A few people (actually, a lot of people) have written to me asking me to address Kirk Durston's probability argument that supposedly makes evolution impossible. I'd love to. I actually prepared extensively to deal with it, since it's the argument he almost always trots out to debate for intelligent design, but — and this is a key point — Durston didn't discuss this stuff at all! He brought out a few of the slides very late in the debate when there was no time for me to refute them, but otherwise, he was relying entirely on vague arguments about a first cause, accusations of corruption against atheists, and very silly biblical nonsense about Jesus. So this really isn't about revisiting the debate at all — this is the stuff Durston sensibly avoided bringing up in a confrontation with somebody who'd be able to see through his smokescreen.
If you want to see Durston's argument, it's on YouTube. I notice the clowns on Uncommon Descent are crowing that this is a triumphant victory, but note again — Durston did not give this argument at our debate. In a chance to confront a biologist with his claims, Durston tucked his tail between his legs and ran away.
Let's start with his formula for functional complexity. He took this from a paper by Hazen, Griffin, Carothers, and Szostack; I know Hazen and Szostak's work quite well, and one thing you have to understand right away is that both are well-known for their work on the origins of life. They are not creationists by any means, and would probably be very surprised to see this paper being touted by a creationist as evidence that evolution is nearly impossible.
Here's the formula that Durston cites:
Doesn't that look impressively sciencey? It's a very simple equation, though, used to quantify the amount of what Szostak calls "functional information",
This big number can be misleading, though. We also want to know what fraction of all those sequences can carry out our function of interest, x, to some degree. This is the value of
To reduce the metric a little more, Hazen takes the negative log base 2 of this number, which simplify specifies the number of bits necessary to specify the functional configuration of the system. In our example of any protein doing the job, the answer is
It's very easy and cheesily fun to churn out big numbers with these kinds of calculations. For instance, here's part of the first sentence of the Hazen paper:
Complex emergent systems, in which interactions among numerous components or agents produce patterns or behaviors not obtainable by individual components, are ubiquitous at every scale of the physical universe
If you strip out the punctuation and spaces from that sentence, there are a total of 181 alphabetic characters there. How many possible arrangements of 26 letters in a sequence 181 characters long can there be? 26181, or 1.3 x 10256. It's huge! If we take the
What the Hazen equation does, though, is include that important
Complicated stuff that is built up by many smaller components interacting with each other to make novel arrangements, arrangements that cannot be seen in the single pieces, are common everywhere in the known universe.
How many sentences like that are there? I don't know, but I'm sure there are a lot; it's also the case that we don't even need to be grammatical or elegant to get the basic message across. This works, too:
There xxxxxx arre l0ts of xxxx big thijngs xxx xxxxxxx xx made of xxxxxxx littler x thangs xx xxxxxx stuck togther xxxxxxxxxxxxxxx xxxxxxxxxxxxxxx xxxxxxxxxxxxxxx xxxxxxxxxxxxxxx xxxxxxxxxxxxxxx xxxxxxxxxxxxx
Hazen is making the point that all 3 of those 181 character sentences are functionally equivalent. To measure the functional complexity of the sequence, you need to at least estimate the number of functional variants and divide by the total number of possible arrangements of letters. This measurement is also only applicable in the context of a specific function, in this case getting across the message of the ubiquity of emergent complexity. This sentence fragment, for instance, would not satisfy the requirements of
It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was th
Keep this in mind. Hazen's formula is used to calculate the information content of a specific function, not all possible functions.
Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree.
Get it? I know, it's a lot of background and a lot of numbers being thrown around, but this is a computational tool they are using in artificial life simulations. Basically, they are asking, if we make a random letter sequence, what is the probability that it will say something about patterns? Or, if they make a random peptide, what is the probability that it will catalyze a particular reaction they are measuring? Or, if they create a random program in an artificial life simulator like Avida, how likely is it that they'll get something that can add two numbers together?
I'm not going to try to give you the details of Hazen's results, since they're largely tangential to my point here — they look at the distribution of solutions, for instance. But they do observe that in Avida, with an instruction set of 26 commands, and randomly generating 100-instruction programs, they find programs that carry out one logic or arithmetic function in about 1 in a thousand cases. There are about 3 x 10141 possible arrangements of 26 instructions taken 100 at a time; any one specific sequence has a
Kirk Durston loves the Hazen paper. He has cited it many times in the various debates recorded on the web. It's wonderful because it's a real scientific citation, it talks about measuring the functional complexity of things, and it's got math — simple math, but it's enough to wow an uninformed crowd. Just watch how he abuses this simple formula!
Start here:
That's it, 3 terms:
Hang on. N, as Hazen defines it, is the number of possible configurations of n possible elements. Durston doesn't have a way to calculate that directly, so he invents a kind of proxy: an estimate of the total number of unique individuals that have ever existed. This is wrong. Here we have a simple metric that we could use, for instance, to calculate the number of different possible poker hands that can be dealt from a deck, and instead, Durston is trying to use the number of times a hand has been dealt. Right away, he's deviated so far from the Hazen paper that his interpretations don't matter.
Now you might say that this is actually a change in our favor. It makes the number N much smaller than it should be, which means the probability of a specific result out of N possibilities is improved. But that's not even how Durston uses it! Suddenly, he tells us that N is a limit on an evolutionary search (again, that's not at all how Hazen is using it).
Here's the game he's playing. Durston shows up with a deck of cards for a game of poker; he knows, and you know, that the odds of getting a specific sequence of cards in a 5-hand deal are really low (about 1 in 3 x 108). Then he tells you he only has time to deal out 100 hands to you, and wants to know if you want to just give him the money he'd win right now, since with only 102 trials to test over 108 possibilities, you are going to fall far short of exhausting the search space, and are highly unlikely to find the one specific hand he has in mind…which is true. Of course, none of that has any bearing on how poker is played.
So, he's basically abandoned the Hazen paper altogether — it was a veneer of scientific respectablity that he initially holds up in front of us, and then he ignores it to plug numbers he wants into the equation. Then he lowballs his irrelevant version of the number N, and redefines it to be a limit on the number of trials. Sneaky.
What about the next parameter?
He ignores it. He simply sets it to 1.
He slides right over this rather significant fact. The next thing we see is that he announces that 140 bits (which is the log base 2 of 1042) is the upper bound of information that can be generated by an evolutionary search, and suggests that anything above this magic number number is unreachable by evolution, and anything below it could be reached by random processes.
What that means is that he only accepts one possible solution in an evolutionary lineage. He is estimating the probability that an organism will have precisely the genetic sequence it has, as derived from a purely random sequence, within a limited amount of trials. No incremental approach is allowed, and worse, it is the one and only sequence that is functionally relevant. The only way he imagines a sequence can be reached is by randomization, and all he considers is the conclusion. It really is a gussied-up version of the '747 in a junkyard' argument that the old school creationists still use.
To summarize, what we're dealing with is a guy who drones on about basic mathematics and pretends that his conclusions have all the authority of fundamental math and physics behind them. He waves a paper or two around to claim the credibility of the scientific literature, and then ignores the content of that paper to willfully distort the parameters to reach his desired conclusion, in contradiction to the actual positions of the authors. And then he further ignores the actual explanations of evolutionary biology to use a hopelessly naive and fallacious model of his own invention to claim that evolution is false. He's a pseudoscientific fraud.
I understand he's actually in a doctoral program in Canada. I hope that, before his thesis defense, a few competent people look over his thesis and check his interpretations of his sources. I just looked over the Hazen paper and compared it to what he's claiming about it, and his version is completely bogus.
Hazen RM, Griffin PL, Carothers JM, Szostak JW (2007) Functional information and the emergence of biocomplexity. Proc Natl Acad Sci U S A 104 Suppl 1:8574-81.
181 Comments
Mike Elzinga · 31 January 2009
Rann · 31 January 2009
KIRK DURSTON, B.Sc (Physics), B.Sc. (Mech. Eng.), M.A. (Philosophy), Ph.D. Candidate (Biophysics) at the University of Guelph
Kirk Durston is the National Director of the New Scholars Society. He is currently a Ph.D. candidate in Biophysics at the University of Guelph, specializing in the application of information to biopolymers.
Joe Felsenstein · 1 February 2009
Mark Frank · 1 February 2009
Obviously you heard Durston speak and I only have the Youtube video plus his comments on UD but I think you are being unfair. His presentation is erroneous - but not for the reasons you give. Peter Olafsson (and to a less extent myself) has commented on his presentation on UD and explained the statistical errors which are severe but not the ones you describe.
(1) His 10^42 number appears to be an estimate of the total number of DNA/RNA mutations that have taken place since life began. He does not use this as a substitute for N in Hazen's formula. He uses it to estimate the chances of nature stumbling across something that meets the criteria of Hazen's formula. In one sense this is quite reasonable. If you want to estimate the chances of dealing a Straight Flush during a poker marathon - you need to know how many hands were dealt. Of course the rub here is the role of natural selection. See (3) below.
(2) In the example of Venter's watermarks I think he does set M(Ex)to 1. However, in the next example, folding proteins, he clearly doesn't. He considers all folding proteins.
(3) Initially he ducks the role of natural selection in reducing the odds but he does come back to it in two ways. One is a fleeting reference to the NFL theorem about fitness functions having to be more complex than the target they are leading to. This is absolute rubbish as in evolution the fitness function comes first and defines the target. But I don't think he understood what he was talking about anyway. The second relies on a knowledge of biochemistry which I am unable to challenge. In the case of folding proteins he claims that:
a. Only folding proteins (plus a small amount of others) are any use in life.
b. These comprise a minuscule proportion of all possible proteins
c. The folding proteins are in clusters of similar proteins but these clusters have no relationship to each other - they are scattered across the space of possible proteins.
If all of these are true I think it presents an interesting problem for evolutionary biology. How did replication and mutation get from the original RNA/DNA across the wide open spaces to these clusters of folding proteins. There does not appear to be any fitness advantage in generating non-folding proteins so natural selection cannot have driven replication that way. And the chances of stumbling on another cluster through genetic drift seem to be negligible.
However, I am not aware of this being considered a big problem in evolutionary biology so I am sure there is something wrong with this argument. But I think the fault lies in the biochemistry. Are a, b and c really true?
Even if this does present a genuine problem for evolutionary biology it is another giant step to deduce an intelligent source. It is really just a problem to be addressed.
JGB · 1 February 2009
point b listed above has been shown experimentally with alpha helix bundles to be nonsense. I don't not have the citation handy, but a reasonably robust number of random sequences where capable of folding into 4 helix barrels.
point c is guesswork because we do not actually have good data on the extent of possible overlap between different folding motiffs. It's a good question to investigate seriously.
mrg (iml8) · 1 February 2009
"Probability calculations are the last refuge of a scoundrel." -- Jeff Shallit
Cheers -- MrG / http://gvgpd.proboards.com
mrg (iml8) · 1 February 2009
Frank J · 1 February 2009
I admit that I haven't carefully read every word of the original article, so I might have missed it. But from a quick read I see no indication of what Durston proposes instead, other than "some designer did something at some time." The obvious questions are: Did the designer - or a yet-undiscovered "naturalistic" mechanism that Durston did not rule out - operate in-vivo, as Michael Behe thinks? Or does Durston have an “in vitro” alternative that no major IDer has yet to propose, let alone test? And when did those “blessed events” occur? Last Thursday? Over the course of billions of years? Once at the beginning of life ~4 billion years ago, as Behe once suggested? At the beginning of the Universe ~14 billion years ago, as Dembski once suggested?
