sentient) species and things in the environment do.
ID creationists are forever touting artificial selection as an example of design, but it isn't. One is simply replacing nature with the breeder to provide selection pressure. The breeder isn't designing anything, rather, hoping for the best. Even supposedly pure bred black poodles will occasionally produce spotted pups.
If you're going with 'direct genetic replacement/substitution/insertion' as a signal of design, then possibly some viruses would count as designers. Assuming you aren't hung up on requiring a designer to be sentient or have intention.
Have the advocates of ID told us anything about what they mean by "intelligent"?

DS · 8 December 2015

TomS said: Have the advocates of ID told us anything about what they mean by "intelligent"?
They weren't intelligent enough to do that. I guess "No intelligence allowed" is actually their motto.

DS · 8 December 2015

Or maybe the intelligent designer just has Alzheimer's. You know, intelligent enough to design an elephant, but can't seem to remember how she did it.

harold · 8 December 2015

Have the advocates of ID told us anything about what they mean by “intelligent”?
Just in case there is anyone who doesn't know this reading, I'll explain why they haven't. ID is not an example of spontaneous generation. It evolved from creation science due through incremental changes, which were contingent on what was already there. Essentially, creation science encountered a challenge in the environment. It was ruled illegal to teach it in tax payer funded public school science class, due to its rather comically obvious unconstitutional nature. All parts of creation science that openly referred to the right wing Christian God actually doing miracles, or to open dating of events based on "literal interpretation of Genesis" were selected against. These elements were not replaced. Rather, in the face of environmental challenge, a camouflage strategy quickly evolved. ID consists of creation science, except where creation science would say something like "these data provide scientific evidence that God created a global flood 4000 years ago, in which everyone but Noah and his family perished"; ID uses a dissembling camouflage strategy that occasionally fools some observers. ID advocates may even make comments along that lines that the Earth "may" be more than 10,000 years old. Anyone with a brain can see that this is just disguised creation science. If I say the sky is green, Bubba says it's blue, and Buck comes along and says it might be blue or green, Buck and I are both wrong and Buck is pandering to me and/or claiming that the sky is green in a dissembling way. Asking ID to tell you who the designer is and what the designer did is like asking chameleons to stop changing color. The point of ID is to support creationist claims by "attacking" evolution, by promoting those claims in a disguised way. The "designer" is always secretly the Liberty University God, but it can't be stated out loud.

harold · 8 December 2015

harold said:
Have the advocates of ID told us anything about what they mean by “intelligent”?
Just in case there is anyone who doesn't know this reading, I'll explain why they haven't. ID is not an example of spontaneous generation. It evolved from creation science due through incremental changes, which were contingent on what was already there. Essentially, creation science encountered a challenge in the environment. It was ruled illegal to teach it in tax payer funded public school science class, due to its rather comically obvious unconstitutional nature. All parts of creation science that openly referred to the right wing Christian God actually doing miracles, or to open dating of events based on "literal interpretation of Genesis" were selected against. These elements were not replaced. Rather, in the face of environmental challenge, a camouflage strategy quickly evolved. ID consists of creation science, except where creation science would say something like "these data provide scientific evidence that God created a global flood 4000 years ago, in which everyone but Noah and his family perished"; ID uses a dissembling camouflage strategy that occasionally fools some observers. ID advocates may even make comments along that lines that the Earth "may" be more than 10,000 years old. Anyone with a brain can see that this is just disguised creation science. If I say the sky is green, Bubba says it's blue, and Buck comes along and says it might be blue or green, Buck and I are both wrong and Buck is pandering to me and/or claiming that the sky is green in a dissembling way. Asking ID to tell you who the designer is and what the designer did is like asking chameleons to stop changing color. The point of ID is to support creationist claims by "attacking" evolution, by promoting those claims in a disguised way. The "designer" is always secretly the Liberty University God, but it can't be stated out loud.
To elaborate, as I have noted before - 1) They can never say that the designer is the American (and Australian and Canadian) Right Wing God, because the fundamental theorem of ID - which has been proven false - is that ID can get around Edwards and get evolution denial into public school science class. 2) They can also never say that the designer is NOT the Right Wing God, either, because all their supporters support them based on the tacit understanding that it is. By definition, they cannot ever comment on who the designer is, what the designer did, when the designer did it, etc.

Michael Fugate · 8 December 2015

Ravi said:
Michael Fugate said: And a gene can arise "de novo" by a point mutation leading to a start codon in a noncoding region of the genome - it's as simple as that. Links to Carl Zimmer - http://phenomena.nationalgeographic.com/2014/04/29/where-genes-come-from/
This is a controversial claim. The non-coding sequence was already functional and may some transcripts may code for both RNAs and proteins alike.
So everything is designed. Good to know.

eric · 8 December 2015

TomS said: Have the advocates of ID told us anything about what they mean by "intelligent"?
I think it's safe to say that cdesign proponentists think its the cdesignertor.

harold · 8 December 2015

Michael Fugate said:
Ravi said:
Michael Fugate said: And a gene can arise "de novo" by a point mutation leading to a start codon in a noncoding region of the genome - it's as simple as that. Links to Carl Zimmer - http://phenomena.nationalgeographic.com/2014/04/29/where-genes-come-from/
This is a controversial claim. The non-coding sequence was already functional and may some transcripts may code for both RNAs and proteins alike.
So everything is designed. Good to know.
"Everything is designed but we can see how an atheist might not think a rock is designed but a living cell is like, really obviously designed too much for anyone to deny it" would be the actual argument.

harold · 8 December 2015

Michael Fugate said:
Ravi said:
Michael Fugate said: And a gene can arise "de novo" by a point mutation leading to a start codon in a noncoding region of the genome - it's as simple as that. Links to Carl Zimmer - http://phenomena.nationalgeographic.com/2014/04/29/where-genes-come-from/
This is a controversial claim. The non-coding sequence was already functional and may some transcripts may code for both RNAs and proteins alike.
So everything is designed. Good to know.
And yes, this is another corner they've painted themselves into. Dissembling is tricky work. 1) They can't say the designer isn't Liberty University God because all their money comes from the tacit understanding that it is. 2) They can't say the designer is Liberty University God either, because the whole point of ID is to disguise that fact as a silly legal strategy. So they can't ever say anything positive about who the designer is, what it did, when it did it, etc. And also... 3) They can't say that anything isn't designed, because again, their funding comes from people who think that everything is designed. 4) They can't say that everything is designed, either, because their silly game is pretending to prove that some things are designed, which at least implies that some other things aren't, or are less designed, or something. So they can't really do much of anything. They can't offer a test of whether things are designed or not that really works, of course. They can't look for evidence of who the designer is, of course. All they can do is repeat silly anti-evolution arguments.

eric · 8 December 2015

harold said: So they can't really do much of anything. They can't offer a test of whether things are designed or not that really works, of course. They can't look for evidence of who the designer is, of course.
Well on that last point I think its more accurate to say that their funders want the money spent on Christian outreach rather than looking for who the designer is. Folk like Ahmanson would rather their 'research' money go to the research of convincing communities to put prayer back in school and God back in science classes, than doing science. But otherwise, I generally agree. To extend a metaphor (...badly), the tent is so big that only meaningless platitude-poles can hold it up.

TomS · 8 December 2015

harold said:
Michael Fugate said:
Ravi said:
Michael Fugate said: And a gene can arise "de novo" by a point mutation leading to a start codon in a noncoding region of the genome - it's as simple as that. Links to Carl Zimmer - http://phenomena.nationalgeographic.com/2014/04/29/where-genes-come-from/
This is a controversial claim. The non-coding sequence was already functional and may some transcripts may code for both RNAs and proteins alike.
So everything is designed. Good to know.
And yes, this is another corner they've painted themselves into. Dissembling is tricky work. 1) They can't say the designer isn't Liberty University God because all their money comes from the tacit understanding that it is. 2) They can't say the designer is Liberty University God either, because the whole point of ID is to disguise that fact as a silly legal strategy. So they can't ever say anything positive about who the designer is, what it did, when it did it, etc. And also... 3) They can't say that anything isn't designed, because again, their funding comes from people who think that everything is designed. 4) They can't say that everything is designed, either, because their silly game is pretending to prove that some things are designed, which at least implies that some other things aren't, or are less designed, or something. So they can't really do much of anything. They can't offer a test of whether things are designed or not that really works, of course. They can't look for evidence of who the designer is, of course. All they can do is repeat silly anti-evolution arguments.
And then there is the question about the state of things before they were designed. Were the pre-flagellum bacteria designed? Necessity is the mother of invention. What necessity does a Intelligent Designer confront that leads to design? There is a good reason (aside from the legal one) not to go into details about design.

Just Bob · 8 December 2015

Still there, Ravi?

Ravi, could you give us an example of something – some part of the natural world – which is NOT designed?

DS · 8 December 2015

Three days ago Nick gave Ravi a link that included several papers published on the evolution of protein folds. You know, papers published by the experts, the guys who have all of the knowledge required in order to satisfy the incredulous. in other words, exactly what Ravi demanded. Here is an example:

http://www.sciencedirect.com/science/article/pii/S0959440X0200338X

So, did the expert conclude that the evolution of protein folds could not occur? No he did not. In fact, he identified mechanisms by which such evolution has occurred. Imagine that.

Now Ravi has yet to read these papers, or comment on them. Not too surprising really, since the topic of this thread was the no free lunch scam perpetrated by Dembski. But after admitting that Dembski didn't know what he was talking about, Ravi just had to find some way to deflect the conversation. That he did accomplish. The ensuing tirades would make Gish himself proud. And of course along the way he succeeded in demolishing several creationist icons, conservation of information, beneficial mutations, etc.

Way to go Ravi. Are you proud of you accomplishments? And I notice that you still haven't had the guts to show up on the bathroom wall to defend your nonsense. I wonder why?

Doc Bill · 8 December 2015

TomS said: And then there is the question about the state of things before they were designed. Were the pre-flagellum bacteria designed?
This is jet-powered goal post moving. Even the IDiots can barely hang on. Little Stevie Meyer threw this Hail Mary during his "debate" with Charles Marshall some years ago. Marshall had deftly knocked all the wind out of Meyer's arguments for the rise of Cambrian fauna etc. Meyer finally spluttered, "Well, you haven't explained the origin of information at the beginning of life" or some such nonsense. Marshall ended by observing that there was no point in having a rational scientific discussion Meyer the IDiot. So, yeah, the hairless bacterium had to have been designed and the Designer (blessed be he!) knew the flagella motor would come later which, lo and behold, it did. It's a pathetic level of detail that Dembski didn't address either, lest it cost him another bottle of scotch.

harold · 8 December 2015

Doc Bill said:
TomS said: And then there is the question about the state of things before they were designed. Were the pre-flagellum bacteria designed?
This is jet-powered goal post moving. Even the IDiots can barely hang on. Little Stevie Meyer threw this Hail Mary during his "debate" with Charles Marshall some years ago. Marshall had deftly knocked all the wind out of Meyer's arguments for the rise of Cambrian fauna etc. Meyer finally spluttered, "Well, you haven't explained the origin of information at the beginning of life" or some such nonsense. Marshall ended by observing that there was no point in having a rational scientific discussion Meyer the IDiot. So, yeah, the hairless bacterium had to have been designed and the Designer (blessed be he!) knew the flagella motor would come later which, lo and behold, it did. It's a pathetic level of detail that Dembski didn't address either, lest it cost him another bottle of scotch.
Yes, that's another "paradox" of ID, isn't it? They argue against abiogenesis. Why argue that the bacterial flagellum is designed if the whole bacterium itself is descended from a magically designed ancestor? The final answer is, ID has ideological consistency, but not logical consistency. ID follows three rules = 1) Always deny evolution. 2) Never overtly admit or deny that the designer is the fundamentalist god. 3) Use BS that sounds kind of like science. No requirement for logical coherence exists. They thought (wrongly) that talking about the "bacterial flagellum" would make people think they were science experts. Their discussions of it are literally not even wrong. The bacterial flagellum clearly evolved, but that's not the point. They aren't even arguing for a specific miraculous event that particularly caused the bacterial flagellum. They just wanted to say "The (fancy words) is too complicated to have evolved. Therefore the theory of evolution must be completely wrong". Although ID advocates are not consciously deceiving, they are by habit deeply dishonest with themselves and others. ID is a deeply dishonest body of work. It is an attempt to create an implied version of right wing Protestant "creation science" than can't be recognized in a court of law as having religious motivations. Therefore, although not consciously liars in a personal sense, they run into the same problem that deliberate liars do, especially in a court of law. They cannot make their story make sense, because they are trying to disguise their motivations and deny the obvious evidence against them.