Just because his misleading negative arguments need to be addressed is no reason to let him off the hook from providing anything meaningful about his own alternative.
Mark Frank · 1 February 2009
Brian Shewchuk · 1 February 2009
Regarding the assertion that only folded proteins are of any utility: There is quite a bit of recent research that has revealed that many proteins (fesselin and synaptopodin, for example - involved in muscle contraction; several transcription factors; etc.) are in fact natively UNFOLDED. They adopt structure when interacting with a particular partner - an "induced fit" model of folding. In fact, it appears that this may be more the rule than the exception, for at least a portion of most proteins. What this appears to accomplish is it allows for divergent functions of a single polypeptide depending on the substrate or interaction partners. This dramatically expands the functional utility and freedom of single protein, and in my mind further diminishes these types of already erroneous probability arguments.
If interested, search "natively unfolded protein" on Medline or equivalent.
Dave Wisker · 1 February 2009
Doesn't the cumulative nature of natural selection preclude a totally random search?
mrg (iml8) · 1 February 2009
Frank J · 1 February 2009
DS · 1 February 2009
So at best, even if all of his arbitrary and biologically nonsensical assumptions are considered to be correct, this guy has shown that evolution couldn't possibly occur without natural selection. Great. Just 150 years behind the times. That should be good enough to get a PhD.
Dave Wisker · 1 February 2009
Mark Frank · 1 February 2009
SteveF · 1 February 2009
Mark Frank,
A large part of Durston's argument relies on the isolation of new protein folds in sequence space. It seems to me that there remains a fair bit to learn about this aspect of protein evolution. In this sense he is taking advantage of a gap in understanding. Having said that, when he discusses this topic, for example here:
http://www.newscholars.com/papers/Origins%20and%20Explanations.pdf
he doesn't present the full picture. The gap in our knowledge isn't quite so extreme. For example:
Tuinstra, R.L., Peterson, F.C., Kutlesa, S., Elgin, E.S., Kron, M.A., and Volkman, B.F. (2008) Interconversion between two unrelated protein folds in the lymphotactin native state. Proc. Nat. Acad. Sci. (USA) 105:5057-5062
One thing that he uses to support his argument is work by Douglas Axe, research that IDers (Axe is one) have picked up on to support the notion of isolation in sequence space. However, Arthur Hunt does a very good job of showing how such an interpretation is flawed:
http://pandasthumb.org/archives/2007/01/92-second-st-fa.html
Note that I'm not an expert and shouldn't be considered as such!
Mark Frank · 1 February 2009
Eamon Knight · 1 February 2009
The bit about NS seems to involve some rather furious handwaving. OK: he's shown that random search can't generate more than X bits of FI in the allowed number of trials. But he seems to simply assert without justification that no selection algorithm can make up the deficit. If we start with an initially low value for Ex (maybe we don't much care about the substrate, as long as something gets catalyzed, a little bit), then M(Ex) might be quite large, and the FI correspondingly low. Then iterate using a slightly higher Ex threshold (or more specific x), and generating new candidates only from those with the highest Ex of the previous round (which is of course classically Darwinian....).
Arthur Hunt · 1 February 2009
Venus Mousetrap · 1 February 2009
John Kwok · 1 February 2009
Durston's argument almost sounds similar to Behe's assertion that he's found the "mathematical limits to Darwinism", as noted in his second pathetic exercise in mendacious intellectual pornography, "The Edge of Evolution". Thankfully a few others, most notably Mark Chu-Carroll, were among the first to "deconstruct" Behe's acute ignorance of probability theory, in his effort to explain why certain mutations had to occur simultaneously in the Plasmodium malarial parasite. Wonder when Durston and Behe will try calculating the probability of the existence of an Intelligent Designer (IMHO, such an entity was most likely a Klingon scientist who travelled backward in time to the primordial Earth and seeded it with life, billions and billions of years ago.).
Mike Elzinga · 1 February 2009
mrg (iml8) · 1 February 2009
Stepping back a bit and taking a more distant view of Dunston's argument, the irony is that it is operating at a level of technical elaboration -- I was tempted to say "sophistication" but concluded I would regret it -- such that the only audience with enough background to seriously examine it
consists of the people who know perfectly well it's
bogus.
Of course the real intent is to hand the charmless
visitors who show up on PT to pick fights (and their like) yet another exercise in windy muddying of the waters.
Cheers -- MrG / http://gvgpd.proboards.com
RBH · 1 February 2009
Frank J · 1 February 2009
Frank Lovell · 1 February 2009
Why do we allow the ID-as-science crowd to continue to successfully conflate supernatural "intelligent design" with natural "intelligent design?"
The IDers (on purpose!) get away with this conflation all the time in front of the general public in their writings, their public presentations, and even in their public debates on the subject of what should be included in public science education curricula. They argue: "There are scientific ways and methods of discerning "intelligent design" that are employed in archaeology and even in the SETI program, and so what's the big deal, we [IDers] merely want to do the same thing as applies to biology [biologically functional processes and structures]." And whenever they say things like that and somebody does not promptly and emphatically point out that IDers want to employ such scientific "ways" to discern NOT natural "intelligent design" (which is the sort of "design" that archaeology and the SETI program seek to discern/discover), but rather supernatural "intelligent design," their purposeful conflation succeeds and the public fails to recognize the (perhaps subtle but nonetheless) vital difference between what scientific methods for discerning "intelligent design" can legitimately succeed in discerning (namely, natural "intelligent design") and cannot legitimately succeed in discerning (namely, supernatural "intelligent design").
And so I ask again: Why do we let the ID crowd to continue to successfully conflate supernatural "intelligent design" with natural "intelligent design?"
Every time an IDer speaks of "intelligent design" we should interrupt and ask: "Excuse me, you mean supernatural "intelligent design," right?" Make them confess and clarify (sorting-out and thwarting their hoped-for conflation), or make them lie. Each and every time.
mrg (iml8) · 1 February 2009
mrg (iml8) · 1 February 2009
Gary Hurd · 1 February 2009
Nicely done, PZ.
Vince · 1 February 2009
JimmyJ · 1 February 2009
Just stop debating these clowns. I swear debating them is competing in a Roshambo championship tournament - even if you win, you still lose.
sledgehammer · 1 February 2009
I posted this on AtBC before I saw this thread. I would have posted here had I known. Apologies to the double-dippers.
I suspect Durston understands all too well the math he's "parading around", and is being deliberately dishonest when he thinks he can get away with it.
Here's why I have come to that conclusion:
After watching that you-tube lecture with it's tornado-in-a-junkyard conclusion, I had all but dismissed his reasoning as obviously bogus, if only due to naivete, but his 70-bit limit on the "functional information" that nature was capable of intrigued me enough to his reasoning behind that, since Dembski's UPB was 500 bits.
A google on "Durston 70 bits" yielded only 9 hits, one of which was this ISCID discussion from 2002 [http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000145;p=4], where he introduces the same equations as he displayed in that you-tube. Towards the end of the discussion, a commenter (Grape Ape) asked about the information
increase from gene duplication followed by mutation, producing a paralogous protein with a new function. His answer was telling.
Here's the comment in it's entirety (apologies for the length, emphasis mine):
[QUOTE]
Kirk Durston Member # 174 posted 12. September 2002 19:32
Post Resp to Grape Ape:
I agree with you; a gene duplication followed by a sequential divergence of one of the paralogues, if it achieved a new function, would produce
an increase in functional information. I also grant that such a thing can happen without the need for ID, provided the increase in functional information is not greater than 70 bits.
It was a bit sloppy of me to say, "The problem arises when we calculate the probability of achieving the novel protein and then realize that it is too small." I see no need for ID in obtaining novel proteins, or paralogues with novel functions, provided that the additional functional information required does not exceed 70 bits.
I suppose a next question could be regarding the possibility that the paralogue, which has achieved a novel function with less than 70 bits of
information, could also duplicate, diverge, etc, and achieve yet another protein with a novel function, all within the stable folding sequence space for that family of proteins.
My answer would be, only if the total information required to generate both paralogues was less than 70 bits. The reason for this is that [B]the
probability of achieving a second paralogue with a second novel function, from the first paralogue with the first novel function is the probability of achieving the first paralogue, [i]multiplied[/i] by the probability of achieving the second paralogue given the existence of the first paralogue.[/B] So the addition of required functional information is proportional to the product of each of their probabilities, where each probability refers to the chance of making the step from the parent gene. I should say that if the new function can be achieved by a paralogue that is less than 70 bits of functional information away within the same region of stable, folding sequence space, I would question whether a new function has been achieved, or a previously existing function has been regained. We might have to look at the fitness the new function provided. If it was not significant enough to prevent its loss, it may have been lost. If it was very significant, then there is a chance that it is a genuine novel function. But even at that, it could still have been lost in a bottle neck event somewhere in the past. One thing that ID, combined with the ITT predicts, is that there ought to be a slow loss of functions over time, depending upon the size of the population and the selective advantage such functions confer. We may have psuedogenes that are nothing more than ancient genes that can be reactivated, given the appropriate genetic engineering So in summary, you are right. Paralogues that achieve new functions increase the functional information content of the genome, but the upper limit for how far this can go is 70 bits, if my hypothesis is correct. If 70 bits is too low, it certainly would not exceed 400 bits.
[/QUOTE]
Grape's response:
[QUOTE]
I don't see how I could agree with you here. The key element you're leaving out is selection and subsequent fixation. If
the first duplication event creates a new gene with a novel function, and that function is of some use to the cell (which is probably a rerequisite for the novel funciton evolving anyway), the extra gene should quickly spread throughout the population and exist in thousands (or millions or billions) of copies. Now that everyone has the first paralogue, the probability of a second occurance is the same (actually lower)than the first. The scenario that you put forth would only apply AFAICT if you're talking about a single individual which only reproduces to replacement (making an effective population of 1). In that case, the probability of two duplications happening to the same individual would be the square of the probability of one duplication occuring over a given time frame. But of course we're talking about a population with many individuals where events can happen in parallel, so this wouldn't apply.