Michael Fugate · 8 December 2015

Doc Bill said:
TomS said: And then there is the question about the state of things before they were designed. Were the pre-flagellum bacteria designed?
This is jet-powered goal post moving. Even the IDiots can barely hang on. Little Stevie Meyer threw this Hail Mary during his "debate" with Charles Marshall some years ago. Marshall had deftly knocked all the wind out of Meyer's arguments for the rise of Cambrian fauna etc. Meyer finally spluttered, "Well, you haven't explained the origin of information at the beginning of life" or some such nonsense. Marshall ended by observing that there was no point in having a rational scientific discussion Meyer the IDiot. So, yeah, the hairless bacterium had to have been designed and the Designer (blessed be he!) knew the flagella motor would come later which, lo and behold, it did. It's a pathetic level of detail that Dembski didn't address either, lest it cost him another bottle of scotch.
Now I see where Ravi is coming from. When the designer made the first fruit fly, it made the fly's genome totally functional, but only turned on the genes it needed then. Over the course of time, it has occasionally turned on other genes as needed. There are still genes in the non-coding regions of the fly's genome that the designer has yet to turn on, but they're there. The designer knew perfectly well when, where, how, what and why the day the first fly was designed all the genes stand all of its descendants would ever need. The designer is a mighty, might designer.

TomS · 8 December 2015

Michael Fugate said:
Doc Bill said:
TomS said: And then there is the question about the state of things before they were designed. Were the pre-flagellum bacteria designed?
This is jet-powered goal post moving. Even the IDiots can barely hang on. Little Stevie Meyer threw this Hail Mary during his "debate" with Charles Marshall some years ago. Marshall had deftly knocked all the wind out of Meyer's arguments for the rise of Cambrian fauna etc. Meyer finally spluttered, "Well, you haven't explained the origin of information at the beginning of life" or some such nonsense. Marshall ended by observing that there was no point in having a rational scientific discussion Meyer the IDiot. So, yeah, the hairless bacterium had to have been designed and the Designer (blessed be he!) knew the flagella motor would come later which, lo and behold, it did. It's a pathetic level of detail that Dembski didn't address either, lest it cost him another bottle of scotch.
Now I see where Ravi is coming from. When the designer made the first fruit fly, it made the fly's genome totally functional, but only turned on the genes it needed then. Over the course of time, it has occasionally turned on other genes as needed. There are still genes in the non-coding regions of the fly's genome that the designer has yet to turn on, but they're there. The designer knew perfectly well when, where, how, what and why the day the first fly was designed all the genes stand all of its descendants would ever need. The designer is a mighty, might designer.
How did the change of the world come about which called for a change in the bacteria? It begins to sound like the designer designed a changing world. Just how was the potential for producing flagella built into the original complement of DNA? One way would be to put the sequence of genes present in the full form but inactivated. But that is subject to disruption when it is not being used. It would not be beyond the capability of the designer to allow some other way for the genes to appear. How can we rule out that the designer designed life with evolution built in?

Michael Fugate · 8 December 2015

TomS said:
Michael Fugate said:
Doc Bill said:
TomS said: And then there is the question about the state of things before they were designed. Were the pre-flagellum bacteria designed?
This is jet-powered goal post moving. Even the IDiots can barely hang on. Little Stevie Meyer threw this Hail Mary during his "debate" with Charles Marshall some years ago. Marshall had deftly knocked all the wind out of Meyer's arguments for the rise of Cambrian fauna etc. Meyer finally spluttered, "Well, you haven't explained the origin of information at the beginning of life" or some such nonsense. Marshall ended by observing that there was no point in having a rational scientific discussion Meyer the IDiot. So, yeah, the hairless bacterium had to have been designed and the Designer (blessed be he!) knew the flagella motor would come later which, lo and behold, it did. It's a pathetic level of detail that Dembski didn't address either, lest it cost him another bottle of scotch.
Now I see where Ravi is coming from. When the designer made the first fruit fly, it made the fly's genome totally functional, but only turned on the genes it needed then. Over the course of time, it has occasionally turned on other genes as needed. There are still genes in the non-coding regions of the fly's genome that the designer has yet to turn on, but they're there. The designer knew perfectly well when, where, how, what and why the day the first fly was designed all the genes stand all of its descendants would ever need. The designer is a mighty, might designer.
How did the change of the world come about which called for a change in the bacteria? It begins to sound like the designer designed a changing world. Just how was the potential for producing flagella built into the original complement of DNA? One way would be to put the sequence of genes present in the full form but inactivated. But that is subject to disruption when it is not being used. It would not be beyond the capability of the designer to allow some other way for the genes to appear. How can we rule out that the designer designed life with evolution built in?
Of course there can be corruption - the FALL happened - so even though the designer made the first fly perfect and able to adapt to any and all future environmental changes (the designer knew organisms would alter the environment just by being alive) it wouldn't ever be able to reach it full godly flyness because Adam and Eve sinned. Sad, but true.

Dave Luckett · 8 December 2015

So, if we stipulate a designer, it has to be an agency that has perfect knowledge of all interactions of everything in the Universe throughout all time and all space. Nothing else could possibly possess the infinite foresight required.

Umm. I can't think what that might be.

Steve · 8 December 2015

Nick Matzke,

Nonsense. The active information is in excess reproduction (repeated queries).

Excess reproduction drives the variation, which is then optimized by natural selection.

Hence, variation and selection cannot account for excess reproduction. That would be putting the cart before the horse.

So no, non-teleological step-wise change (NTSWC) cannot and does not create new information. It only optimizes (rearranges) what has already been produced.

Design uses the frequency and quantity of excess reproduction to provide enough variation, which natural selection can optimize. This allows for organisms to withstand any change in the environment without having any foresight, since the foresight is in the design of the system.

DEM are right, and English/Felsenstein/and now Matzke are wrong.

Game, set, match for DEM.

Steve · 9 December 2015

Dave Luckett, The designer's foresight is in understanding what is required of organisms to survive within a changing biosphere. Excess reproduction creating variaton optimized by natural selection provides the perfect solution that does not require each individual organism to itself possess foresight. They throw out numerous offspring, guaranteeing at least one survives, no matter what the changes in the environment present. The offspring that do not survive are early participants in the food chain, meaning organisms pay their rent in advance. The neighbors are happy, they are happy and life persists. NTSWC cannot account for these integrated, interactive systems that we call the biosphere. Design can, precisely because design is teleological and uses foresight to build a system. The better the foresight, the better the system.
Dave Luckett said: So, if we stipulate a designer, it has to be an agency that has perfect knowledge of all interactions of everything in the Universe throughout all time and all space. Nothing else could possibly possess the infinite foresight required. Umm. I can't think what that might be.

Yardbird · 9 December 2015

Steve said: Excess reproduction.
Excess to what?

Mike Elzinga · 9 December 2015

Steve said: Nick Matzke, Nonsense. The active information is in excess reproduction (repeated queries). Excess reproduction drives the variation, which is then optimized by natural selection. Hence, variation and selection cannot account for excess reproduction. That would be putting the cart before the horse. So no, non-teleological step-wise change (NTSWC) cannot and does not create new information. It only optimizes (rearranges) what has already been produced. Design uses the frequency and quantity of excess reproduction to provide enough variation, which natural selection can optimize. This allows for organisms to withstand any change in the environment without having any foresight, since the foresight is in the design of the system. DEM are right, and English/Felsenstein/and now Matzke are wrong. Game, set, match for DEM.
According to a Dembski, Ewert, and Marks calculation, the "information" in 64 grams of copper is - log21186x10^23. Can you do their math for them? There is twice as much information in 128 grams of copper. Not only can copper nuggets of mass 64 grams not exist in the lifetime of the universe, they can't increase in information either. Maybe you can explain why DE&M didn't win the 2013 Nobel Prize in chemistry for their mathematical calculations of the probabilities of molecular assemblies. Shouldn't that be a major slight for you ID/creationists? I also recall that you ran away from a little concept test about entropy quite a while back. Have you made any progress on that test yet? You seem to "know" so much about everything that I would think it would have been a piece of cake for you.

TomS · 9 December 2015

Mike Elzinga said:
Steve said: Nick Matzke, Nonsense. The active information is in excess reproduction (repeated queries). Excess reproduction drives the variation, which is then optimized by natural selection. Hence, variation and selection cannot account for excess reproduction. That would be putting the cart before the horse. So no, non-teleological step-wise change (NTSWC) cannot and does not create new information. It only optimizes (rearranges) what has already been produced. Design uses the frequency and quantity of excess reproduction to provide enough variation, which natural selection can optimize. This allows for organisms to withstand any change in the environment without having any foresight, since the foresight is in the design of the system. DEM are right, and English/Felsenstein/and now Matzke are wrong. Game, set, match for DEM.
According to a Dembski, Ewert, and Marks calculation, the "information" in 64 grams of copper is - log21186x10^23. Can you do their math for them? There is twice as much information in 128 grams of copper. Not only can copper nuggets of mass 64 grams not exist in the lifetime of the universe, they can't increase in information either. Maybe you can explain why DE&M didn't win the 2013 Nobel Prize in chemistry for their mathematical calculations of the probabilities of molecular assemblies. Shouldn't that be a major slight for you ID/creationists? I also recall that you ran away from a little concept test about entropy quite a while back. Have you made any progress on that test yet? You seem to "know" so much about everything that I would think it would have been a piece of cake for you.
Has it been determined that information is an extensive property? How much information is there is one atom of copper? In one neutron in a copper nucleus? A quark?

Steve · 9 December 2015

If Im not mistaken Mike, this OP is responding to DEM's assertion that non-teleological step-wise change (NTSWC) cannot create new information, only optimize it. Find an OP on entropy and we can talk there. Also, in the context of this OP, information is not being calculated. The issue is with the probability that NTSWC creates new information. DEM show that it does not, which is a no-brainer since we (both sides of the aisle) agree natural selection is an optimizer, thus implying that it works on something that already exists, not something that it is in the process of making. Again, variation and selection only happen because there is enough frequency and quantity of offspring to work off of. Variation and selection are components of a designed system that is driven by excess reproduction, not the other way around.
Mike Elzinga said:
Steve said: Nick Matzke, Nonsense. The active information is in excess reproduction (repeated queries). Excess reproduction drives the variation, which is then optimized by natural selection. Hence, variation and selection cannot account for excess reproduction. That would be putting the cart before the horse. So no, non-teleological step-wise change (NTSWC) cannot and does not create new information. It only optimizes (rearranges) what has already been produced. Design uses the frequency and quantity of excess reproduction to provide enough variation, which natural selection can optimize. This allows for organisms to withstand any change in the environment without having any foresight, since the foresight is in the design of the system. DEM are right, and English/Felsenstein/and now Matzke are wrong. Game, set, match for DEM.
According to a Dembski, Ewert, and Marks calculation, the "information" in 64 grams of copper is - log21186x10^23. Can you do their math for them? There is twice as much information in 128 grams of copper. Not only can copper nuggets of mass 64 grams not exist in the lifetime of the universe, they can't increase in information either. Maybe you can explain why DE&M didn't win the 2013 Nobel Prize in chemistry for their mathematical calculations of the probabilities of molecular assemblies. Shouldn't that be a major slight for you ID/creationists? I also recall that you ran away from a little concept test about entropy quite a while back. Have you made any progress on that test yet? You seem to "know" so much about everything that I would think it would have been a piece of cake for you.

gnome de net · 9 December 2015

Steve said:
Dave Luckett said: So, if we stipulate a designer, it has to be an agency that has perfect knowledge of all interactions of everything in the Universe throughout all time and all space. Nothing else could possibly possess the infinite foresight required. Umm. I can't think what that might be.
The designer's foresight is in understanding what is required of organisms to survive within a changing biosphere. Excess reproduction creating variaton optimized by natural selection provides the perfect solution that does not require each individual organism to itself possess foresight. They throw out numerous offspring, guaranteeing at least one survives, no matter what the changes in the environment present. The offspring that do not survive are early participants in the food chain, meaning organisms pay their rent in advance. The neighbors are happy, they are happy and life persists. NTSWC cannot account for these integrated, interactive systems that we call the biosphere. Design can, precisely because design is teleological and uses foresight to build a system. The better the foresight, the better the system.
So your proposed designer lacks perfect knowledge and foresight?

eric · 9 December 2015

Steve said: The active information is in excess reproduction (repeated queries). Excess reproduction drives the variation, which is then optimized by natural selection. Hence, variation and selection cannot account for excess reproduction. That would be putting the cart before the horse.
I think you're wrong in describing where Dembski, Ewart, and others place active information. AFAIK they don't place it solely or even at all in 'excess reproduction.' They place it in the environment; it is the external information that contributes to fitness definition or fitness goals if you will. So I think you are mischaracterizing the ID side, at least as Ewart (the subject of the OP) would describe it. Having said that, I don't think anyone is claiming variation and selection account for 'excess' reproduction (scare quotes because...what do you consider excess? How do we decide what excess is? In excess of what standard?). Nonbiological inorganic and organic catalytic reactions can occur more than once, so it seems to me very safe to say that under abiogenesis we would expect the replicators to have had that 'reproduce more than once' capability originally, from "generation zero" as it were. Because that capability is shared by pretty much all chemical compounds, biological and nonbiological both, due to how chemistry works.
So no, non-teleological step-wise change (NTSWC) cannot and does not create new information. It only optimizes (rearranges) what has already been produced.
Define information. Does a change in a string from "ABAB" to "ABABABAB" increase information?

Just Bob · 9 December 2015

Steve said: They throw out numerous offspring, guaranteeing at least one survives, no matter what the changes in the environment present.
"Survives to reproduce" I assume you mean; otherwise what's the point? But -- really now -- I'd like you to name any creature on Earth that can guarantee that even one of its offspring will survive, "no matter what the changes in the environment."

Michael Fugate · 9 December 2015

The creationist overlords at ID Central must have noticed Ravi was floundering so they benched him in favor of Steve. Steve, in typical fashion, throws out new undefined terms to deflect criticism. So Steve can you operationally define "active information" and "excess reproduction"? Doesn't fitness depend on both survival and reproduction and doesn't this mean Steve doesn't have a clue?

Daniel · 9 December 2015

Michael Fugate said: Of course there can be corruption - the FALL happened - so even though the designer made the first fly perfect and able to adapt to any and all future environmental changes (the designer knew organisms would alter the environment just by being alive)
gnome de net said: So your proposed designer lacks perfect knowledge and foresight?
And of course, according to creationists, before the Fall the Creation was perfect, an unchanging paradise with no predation nor any kind of selective pressure. So The Designer made the first fly able to adapt to any and all future environmental changes, even thou there were none in the beginning... which of course leads to the inevitable conclusion that The Designer knew beforehand that Adam and Eve would be convinced by a talking snake to eat the forbidden fruit, which would lead to The Fall, which would lead to death and disease and hunger and migration and runaway plate tectonics creating all the different environments, which would lead to organisms having to adapt... therefore praise the foresight of The Designer for making the fly able to adapt to anything. Of course, this also begs the question... if The Designer knew beforehand that there would be a Fall and death and suffering, why did he simply NOT plant that tree? Or why not just, you know, shrug his shoulders and say "no biggie"?

Doc Bill · 9 December 2015

Steve said: design is teleological and uses foresight to build a system.
How do you know that design is teleological? What exactly does that mean? A real example from biology would be nice. You have that, right?

Michael Fugate · 9 December 2015

Doc Bill said:
Steve said: design is teleological and uses foresight to build a system.
How do you know that design is teleological? What exactly does that mean? A real example from biology would be nice. You have that, right?
Theodicy Steve theodicy - what's yours?

TomS · 9 December 2015

Steve said: Dave Luckett, The designer's foresight is in understanding what is required of organisms to survive within a changing biosphere. Excess reproduction creating variaton optimized by natural selection provides the perfect solution that does not require each individual organism to itself possess foresight. They throw out numerous offspring, guaranteeing at least one survives, no matter what the changes in the environment present. The offspring that do not survive are early participants in the food chain, meaning organisms pay their rent in advance. The neighbors are happy, they are happy and life persists. NTSWC cannot account for these integrated, interactive systems that we call the biosphere. Design can, precisely because design is teleological and uses foresight to build a system. The better the foresight, the better the system.
Dave Luckett said: So, if we stipulate a designer, it has to be an agency that has perfect knowledge of all interactions of everything in the Universe throughout all time and all space. Nothing else could possibly possess the infinite foresight required. Umm. I can't think what that might be.
Design does not build anything. For example, the "Penrose triangle". Or see the Wikipedia article on "Unfinished created work".

Mike Elzinga · 9 December 2015

TomS said: Has it been determined that information is an extensive property? How much information is there is one atom of copper? In one neutron in a copper nucleus? A quark?
If you use Dembski's type of calculation, yes. log21186x10^23 = (6x1023) x log2118. Twice as many moles, twice the "information." This is one of the major reasons that D/creationist calculations make no sense whatsoever- besides the fact that they have absolutely nothing to do with the properties and behaviors of atoms and molecules; or even other things that interact among themselves.

Just Bob · 9 December 2015

Hey Steve! Ravi didn't seem to want to touch this, but I bet you could do it in your sleep:
Just Bob said: Ravi, could you give us an example of something – some part of the natural world – which is NOT designed?

TomS · 9 December 2015

Mike Elzinga said:
TomS said: Has it been determined that information is an extensive property? How much information is there is one atom of copper? In one neutron in a copper nucleus? A quark?
If you use Dembski's type of calculation, yes. log21186x10^23 = (6x1023) x log2118. Twice as many moles, twice the "information." This is one of the major reasons that D/creationist calculations make no sense whatsoever- besides the fact that they have absolutely nothing to do with the properties and behaviors of atoms and molecules; or even other things that interact among themselves.
So, when a bacterium divides, it is doubling the amount of information. Presumably by purely naturalistic, physical, materialistic means. When a plant or animal grows, it is increasing the amount of information. When a crystal grows.

DS · 9 December 2015

Just Bob said:
Steve said: They throw out numerous offspring, guaranteeing at least one survives, no matter what the changes in the environment present.
"Survives to reproduce" I assume you mean; otherwise what's the point? But -- really now -- I'd like you to name any creature on Earth that can guarantee that even one of its offspring will survive, "no matter what the changes in the environment."
So design cannot account for extinction either. Good to know.

Mike Elzinga · 9 December 2015

TomS said:
Mike Elzinga said:
TomS said: Has it been determined that information is an extensive property? How much information is there is one atom of copper? In one neutron in a copper nucleus? A quark?
If you use Dembski's type of calculation, yes. log21186x10^23 = (6x1023) x log2118. Twice as many moles, twice the "information." This is one of the major reasons that D/creationist calculations make no sense whatsoever- besides the fact that they have absolutely nothing to do with the properties and behaviors of atoms and molecules; or even other things that interact among themselves.
So, when a bacterium divides, it is doubling the amount of information. Presumably by purely naturalistic, physical, materialistic means. When a plant or animal grows, it is increasing the amount of information. When a crystal grows.
Exactly! And, as you can see from the response of a typical follower of ID/creationism,

If Im not mistaken Mike, this OP is responding to DEM’s assertion that non-teleological step-wise change (NTSWC) cannot create new information, only optimize it. Find an OP on entropy and we can talk there. Also, in the context of this OP, information is not being calculated. The issue is with the probability that NTSWC creates new information. DEM show that it does not, which is a no-brainer since we (both sides of the aisle) agree natural selection is an optimizer, thus implying that it works on something that already exists, not something that it is in the process of making. Again, variation and selection only happen because there is enough frequency and quantity of offspring to work off of. Variation and selection are components of a designed system that is driven by excess reproduction, not the other way around.

none of these poor guys has any clue about what "information" is, how Dembski calculates it, and that it makes no sense in any real context of physical objects that can vary in size and in their access to resources; the latter showing up in the log2118 in my example. This math, no matter how simple and irrelevant, is far, far over the heads of any ID/creationist followers. There is no hope of explaining its irrelevancy to them.

Michael Fugate · 9 December 2015

Mike says
...none of these poor guys has any clue about what “information” is...
Ain't that the truth.

prongs · 9 December 2015

SETI seeks to discover intelligence in electromagnetic signals from outer space. Their criterion to judge their success is human-invented electromagnetic signals, in both physics and statistics.

Historically creationists, like Paley, have sought to discover intelligence in Nature (like a watch laying out on the heath). Their criterion to judge their success was "Is it complicated, like a human-invented watch?" (Aha! A watch laying out on the heath. Is it complicated, like a human-invented watch? Yes? Then it must be designed, and if it wasn't designed by a human, it must have been designed by the Great Designer.)

Modern-day creationists seek to discover intelligence in Nature. Their criterion to judge their success is, "Is it complicated, so complicated I can't imagine how anyone could design it. Since we mere humans can barely understand it, it must have been designed by the Great Designer. Case closed."

And you know who the Great Designer is.

We are still in the Stone Age.

Dave Luckett · 9 December 2015

In fairness, Paley did go a little further than mere complication. He also observed that a watch is made to perform a specific function, which it achieves by the purposeful arrangement of parts. He attempted to argue that living things also demonstrate such a purposeful arrangement of parts, hence that design may be inferred.

The argument breaks down when one makes these further observations of living things: that their purpose, if you can call it that, is simply to survive and to successfully reproduce, BUT they do not invariably perform that function, AND that their unique property is reproduction with variation. The rest of evolution follows from that simple understanding.

Doc Bill · 9 December 2015

Looks like IDiot Steve and IDiot Levi hit the road because - D'oh!

gnome de net · 9 December 2015

They've negotiated the obstacles of the PT proving ground and are now ready to go out in the world to convert the heathen hordes.

Steve · 10 December 2015

Active information is not a new undefined term. It is defined as repeated queries. It is easy to understand excess reproduction (defined as more than one offspring) as that active information since it entails more than one query. (in the case of most genomes it is hundred and thousands of queries). It appears only in the case of mammals where only a few to several queries are needed). There is never any question of the survival of genomes. Otherwise they would be classified as extinct. Fitness is too often mischaracterized as a struggle. In actuality, there is vastly more examples of cooperation than struggle and competition. Excess reproduction IMO is circumstantial and inferential evidence of a designed object since it is multifunctional. It not only guarantees a reproduction continuum, it also contributes to the stability of the food chain (and consequently the biosphere) by supplying the offspring that didnt reproduce to the food kitty. It makes more sense to see offspring as those that went right and continued the reproductive cycle and those that went left and contributed to the food chain, rather than seeing offspring as fit and unfit. But I can see why an evolutionary biologist would want to keep it that way since it fits (no pun intended) nicely with the struggle/undesigned/kluge narrative popular in evolutionary circles.
Michael Fugate said: The creationist overlords at ID Central must have noticed Ravi was floundering so they benched him in favor of Steve. Steve, in typical fashion, throws out new undefined terms to deflect criticism. So Steve can you operationally define "active information" and "excess reproduction"? Doesn't fitness depend on both survival and reproduction and doesn't this mean Steve doesn't have a clue?

Steve · 10 December 2015

No, actually who/whatever designed the evolutionary cycle had perfect foresight. As I mentioned, the foresight is in the design. Only excess reproduction can drive variation and selection. If early organisms were not already embedded with excess reproductive ability, then evolution could not get off the ground. How would a single offspring provide enough variation for selection to optimize?
gnome de net said:
Steve said:
Dave Luckett said: So, if we stipulate a designer, it has to be an agency that has perfect knowledge of all interactions of everything in the Universe throughout all time and all space. Nothing else could possibly possess the infinite foresight required. Umm. I can't think what that might be.
The designer's foresight is in understanding what is required of organisms to survive within a changing biosphere. Excess reproduction creating variaton optimized by natural selection provides the perfect solution that does not require each individual organism to itself possess foresight. They throw out numerous offspring, guaranteeing at least one survives, no matter what the changes in the environment present. The offspring that do not survive are early participants in the food chain, meaning organisms pay their rent in advance. The neighbors are happy, they are happy and life persists. NTSWC cannot account for these integrated, interactive systems that we call the biosphere. Design can, precisely because design is teleological and uses foresight to build a system. The better the foresight, the better the system.
So your proposed designer lacks perfect knowledge and foresight?

Yardbird · 10 December 2015

Steve said: Bullshit.

Yardbird · 10 December 2015

Steve said: More bullshit.
Sounds just like my college blue books when I hadn't read the material.

Steve · 10 December 2015

Obviously. The difference is that the evolutionary narrative see the unsurviving offspring as a kluge, a waste, a poor design. Yet, the unsurviving offspring play an important role in the stability of the food chain. So there is no inefficiency, no waste, no roundabout make-shift solution. From the get go, surviving organisms reproduce, unsurviving organisms contribute to the food kitty. A simple, effect design that creates an interdependent, interactive, robust biosphere. As for naming one, they all do. Thats why the definition of species is specious (pun intended). If we view species as distinct, then sure many go extinct. But if you see species as varities of an organism, we can see that the organism does indeed persist. As an example, varieties of insects come and go but Insects persist. In fact, it is precisely because varieties of insects come and go that Insects can stay in the game.
Just Bob said:
Steve said: They throw out numerous offspring, guaranteeing at least one survives, no matter what the changes in the environment present.
"Survives to reproduce" I assume you mean; otherwise what's the point? But -- really now -- I'd like you to name any creature on Earth that can guarantee that even one of its offspring will survive, "no matter what the changes in the environment."

Mike Elzinga · 10 December 2015

Steve said: Fitness is too often mischaracterized as a struggle.
Oh my!

Steve · 10 December 2015

Well of course it is all bullshit to you Yardbird.

It would rock your world if it was any different than a messy kluge of a struggle to exist.

If life were in fact as you say, it would have vaporized long ago. It is the design that makes it all work.

NTSWC only works when it co-opts design but dare not speak its name.

Whatever works for you. Im good with it.

Steve · 10 December 2015

Hey, Mike

Love that tidbit sound bite.

It kicks ass.

The creationistists are shakin' in their boots.

Sylvilagus · 10 December 2015

Steve said: If life were in fact as you say, it would have vaporized long ago. It is the design that makes it all work. NTSWC only works when it co-opts design but dare not speak its name
You keep asserting this, but I have yet to see an argument supporting your assertion, let alone any actual evidence. You know, evidence... That stuff real scientists use.