Incidentally, once there is one paralogue, the probability of subsequent duplications becomes greater. The reason is simply because there are now two targets to be duplicated rather than just one. Also, given that the most common mechanism for generating duplicates is unequal crossing-over, the chances of this happening increase when you have similar sequences next to each other on a chromosome. This is, for example, why short tandem repeats grow like they do, and it also allows for gene families to rapidly expand. This is the most likely explanation for why genes tend to follow a power law distribution IMO. quote:
So the addition of required functional information is proportional to the product of each of their probabilities, where each probability refers to the chance of making the step from the parent gene. Again, the whole point of mutation/selection is that things can be "ratcheted up" such that each step, if it's not highly improbable itself, can be additive such that it can create cumulative change that would be too improbable given a single step. Multiplying the probabilities only assumes a single step. In other words, I think it's a legitimate argument to talk about "functional islands", but in order for the argument to work, you must show that these islands are not connected or cannot be bridged via a low probability event. (This is the essence of Behe/Dembski's IC argument.) In our situation here, we have a duplication/divergence event which is not itself too improbable, so therefore there is no intrinsic limit to how many iterations that this process can proceed. And since we now we have a situation where some amount of functional information -- say 10 bits -- can be added to the genome, then a repetition of this process can surely add up to more than 70. The only way I can see your argument working (at least in regards to this scenario) is to show that a [i]single[/i] step must have been greater than 70 bits. [/QUOTE]
Durston back down from his multiplicative probabilities, and after a paragraph of hand-waving obfuscation, gives this surprising admission on the effects of selection:
[QUOTE]
Grape, I specifically included the phrase 'given the existence of the first paralogue' to account for what you have pointed out. You are right in that the generation of the second functional paralogue is not independent of the existence of the first. The effect of fixation merely increases the number of opportunities for the second paralogue to evolve. The probability that a paralogue will achieve a new function via a random walk is R!/R^R x (Nf/N). If there is an incremental, but significant advantage for each step closer in sequence space, then the R!/R^R disappears, as the fixation insures that we at least don't go backward, although we could go sideways, which still slows things down. Selection can't cut in until a mutation has occurred, which is largely random in nature (though not always). The right mutations have to occur to produce the function, even with selection operating, and the probability that the right mutations occur is related to Nf/N and the size of the population, if we ignore the possibility of sideways, or neutral mutations. Of course, the greater the population, the greater the probability that the right mutations will occur. But the likelihood that the second paralogue will become functional is dependent upon the Nf/N of both functional paralogues and probabilistic limitations, which are also related to Nf/N. That is why I say the second function won't happen unless the total information required is less than 70 bits.[B]So the effect of selection (or more accurately, elimination), if the fitness advantage is large enough, is to get rid of the random walk. The Nf/N still remains, however, as the target for which the random mutations must arrive at, one step at a time. Selection merely preserves gains. [B] The number of generations and the size of the population, however, may virtually guarantee that the target is reached by this ratcheting processes, if Nf/N is high enough.[/B]
[/QUOTE]
Immediately after this exchange, he dismisses himself, UD Patrick-style:
[QUOTE]
I'm going to have to sign off now. I'm bug-eyed from staring at this screen and I feel a little fried from generating all these essays today. I won't be able to continue this discussion, as I already indicated. I realize I probably have not convinced even one person, but I do hope I've introduced a few things to think about. My apologies to anyone who might post anything further on this subject, I just can't afford to get any further behind in my work.
I've enjoyed this discussion and feel that being involved in it was well worth my time. [/QUOTE]
Now that was in 2002. He has basically admitted that natural selection can increase the functional information in the genome by arbitrarily more than 70 bits.
Do any of his subsequent lectures and discussions in the next 6-7 years touch on this aspect of selection? No way! In fact, like in the you-tube lecture, he introduces selection only to dismiss it as ineffective in creating "functional information".
I call that intellectual dishonesty.
bdeller · 1 February 2009
I will confess, as a biology teacher much of the math is beyond my reach of understanding. But if I understand Durston's assertion correct random changes in proteins, thus genetic coding would be mathematically improbable. So would it follow that the "Random" mutations observed in HIV is not product of natural selection, but rather the work of an intelligent agent?
I ask this in all seriousness.
PZ thank you for this analysis.
Frank J · 2 February 2009
snaxalotl · 4 February 2009
snaxalotl · 4 February 2009
so, again, we're seeing the thinly disguised 747. I think what people are missing is WHY creationists keep returning to the 747 argument. I suggest that the underlying thread is "yes I KNOW there's all this stuff about evolutionary mechanisms (that I don't/partly understand), but you START with chaos and you END UP with something that must be far rarer than statistical noise" (analagous to the fact that most real numbers are uninteresting/incompressible). This intuition then drives all the variously sophisticated/confusing attempts at a mathematical justification of the intuition.
If this is true, what many creationists require is an understanding that the laws of physics inherently support feedback loops. Therefore we should expect that ALL possible histories of the universe involve "bizarre and unlikely" entities that exhibity "loopy" behavior in a way that "random configurations" of matter do not. Creationists think there's an elephant in the room (chaos -> structure) that entitles them to look for fault in established theory, and I suspect it might help to puncture this elephant
snaxalotl · 4 February 2009
ooer, I wish I'd used a phrase I just saw in a P. Z. Myers post: the physical universe is a "a tangled web of interdependent processes" because of it's inherent ability to support feedback loops
Durston · 26 February 2009
While having a Guinness with several fine young atheists at Doctor's pub in Edinburgh this past week, one of them informed me of PZ Meyers' write-up of how he supposes I estimate the empirical probability of protein families. Meyers' analysis, unfortunately, is incorrect on all the major points. I am grateful to Mark Frank for correcting some of Meyers' misconceptions, though Frank himself remains unpersuaded by my arguments, and raises his own misgivings about my view on fitness functions and natural selection.
It would surely help the clarity of the discussion to hear it straight from the source, so here are a few comments to correct some of Meyers' more significant mistakes and address the natural selection/fitness function problem raised by Frank.
As Mark Frank pointed out, and as stated right on the slide that Meyers referred to, the 1042 number is the maximum estimated number of trials that biological life has available to it over 4 billion years, given the parameters listed there. It does not represent N.
With regard to how I calculate M(Ex), the simple answer is that I most certainly do not use the value of 1 for proteins, as Meyers mistakenly assumes. In fact, I do not calculate M(Ex) at all, only the ratio M(Ex)/N, which gives the target size in sequence space and an estimation of the empirical probability if real data is used.
There is a significant problem with Hazen's approach when applied to proteins. One cannot directly obtain an empirical value for M(Ex), and Hazen supplies no reasonably attainable method in his paper for even calculating it. Hazen's eqn. is a simplified form of Shannon complexity, with the additional requirement of functionality. He assumes that all sequences are equally probable, which is almost certainly not the case. A more accurate way to measure the functional information of a protein is to use the following eqn.
If = ∑[log20 + ∑ P(af) logP(af)]
where the inner sum gives the functional information for a given site in the protein and P(af) is the probability of each of the commonly occurring 20 amino acids at a given site for a functional sequence as determined by natural selection. The outer sum, sums the functional information for each site in the sequence to give the total functional information required to code for the particular protein family. To actually calculate the functional information for a protein family, one can do the following:
Step 1: download the sequence alignment for a protein family, using Pfam as the source. The alignment is in the form of a 2–D array where each column represents an aligned site and each row represents a particular sequence for that protein family. An underlying assumption here is that the protein family sequences listed on Pfam, are functional, i.e., the non-functional sequences have been eliminated by natural selection/elimination thus satisfying Hazen's Ex. To clarify, the protein family sequences on Pfam have been filtered for functionality by natural selection. To give an adequate sampling of sequence space, at least 1,000 sequences is preferable for reasons stated shortly.
Step 2: remove insertions to reduce the number of columns to approximately the standard length of the protein. This is done by removing those columns which contain data that occurs less than a given percentage, usually 5 or 10 percent. The assumption here is that spurious insertions are not required for function (which is likely to be a safe assumption, but not always). (Note: I have written software that carries out steps 2 -5.)
Step 3: each column is analyzed to calculate the empirical probability of each of the 20 common amino acids. There will be 20 probabilities for each column. This is done by moving down a column and counting up the number of occurrences of each of the 20 amino acids and dividing the number of occurrences of each amino acid by the total number of sequences (rows) in the array. This procedure is repeated for each column/aligned site.
Step 4: The ground state is assumed to be the null state, which reduces to a Shannon complexity log 20 for proteins.
Step 5: The functional information required to produce any functional sequence for the protein family is calculated using the equation mentioned earlier above.
Step 6: to check if an adequate sampling of functional sequence space has occurred, one can plot the functional information If vs sample size. The slope of the curve at any point represents the change in functional uncertainty between the non-functional ground state and the functional state. As the curve becomes horizontal, the change in functional uncertainty with additional sequences becomes minimal, indicating that the sample size is sufficient to give an adequate approximation of the probability distribution for each amino acid at each site. As a general rule of thumb, at least 1,000 sequences are required to give an adequate sample size, certainly no less than 500. Be aware that these sequences are not even remotely equal to M(Ex). One must be aware that Pfam sorts sequences by a HMM and it is not error free. The inclusion of falsely sorted sequences will lower the estimated value of functional information for the protein family.
Once a value for the functional information for a protein family has been estimated as outlined above, one can then solve for the ratio M(Ex)/N by using Hazen's equation. This will give you the target size of a protein family in sequence space as well as the empirical probability of locating it in a single random trial. The actual probability of finding it, of course, will depend upon the number of trials available for the search. I'll say something about natural selection/elimination shortly.
Just a quick comment about PZ Meyers' surprise that I did not use a biological argument in the University of Edmonton formal debate on the existence of God. The debate was on the existence of God, not intelligent design. Of course, one might possibly construct an argument from design in biology for the existence of God, but the problem with constructing an argument using biology is that one must spend far too much time educating the audience on various technical details before one can even present ones argument. Thus, it is a tactical mistake to attempt to use a biological argument for the existence/non-existence of God in a timed, formal debate where one simply does not have the time to both educate the audience in the necessary background biological information, as well as present the emergent argument. This tactical mistake was aptly demonstrated by Meyers in his opening argument, where he used up his time giving a pleasant lecture about the hox gene complex, and had no time to present an argument against the existence of God.
Now to respond to Mark Frank's comment about natural selection. I believe that it is time for science to acknowledge that evolutionary biology has a very serious problem on its hands. Regardless of whether we are talking about molecular machines, molecular computers, or the discovery of novel protein families, 'natural selection diddit' is the standard response. Natural selection has become the new 'god' of the gaps. It has reached the point where natural selection is credited with truly phenomenal powers far exceeding anything it has been empirically shown to be able to do. No one disputes that natural selection can fine-tune an existing organism in a fluctuating environment, but with each discovery of yet more intricately designed molecular machines, meta information encoded in genomes, and regulatory cybernetic programming, the standard response is to credit yet more fantastic powers to natural selection. The testing of these phenomenal powers is painfully lacking. Call me a skeptic, but I just don't think natural selection can do all its cracked up to do. This isn't my problem; the onus is on those who actually think that natural selection can somehow guide evolutionary paths through sequence space to find novel protein fold-sets/families which, by the way, are determined by physics and not biology, to test that hypothesis. My graduate-level experience with genetic algorithms (which includes the writing of numerous algorithms ranging from basic to state of the art) tells me that natural selection actually found in nature is pathetically under programmed by orders of magnitude to do the fantastic things it is being credited with. Natural selection, as talked about in evolutionary biology (yet badly under-tested) is becoming a pantheistic Mother Nature. As I said, this is not my problem, it is the problem of the true believer in the new deity, Natural Selection. So, lets stop talking about natural selection as being able to guide the search for novel protein families and lets start doing science by putting forward a real hypothesis and then testing it. Until that is done, I think we all need a healthy dose of skepticism.
DS · 26 February 2009
Durston wrote:
"So, lets stop talking about natural selection as being able to guide the search for novel protein families and lets start doing science by putting forward a real hypothesis and then testing it. Until that is done, I think we all need a healthy dose of skepticism."
You seem to have some pretty basic misconceptions about the role of natural selection. Why on earth would natural selection "guide the search"? As for testing hypotheses, we do in fact know where novel genes and novel gene functions come from. The hypothesis has been tested and has been confirmed countless times.
You can be skeptical all you want. That won't change reality.
Durston · 26 February 2009
DS wrote:"As for testing hypotheses, we do in fact know where novel genes and novel gene functions come from. The hypothesis has been tested and has been confirmed countless times."
Novel genes that code for a protein within an existing protein family are trivial to generate. Novel functions within an existing protein family can also be produced. Also novel folds within a protein family can also be produced. However, we are not concerned with novel genes/functions/folds within an existing protein family. What we are concerned with is a novel gene that codes for a novel protein family. That has never been demonstrated and given our growing knowledge of the rarity of stable 3-D structures in sequence space, it is not likely to ever be demonstrated (unless we do it ourselves, which then becomes an example of intelligent design, where intelligent design is defined as an effect that requires a mind to produce).
Since the stable 3-D structures are determined by physics, an evolutionary search engine must search amino acid sequence space to find these structures. Since actual data indicates that the target sizes are extremely miniscule, a random search will never find any. Therefore, it is assumed, natural selection diddit. If natural selection cannot guide the search by radically reducing the non-functional search space, then the search for the protein families will degenerate to a random walk. I agree with you that natural selection is badly underpowered to provide any guidance in a search of amino acid sequence space, but that is not my problem; it is the problem of those who think it can. If you think it cannot, then you are faced with a large problem .... finding the protein families in a random search. I don't think you want to do that.
mrg · 26 February 2009
This is fascinating. It's the "bombardier beetle" argument rearranged in terms of protein structures -- with
"Hoyle-type probability arguments"
thrown in.
I sometimes suspect that there are basically no more than about a dozen fundamental Darwin-basher arguments -- they never come up with any new ones, they just dress them up in different clothes and claim they're new. One of these days I'll write up the list.
The Darwin-bashers like the archerfish, too: "This couldn't have evolved!" They also like to point to elaborate symbiotic relationships ... one even pointed to the clearly symbiotic nature of the eukaryotic cell as evidence of Design. I think I just stared at that one for a moment ... I just picked up the saying that fits the moment: "It puts the DUMB in DUMBFOUNDED."
Cheers -- MrG / http://www.vectorsite.net/gblog.html
Durston · 26 February 2009
MrG, I'm not a Darwin basher, I'm a realist. If you think that there is some evolutionary process out there that can produce novel protein families, then table your hypothesis and test it. I see Natural Selection being credited with a phenomenal amount of creative power and not a whole lot of testing to see if the credit is deserved.
mrg · 26 February 2009
Well fancy that, I'm a realist as well. I believe that the Moon is made of green cheese and I want you to show me that it isn't.
Henry J · 26 February 2009
Frank J · 26 February 2009
mrg · 26 February 2009
mrg · 26 February 2009
Durston · 26 February 2009
Frank J. wrote, "Whatever (apparently non-evolutionary) process you think produces novel protein families, would you mind telling us whether you agree with Michael Behe that such processes occur in a “biological continuum”, that humans and other species share common ancestors, and that life has existed on Earth for ~4 billion years?"
Is that the new 'Apostles' Creed'? I am always reluctant to pledge allegiance to a series of hypotheses before the testing has been adequately done. It is better to say, 'We are not sure exactly what processes were involved, but we are testing various hypotheses. When we are sure, we will make the announcement.' I see lot of people making announcements or making pledges of allegiance, when the actual testing has been woefully inadequate. As I said before, a healthy dose of skepticism is in order in such cases.
Here is an interesting alternative, which I am not endorsing, but is still fascinating .... Sherman, M. (2007), ‘Universal genome in the origin of metazoa’, Cell Cycle, 6:15, 1873-1877.
Frank J · 26 February 2009
Durston · 26 February 2009
A scientist starts walking on pretty shaky ground when he/she starts guessing. Guessing does not replace a careful, methodical, step-by-step testing of hypothesis. I do not know Behe's approach well enough to even comment on it, but I will say in which direction the evidence is causing me to lean. It is in the direction of Sherman's paper cited above. But as I said, I am only 'leaning' in that direction. I still see a lot of testing that needs to be done with Sherman's hypothesis before I would even go so far as to say it is credible. In the meantime, I am aware of a few other papers that are consistent with Sherman's hypothesis. However, 'consistent' does not constitute verification. In other words, although I lean toward Sherman's hypothesis, I still have a healthy does of skepticism about it for the time being.
Frank J · 26 February 2009
Frank J · 26 February 2009
I have not been able to access Sherman's paper. Does he state his estimate of the age of life, or is he only concerned with mechanisms?
mrg · 26 February 2009
I think the word is not "skeptic" but "pseudoskeptic".
Cheers -- MrG / http//www.vectorsite.net/gblog.html
Durston · 26 February 2009
Sherman does not concern himself with the age of life. I have not concerned myself with the age of life either. I'm concerned only with the origin and disparity of life, not with its age. I believe the current estimate is about 4.5 byrs, an age far too young to allow for the time required to find the protein families in sequence space. I would recommend Sherman's paper if for no other reason than as a discussion piece. From what I've heard about Hovind, he has no credibility.
Frank J · 26 February 2009
Durston · 26 February 2009
At this point, the only problem I see is that an alternate mechanism is required to fit within that time frame. Increasing the age estimates is not going to solve the problem, as even 12.5 Byrs is far too short to find even one average protein family. Sherman's proposal does fit within current age estimates, solving a lot of problems and lining up with some observations. As I said before, however, I'm only leaning in his direction. I'd like to see a lot more research into the hypothesis he suggests. A third proposal is Koonan's (Eugene Koonin, ‘The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life’, Biology Direct, 6/27/2007). However, I see appealing to an infinite number of worlds to overcome the probability problems, raises new problems; it isn't testable, it is the opposite of parsimonious, and it seems ad hoc. Appealing to an infinite number of worlds solves all sorts of problems, but raises the Boltzmann Brain problem. I feel that Koonan's solution to the origin of life is too bizarre to give serious consideration to. In the end, I do not see a Darwinian or a Koonanian solution to the problem of locating the physics-determined stable 3-D folds in sequence space. Sherman's model, however, does work within the time constraints we have.
Mike Elzinga · 26 February 2009
This discussion is a bit peculiar to watch. I never see these kinds of skeptical avoidances in the research community; only in the intersections with science, anti-science, and politics.
It reminds me of the old story that aerodynamic calculations show it is impossible for bumblebees to fly; yet they do.
If actual researchers avoided carrying out investigations on the basis of someone’s calculations, most areas of research would remain unexplored. No doubt, if Mother Nature had any awareness of the “impossibility calculations” of the evolution skeptics, she would just smile and think, “How dumb!”, and then go ahead and do it anyway.
The real motivator for the actual research community is the fact that we know of thousands of instances in which novel systems emerge unexpectedly from the most unexpected circumstances.
Not only do we have enough time for evolution to have occurred, along with a fossil record showing that it actually did, we have thousands of examples from all levels of evolving systems that we now understand.
Just because all issues haven’t been settled is not a sufficient reason, in the light of already available knowledge, to argue that the situation is impossible.
Almost everyone I know in the research community knows that the search space is enormous. Going through it systematically might be the way research does it, but that is not the way that Nature does it, and most researchers know that.
Some of the more subtle approaches to novel evolving systems do not work from some artificial evolutionary landscape concocted by evolutionary models. They emerge from adjacent realms involving different energy ranges (temperatures and pressures) and working materials and systems. The novel systems that emerge are not part of that adjacent realm, and could not survive long in that realm, but they have been “pumped” into an adjacent set of conditions where they become relatively stable.
This is analogous to simpler systems reaching “forbidden” states by way of being pumped into states from which the “forbidden” state can be reached.
The point here is that most people working in these areas are familiar with these approaches to the evolution of novel complex systems, and they are working on them even as the evolution skeptics make their models showing it to be impossible. Modeling these processes is often out of reach of current modeling methods, and at worst, misleading.
mrg · 26 February 2009
DS · 26 February 2009
Durston wrote:
"Novel genes that code for a protein within an existing protein family are trivial to generate. Novel functions within an existing protein family can also be produced. Also novel folds within a protein family can also be produced. However, we are not concerned with novel genes/functions/folds within an existing protein family. What we are concerned with is a novel gene that codes for a novel protein family."
So you admit that is possible to evolve new genes and new functions through random mutation and natural selection? Great. So exactly why do you conclude that no "novel" genes could evolve this way? Are you claiming that no "novel" genes could just poof into existence without devine intervention? Agreed, there is definately no evidence for that. What we definately do observe is that genes can undergo mutations that are selected on to produce new genes and new functions. They all come from preexisting genes. There is plenty of evidence for this and plenty of examples.
You need remain skeptical no longer. If you choose to remain skeptical you should get to work right away testing your alternative hypothesis. What was that again?
Oh, and once again, natural selection is not searching for anything, letalone a single "solution". Quit saying that.
Mike Elzinga · 26 February 2009
mrg · 26 February 2009
Frank J · 27 February 2009
Frank J · 27 February 2009
mrg · 27 February 2009
Frank J · 27 February 2009
Mr. G.:
Thanks for the reference. I’ll give it more exposure on Talk.Origins.
The only recent ones I know that propose “naturalistic” alternatives that are (1) based almost exclusively on “Darwin doesn't work” and (2) provide any comfort to biblical creationists (even more than Behe in that they reject common descent) are Schwabe and Senapathy. Schwabe is even mentioned in the DI’s “Explore Evolution” which is apparently its latest attempt to distance itself from design as well as YEC and OEC, in hopes of convincing a judge (who isn’t a GWB-appointed conservative Christian? ;-)) to allow their pseudoscience in public schools.
Unless they have another trick that I’m aware of (Lord knows they have plenty), invoking Schwabe is quite risky because (1) it could alert students to the false dichotomy that they are trying to peddle wherever legal, and (2) it conflicts with Behe’s model. Which means that at least some students might critically analyze claims that the DI does not want placed under scrutiny.
For me, if not for most critics of ID/creationism, it’s not the stealth “some designer did it” that’s worrisome, but how they are increasingly vague about what that designer did, when and how. As Ken Miller notes in “Only A Theory” ID activists have succeeded in uniting YECs, OECs and IDers under the “big tent,” while dividing “evolutionists” who get distracted into their own internal theology debate. That needs to change.
Wesley R. Elsberry · 1 June 2009
AJ · 15 July 2009
Stumbling across this board, I am impressed by the mathematical discussion of the chance elements of evolution, but from what I read recently in a new book on Amazon, "The Darwin Delusion", some "experts" are worried about the lack of real proof it ever happened at all. I was surprised to read, for example, that the loquacious Prof Steve Jones states that the fossil record simply does not show the finely graded spectrum of intermediate forms that Darwin required as the crucial test of his theory. Isn't that a bit worrying?