Dave Lovell · 10 December 2015

Steve said: It would rock your world if it was any different than a messy kluge of a struggle to exist.
That has to be a text book example of projection Steve. It really wouldn't rock their world, at least not in the way you imagine. The mearest suggestion that there was some gamechanging evidence in the pipeline would set every scientists heart racing. A once in a lifetime quantum leap in human understanding they would be desperate to be a part of. Going back up the page to your earlier comments you say in one post:
Excess reproduction IMO is circumstantial and inferential evidence of a designed object since it is multifunctional. It not only guarantees a reproduction continuum, it also contributes to the stability of the food chain (and consequently the biosphere) by supplying the offspring that didnt reproduce to the food kitty.
and then in the very next one:
If early organisms were not already embedded with excess reproductive ability, then evolution could not get off the ground. How would a single offspring provide enough variation for selection to optimize?
Do you not see the problem there? You concede that excess reproduction is essential for Darwinian Evolution but then claim it is also proof of design. How does that contribute to human understanding of whether evolution is by design or unintelligent processes, or through struggle or co-operation? How do you decide between the two possibilities?

eric · 10 December 2015

Steve said: Active information is not a new undefined term. It is defined as repeated queries.
No, you're still mischaracterizing the ID position. AI is information that is either front-loaded into the search algorithm (i.e., by the designer), or supplied by an outside source (i.e., the designer or some other outside source). 'Repeated queries' could be a source of external information and thus AI, but it is certainly not the only source and it is certainly not the definition of AI.
Excess reproduction IMO is circumstantial and inferential evidence of a designed object since it is multifunctional.
Again, the way chemistry works the notion of repeated reactions is more the rule than the exception. There is nothing particularly remarkable or miraculous about the same molecule or biological structure performing the same reaction more than once. Moreover by your definition of 'excess', its actually required for sexual reproducing life, not some sort of optional benefit. Because each reproduction requires two parents, the replacement rate has to be 2 kids/parent, not 1 kid/parent (and this is excluding expectations of premature death). If every sexually reproducing animal had exactly 1 kid, the population of every species would decline by half every generation. IOW, put simply, you're not even getting your basic math right. The rest of your post, I have to admit, I didn't really understand. Sounded like gobbledygook to me.

DS · 10 December 2015

Stevie boy is just making shit up as usual. And as usual, provides absolutely no evidence at all for anything. Take this little gem for example:

"No, actually who/whatever designed the evolutionary cycle had perfect foresight. As I mentioned, the foresight is in the design. Only excess reproduction can drive variation and selection."

Really? So a population of a million breeding pairs, only producing one offspring per pair, thus reducing the population size by half every generation, could not possibly generate any genetic variation and so could not undergo natural selection. Really? Why on earth not? This is just poor logic combined with ignorance in a desperate attempt at obfuscation. This guy will say anything to try to deny real science, no matter how ridiculous.

And perfect foresight? Really? So no population ever have massive die offs? No species has ever gone extinct? Really? Wasn't such good foresight with the trilobites or the dinosaurs now was it? Seems like the perfect foresight didn't work so well there did it? Sure, just ignore all the evidence, make up bullshit that is completely meaningless and presto, instant science denial.

Since Stevie is not discussing the topic of the thread, time for another dump to the bathroom wall.

eric · 10 December 2015

Steve said: Obviously. The difference is that the evolutionary narrative see the unsurviving offspring as a kluge, a waste, a poor design.
I have never heard any biologist describe reproduction above the replacement rate as a kluge, waste, or poor design/adaptation. You are arguing against a very weird straw man version of evolutionary theory here.
As an example, varieties of insects come and go but Insects persist. In fact, it is precisely because varieties of insects come and go that Insects can stay in the game.
Taxonomically, 'insect' is a class. Are you claiming that under ID, taxonomic classes never go extinct? That is at least an empirically testable claim of the hypothesis.

DS · 10 December 2015

Well you know Steve is a carpet salesman. He obviously never studied any real biology. To fill this yawning chasm in his knowledge, he constructs elaborate scenarios about the ridiculous things that biologists supposedly believe. Then he spends his time denigrating his own misconceptions and congratulating himself for how superior he is to all of the foolish scientists who supposedly believe the things he made up. It really must stroke his ego to be so superior to all the real experts. It must also be quite a shock for him to come here and receive nothing but ridicule.

gnome de net · 10 December 2015

DS said: And perfect foresight? Really? So no population ever have massive die offs? No species has ever gone extinct? Really? Wasn't such good foresight with the trilobites or the dinosaurs now was it? Seems like the perfect foresight didn't work so well there did it?
I fully expected Steve to respond as he did. Had I not overslept, DS, I would have responded as you did.

eric · 10 December 2015

DS said: To fill this yawning chasm in his knowledge, he constructs elaborate scenarios about the ridiculous things that biologists supposedly believe.
Ah, but he's somewhat unusual in getting the ID piece wrong too. So in this case he's set up a straw man vs. straw man joust. May the best scarecrow win!

Yardbird · 10 December 2015

Steve said: Well of course it is all bullshit to you Yardbird. It would rock your world if it was any different than a messy kluge of a struggle to exist. If life were in fact as you say, it would have vaporized long ago. It is the design that makes it all work. NTSWC only works when it co-opts design but dare not speak its name. Whatever works for you. Im good with it.
You don't know my opinion on the topic of ID/creationism because I have not stated one. The only opinion I have stated is that what you have stated is bullshit. Here's another opinion. You are an asshole.

DS · 10 December 2015

eric said:
DS said: To fill this yawning chasm in his knowledge, he constructs elaborate scenarios about the ridiculous things that biologists supposedly believe.
Ah, but he's somewhat unusual in getting the ID piece wrong too. So in this case he's set up a straw man vs. straw man joust. May the best scarecrow win!
Well perhaps we should just sit back and let him argue with himself, secure in the knowledge that real science is immune to his bumbling efforts.

John Harshman · 10 December 2015

eric said:
Steve said: As an example, varieties of insects come and go but Insects persist. In fact, it is precisely because varieties of insects come and go that Insects can stay in the game.
Taxonomically, 'insect' is a class. Are you claiming that under ID, taxonomic classes never go extinct? That is at least an empirically testable claim of the hypothesis.
He does seem to be making that claim. Somebody tell the trilobites. Oh, wait. We can't.

DS · 10 December 2015

John Harshman said: He does seem to be making that claim. Somebody tell the trilobites. Oh, wait. We can't.
Or the dinosaurs. Unless of course he is willing to stipulate that birds are descended from dinosaurs. Now why do I think that that is unlikely? Man, with just a little foresight, you could have warned all of the dinosaurs to hide somewhere safe the day the meteor hit. Or maybe, with a little more foresight, you could have altered the orbit to prevent it from hitting the earth. So, either no foresight, or a real hatred of dinosaurs. What, did they eat the magic apple to?

eric · 10 December 2015

DS said:
John Harshman said: He does seem to be making that claim. Somebody tell the trilobites. Oh, wait. We can't.
Or the dinosaurs. Unless of course he is willing to stipulate that birds are descended from dinosaurs. Now why do I think that that is unlikely?
I thought of the dinosaurs, but then rejected it as an example precisely because there's a bunch of theropod descendants still around. But trilobites, OTOH - good example.

CJColucci · 10 December 2015

I'm having trouble understanding how Steve's version of ID differs from natural selection, except by calling all natural selection's mechanisms, and natural selection itself, "designed."

Yardbird · 10 December 2015

Firesign Theatre on evolution

Animals without backbones hid from each other or fell down. Clamasaurs and Oysterettes appeared as appetizers. Then came the sponges which sucked up about ten percent of all life. Hundreds of years later, in the Late Devouring Period, fish became obnoxious. Trailerbites, chiggerbites, and mosquitoes collided aimlessly in the dense gas. Finally, tiny edible plants sprang up in rows giving birth to generations of insecticides and other small dying creatures.

There's a humorous look at taxonomy in the linked article. It's a little too long to relate.

John Harshman · 10 December 2015

DS said:
John Harshman said: He does seem to be making that claim. Somebody tell the trilobites. Oh, wait. We can't.
Or the dinosaurs. Unless of course he is willing to stipulate that birds are descended from dinosaurs. Now why do I think that that is unlikely?
Dinosauria, whether or not birds are a part of it, isn't officially a class. Of course the designation is arbitrary, but that's something for Steve to deal with.
Man, with just a little foresight, you could have warned all of the dinosaurs to hide somewhere safe the day the meteor hit. Or maybe, with a little more foresight, you could have altered the orbit to prevent it from hitting the earth. So, either no foresight, or a real hatred of dinosaurs. What, did they eat the magic apple to?
As long as the beetles are safe, god doesn't care.

Mike Elzinga · 10 December 2015

John Harshman said:
eric said:
Steve said: As an example, varieties of insects come and go but Insects persist. In fact, it is precisely because varieties of insects come and go that Insects can stay in the game.
Taxonomically, 'insect' is a class. Are you claiming that under ID, taxonomic classes never go extinct? That is at least an empirically testable claim of the hypothesis.
He does seem to be making that claim. Somebody tell the trilobites. Oh, wait. We can't.
Or maybe we should start thinking of DNA as a "class?"

eric · 10 December 2015

Mike Elzinga said:
John Harshman said:
eric said:
Steve said: As an example, varieties of insects come and go but Insects persist. In fact, it is precisely because varieties of insects come and go that Insects can stay in the game.
Taxonomically, 'insect' is a class. Are you claiming that under ID, taxonomic classes never go extinct? That is at least an empirically testable claim of the hypothesis.
He does seem to be making that claim. Somebody tell the trilobites. Oh, wait. We can't.
Or maybe we should start thinking of DNA as a "class?"
"That's not an example of evolution, its still a chordata!"

Michael Fugate · 10 December 2015

Steve is claiming a key premise - that more offspring are produced than survive to reproduce - of Darwin's evolution by natural selection is wrong. Darwin who was a careful observer of nature blew this? Really, Steve? Anyone who has spent any time observing would know this premise not wrong. Ever seen an oak tree with acorns, Steve? Ever cut open a fish before spawning? Ever ejaculated? 180 million pieces of active information to fertilize one egg? An egg that if fertilized only has a slim chance of implanting? And you claim this for intelligent design?

Then on to ID analogy for intelligent design - human design. Have you ever designed anything, Steve? Did it happen like magic? or did you plan it out measuring and remeasuring, imagining how it would look or work and then reimagining, building a prototype and then another, going back to the plan and reimagining? Excess production all the way down. Then there are the finished designs - we use homeostatic mechanisms to keep things working - excess and deficit, excess and deficit - not constants. Please try to study some before coming back.

Tom English · 10 December 2015

John Harshman said: As long as the beetles are safe, god doesn't care.
As long as Ewert can turn a bug into a beetle, god is safe. (It was Joe who first noticed the photo. It was I who first noticed that Ewert had changed our model -- from a GUC Bug to a GUC Beetle, I suppose.)

John Harshman · 10 December 2015

Tom English said:
John Harshman said: As long as the beetles are safe, god doesn't care.
As long as Ewert can turn a bug into a beetle, god is safe. (It was Joe who first noticed the photo. It was I who first noticed that Ewert had changed our model -- from a GUC Bug to a GUC Beetle, I suppose.)
What's all this then?

John Harshman · 10 December 2015

Michael Fugate said: Steve is claiming a key premise - that more offspring are produced than survive to reproduce - of Darwin's evolution by natural selection is wrong.
No, I don't think he is. What he's claiming is that excess reproduction exists and is evidence of design, because it would have to be designed in and could never occur naturally.

Michael Fugate · 10 December 2015

John Harshman said:
Michael Fugate said: Steve is claiming a key premise - that more offspring are produced than survive to reproduce - of Darwin's evolution by natural selection is wrong.
No, I don't think he is. What he's claiming is that excess reproduction exists and is evidence of design, because it would have to be designed in and could never occur naturally.
Yeah, I misread his earlier comment. It is worse than I thought - he must be some sort of Calvinist - his god decides which individuals survive and reproduce and which get eaten before they are even born. What a bizarre worldview.