Of course Jones then tries to explain why the evidence is missing, apparently because very few dead organisms get fossilized. I can see that, but how come the millions that did always seem to be of incredibly complex, fully functioning organisms. Is that what Darwin meant by the "survival of the fittest"?
fnxtr · 15 July 2009
What did you expect, AJ? Soft parts don't fossilize. Most early creatures were all soft parts. And of course they're fully functioning organisms. If they weren't, they wouldn't be around to fossilize in the first place.
"Survival of the Fittest" was Spencer's phrase, not Darwin's. It means "fit" as in "best suited to the current environment". There's nothing particularly buff or muscular about slugs, but they manage to reproduce.
Try reading "Wonderful Life" by Stephen Jay Gould, or you could go to Steve Jones' own words and find out for yourself what he really said, and why.
I recommend your local library for starters.
All of this is assuming you're being sincere and not a concern troll just plugging that book you mentioned.
Dan · 15 July 2009
AJ · 16 July 2009
fnxtr
Thanks for your polite reply. It's just astonishing how different groups can draw opposite conclusions from the same facts -- as with politics I suppose.
Funny how we seem to have an intuitional bias one way or the other. I get the feeling that creationists are just as adamant about what I see as their errors (e.g. an earth only 6000 years old, or Noah's flood supposedly creating all or most sedimentary rocks, yet leaving an olive tree growing) as evolutionists are about theirs.
"Derek Hough, for example ("Evolution -- a case of stating the obvious) also says the fossil evidence is missing, and that Darwin's concept of complexity resulting from the accumulation of tiny difference is infantile, yet he is still convinced that macro-evolution is a fact. He is still looking for a credible mechanism.
Stanton · 16 July 2009
AJ, you have to be aware that biologists have come a long way since Darwin, and have accumulated literal mountains of evidence for evolution. Evidence which has lead to numerous changes and revisions of how people understand and explain evolution.
Simply because Precambrian fossils are rare does not mean that they don't exist, nor does the fact that people are still studying and hypothesizing about the origins of life change the fact that biological evolution occurred/still is occurring. Furthermore, 3 billion year old fossils of what appear to be bacteria in chert, together with chemical byproducts.
I strongly recommend you read the book The Rise of Animals, which talks about Precambrian fossils.
And the way anti-evolutionists wail and rail about the horrible impossibility of "random chance" makes one wonder if they have never ever ever heard of games like poker or bingo.
Dan · 16 July 2009
fnxtr · 16 July 2009
The difference, AJ, in case you hadn't noticed, is creationists start with their conclusion. "It's in the book, this must be the way it is.".
Scientists start with the evidence and try to understand how it got there.
Maybe there's a God, maybe there isn't. How do you test for God? You can't. It isn't helpful, practical, or useful to the scientific endeavour. Of course it may be important socially, spiritually, culturally, whatever, but it is not relevant to the observations of science.
There are many, many, many deeply devout scientists and laypersons who also accept the fact of evolution. Couple of obvious names come to mind: Kenneth Miller and the Pope.
Then there are nutjobs like FL who insist that their particular sectarian interpretation of a 2000+ year old book means evolution can't possibly be true, and those said devout individuals are not True Christians(tm).
Look at it this way: men and women all over the world from all religions have converged on the current scientific consensus.
E=mc^2. So atomic theory is a reasonably accurate representation of reality, therefore so is chemistry, so is radio-isotope dating, so is cosmology, so is biology. It's all of a piece.
Meanwhile, disagreements in religion don't lead anyone closer to the truth, they lead to sectarianism and religious wars.
AJ · 17 July 2009
Stanton,
I think Fred Hoyle knew about games of chance, and was a brilliant mathematician -- but he realized that the chance of the a cell, for example, forming by the chance accretion of atoms and molecules was like a tornado assembling a 747 from the bits and pieces in a scrap yard. i.e. Impossible to any rational person.
Yet macro-evolution claims that not just a cell, but the unfathomable complexity of life on earth, much of which has yet to be discovered and classified, created itself by the accumulation of random DNA copying errors in reproduction. In my opinion that is impossible. I know it doesn't trouble Dawkins who thinks a statue may one day wave at him -- but that again would be a minor baby miracle compared to the imagined achievements of macro-evolution.
Sean Carrol explains the Cambrian explosion by "they must have invented toolbox genes", multi-level hierarchies of slave and master genes. A vague simplistic answer that ignores cause-and-effect reality. Just not credible to most people, but not, as Darwin commented, for those who believe. Again, it comes down to personal interpretation of the observed facts.
The book I mentioned talks about the star-nosed mole, which blows out bubbles and immediately breaths them in again to track the scent of worms. Amazing. And why are the young of migratory birds born knowing how to navigate by sun and stars? Incredible. Dare I mention Rupert Shelrake, a keen evolutionist who realizes things ain't quite so simple and cut and dried as many would have us believe. An opinion shared by Lewontin I believe.
DS · 17 July 2009
AJ wrote:
"Yet macro-evolution claims that not just a cell, but the unfathomable complexity of life on earth, much of which has yet to be discovered and classified, created itself by the accumulation of random DNA copying errors in reproduction. In my opinion that is impossible."
Um, "macroevolution' doesn't claim anything, but you did. And in this case you claimed something that no real scientist claims. See you forgot about the role of cumulative selection in the process. Now if you include that then there is no problem. If you forget about that, all you get is some nonsensical calculations about how improbable something is without any selection. Who cares, no one claims that is how it happened except you.
Why don't you read the book that Stanton recommended and increase your knowledge before trying to argue with real scientists about things you know nothing about? Oh and try a little poker while you're at it. I recommend seven card stud for starters. You might learn something about probabliity as well.
DS · 17 July 2009
Oh, I almost forgot about those little "toolbox genes". You do know that there is a vast literature about the origin and evolution of HOX genes right? Do try not to ridicule things you don't understand. I could provide hundreds of references, but guys like you never seem to be interested. I wonder why that is?
AJ · 18 July 2009
DS
Why are evolutionists as a breed so abusive? I thought real scientists were rational, reasonable chaps, but as Lewontin points out they are, of course, human. So although they are supposedly sincere searchers after truth, paradoxically, they can get angry and impatient with people who question accepted convention.
Anyway, if I have misrepresented the situation, please give me, without referring me to several books to do the job for you, a concise and credible explanation of the mechanism by which evolution did create DNA, toolbox genes, the cell and the complexity of life on earth as we know it.
Dave Luckett · 18 July 2009
AJ, you are asking questions that have long, long ago been answered by mathematicians far greater than you or me. Fred Hoyle was a great astronomer, but towards the end of his career was quirky and contrarian to an unreasonable degree. His stubborn refusal to credit the necessary implications of an expanding universe ended in embarrassment, for instance.
The fact that you're hauling out yet again his false-to-fact analogy about the 747 and the junkyard demonstrates that you don't understand the theory. Nobody has ever thought for a moment that evolution works that way.
And while we're talking about assessment of data, you received extremely polite answers from fnxtr, Stanton, and Dan, and a slightly less diplomatic, but not by any standard abusive one from DS. And then you complain about "evolutionists" (which means "mainstream scientists", I guess) being "abusive". Do check the sample. Alternatively, it might be time to recalibrate your abuse meter.
DS · 18 July 2009
AJ,
Why are creationists so dense? The tired old creationist claptrap you have been spouting has been debunked for over fifty years. Why do you keep spewing it out as if it were a valid argument? Now, do you or do you not admit that the 747 in a junkyard analogy is fundamentally flawed and in no way a valid argument against evolution?
And by the way, I was not in the least "abusive" as your misleading question implies. Just ask yourself, if a child continuously poked you in the eye with a stick and refused to stop, would you be justified in taking the stick away? Would that be "abusive"? Well now you understand how scientists feel when you use such tired old debunked arguments that demonstrate such a lack of knowledge of the relevant issues. It is really insulting to the millions of scientists, who have worked so hard and so long to provide the evidence for one of the greatest theories in the history of science, that you dismiss them entirely based on some nonsensical creationist misrepresentation.
As for your request, once again it betrays your lack of knowledge. There is no simple answer for the questions you pose. There is however a voluminous scientific literature regarding each one. Now if you don't know what HOX genes are, you are hardly in a position to argue about their evolution. If you are willing to read the scientific literature I would be happy to provide references. But if that is the case, why haven't you already read the relevant literature?
Stanton · 18 July 2009
AJ, being told that macro-evolution doesn't work by magically smushing stuff together to form the first (eukaryotic) cell does not constitute "abuse." Being told that Sir Fred Hoyle didn't know a single thing about evolution does not constitute "abuse," either. I mean, you deserve the most harshest responses possible for trusting the word of a man who couldn't tell the difference between Archaeopteryx's tail, and a single feather, or who thought that a small group of men could produce a series of allegedly perfect counterfeits over a series of over eighty years, with absolutely no evidence to suggest otherwise beyond one astrophysicist's hubris and paranoia.
Or, perhaps you could go back and point out specifically how having your recycled "arguments" taken apart for the hundred thousandth time constitutes as "abuse," please.
AJ · 18 July 2009
I have read some papers on the supposed evolution of homeobox genes -- and to my mind they simply demonstrate the unfathomable complexity of the mutational mechanism God engineered into the Genesis kinds enabling them to reproduce "after their kind", so that, for example, all the varieties of dogs have resulted from one original pair. Likewise for dinosaurs in Buckland's prehistoric world, I suppose. Hough postulates a remarkably similar mechanism thathe calls the Self-developing genome. Understandably, the papers ask more questions than they answer.
Darwin, of course, wanted all present day organisms to have a single common ancestor rather than the initial range created in Genesis. He therefore had to extrapolate the limit-ed variation already familiar to plant and animal breeders into the mythical limit-less variation required for macro-evolution. That , I understand, is "The Darwin Delusion", an elementary mathematical faux pas. Hence the need to devise imaginary trees of descent using extinct organisms.
That delusion also required the infinitely graduated spectrum of fossil remains that do not exist. And that, like the complex scheme of heavenly spheres required to explain planetary motion prior to Newton, never did exist. The simple G-Theory scenario solves the mystery of the missing intermediate forms.
DS · 18 July 2009
AJ,
Once again, you have been sadly misinformed. Reading "some papers" can hardly provide you with a decent overview of the last fifty years of genetic research. Is does however put you head and shoulders above our resident trolls on this site.
You do know that all animals have HOX genes right? You do know that the number of genes and the number of gene complexes increases steadily through evolutionary time right? You do know that a phylogenetic analysis of HOX gene sequences reproduces exactly the same hierarchical relationships produced by ribosomal and histone genes, as well as mitochondrial genes, right? You do know that this hierarchy corresponds precisely to the time of appearance of the major groups of animals in the fossil record right? If you are not familiar with this evidence, I suggezxt that you read the following reference:
American Scientist 85(2):1-10 (1997)
As for Darwin, he didn't want anything. His conclusions were based on the evidence.
And of course you are entirely wrong about the fossill recored as well. In the one hundred and fifty years since Darwin published the Origin, there have been literally hundreds of intermediate fossils species discoivered. Add to that the dramatic confirmation of the idea of descent with modification by modern genetics and you will see that Darwin has been completely vindicated by history.
Now, one last time just to be fair, do you or do you not admit that the junkyard analogy is bogus?
Stanton · 18 July 2009
Everything about AJ's arguments is bogus, from his inaccurate caricatures of Darwin, evolution, and "evolutionists" to his use of whiny appeals to ignorance in place in place of actual evidence for his position.
That, and then there's his whiny concern trolling over "abuse" because we were so mean in taking apart his shoddy arguments.
AJ · 19 July 2009
DS and Stanton
I will study those references you gave me: "The Rise of Animals" and "American Scientist 85(2):1-10 (1997)"
As you will have gathered, I am a Bible literalist who believes that Genesis properly understood is scientifically accurate. Not saying it is a "science textbook", but not unscientific if read carefully. Do we think an astronaut is an ignoramus if he talks about the sun rising or going down? Of course not. But people want to apply very rigid rules to Bible language. Like a scientist, the Bible uses metaphorical language, for example, comparing the water in rain clouds to "water jars". It has to be read with intelligence. Of course, most Bible scholars and many supposed Christian ministers also think Genesis is error, superstition and myth -- their vision also being distorted by an evolutionary outlook.
A tiny but interesting point about the creation of Eve from Adam's rib. I read somewhere in an account of a heart surgery that the ribs are the only bones that will grow back if cut off. Odd.
I also believe there is more to man and animals than atoms and molecules, there is a "spirit" that imparts intellect, given at birth and returning to God at death. Our knowledge of the world, despite those vast piles of research papers, really is very limited. All that stuff about slime molds, bird migration, etc. No doubt your reasonable response will be that by the nature of science, we do not (yet) know everything, but we are working on it.
So, a final question -- can atoms and molecules have talent, e.g. Paul McCartney? I don't think so.
And Is Kathryn Jenkins the outcome of evolution? Absolutely not!
Not trying to annoy you. Just trying to find out how you think, and why you embrace Darwin with such certainty, when there are so may hard questions and problems.
Dave Luckett · 19 July 2009
AJ, I'm glad that you'll have a look at the references. Some comments:
Biblical literalism is precisely to apply very rigid rules to Biblical language - that is, to proceed on the unwarranted assumption that the language must be literally factual, and the even less warranted assumption that the reader's interpretation of it must be the correct one. The Bible does not actually say anywhere that it must be read literally, only that all the scriptures may be read with profit, and that they contain truth. Genesis does, certainly. It's absolutely true, for instance, that farmers have to work a lot harder than hunter-gatherers to make a living. (The advantage of farming is the ability to support higher population.) It's true that humans have a lot more trouble, danger and pain in bearing young than other mammals. Undeniably, parental favouritism inevitably produces sibling rivalry. Rainbows are associated with the sun coming out after rain. And so on.
But the Universe, and the Earth was not created in six literal days. All life is commonly descended, and was not created in one week. There never was a worldwide flood. These are physical facts that are attested by evidence, and the evidence is all around us. There's mountains of it.
I wish you well as you embark upon the discovery of it.
DS · 19 July 2009
AJ,
You are a breath of fresh air around here. If you do actually read the references provided it will be a first.
No one is trying to say anything about God or souls here except you. The point is that there is evidence about the past history of life on earth. If you can interpret the Bible in such a way as to not conflict with this evidence, more power to you. If your faith is not strong enough to allow you to examine the evidence, then you will suffer the fate you so richly deserve.
Now, about those Hox genes. PZ has an excellent web site which includes a summary of a paper describing the origin and evolution of Hox genes:
http://scienceblogs.com/pharyngula/2006/05/hox_genesis.php
The reference is:
Garcia Fernandez (2005) The genesis and evolution of hox gene clusters. Nature Review Genetics 6:881-892.
I hope you enjoy it. It does not have all the answers, but it does demonstrate conclusively that the evolutionary mechanisms by which these genes arose and diversified are well studied and well documented. There is absolutely nothing that has been discovered about these genes that is in any way a problem for evolutionary theory. On the contrary, what we have learned is that simple genetic changes can indeed produce the diversity of life that we see around us and that all life forms share similarities that all point to their common ancestry. Modern molecular genetics has completely vindicated Darwin and his ideas, which were way ahead of their time.
As for you question, of course "atoms and molecules" can have "talent". It is an emergent property of complex systems. Can you demonstrate that such a thing aas a soul exists or that it is nevessary for things such as "talent"? See the thing is, it can be easily demonstrated that Paul McCartney is composed of atoms and molecules.
Mike Elzinga · 19 July 2009
Stanton · 19 July 2009
stevaroni · 19 July 2009
stevaroni · 19 July 2009
Henry J · 19 July 2009
AJ · 20 July 2009
You guys don't let up, do you -- and you accuse me of repeating lies.
I said I would research some references you gave me, and in so doing came across this article in American Scientist: "May-June 2009 Volume 97, Number 3 Page: 206 The Origin of Life". by James Trefil, Harold Morowitz, and Eric Smith.
Here is their conclusion after several pages of speculation: "The hope is that the interplay of theory and experiment, so familiar to historians of science, will produce a theory that illuminates the physical principles that led to the development of life and, hence, give us the ability to re-create life in our laboratories."
They are still lookiing for a theory! -- yet you guys try to con people that evolution knows the answers to these problems. Who is repeating lies? The article confirms G-Man's claim in the "Darwin Delusion" that evolution has NO credible explanation for the origin of life on earth.
I will now study some articles on the supposed evolution of Hox genes, and report back to you the real facts behind the hype and conveniently vague supposition I will no doubt encounter.
AJ · 20 July 2009
So you accuse me of repeating lies.
I said I would research some references you gave me, and in so doing came across this article in American Scientist: "May-June 2009 Volume 97, Number 3 Page: 206 The Origin of Life". by James Trefil, Harold Morowitz, and Eric Smith.
Here is their conclusion after several pages of speculation: "The hope is that the interplay of theory and experiment, so familiar to historians of science, will produce a theory that illuminates the physical principles that led to the development of life and, hence, give us the ability to re-create life in our laboratories."
They are still lookiing for a theory! -- yet you guys try to con the unwary that evolution knows the answers to these problems. Who is repeating lies? The article confirms G-Man's claim in the "Darwin Delusion" that evolution has NO credible explanation for the origin of life on earth.
I will now study some articles on the supposed evolution of Hox genes, and report back to you the real facts behind the hype and conveniently vague supposition I will no doubt encounter.
Dave Luckett · 20 July 2009
Well, there goes the "honest creationist" hypothesis. The evidence has just invalidated it.
The origin of life is at present unknown. Got that? Not known. There are a number of interesting ideas, several lines of inquiry, quite a bit of experimentation, but the origin of life is at present unknown, and nobody ever said different. The Theory of Evolution accounts for the origin of the species, not for the origin of life. It requires descent with modification, which assumes self-replication, ie life. You are flailing away at a straw man.
And you're no longer fooling anyone.
AJ · 20 July 2009
Thank you for intervening to make make my point for me.
Perhaps the surgeon who wrote the article I read was wrong. So how about this source instead:
Authors: BANIA M. A. ; NEGRIN J. A. ;
Authors: Affiliation(s): North Shore univ. hosp., div. nuclear medicine, Manhasset NY 11030
Journal Title: Clinical nuclear medicine ISSN 0363-9762
Abstract:
Regeneration of a portion of a previously resected rib may occur because periosteum is usually left in place.
I suspect that the God (actually Jesus Christ, Ephesians 3:9, Hebrews 1:2) who designed and created the human body probably knew to leave a bit of the periosteum coating in place, complete with its miraculous network of nerves and blood vessels.
Who is spreading lies now?
Dan · 20 July 2009
Dave Luckett · 20 July 2009
"Regeneration of a portion of resected rib" doesn't mean that "ribs are the only bones that will grow back if cut off". They don't "grow back" in whole if removed. Nobody is lying about that, and nobody accused anyone else of doing it over that, either way.
What you're lying about is being of an open mind. You're not of an open mind. The only reason that you're reading the material at all is to find any interpretation, however strained, of any statement, however irrelevant, that can be twisted to attack the Theory of Evolution.
You're wasting your time. Go back to your Bible, and the dark ages, and wallow in your ignorance.
Stanton · 20 July 2009
DS · 20 July 2009
AJ wrote:
"I will now study some articles on the supposed evolution of Hox genes, and report back to you the real facts behind the hype and conveniently vague supposition I will no doubt encounter."
Good. Why don't you start with the article I recommended and the web site that summarizes it? Here is the web site and the reference again:
Garcia Fernandez (2005) The genesis and evolution of hox gene clusters. Nature Review Genetics 6:881-892.
http://scienceblogs.com/pharyngula/[…]_genesis.php
Don't go to creationist web sites and repeat their ignorant nonsense. And don't complain that we don't have all the answers, that doesn't invalidate the answers we do have. Look dude, if you want to find real scientific answers to real scientific questions then you have to read the real science. So far you have utterly failed to address any of the points that I made. The fact is that all of the evidence points to the evolution of hox genes and the continuitity of all of life. Spouting ignorant nonsense about some things that are not yet understood is not going to change that.
Please prove to us that you are not just another creationist lap dog incapable of reading any real science. Please prove to us that you really are interested in looking for real answers. Not one creationist I know has ever actually read one real scientific paper. Here is your chance to be the first. Until you do, no one here will take anything you say seriously.
Oh, and everyone can see that you still have not admitted that your junkyard crap belongs in the junkyard. You also still have not admitted that Paul McCartney is composed of atoms and molecules and has talent. If you continue to ask inane questions in order to divert the conversation from real science, the least you could do is acknowledge the responses. Talk about hype and vague supposition. Your double standard is showing.
AJ · 20 July 2009
OK, so technically evolution concerns what supposedly happened after life accidentally created itself -- but thank you for confirming that evolutionists do not understand how "life" was formed, despite the the lovely pools of slime and animations used to con a gullible public and school kids that they do. Sorted! Next problem.
Shalom.
Stanton · 20 July 2009
Abiogenesis and Evolutionary Biology are two separate topics, AJ. If we use your train(wreck) of logic, one can always say that Christianity is technically separate from Anti-Semitism and misogyny.
And when you imply that people studying Abiogenesis are still talking about the "primordial ooze," you are either woefully out of date, or being maliciously duplicitous, especially since they have long ago moved on from that idea to studying how organic molecules can replicate themselves either in solution, or with the aid of catalysts.
Either way, it's quite apparent that you were, and still are lying about wanting to learn anything. You not only wish to continue conflating piety with ignorance, but, you also want to drag as many others down with you in your malign ignorance, hence your continued implication that scientists are empty-headed God-deniers who don't know what they're saying or doing.
Stanton · 20 July 2009
DS · 20 July 2009
AJ,
Don't know where you are going with this rib thing. The article you cited proves that ribs do not regenerate. How does that help you prove Biblical literalism? Simple question for you, how many ribs do human males have? How many ribs to female humans have?
See the thing about Biblical literalism is that it's antithetical to the entire purpose of the Bible. For example:
Man shall not live by bread alone (he also needs peanut butter)
Whatsoever a man soweth, that also shall he reap (so don't plant corn and try to harvest wheat)
Let your women keep silence in the church (nuf said)
Several days ago you said you were going to read some scientific articles. You still have not done so. I not only provided references, I even provided a web page with a summary for you, just to make it easier. Look dude, no one here is interested in your musings about Paul McCartney's ribs or your mischaracterizations of the field of abiogenesis. Read the paper already, or go back to the junkyard where you usually get your information.
stevaroni · 20 July 2009
GvlGeologist, FCD · 20 July 2009
stevaroni · 20 July 2009
DS · 20 July 2009
I guess it depends on what kind of bread.
fnxtr · 20 July 2009
I should have known.