Michael Fugate · 10 December 2015

So when theists say "everything happens for a reason", they really mean it. So if I were out camping with my family and my young son wandered off and was eaten by a mountain lion, then he was just "excess reproduction"? Steve's god destined him for mountain lion food before he was conceived? This god doesn't leave anything to chance.

harold · 10 December 2015

CJColucci said: I'm having trouble understanding how Steve's version of ID differs from natural selection, except by calling all natural selection's mechanisms, and natural selection itself, "designed."
I noticed that too. He seems to be vaguely implying that the fact that organisms have more offspring than survive means "design". Incidentally, Steve accidentally got something right. Natural selection is not a "struggle". Most of the time. Humans and maybe a few other highly cephalized mammals and birds can experience an emotional state of "struggle". However, we almost never feel a direct sensation of struggle to have our alleles selected for. We fear death and many of us like sex, but those are indirect urges with respect to natural selection. In rich countries, people are very happy to have a few children and invest many resources in them. In poor countries, where there is inadequate control of infectious disease and nutrition may be inadequate, children die all the time. So those poor people have more children. A much greater proportion of the children die, but the net effect is that human population growth due to birth is mainly occurring in poor countries (some places like the US, Canada, and Australia have also experienced quite a bit of population growth, but due to in-migration). Human populations are all very closely related to each other anyway, but if any alleles are disproportionately associated with living in an area of high childhood mortality, those alleles are being selected for. (Note - of course, they wouldn't be if childhood mortality was so high that natural population growth was below zero despite high birth rate, as in seventeenth century London, but where births outpace deaths the fastest, alleles are being selected for.) It's unlikely that plants or microbes experience any sense of "struggle" whatsoever. It isn't a struggle, it's just what happens. It's not coincidence that as well as being contempraneous with the civil rights movement and widespread birth control, the post-modern political evolution denial movement also emerged exactly as nucleic acid genomes were first being understood by molecular biologists. Life can't not evolve! Darwin saw what was happening but could not see what was going on at the molecular level. Now that we can, it's much, much more obvious how it works. Offspring always carry some genetic differences from their parents, some of those differences affect phenotype and can be passed to their offspring in turn, if they affect phenotype they may be stochastically selected for or against in the context of a given environment. Random chance and things like genetic drift also play a considerable role and would cause evolution of sorts without natural selection, but specialized adaptations are due to natural selection. This can be modeled mathematically in an intelligent way as well as studied directly at the molecular level. This is how it works. It's very hard for humans to accept, not because it's all that complicated (you need to have some intuitive understanding of probability, but only as much as the average decent poker player), but because we experience the biased fantasy that the current biosphere is the result of planning. But life is still evolving. Even if it was "the designer", we aren't the final design. It's just what happens. It's the way life works on Earth.

KlausH · 10 December 2015

Dave Luckett said: In fairness, Paley did go a little further than mere complication. He also observed that a watch is made to perform a specific function, which it achieves by the purposeful arrangement of parts. He attempted to argue that living things also demonstrate such a purposeful arrangement of parts, hence that design may be inferred. The argument breaks down when one makes these further observations of living things: that their purpose, if you can call it that, is simply to survive and to successfully reproduce, BUT they do not invariably perform that function, AND that their unique property is reproduction with variation. The rest of evolution follows from that simple understanding.
I ran into the Paley's watch argument, as well as Pascal's wager in public elementary school in Michigan (Lincoln Elementary, Detroit suburbs). The same teachers that taught this also taught us the ridiculous story about Columbus setting out to prove the world was round, when everyone else mistakenly believed it to be flat. This was all in the 70s. Even at the age of 9 or 10, I could see major flaws in the Paley and Pascal arguments.

Just Bob · 10 December 2015

Steve, are you capable of naming something which is NOT designed?

Henry J · 10 December 2015

You want something that wasn't designed?

How about "cdesign proponentsists".

Just Bob · 10 December 2015

Henry J said: You want something that wasn't designed? How about "cdesign proponentsists".
Nah. Overlapping, conflicting designs. Too much design, not enough quality control.

Rolf · 11 December 2015

The complexity of life is mindboggling.

The inherent instability of DNA making it susceptible to so many errors an faults. It needs a continuous maintenance operation of a complexity far beyond anything imaginable, but it has been revealesd as a fact of life. It makes no sense that a superinteligent designer (not to mention his mindblowing R&D and implementation facilites) with unlimited resources to create a universe in his image, i.e. perfection, did not create that universe and show off his superior design
capability. Instead what we see is kludge uopon kludge all the way both up and down. Just what we should expect from our mother nature.

ID isn't even a kludge, it is a brainfart if I may say so.
With that in mind, no further debate required.

Besides, ID is boring, boring, boring. Goddidit, and then what? Prayer an hallelujahs from sunrise to sundown?

Just Bob · 11 December 2015

Rolf said: Goddidit, and then what?
My point exactly. Even if ID were accepted as true, what can you DO with it? For instance, what great scientific advances have come from ID labs?

Henry J · 11 December 2015

Yeah, if everything was designed, why doesn't our yellow dwarf have waste disposal and refueling mechanisms?

Just Bob · 11 December 2015

And if EVERYTHING is designed -- sometimes the fallback position of an IDiot who realizes he can't say how to detect design -- it is still a useless concept: it doesn't distinguish anything from anything else. We're doing pretty well with physics and chemistry and biology without assuming everything is IDed... what would we gain by assuming everything was?

TomS · 12 December 2015

Even imaginary things are designed. Being imaginary means that they are the products of design. From unfinished creative work to impossible objects.

Design doesn't even distinguish reality from imagination.

Henry J · 12 December 2015

So the square root of -1 was "designed"? :D

Mike Elzinga · 12 December 2015

Henry J said: So the square root of -1 was "designed"? :D
It's really complex; so it has to be.

stevaroni · 12 December 2015

Just Bob said: My point exactly. Even if ID were accepted as true, what can you DO with it? For instance, what great scientific advances have come from ID labs?
That's always been the ironic part for me. Even if tomorrow gave us an enormous ID breakthrough and provided clear, unambiguous evidence that the Bible was literally true, physical science would still have to go on as if the world was billions of years old and physical forces alone were at play, because for some ineffable reason the world is designed to work exactly that way, and we have to understand that model if we want to make any progress. Even if lightning bolts are actually hurled by angry gods, those gods apparently have a great affinity for aiming at grounding rods if they are offered in a convenient manner. Even if there really was a Noachian flood, oil deposits are still best located by trying to find geology that looks like swampy coastal deltas from 300 million years ago, and not, as expected, by trying to find deep mountainous catchment basins from 100 years before the Egyptian age ( a fact of enormous frustration to devout petroleum engineers all over the planet). Likewise in medical research, where it's much, much more useful to work with animal models based on the assumption of their distinct genetic similarity to humans, rather than to have extensive cross-referenced tables about how all the various baraminic "kinds" show details of independent origin that have to be worked around. The great irony for ID is that, even if they're correct, day-to-day science will still have to go on exploring the world as if it isn't, because that's the exact model the designer chose to use. Crafty, designer. I see what you did there. very tricky.

TomS · 12 December 2015

@stevaroni there is one major step before what you mention.

If ID were correct in all that it offers, what they would have gained is that there is a fatal flaw in the scientific account depending on evolution.

Even if that were found out to be the case, that would not provide us with an alternative. It would not tell us what does happen, when or where it happens, how or why it happens, or even anything about who the intelligent designers might be. The designers might, for all that we can imagine, have been directing evolution to operate, producing new species by common descent over billions of years, etc. etc. etc.

Even if there have to be intelligent designers behind it all, they might include "the God of Christianity; an angel--fallen or not; Plato's demi-urge; some mystical new age force; space aliens from Alpha Centauri; time travelers". They might not have had any function since, for example, the Cambrian. Maybe all of naturalistic, materialistic, scientific, goal-less evolution has it 100% correct for the last hundreds of millions of years.

John Harshman · 12 December 2015

Mike Elzinga said:
Henry J said: So the square root of -1 was "designed"? :D
It's really complex; so it has to be.
The square root of -1 isn't complex. But the square root of -1 + 1 is.

gnome de net · 12 December 2015

Intelligent Design and the square root of -1 are both imaginary.

Joe Felsenstein · 12 December 2015

John Harshman said: The square root of -1 isn't complex. But the square root of -1 + 1 is.
No. -1 + 1 = 0, and the square root of 0 is 0. (But if you put in a couple of parentheses in the right place, John would be right.)

John Harshman · 13 December 2015

Joe Felsenstein said:
John Harshman said: The square root of -1 isn't complex. But the square root of -1 + 1 is.
PEMDAS, Joe. No. -1 + 1 = 0, and the square root of 0 is 0. (But if you put in a couple of parentheses in the right place, John would be right.)

harold · 13 December 2015

TomS said: @stevaroni there is one major step before what you mention. If ID were correct in all that it offers, what they would have gained is that there is a fatal flaw in the scientific account depending on evolution. Even if that were found out to be the case, that would not provide us with an alternative. It would not tell us what does happen, when or where it happens, how or why it happens, or even anything about who the intelligent designers might be. The designers might, for all that we can imagine, have been directing evolution to operate, producing new species by common descent over billions of years, etc. etc. etc. Even if there have to be intelligent designers behind it all, they might include "the God of Christianity; an angel--fallen or not; Plato's demi-urge; some mystical new age force; space aliens from Alpha Centauri; time travelers". They might not have had any function since, for example, the Cambrian. Maybe all of naturalistic, materialistic, scientific, goal-less evolution has it 100% correct for the last hundreds of millions of years.
My final comment here, but I seem to see a resistance to just admitting what ID is, in this thread. I get that the resistance is due to the fun of "pretending ID is serious" and picking apart its absurdity, but hey, let's also be realistic about it. I know everybody knows this (certainly TomS does), but in case there are still a few who may not be totally clear... It is the nature of ID that they can't present an alternative. They literally can't, and if they could, they wouldn't be ID. If they showed that the designer was the God of Abraham as interpreted by Jerry Falwell they'd be creation science. If they showed the designer was an alien they'd be Scientologists or Rosicrucians or something similar. 1) They can't say that the designer isn't the God of Abraham as interpreted by Ted Cruz because all their money is from people who want to say that it is. 2) They can't say that the designer is that, either, because all their money comes because they promised to get evolution denial into public schools by disguising all overt reference to religion. An ID advocate is literally a YEC creation science advocate who refuses to overtly admit that he's talking about the Christian God and secretly supporting Biblical literalism. That is all it is. In their own minds, due to bias, they are sincere (although tormented by cognitive dissonance). They believe, at least consciously, that "evolution can't be true, therefore I can ignore all evidence, and my job is to say anything that could be seen by naive people as legitimately casting doubt on evolution. Except that if I'm doing 'ID' instead of 'creation science' I can't refer to God, Jesus, or the Bible, for legal reasons". That's ID. The verbose details are just the tormented process of trying to argue that something obviously observed is "impossible" while not presenting any alternate explanation of the data.

gnome de net · 13 December 2015

Or you could have written "1 plus the square root of -1" with no need to invoke PEMDAS.

Henry J · 13 December 2015

Parenthetically speaking.

TomS · 13 December 2015

I do have a minor disagreement with harold.
I don't think that Young Earth Creationism is the base position. They are surely the loudest, but I think that many of the ID advocates realize that it is ridiculous. One of the reasons that they are taking the "don't ask, don't tell" position is that they would alienate their political base by openly admitting that there is no way to back things like baraminology and Noah's Ark and the vapor canopy. Indeed, "traditional" creationism had rejected YEC before the 1960s.

And it is worth pointing out that anti-evolution has always had a problem which they have addressed by making a point of silence - as ID is to YEC, so "traditional" creationism is to Omphalism. No variety of creationism has ever told us what happens, why and how - with the possible suggestion that it all suddenly appeared with all of the appearance of having a evolutionary history.

Even before the publication of On the Origin of Species, it was pointed out that creationists did not offer an alternative account to an evolutionary one. Herbert Spencer wrote about that in an 1852 essay, "The Development Hypothesis" (see it in Wikisource.org).

Doc Bill · 13 December 2015

TomS said: I do have a minor disagreement with harold. I don't think that Young Earth Creationism is the base position. They are surely the loudest, but I think that many of the ID advocates realize that it is ridiculous. One of the reasons that they are taking the "don't ask, don't tell" position is that they would alienate their political base by openly admitting that there is no way to back things like baraminology and Noah's Ark and the vapor canopy. Indeed, "traditional" creationism had rejected YEC before the 1960s. And it is worth pointing out that anti-evolution has always had a problem which they have addressed by making a point of silence - as ID is to YEC, so "traditional" creationism is to Omphalism. No variety of creationism has ever told us what happens, why and how - with the possible suggestion that it all suddenly appeared with all of the appearance of having a evolutionary history. Even before the publication of On the Origin of Species, it was pointed out that creationists did not offer an alternative account to an evolutionary one. Herbert Spencer wrote about that in an 1852 essay, "The Development Hypothesis" (see it in Wikisource.org).
Just for fun, you can look up through Google the transcripts of the Kansas Kangaroo Kourt of 2005 where a number of creationists were brought in to testify. Look up Stephen Meyer's testimony; he dialed-in to the proceedings. Legal Beagle Pedro Irigonegaray graciously provided representation for Sanity and simply asked each witness the same set of questions. One question was: What is the age of the Earth? Such a simple question. You could get away with 4.5 billion years and move on. But not Meyer. Oh, no! He dances around for page after page of transcript. He really, really, really didn't want to go on record with a question this simple. To me, that exchange typified the abject dishonesty of the Dishonesty Tute.