AJ, I'm disappointed. I thought you really were admitting your ignorance (which is quite a noble gesture, really), and were honestly seeking information.
You have revealed yourself as just another bible-thumping lout with no interest in the real world.
We tried to be polite, we really did. But you went on and on about a bunch of long-rehashed bullshit that tried our collective patience.
Sad, really, you had a chance for a minute there.
AJ · 20 July 2009
OK, I am going to give you guys a chance to calm down while I go and check over those references.
Shalom.
stevaroni · 20 July 2009
Mike Elzinga · 20 July 2009
eric · 20 July 2009
DS · 20 July 2009
AJ wrote:
"OK, I am going to give you guys a chance to calm down while I go and check over those references."
All calm here dude. Now quit the BS and read the paper already. No excuses, no changes of topic, no regenerating ribs, no rock stars, no double standards. Just read the paper. If you can't or won't do that then you will have proven that you are just another willfully igornant drone and we are done here. Don't get hysterical, just go to the web site and read the summary at least. It's free you know. It should take you about fifteen minutes. I can give you hundreds more references once you prove that you are serious about learning some science. You have claimed three times now that you are going to read the references. If you don't want to be called a liar then keep your word.
Mike Elzinga · 20 July 2009
Henry J · 20 July 2009
What does rib regeneration have to do with anything, anyway? Even if one guy did lose one via removal, his descendants wouldn't have fewer ribs due to that.
Henry J
fnxtr · 20 July 2009
DS · 20 July 2009
Henry J,
Darned if I know. AJ is the one who claimed, for some unfathomable reason, that God was smart enough to leave behind enough tissue for the rib to regenerate. Somehow I guess he thinks that if God did not do this then males would somehow have one less rib. Of course, since that is not the case, it matters not at all what tissue was left or whether the rib regenerated or not. Therefore, the entire discussion is completely pointless and can never even in theory provide any evidence concerning the interpretation of events described in the Bible.
My guess is that AJ is simply trying to fixate on such issues in order to draw attention away from the fact that he still hasn't read the references that he promised he would. Ditto with the pointless discussion of Paul McCartney. Now abiogenesis is at least germaine, in the sense that AJ can try to invoke the good old tried and true "you don't know everything so I don't have to believe anything" argument. Of course, the blatant double standard being used never seems to bother those who use this argument.
Oh well, perhaps if we all "calm down" AJ will actually read the references. Until then we can all keep playing whack a creationist on a six month old thread. At least we may eventually get him to admit that the junkyard thing was silly.
Henry J · 20 July 2009
Another thought - AFAIK, the number of ribs is not a sex-linked trait. So if the relevant DNA got modified, it would hit descendants of both genders.
Dan · 20 July 2009
stevaroni · 20 July 2009
Stanton · 21 July 2009
DS · 21 July 2009
AJ,
Where is ya lad? It's been three days since you promised to read that article. What's the problem? It's only about five pages long and it summarizes all of the important stages in the evolution of the hox gene complex in animals for the last 600 million years. Here is the web site again in case you forgot:
http://scienceblogs.com/pharyngula/2006/05/hox_genesis.php
Now on that same website there are also about ten other articles on hox genes, all with references from the scientific literature. Don't waste your time with creationist web sites. This site is administered by a real devemopmental biologist! Of course there are literally thousands of scientific research articles on this topic. You certainly have a lot of catching up to do. Here are a few more references for your consideration:
Current Topics in Developmental Biology (1998) 40:24-54
Evolutionary Development (1999) 1(1):16-23
Nature Review Genetics (2001) 2(1):33-38
You know dude, it might be better if you switched to a more current thread. This one is getting hard to get to. Also, we're way off topic here. Maybe we will have another thread specifically on hox genes in the future. Maybe you will have read the paper by then.
fnxtr · 21 July 2009
If AJ follows the normal creotroll routine, he'll be back in a couple of days on a different thread, pretending this never happened. We shall see.
DS · 21 July 2009
fnxtr,
Maybe.
Or maybe he will try to quotemine the paper to try to expose some supposed weakness. Then he can try the old "you don't know everything" routine again.
Or maybe he will not read the paper, go to some creationist web sites instead and try to peddle some more of their lies.
Or maybe he will simply try to change the subject again. Maybe regenerating appendix stuff or whatever.
Or maybe he will simply start preaching and hope no one notices.
Or maybe he will pretend to read the paper, claim he is unconvinced and then claim victory over the forces of darkness.
Or maybe he will tell us all to calm down and relax again and hope we forget all about the paper.
Or maybe he will claim that asking him to read the paper constitutes abuse of some kind so he isn't going to do it.
Or maybe he will read the paper, learn some real science, realize he can still believe in Jesus and become hooked on knowledge. Yea right. We'll see.
Stanton · 21 July 2009
fnxtr · 21 July 2009
DS · 21 July 2009
Well another day has come and gone and still no word from the honest seeker for truth. I wonder why that is? Man, if it takes him this long to read one paper, no wonder he hasn't learned any science yet.
Oh well, that won't stop me from providing more references. Or maybe I should just start quoting from the summary of the paper. After all, this thread does belong to PZ, so maybe he won't mind.
"Parts of the history of the Hox cluster have been reconstructed. The last common ancestor of insects and vertebrates would have had a bank of 7-9 genes. Later duplications in the protostome lineage would have expanded that to 8-9; vertebrates expanded the original cluster to about 14, and additionally duplicated the whole cluster multiple times. We mammals have 4 clusters, HoxA, HoxB, HoxC, and HoxD, each of which contains up to 14 genes (because we have 4 clusters, there is some redundancy, and individual genes within some of the clusters have been lost.) If we try to look farther back in our history, the best evidence so far suggests that the last common ancestor of insects, vertebrates, and flatworms probably had 4 Hox genes. Even further back, our last common ancestor with cnidarians had at least 2 Hox genes."
So much for the barimin hypothesis. Until AJ can bring himself to comment about this research then I guess we're done here. So to recap: abiogenesis, irrelevant; bariminology, falsified; regenerating ribs, priceless. Science, don't leave home without it.
AJ · 22 July 2009
OK, since you are so impatient for some response, here is some of the stuff I have been reading by you pal PZ while I order the reprint you recommended.
First of all I totally agree with Darwin that the organisms that now exist are the result of descent with modification from ancestral forms. That statement actually agrees with Genesis, depending on the definition of “few”. By virtue of the mutative mechanism that Lamarck postulated and that Derek Hough calls a “self-developing genome”, we now have many breeds of dogs and cattle for example. I also suspect, like Lamarck, that this mechanism is capable of sensing and responding to needs and pressures and adapting accordingly, rather than new forms arising randomly and being screened by natural selection. That was one major advantage of Lamarck’s theory – no need for those elusive intermediates. Darwin’s later theory of pangensis said something similar.
All this gene technology Carroll and others are investigating is simply helping us understand how that mechanism works – and it seems we are just scratching the surface as we learn more about gene expression.
No problem there. We all agree. The problem is that Darwin was not happy for his theory to agree with Genesis, so he moved the goalposts to theorize that all organisms decended from just one, or very very few common ancestors, organisms totally unlike those we now have. As a result he had to theorize that a process of macro “evolutionary” change had taken place – and the tree of life was part of that attempt.
In so doing, Darwin assumed that the extinct organisms of the pre-historic world's paleozoic and mesozoic rock strata were part of that ancestry. A reasonable supposition that suited his purpose. Evolutionists have therefore set about explaining how that process of descent with modification could have happened. Which is why they ideally need all those missing forms to stitch it all together. However to a true believer in evolution, it just happened, and so there must be a logical explanation.
Key point. In explaining how one organims turned into another, perhaps acquiring legs instead of fins, they naturally call on mechanisms that are visibly taking place in nature now – as typified by miraculous changes as tadpoles turn into frogs, for example. And as more gene technology is discovered, they are able to cites more specific mechanism to describe what needed to happen for the imagined evolution to take place – hox genes, duplication, reversal, etc.
Since generalized terms are necessary for efficient communication, people like Carroll and PZ happily “explain” how the changes required, for the evolution of hox genes, for example, occurred with no further explanatoin of how they did take place other than their total faith that evolution is true. In other words , like Darwin, they are extrapolating Filipchenko’s microevolution to create macro-evolution.
In his latest book, Carroll does just this as he tries to explain the Cambrian Explosion. Since segmented creatures like trilobites and opabinia, etc., needed hox genes, he therefore concludes “they must have invented toolbox genes”. A reasonable statement if you are a devout evolutionist. If called on to explain how they “invented” those genes, he will come out with vague jargon and supposition, similar to used by PZ below, that the gullible will find convincing. Let’s face it, most of the general public are in the position of the illiterate peasants of the middle ages who simply had to believe what the priest told them. You of course also rate me as ignorant.
Here is some typical vague verbosity from you pal PZ to illustrate my poiint:
---------------------
Necessary to modify one end for feeding, and the opposite end for mating .
We can surmise where duplications and deletions occurred, we can speculate about how new additions to animal morphology occured.
it must have arisen by an early duplication. . . undergone multiple duplications, followed by variations
An ancestor acquired a duplication of the gene responsible . . . allowed it to add extra specializations to the front end . . . this gave a few limbs. . . the abdominal Hox genes then acquired a property that suppressed limb formation.
---------------------
This is not explanation, but speculative description. But of course if you are convinced that something took place, it is only reasonable to try to explain how it could have taken place by the application of known technology. It’s a free country.
Historians do the same kind of thing, and often get it wrong because of the prejudice they also bring to the job -- which is why it has been said (Archibald Roberston, I believe) that “most history is a tissue of lies and half-truths”.
DS · 22 July 2009
AJ,
The point is that there is a vast literature documenting in great detail exactly what happened and when. No one made it up. It is well documented and self consistent. You have utterly failed to comprehend exactly how consistent this evidence is with all of the other evidence. You have simply assumed that all of these people, everyone from Darwin on, are just trying to fool you or that they have no evidence for their conclusions. No one cares what you believe. Until you can provide an alternative that explains the patterns I described and better explains all the data, all you have is an unwillingness to believe.
The conclusion of gene duplication is based on sequence comparisions and known mechanisms. You can't just dismiss it because someone somewhere at one point summarized all of this evidence and did not give every detail. How do you explain the fact that that conclusion is consistent with all of the other evidence? How do you explain the sequence similarities between these genes and other homeo box genes? How do you explain the sequence similarities between the different hox genes? How do you explain the sequence of the gene duplications, all of which are consistent with phylogenies drawn using other genes and the fossil record?
Why don't you read the web site article I cited and tell us exactly what you disagree with? Quote mining snipets that don't happen to have enough detail for you is not going to make all of the evidence go away. Why don't you provide some reason to reject all of the evidence, other that the fact that you don't want to believe it? Why don't you tell us where you think all of the gene clusters came from if not from gene duplication?