Michael Fugate · 14 December 2015

Doc Bill said:
TomS said: I do have a minor disagreement with harold. I don't think that Young Earth Creationism is the base position. They are surely the loudest, but I think that many of the ID advocates realize that it is ridiculous. One of the reasons that they are taking the "don't ask, don't tell" position is that they would alienate their political base by openly admitting that there is no way to back things like baraminology and Noah's Ark and the vapor canopy. Indeed, "traditional" creationism had rejected YEC before the 1960s. And it is worth pointing out that anti-evolution has always had a problem which they have addressed by making a point of silence - as ID is to YEC, so "traditional" creationism is to Omphalism. No variety of creationism has ever told us what happens, why and how - with the possible suggestion that it all suddenly appeared with all of the appearance of having a evolutionary history. Even before the publication of On the Origin of Species, it was pointed out that creationists did not offer an alternative account to an evolutionary one. Herbert Spencer wrote about that in an 1852 essay, "The Development Hypothesis" (see it in Wikisource.org).
Just for fun, you can look up through Google the transcripts of the Kansas Kangaroo Kourt of 2005 where a number of creationists were brought in to testify. Look up Stephen Meyer's testimony; he dialed-in to the proceedings. Legal Beagle Pedro Irigonegaray graciously provided representation for Sanity and simply asked each witness the same set of questions. One question was: What is the age of the Earth? Such a simple question. You could get away with 4.5 billion years and move on. But not Meyer. Oh, no! He dances around for page after page of transcript. He really, really, really didn't want to go on record with a question this simple. To me, that exchange typified the abject dishonesty of the Dishonesty Tute.
Not to mention his dancing around common descent. You can see his little brain spinning even on paper - do I want to look like a loon to every scientist in the world and deny common descent or do I jettison credibility with my base who are themselves a bunch of loons? Do you want maple syrup or blueberry on that waffle?

Doc Bill · 14 December 2015

Michael Fugate said: Not to mention his dancing around common descent. You can see his little brain spinning even on paper - do I want to look like a loon to every scientist in the world and deny common descent or do I jettison credibility with my base who are themselves a bunch of loons? Do you want maple syrup or blueberry on that waffle?
Decisions, decisions! I can look like a loon to every scientist in the world who doesn't pay me a farthing, or I can be true to Teh Base who pays my salary? Hmmmmmmm, decisions, decisions ...

eric · 14 December 2015

John Harshman said:
Michael Fugate said: Steve is claiming a key premise - that more offspring are produced than survive to reproduce - of Darwin's evolution by natural selection is wrong.
No, I don't think he is. What he's claiming is that excess reproduction exists and is evidence of design, because it would have to be designed in and could never occur naturally.
Very innumerately, he's claiming "excess reproduction" includes >1 offspring/parent, which is not even the replacement rate.

John Harshman · 15 December 2015

eric said:
John Harshman said:
Michael Fugate said: Steve is claiming a key premise - that more offspring are produced than survive to reproduce - of Darwin's evolution by natural selection is wrong.
No, I don't think he is. What he's claiming is that excess reproduction exists and is evidence of design, because it would have to be designed in and could never occur naturally.
Very innumerately, he's claiming "excess reproduction" includes >1 offspring/parent, which is not even the replacement rate.
Of course it's replacement rate. In sexual reproduction, each offspring provides only half a credit to each parent. So you need to provide half your genes to two kids in order to be credited with one full offspring.

Ray Martinez · 16 December 2015

Nick Matzke: GAME OVER, MAN. GAME OVER! The whole point of Dembski et al. invoking “No Free Lunch” theorems was to argue that, if evolutionary searches worked, it meant the fitness function must be designed, because (logical jump herein) the No Free Lunch theorems showed that evolutionary searches worked no better than chance, when averaged over all possible fitness landscapes.
Don't get too excited, you seem to forget that all Dembski is really fighting for is one creative law programmed deistically into life four billion years ago. This is not any historic mainstream position of Creationism or design. Since the same presupposes design and evolution not mutually exclusive, when in fact they are, all one really needs to conclude game over for Dembski is his acceptance of the concept of evolution existing in nature.

Yardbird · 16 December 2015

Ray Martinez said: Since the same presupposes design and evolution not mutually exclusive, when in fact they are...
How do you know that?

Ray Martinez · 16 December 2015

Yardbird said:
Ray Martinez said: Since the same presupposes design and evolution not mutually exclusive, when in fact they are...
How do you know that?
Two Reasons 1. Design, as an effect, presupposes Intelligent agency; evolution, as an effect, presupposes unintelligent agencies. 2. No evolutionary scientist, since Darwin, accepts both concepts existing in nature at the same time because these persons understand the logic of reason #1 as conveying mutual exclusivity. Existence of one precludes existence of its antonym and falsifies existence of its antonym. To say, as Demsbki says, that both concepts exist in nature (design and evolution) is to say God created a concept that falsifies His own existence. Dembski rejects mutual exclusivity because he has, since college, accepted the concept of evolution existing in nature. In short he has misunderstood the main claim of accepted evolution as it relates to any objective understanding of design in science: existence of unintelligent agencies dictates that no effect can be described as designed. If Dembski were to respond he would be forced to make an invalid argument-from-authority (he is only right because of his credentials).

phhht · 16 December 2015

Ray Martinez said:
Yardbird said:
Ray Martinez said: Since the same presupposes design and evolution not mutually exclusive, when in fact they are...
How do you know that?
Two Reasons 1. Design, as an effect, presupposes Intelligent agency ...
You said:

Design observed infers implies the work of Intelligence.

You can't have it both ways, stupid. You said:

...evolution, as an effect, presupposes unintelligent agencies.

That's simply false. Evolution presupposes no such thing. It's just that there is no reason in evolution to believe otherwise.
Say, this Dembski guy you mention, didn't he leave the ID movement?

Yardbird · 16 December 2015

Ray Martinez said: 2. No evolutionary scientist, since Darwin, accepts both concepts existing in nature at the same time because these persons understand the logic of reason #1 as conveying mutual exclusivity. Existence of one precludes existence of its antonym and falsifies existence of its antonym.
What is an evolutionary scientist? Maybe that's a dumb question but I'm just a bass player and I don't understand all this evolution stuff.

Steve · 16 December 2015

Excess reproduction IS the front loading of information into the genome. Repetitive chemical reactions and reproduction are different animals. They are more like different universes. What an extraordiary logical stretch to assume that the repetitive nature of a chemical reaction is supporting evidence for the the coordinated, timed execution of a myriad set of chemical reactions which is reproduction. It seems your misunderstanding is due to your consideration of what is now, and not the contemplation of how they got where they are. 'Optional benefit' is your mischaracterization. I have never implied such. In fact, I assert that it is an logical impossibility that variation and selection could work without excess reproduction. Excess reproduction is a pre-requisite to the onset of variation and selection. Therefore, by your own admission, sexually reproducing organisms could not logically have emerged through non-teleological step-wise change. Oh, and sure, gobbledygook is what one sees when steeped too long in (non-teleological) evolutionary memes.
eric said:
Steve said: Active information is not a new undefined term. It is defined as repeated queries.
No, you're still mischaracterizing the ID position. AI is information that is either front-loaded into the search algorithm (i.e., by the designer), or supplied by an outside source (i.e., the designer or some other outside source). 'Repeated queries' could be a source of external information and thus AI, but it is certainly not the only source and it is certainly not the definition of AI.
Excess reproduction IMO is circumstantial and inferential evidence of a designed object since it is multifunctional.
Again, the way chemistry works the notion of repeated reactions is more the rule than the exception. There is nothing particularly remarkable or miraculous about the same molecule or biological structure performing the same reaction more than once. Moreover by your definition of 'excess', its actually required for sexual reproducing life, not some sort of optional benefit. Because each reproduction requires two parents, the replacement rate has to be 2 kids/parent, not 1 kid/parent (and this is excluding expectations of premature death). If every sexually reproducing animal had exactly 1 kid, the population of every species would decline by half every generation. IOW, put simply, you're not even getting your basic math right. The rest of your post, I have to admit, I didn't really understand. Sounded like gobbledygook to me.

Steve · 17 December 2015

This is precisely what I am claiming. Let's take that first multi-cellular organism for a start. It has maximum fitness by virtue of its very existence. This logically implies it has the correct set of components and cellular processess to stay alive. Next we assume (from a non-teleological, step-wise change POV) this first multi-cellular organism was capable of only a single replication. Also, in this original multi-cellular configuration the cell would not have had the sophisticated DNA error detection and repair capabilities (design assumes the opposite for the obvious logical reasons) to eliminate deleterous mutations. Using the popular non-teleological step-wise change evolutionary meme again, what would be the effect of a single, random variation in any one of the components/chemical processes of this obviously extraordinarily successful configuation of matter? Further, assuming the super successful organism was able to repeatedly defy the odds and hang on despite repeated challenges from variations that would steer the organism away from its current maximum fitness, what would trigger these variations that are void of selection (since there is only one offspring, and nothing to select for) to 'improve' an organism already at maximum fitness? How was it logically possible for this organism to survive even one single variation without pre-existing machinery (information)? This is what I ask Harshman, Elsberry, Matzke, et al Oh, and for DS' benefit, this goes directly to the heart of the OP. Are non-teleological processes capable of creating information? So John Harshman (or Nick Matzke, Wesley Elsberry, et al for that matter), where's the free lunch coming from? How did variation in that single, maximumly fit multi-cellular organism create something new and improved?
John Harshman said:
Michael Fugate said: Steve is claiming a key premise - that more offspring are produced than survive to reproduce - of Darwin's evolution by natural selection is wrong.
No, I don't think he is. What he's claiming is that excess reproduction exists and is evidence of design, because it would have to be designed in and could never occur naturally.

Steve · 17 December 2015

Dave Lovell, Yes, excess reproduction is essential for evolution to take place, therefore non-teleological step-wise change is an evolutionary myth. variation and selection are sub-components in a designed system. Excess reproduction provide the quantity and frequency that variation and selection need to do their work. Therefore, logically excess reproduction cannot be defined by non-teleological step-wise change. This contributes to our knowlege by starting inquiry from a productive basis. HOW was life designed? WHAT tools were used to create the design? WHY were these tools chosen? WHERE are these tools? HOW do they work? WHAT are the fundament elements of the design? HOW many elements are there? Were all the elements introduced at the same time? If not, WHEN were each element introduced? WHAT order were each element introduced? WHY were they introduced in this particular order? With the evolutionary memes infecting our thought on biology right now, none of the above questions are being asked. In fact, this board is dedicated to seeing that NONE of the above questions are introduced into any of the life sciences. And especially not in any classroom, regardless of the institution, be it elementary school or university. Now this is a major problem. If i was a scientist I would be eager to work on those questions. In fact, asking and answering these questions are the only way forward for the biological sciences and AI. Non-teleological evolutionary memes get us nowhere. In fact, they are science stoppers. These memes tell us to not look here (teleology), don't look there (design). Just look my way (non-teleological step-wise change).
Do you not see the problem there? You concede that excess reproduction is essential for Darwinian Evolution but then claim it is also proof of design. How does that contribute to human understanding of whether evolution is by design or unintelligent processes, or through struggle or co-operation? How do you decide between the two possibilities?

Yardbird · 17 December 2015

Steve said: If i was a scientist...
Yeah, I'm not a scientist either, but I can tell you're full of shit.

stevaroni · 17 December 2015

Steve said: Let's take that first multi-cellular organism for a start. It has maximum fitness by virtue of its very existence.
No, it has adequate fitness to survive. That is all it needs. It may be the one of the fittest organisms on the planet at this particular point, but that doesn't matter all that much at the moment, since the survival landscape is mostly driven by the need to survive the environment.
This logically implies it has the correct set of components and cellular processess to stay alive.
No, this logically implies that it has a sufficient set to survive. There will eventually be much better sets, but at the moment, this one is good enough.
Next we assume (from a non-teleological, step-wise change POV) this first multi-cellular organism was capable of only a single replication.
Why?
Using the popular non-teleological step-wise change evolutionary meme again, what would be the effect of a single, random variation in any one of the components/chemical processes of this obviously extraordinarily successful configuation of matter? How was it logically possible for this organism to survive even one single variation without pre-existing machinery (information)?
Ah. now we get to the meat of your argument. But it's a straw argument, isn't it? Your entire model imagines one organism that replicates one time, and that's not how it works. Most simple organisms (aided by their offspring) would have been capable of multiplying zillions of times. And, of course, some of them would be mutated, especially with a simple primitive genome with little backup. And, of course, most of those mutations would have been disastrous, because there was very little DNA to begin with, and it was all pretty important and the odds of having a useful mutation are tiny, and therefore almost all mutations would have been fatal. This is readily apparent by the slow, slow rate of progress from single celled organisms 3+ billion years ago to even simple multicellular animals maybe 700mya. Compare that rate of change to modern rates and the progress is glacial. But this is to be expected, if you want to use the "computer program" analogy, in the early days you're a simple machine with not much more than an operating system aboard, and almost any change will break you, not make anything better, and the record shows this. In fact, you probably couldn't have many mutations at all until you had initial mutations that duplicated some of the DNA so there were pieces that could break in the first place without killing the organism. But "almost none" is not none, and even astonishingly long odds, when multiplied by enough tries, turns up winners. Just ask these lottery winners, who all beat vanishingly tiny odds to score that winning ticket.

Mike Elzinga · 17 December 2015

Steve said: Repetitive chemical reactions and reproduction are different animals. They are more like different universes. What an extraordiary logical stretch to assume that the repetitive nature of a chemical reaction is supporting evidence for the the coordinated, timed execution of a myriad set of chemical reactions which is reproduction. It seems your misunderstanding is due to your consideration of what is now, and not the contemplation of how they got where they are.
Here is an extremely important question that simply sails way over the heads of all ID/creationists (and I do mean all ID/creationists); namely, what do your "theories" predict if the temperature of the organism drops below, say, 5 degrees Celsius or goes above, say, 80 degrees Celsius? A second question is why does temperature never enter into your theories? Those of us who actually know something about this stuff know why these questions mean absolutely nothing to an ID/creationist.

Just Bob · 17 December 2015

Steve! You're back!

Maybe you've had time to think of just one little example of something which is NOT designed. If you can't think of one, just say so.

gnome de net · 17 December 2015

Hey, Steve, if you'd post your response below/after the comment you're responding to, your response would be easier to interpret.

DS · 17 December 2015

Steve said: Non-teleological evolutionary memes get us nowhere. In fact, they are science stoppers. These memes tell us to not look here (teleology), don't look there (design). Just look my way (non-teleological step-wise change).
So that's why science hasn't made any progress in the last two thousand years. Now I get it!

John Harshman · 17 December 2015

There's really no point in a
Steve said: This is precisely what I am claiming.
But you have no justification for such a claim.
Let's take that first multi-cellular organism for a start. It has maximum fitness by virtue of its very existence. This logically implies it has the correct set of components and cellular processess to stay alive.
This, I'm afraid, is word salad. Nothing has maximum fitness "by virtue of its very existence". All we can say is that it's more fit than an organism that isn't able to survive. Also, there is no "first multi-cellular organism"; evolution happens to populations.
Next we assume (from a non-teleological, step-wise change POV) this first multi-cellular organism was capable of only a single replication.
There seems no reason for such an assumption.
Also, in this original multi-cellular configuration the cell would not have had the sophisticated DNA error detection and repair capabilities (design assumes the opposite for the obvious logical reasons) to eliminate deleterous mutations.
Demonstrably false, since multicellular organisms (several separate groups) are well nested within eukaryotes, all of which have these sophisticated capabilities. They evolved well before multicellularity.
Using the popular non-teleological step-wise change evolutionary meme again, what would be the effect of a single, random variation in any one of the components/chemical processes of this obviously extraordinarily successful configuation of matter?
Usually, none, since most mutations are neutral. Sometimes, deleterious. Other times, advantageous, and the latter would increase in frequency in the population. If, for example, greater fecundity were advantageous, a mutation that resulted in greater fecundity would be advantageous.
Further, assuming the super successful organism was able to repeatedly defy the odds and hang on despite repeated challenges from variations that would steer the organism away from its current maximum fitness, what would trigger these variations that are void of selection (since there is only one offspring, and nothing to select for) to 'improve' an organism already at maximum fitness?
Still thinking of individuals, not populations. Variations that steer away from maximum fitness won't spread in the population. It's very unlikely that there is one one offspring, but even if there were, selection would still take place, if only to eliminate deleterious variants.
How was it logically possible for this organism to survive even one single variation without pre-existing machinery (information)? This is what I ask Harshman, Elsberry, Matzke, et al Oh, and for DS' benefit, this goes directly to the heart of the OP. Are non-teleological processes capable of creating information? So John Harshman (or Nick Matzke, Wesley Elsberry, et al for that matter), where's the free lunch coming from? How did variation in that single, maximumly fit multi-cellular organism create something new and improved?
You set up an absurd straw man in which a population consists of a single individual, without a repair mechanism, that makes one copy of itself and dies. That's a recipe for quick extinction even if there were some kind of pre-existing machinery, whatever that means. And we know quite well that no such thing ever existed. There are models for the evolution of multicellularity around today, Dictyostelium being the most popular. It has huge populations, becomes multicellular under special conditions, and produces a multitude of spores. As do a number of single-celled organisms.

TomS · 17 December 2015

Steve said: This contributes to our knowlege by starting inquiry from a productive basis. HOW was life designed? WHAT tools were used to create the design? WHY were these tools chosen? WHERE are these tools? HOW do they work? WHAT are the fundament elements of the design? HOW many elements are there? Were all the elements introduced at the same time? If not, WHEN were each element introduced? WHAT order were each element introduced? WHY were they introduced in this particular order?
For with what eyes of the mind was your Plato able to see that workhouse of such stupendous toil, in which he makes the world to be modelled and built by God? What materials, what bars, what machines, what servants, were employed in so vast a work? How could the air, fire, water, and earth, pay obedience and submit to the will of the architect? From whence arose those five forms, of which the rest were composed, so aptly contributing to frame the mind and produce the senses? Cicero: De Natura Deorum (On the Nature of the Gods) Book I, section 19

Michael Fugate · 17 December 2015

Just Bob said: Steve! You're back! Maybe you've had time to think of just one little example of something which is NOT designed. If you can't think of one, just say so.
Let me start the list for you Steve. Designed 1. Organisms 2. 3. 4. Not Designed 1. 2. 3. 4. We are especially interested in the "Not Designed" items. If the universe were designed, doesn't all it's prescribed pain, death and indifference give you pause?

Just Bob · 17 December 2015

Steve said: This contributes to our knowlege by starting inquiry from a productive basis. HOW was life designed?magic Miracle. WHAT tools were used to create the design? God's will. WHY were these tools chosen? Only God knows. WHERE are these tools? In the mind of God. HOW do they work? Miraculously. WHAT are the fundament[al] elements of the design? Divine thoughts. HOW many elements are there? As many as God wanted. Were all the elements introduced at the same time? God is omnitemporal, so yes and no If not, WHEN [was] each element introduced? Whenever it pleased God. [In] WHAT order [was] each element introduced? He is the alpha and the Omega. WHY were they introduced in this particular order? The answer will come through prayer.
Intelligent Design answers supplied (and grammar corrected). Now, how does that "productive basis" advance the enterprise of science?

Michael Fugate · 17 December 2015

Mike Elzinga said:
Steve said: Repetitive chemical reactions and reproduction are different animals. They are more like different universes. What an extraordiary logical stretch to assume that the repetitive nature of a chemical reaction is supporting evidence for the the coordinated, timed execution of a myriad set of chemical reactions which is reproduction. It seems your misunderstanding is due to your consideration of what is now, and not the contemplation of how they got where they are.
Here is an extremely important question that simply sails way over the heads of all ID/creationists (and I do mean all ID/creationists); namely, what do your "theories" predict if the temperature of the organism drops below, say, 5 degrees Celsius or goes above, say, 80 degrees Celsius? A second question is why does temperature never enter into your theories? Those of us who actually know something about this stuff know why these questions mean absolutely nothing to an ID/creationist.
And of course there is concentration. The non-directed formation of micelles would concentrate molecules and this would affect reaction rates. Chemistry, Steve, is it random collision of molecules?

eric · 17 December 2015

Ray Martinez said: 2. No evolutionary scientist, since Darwin, accepts both concepts existing in nature at the same time because these persons understand the logic of reason #1 as conveying mutual exclusivity.
[Looks at German Shepherd], [looks back at Ray]...are you daft? And are you seriously claiming that Darwin did not accept that artificial selection happened because it was mutually exclusive with evolution? Have you read OOS?

eric · 17 December 2015

Steve said: Excess reproduction IS the front loading of information into the genome.
Then as far as I can tell, you're just making the 'everything is designed" argument.
Repetitive chemical reactions and reproduction are different animals. They are more like different universes. What an extraordiary logical stretch to assume that the repetitive nature of a chemical reaction is supporting evidence for the the coordinated, timed execution of a myriad set of chemical reactions which is reproduction.
What law of physics, chemistry, or biology would prevent an RNA polymerase from reacting more than once with a DNA strand? What law of chemistry or physics are you claiming makes these molecules 'one use only' unless God intervenes?
In fact, I assert that it is an logical impossibility that variation and selection could work without excess reproduction.
Well it would work as long as the organism existed, but with a steadily decreasing population, that probably wouldn't be very long. Let's work through a toy example. I have 100 bacteria. Each initial 'parent' will produce exactly one and only one offspring, but not all of those offspring will survive. The situation will then look like this: 1. 100 parents ("Gen 0") produce 100 slightly varied offspring ("Gen 1"). Because of varied fitness, competition, and environmental dangers, some of these offspring (let's say...10%) die before they can reproduce in turn. 2. The successful 90 Gen 1 bacteria produce 90 slightly varied offspring ("Gen 2"). Again, there is selection based on fitness. 3. The successful 81 Gen 2 bacteria...and so on. ... 28: After 27 generations (for this exercise, I round 'fractional' children down)humans observe the remaining 2 bacterium and quite correctly say, 'these are the survivors of evolution via random mutation and natural selection.' The point being: even without "excess reproduction," there can be random mutation and natural selection, which is one of the key mechanisms of Darwinian evolution. It won't last long because the organism will quickly become extinct if it doesn't reproduce at least at the replacement rate, but evolution via natural selection can and will still occur.

Michael Fugate · 17 December 2015

eric said:
Ray Martinez said: 2. No evolutionary scientist, since Darwin, accepts both concepts existing in nature at the same time because these persons understand the logic of reason #1 as conveying mutual exclusivity.
[Looks at German Shepherd], [looks back at Ray]...are you daft? And are you seriously claiming that Darwin did not accept that artificial selection happened because it was mutually exclusive with evolution? Have you read OOS?
Genetic engineering? So its all or none, Ray? God controls everything - and yet we have free will. How can two ideas be in less agreement?

Ray Martinez · 17 December 2015

Michael Fugate said: So its all or none, Ray? God controls everything - and yet we have free will. How can two ideas be in less agreement?
Yes, it's all or nothing. Science supports wholeheartedly: it completely rejects Intelligence to have any role in the production of reality. That said, where did you obtain the idea that God's control has exceptions?

John Harshman · 17 December 2015

Ray Martinez said: Science supports wholeheartedly: it completely rejects Intelligence to have any role in the production of reality.
I protest. Science rejects intelligence to have any role in the production of Ray's posts. But Ray's posts should not be confused with reality.

Ray Martinez · 17 December 2015

John Harshman said:
Ray Martinez said: Science supports wholeheartedly: it completely rejects Intelligence to have any role in the production of reality.
I protest. Science rejects intelligence to have any role in the production of Ray's posts. But Ray's posts should not be confused with reality.
Why is Atheist John Harshman attempting to undermine his own position (complete rejection of Intelligence to have any role in the production of reality)?

Ray Martinez · 17 December 2015

John Harshman said:
Ray Martinez said: Science supports wholeheartedly: it completely rejects Intelligence to have any role in the production of reality.
I protest. Science rejects intelligence to have any role in the production of Ray's posts. But Ray's posts should not be confused with reality.
Ray Martinez said:
John Harshman said:
Ray Martinez said: Science supports wholeheartedly: it completely rejects Intelligence to have any role in the production of reality.
I protest. Science rejects intelligence to have any role in the production of Ray's posts. But Ray's posts should not be confused with reality.
Why is Atheist John Harshman attempting to undermine his own position (complete rejection of Intelligence to have any role in the production of reality)?
I get the distinct impression that John is seeking relief from a Moderator. He has been domineered.

eric · 17 December 2015

Ray Martinez said: [Science] completely rejects Intelligence to have any role in the production of reality.
How can you type that into a computer without seeing the idiocy of your own claim?

Ray Martinez · 17 December 2015

eric said:
Ray Martinez said: [Science] completely rejects Intelligence to have any role in the production of reality.
How can you type that into a computer without seeing the idiocy of your own claim?
What idiocy? Your bluff is called.

Steve · 23 December 2015

1. There is no such thing as adequate fitness or the fittest organism. Its just one of those evolutionary memes that muddy your thinking. The organism is either fit (alive) or unfit (dead). Changes to organisms are made in order to keep the lineage fit (alive). Saying one offspring is fitter than another is meaningless. There will always be at least one fit offspring or the lineage will die off. There is no chance or question on the matter. Organisms dont run through the jungle blind. They have always had the tools to make the changes that are required to stay fit (alive). 2. There is no such thing as better sets (another evolutionary meme). It only has different sets. A better set today is a worse set tomorrow so it adds nothing to talk about better or worse. Only what works. The organism that has the right set today could kill it tomorrow. That is why excess reproduction is a prerequisite for variation and selection. A continouse stream of variation guarantees a minimum of offspring will survive to the next reproductive round. There is no question about it. These evolutionary memes create the impression that organisms are always on the precipice of oblivion. Its just not the case. They are in continuous flux as is the environment. And that's no thanks to non-teleological step-wise change. 3. There is no strawman argument. The strawman is you imagining organisms could reproduce zillions from the get-go. You have no supporting evidence for this. In fact, non-teleological step-wise change requires the first proto-cell to start from 0 to 1, then 1 to 2, etc. How did early organisms go from 0 to a zillion in 6 seconds? Unless they were Bugatti's. But then in that case you would be talking teleology and design. 4. Your lottery analogy is also yet another evolutionary meme. Even a billionth of a chance you will take as evidence for non-teleological step-wise change. But look closer at your analogy. The lottory is in fact designed to have winners. That is why they chose 6 numbers from 1-60. But lets say we design a new lottery with 12 numbers from 1-150. What do you think the results will be? Needless to say, the lottory designers would either get beaten up in a back alley by frustrated lottery buyers or jailed for fraud. Either way, there won't be any winners in several lifetimes. In fact, your lottery analogy works better as a designed explanation, i.e. the amount of excess reproduction is calibrated to ensure there is always at least one winner within the reproductive lifespan of the organism.
stevaroni said:
Steve said: Let's take that first multi-cellular organism for a start. It has maximum fitness by virtue of its very existence.
No, it has adequate fitness to survive. That is all it needs. It may be the one of the fittest organisms on the planet at this particular point, but that doesn't matter all that much at the moment, since the survival landscape is mostly driven by the need to survive the environment.
This logically implies it has the correct set of components and cellular processess to stay alive.
No, this logically implies that it has a sufficient set to survive. There will eventually be much better sets, but at the moment, this one is good enough.
Next we assume (from a non-teleological, step-wise change POV) this first multi-cellular organism was capable of only a single replication.
Why?
Using the popular non-teleological step-wise change evolutionary meme again, what would be the effect of a single, random variation in any one of the components/chemical processes of this obviously extraordinarily successful configuation of matter? How was it logically possible for this organism to survive even one single variation without pre-existing machinery (information)?
Ah. now we get to the meat of your argument. But it's a straw argument, isn't it? Your entire model imagines one organism that replicates one time, and that's not how it works. Most simple organisms (aided by their offspring) would have been capable of multiplying zillions of times. And, of course, some of them would be mutated, especially with a simple primitive genome with little backup. And, of course, most of those mutations would have been disastrous, because there was very little DNA to begin with, and it was all pretty important and the odds of having a useful mutation are tiny, and therefore almost all mutations would have been fatal. This is readily apparent by the slow, slow rate of progress from single celled organisms 3+ billion years ago to even simple multicellular animals maybe 700mya. Compare that rate of change to modern rates and the progress is glacial. But this is to be expected, if you want to use the "computer program" analogy, in the early days you're a simple machine with not much more than an operating system aboard, and almost any change will break you, not make anything better, and the record shows this. In fact, you probably couldn't have many mutations at all until you had initial mutations that duplicated some of the DNA so there were pieces that could break in the first place without killing the organism. But "almost none" is not none, and even astonishingly long odds, when multiplied by enough tries, turns up winners. Just ask these lottery winners, who all beat vanishingly tiny odds to score that winning ticket.

DS · 23 December 2015

Poor Steve once again displays his ignorance. Look up the word "fitness" Steve. It doesn't mean what you think it means. And calling something a meme is not an argument. All of your bluster is meaningless. Grow up, learn some real biology, then go away, not necessarily in that order.

Time to close this thread. Game over indeed.

eric · 23 December 2015

Ray Martinez said:
eric said:
Ray Martinez said: [Science] completely rejects Intelligence to have any role in the production of reality.
How can you type that into a computer without seeing the idiocy of your own claim?
What idiocy? Your bluff is called.
Computers are part of reality, Ray. Scientists don't reject the notion that intelligence was involved in their production, and its incredibly silly to claim that they do. Yes, there are intelligently designed things in reality. That does not mean every ID hypothesis is good or scientific; each must be evaluated on its strength, and "species were poofed into existence in their present form via divine miracle from an intelligence which shall go unnamed" is a much weaker ID hypothesis than, for instance "this computer was designed by humans" or "this rock's fractured surface is a result of hominid intentional sharpening rather than tumbling."

eric · 23 December 2015

Steve said: 3. There is no strawman argument. The strawman is you imagining organisms could reproduce zillions from the get-go. You have no supporting evidence for this.
Sure we do; organisms that produce more than once. Chemical catalysts that catalyze the same reaction more than once. Cyclical biochemical reactions, where the cycle occurs over and over again. We observe the process you claim is impossible, and so we reject your claim. You have yet to answer Stevaroni's question: why assume replication reactions can only occur once per organism? What law of physics or chemistry prevents a set of biochemicals from going through the same set of reactions second time?

Steve · 28 December 2015

Ahh, but Eric, reproduction and repetitive chemical reactions are two different animals. Its understandable that you would want to try and shift the focus to the simplest aspect of what's happening during reproduction. That way you feel you won't have to confront the teleology that is apparent; like the timing of reactions, the ordering of processes, etc. Chemical reactions are the most mundane and uninteresting of aspects of what is taking place during reproduction. As to Stevaroni's question, I have indeed answered it. Non-teleological step-wise change inherently starts with a single reproduction at a single speed (assumed to be the speed of replicating amino acids since that is the only evidence we have of replication speed in early life). It DOES NOT start with a rapid replicating capability. But that won't do for your non-teleological step-wise change explanation. In order to kick start it, you have to assume rapid reproduction, you have to assume replication errors occurred from the get-go, you have to assume the variation would not hinder the organism's next round of reproduction, you have to assume that if the organism could successfully reproduce with the variation, that the variation would not weaken the offspring's viability and shorten its lifespan. With such a long string of unwarranted assumptions being made on your (pl) part, we are justified in rejecting YOUR claims that non-teleological step-wise change can do much of anything without a slew of already designed objects already in place.
eric said:
Steve said: 3. There is no strawman argument. The strawman is you imagining organisms could reproduce zillions from the get-go. You have no supporting evidence for this.
Sure we do; organisms that produce more than once. Chemical catalysts that catalyze the same reaction more than once. Cyclical biochemical reactions, where the cycle occurs over and over again. We observe the process you claim is impossible, and so we reject your claim. You have yet to answer Stevaroni's question: why assume replication reactions can only occur once per organism? What law of physics or chemistry prevents a set of biochemicals from going through the same set of reactions second time?

eric · 28 December 2015

Steve said: As to Stevaroni's question, I have indeed answered it. Non-teleological step-wise change inherently starts with a single reproduction at a single speed (assumed to be the speed of replicating amino acids since that is the only evidence we have of replication speed in early life). It DOES NOT start with a rapid replicating capability.
This is so much gobbledygook. A biochemical system will do the same thing every time you create the same circumstances. If the system is one that can create a copy of itself, then every time you give it the same environment and reactants it will make copies of itself. The equations governing reactions don't distinguish between DNA strand #1 original and DNA strand #1,000,000 clone; if the former would replicate in some circumstance, the latter would too. The ability to "reproduce" on a biochemical scale is just a consequence of how physics works.
In order to kick start it, you have to assume rapid reproduction,
Define 'rapid.' I think mainstream science expects that carbon backbone polymer reactions 3 billion years ago operated at the same speed we observe carbon backbone polymer reactions occurring today.
you have to assume replication errors occurred from the get-go, you have to assume the variation would not hinder the organism's next round of reproduction, you have to assume that if the organism could successfully reproduce with the variation, that the variation would not weaken the offspring's viability and shorten its lifespan.
We don't make these assumptions. The first is an observation rather than an assumption: we observe the rate at which errors occur. Your complaints #2 and #3 show you don't understand evolution, because evolution expects that many if not most variations will inhibit reproduction or weaken the organism.
With such a long string of unwarranted assumptions being made on your (pl) part, we are justified in rejecting YOUR claims that non-teleological step-wise change can do much of anything without a slew of already designed objects already in place.
Well, except that all of your assumptions are wrong. The first isn't an assumption and in the last two cases we appear to agree with you about the expected result of most variation.

Scott F · 28 December 2015

stevaroni said: This is readily apparent by the slow, slow rate of progress from single celled organisms 3+ billion years ago to even simple multicellular animals maybe 700mya. Compare that rate of change to modern rates and the progress is glacial.
This is one of the arguments that's always bothered me. Why is it assumed that the rate of evolution was "glacial" in the first 3 billion years, or so? Presumably, since the first self-replicator, evolution was occurring. By the time we get to the first multi-cellular organism, the individual cell is, itself, very, very complex and highly evolved. Just because we can't see it in the fossil record, evolution must have been occurring at a furious pace to create all of the various cellular "engines", repair mechanisms, etc. I'm not a biologist in any sense. But it's always seemed to me that all of the grand variation in multi-cellular forms is nothing compared to the inner mechanisms of the cell itself. Also, the notion that there was just one least common ancestor, just a single "first replicator". To my untrained eye, the eukaryotic cell itself appears to be a fossil record of multiple origins of life. Just look at its components: mitochondria, chloroplasts, the nucleus itself. This suggests that there were different kinds of replicating organisms, some of which eventually cooperated (or were co-opted) into creating a more complex replicator.

Scott F · 28 December 2015

Steve said: on Dec 17 Let’s take that first multi-cellular organism for a start. It has maximum fitness by virtue of its very existence.
Steve said: on Dec 23 1. There is no such thing as adequate fitness or the fittest organism.
This is nonsense. You can't have it both ways. First you claim that an organism can have "maximum fitness". A week later (in the same thread) you claim there is no such thing as "the fittest organism". If an organism has "maximum fitness", then by definition it must be "the fittest organism".

eric · 28 December 2015

Scott F said: Also, the notion that there was just one least common ancestor, just a single "first replicator". To my untrained eye, the eukaryotic cell itself appears to be a fossil record of multiple origins of life. Just look at its components: mitochondria, chloroplasts, the nucleus itself. This suggests that there were different kinds of replicating organisms, some of which eventually cooperated (or were co-opted) into creating a more complex replicator.
I'm not a biologist either, but I believe you're expressing an idea similar to one current hypothesis: that lateral gene (and larger structure) transfer between organisms played a big role in early life. This would mean that we wouldn't have a "family tree" with a traditional trunk and branches early on. Instead, the early 'tree' would look more like interconnected webbing; all organisms related, but not hierarchically so, because lineages would trade or aggressively co-opt components of other lineages a lot more than multicellular life can or does today.

Scott F · 28 December 2015

Steve said: Chemical reactions are the most mundane and uninteresting of aspects of what is taking place during reproduction.
What do you think that reproduction is, if it isn't mundane and "uninteresting" chemical reactions? I'm not a Reductionist by any means (I'm a big fan of Mike's "emergent properties" at all levels of organization of condensed matter), but "life" is chemical reactions. The former would not exist without the latter. (Well, to be precise, that's an unproven assumption. We don't know for certain that "life" (of some sort) could not exist without chemistry. But it certainly holds true for "life" as we know it.) Despite what creationists say, there is no magic poof-ism line separating "life" from "chemistry".

Scott F · 28 December 2015

eric said:
Scott F said: Also, the notion that there was just one least common ancestor, just a single "first replicator". To my untrained eye, the eukaryotic cell itself appears to be a fossil record of multiple origins of life. Just look at its components: mitochondria, chloroplasts, the nucleus itself. This suggests that there were different kinds of replicating organisms, some of which eventually cooperated (or were co-opted) into creating a more complex replicator.
I'm not a biologist either, but I believe you're expressing an idea similar to one current hypothesis: that lateral gene (and larger structure) transfer between organisms played a big role in early life. This would mean that we wouldn't have a "family tree" with a traditional trunk and branches early on. Instead, the early 'tree' would look more like interconnected webbing; all organisms related, but not hierarchically so, because lineages would trade or aggressively co-opt components of other lineages a lot more than multicellular life can or does today.
Yes, indeed. That's an interesting way of expressing it too. The notion that organisms could "attack" other organisms, not to acquire raw materials for growth, but to acquire new capabilities. Almost like an organism soup. Only later does Evolution settle down to the notion of "separate" and distinct organisms that cooperate to achieve new capabilities. (Maybe. That's just a vague notion, rather than a well thought-out proposal.)

DS · 28 December 2015

Scott F said:
Steve said: on Dec 17 Let’s take that first multi-cellular organism for a start. It has maximum fitness by virtue of its very existence.
Steve said: on Dec 23 1. There is no such thing as adequate fitness or the fittest organism.
This is nonsense. You can't have it both ways. First you claim that an organism can have "maximum fitness". A week later (in the same thread) you claim there is no such thing as "the fittest organism". If an organism has "maximum fitness", then by definition it must be "the fittest organism".
Well remember, this is the guy who refused to define the term "fitness" and refused to identify which type of fitness he was trying to describe. Apparently to him it means "something I don't understand and don't care to become educated about." So when you refuse to define the term, is it any surprise when you try to switch meanings? Steve can argue his own misconceptions into the ground. No one cares. In the end he won't have touched the modern theory of evolution at all, except of course in his own mind. Must be a lot of echos because of all the empty space in there.

eric · 28 December 2015

Scott F said: The notion that organisms could "attack" other organisms, not to acquire raw materials for growth, but to acquire new capabilities.
Well it was more the reverse situation I was thinking of. Like a virus: one organism injects its own DNA into a second, and the second then propagates a "chimera" daughter. Generally organisms try to be the invader, not the invadee. Though I guess if you think of examples such as mammalian gut bacteria, there's an argument to be made that organisms still sometimes practice a successful 'be an invadee' strategy in an epigenetic rather than genetic manner.