Exactly how many different origins of life do you think that there were? Where did they come from? How much can they evolve? How do you explain the nested hierarchy of genetic similarities between all organisms? How do you explain the fact that all organisms use the same genetic code? How do you explain the fact that all animals share essentially the same hox genes? How do you explain all of the intermediatee forms between major groups in the fossil record? If descent with modification is fine with you, why do you place arbitrary limits on it? What prevents major clades from evolviing?
Gook luck on your quest for knowledge.
DS · 22 July 2009
AJ,
If you really do want more details, I can probably provide references for all of the claims made in the PZ summary. Of course, when you finally do get the actual paper, you will find that it is a review article that contains many references. This is where the actual evidence for the claims made can be found.
"An ancestor acquired a duplication of the gene responsible … allowed it to add extra specializations to the front end … this gave a few limbs… the abdominal Hox genes then acquired a property that suppressed limb formation."
There is doscumeted evidence for all of these claims. Just because you are not familiar with the evidence does not mean that it does not exist. For example, we know about the control mechanisms regulate hox gene expression patterns. We also know about mutations that affect these regulatory mechanisms. We know when some of these mutations arose and how they affected limb formation in different lineages. Here is one good example:
Current Biology 12:R291-R293 (2002)
This article describes the sequence of mutation events that was responsible for the production of different limb patterns within different lineages of arthropods. The patterns can be explained by simple genetic changes to regulatory mechanisms controlling hox gene expression. The important point is that the sequence of the changes is exactly consistent wth arthropod phylogeny. Quite a coincidence!
Look dude, go ahead and believe anything you want. But there really are hundreds of thousands of references like this out there. Unless you are familiar with them you have no idea what is known and what is not. Simply assuming that no evidence exists won't get you anywhere. Simply demanding more and more evidence no matter what won't get you anywhere.
DS · 22 July 2009
AJ,
There are also references detailing the mechanisms of hox gene changes in the evolution of Crustacean limbs:
Nature (1997) 388:682-686
and insect hindwings:
Nature (1995) 376:420-443
Just think of how much we have learned since then. Isn't science wonderful?
KP · 22 July 2009
DS · 22 July 2009
AJ,
It might take a while to get a reprint of that article. Why don't you just go to the journal web site and download a copy. The reference is:
Nature Reviews Genetics (2005) 6(12):881-892
There are eighty references at the end of the article. If you want to look at the evidence you should start there. In fact, there is another interesting article in the exact same issue:
Pearson, Lemons nd McGinnis (2005) Modulating Hox gene functions during animal body patterning. Nature Review Genetics 6(12):893-904
It has lots of details about the mechanisms that regulate hox gene expression and how they have evolved over time. Of course it contains 127 references as well. You better get buzy, this could take a while.
Of course, if you just plan on quote mining the references to prove that we don't have all the answers yet, don't bother. Everyone already knows that we don't have all the answers. So what? First you have to learn what is known and then you will have earned the right to complain about what we don't know yet. Then you could get in the lab and make some new discoveries, or you could just keep complaining.
fnxtr · 22 July 2009
stevaroni · 22 July 2009
Henry J · 22 July 2009
fnxtr · 22 July 2009
AJ · 23 July 2009
And what EXACTLY is the biological definition of a "species"?
A "clade" is an imaginary grouping based on Darwin's infantile ASSUMPTION that any similarity proves a common ancestry. Surely you know that cladistics is a highly subjective technique, a new "dogma", absolute faith in which concerns well-informed and serious-minded biologists. (See "The Darwin Delusion", or Henry Gee's "Deep Time")
In the absence of all those zillions of intermediate forms that Darwin requires, cladistics is the final desperate attempt to create intermediates where none existed before. In reality, it simply confirms the handiwork of a common Designer.
I really think some of you guys (with a couple of exceptions) need to take part in that old evolutionary process known as "growing up"!
PZ Myers · 23 July 2009
There are multiple definitions of species. One of the things that supports evolution is precisely that "species" is a fuzzy concept, because populations and species grade into one another.
I know Henry Gee. Gee is a confident evolutionist -- he regards creationism as infantile. You haven't read his book, obviously, so don't try to cite it in support of your nonsense.
You also don't understand cladistics. Pure cladistics is a discipline free of evolutionary assumptions altogether: species are classified and grouped entirely by evidence, characters present in the organism. The resulting hierarchy of forms can be used as evidence for evolution, because the theory is not used in generating it.
We're grown up already. Your embarrassing performance here suggests that you need to take part in that old intellectual process known as "wising up".
Ichthyic · 23 July 2009
And what EXACTLY is the biological definition of a "species"?
Ask Ernst Mayr
A "clade" is an imaginary grouping based on Darwin's infantile ASSUMPTION that any similarity proves a common ancestry.
nope.
also easy to look that one up.
a new "dogma"
you need to learn the definition of that word, too.
In reality
This is where you really need to work, 'cause it's obvious your failing at living in it.
386sx · 23 July 2009
Everybody who has absolute faith in cladistics please raise your hands! Lol.
Stanton · 23 July 2009
AJ, you are a liar: your so-called quest for knowledge is, at its very best, a pathetic sham.
You're not seeking knowledge, and you have absolutely no intention of learning anything, given as how you're insistent that we join you in your disgusting ignorance-cum-piety. So please go and proselytize your Lies for Jesus somewhere else.
a lurker · 23 July 2009
Toidel Mahoney · 23 July 2009
stevaroni · 23 July 2009
Dan · 23 July 2009
DS · 23 July 2009
AJ wrote:
"A “clade” is an imaginary grouping based on Darwin’s infantile ASSUMPTION that any similarity proves a common ancestry."
This is so wrong on so many different levels.
First, "any similarity" is NOT taken as evidence of common ancestry.
Second, it is not an assumption that similarity is produced by common ancestry.
Third, the nested hierarchy of genetic similarities is congruent between data sets and has already been pointed out to you. You have laready ignored this fact several times.
Third, even genetic mistakes such as SINE insertions can be used to reconstruct phylogeny. Guess what, they are definately evidence of common ancestry and they give exactly the same answer as all of the other genetic data which is completely consistent with the developmental and fossil evidence. I can of course provide lots of references, but why bother?
Look AJ, this ignorance routine is wearing thin. You have had a week to look at a web page and so far no evidence that you have actually read anything. You demand infinite detail from everyone else yet provide exactly none yourself. Get on with it man. Ducuation is hard, but you can at least start to try.
DS · 23 July 2009
Fifth, the second third should be fourth (because he that is first shall be last). And while I agree that ducuation is hard, education is even harder.
eric · 23 July 2009
Toidel, you made my day.
AJ, any definition of "kind" that reduces the number of progenitor species to a few is going to permit human and chimpanzees to have evolved from the same ancestor (i.e. be in the same kind). Any genetic definition of kind that strives to keep humans separate from chimpanzees is going to result in millions of different kinds.
So, one does not need to know the precise definition of "kind" to know the concept is nonsense, because every possible definition is nonsense. Pick any definition, and it will either run afoul of the biblical claim that humans are separate or it will run afoul of the biblical claim that there were few kinds.
fnxtr · 23 July 2009
Dave Luckett · 23 July 2009
He's priceless, isn't he? Every time you think you've heard the last word in loopy, along comes Toidel and readjusts your loopometer. I think we're going to need a logarithmic scale for the next one.
Kevin B · 23 July 2009
Dan · 23 July 2009
eric · 23 July 2009
DS · 23 July 2009
Well it has been nearly a week since AJ promised to read a paper. So far no evidence that he has done so. For anyone who really is interested in hox gene evolution, the following references document how gene duplications, followed by functional divergence, have resulted in the evolution of body plans in many different groups of animals:
Science (2006) 313(5795):1918-1922
American Zoologist (2001) 41(3):676-686
Nature (2000) 403:661-665
Current Biology (1997) 7(10):R634-R636
Development (1995) 121(2):333-346
AJ has utterly failed to address any evidence and has also failed to provide any alternative explanation. He keeps demanding definitions for "species" but refuses to give a definition for "kind". He has consistently displayed the double standard so typical for creationists, demanding excrutiating detail for your hypothesis and providing none whatsoever for his own, in this case including a complete lack of said alternative. Unless and until he can bring himself to address the evidence there is nothing more that need be said.
DS · 24 July 2009
Of course, it's not just hox genes that undergo duplication and divergence. Globin genes, ribosomal genes, genes for smell and taste receptors and countless others have also undergone this process. In fact, this is the major maechanism by which gene families and new genes arise. And of course, the pathways that lead from the original duplication to gene divergence and the acquisition of new functions are well known. I could post those references as well, but I think I'll wait until AJ has read at least one paper first.
I bet that AJ is gong to demand eye witness evidence before he is willing to believe any of this. But of course DNA evidence is more reliable that eye witness evidence any day.
DS · 25 July 2009
Well another day has come and gone and AJ still hasn't gotten ahold of that reprint. He is really getting behind in his reading. I am sure that he will want more information about gene duplications. Here are a few more references:
Nature Reviews Genetics (2002) 3(1):65-72
Nature (2007) 440:677-681
Science (2008) 319(5867):1527-1530
Trends in Genetics (2009) 25(4):152-155
These articles document the processes of gene duplication and mutational divergence and how it produces morphological evolution in various groups. This is a major mechanism of evolutionary change that has been well understood for many years. Man, I sure hope that AJ will be convinced, otherwise, ... whatever.
AJ · 26 July 2009
I didn't see any option of downloading that paper free, and have paid good money to get a hard copy mailed to me. Hopefully it will arrive this week and I can give you my analysis of it,
Meanwhile I have been re-reading "The Making of the Fittest" by Sean Carroll which attempts to trace the evolution of colour vision using cladistic principles. He probably now outranks Richard Dawkins as the world's leading impossibility thinker. Funny how he can spout such rubbish as "the pattern of opsin gene evolution . . . was one of initial abundance (i.e. the jawless lamprey had 5 opsin genes, we only have 3), then a loss in the ancestors of mammals, and then an expansion again . . . "
Like your pal PZ (who clearly thinks he has supernatural powers, claiming to know I have not read Gee's book -- which like Carroll's is based on the grand assumption that all living organisms share a common ancestor), Carroll shares the Darwin delusion -- using the usual vague language, such as : go their separate ways, they arose, by making replacements, duplication, retuned, evolution repeats itself, gained, etc. And when convenient, evolution repeats itself on demand apparently.
Incidentally, Gee actually admits that "everything we knew about evolution" before cladistics came to the rescue "was wrong". But still those errors (lies?) were foisted on a gullible public, like false doctrines on peasants of the middle ages.
Carroll claims to "vaporize" the arguments of creationists -- but all he does is describe the miraculous complexity of God's creative genius -- like the ice fish that adapts to freezing conditions by absorbing oxygen through its skin rather than having bigger gills, meanwhile generating extra antifreeze chemicals to avoid freezing solid. As with the fine tuning of the spectral responses of opsin genes, those amazing changes are not the outcome of natural selection working on zillions of accidental DNA copying errors -- leaving an invisible trail of failed intermediate forms.
I suppose it comes down to what you prefer to believe in -- God, or the fortuitous accumulation of random DNA copying errors.
One final comment -- Darwin was not seeking Truth, but desperately pursuing a personal agenda. He didn't want Genesis to be true. As a result, he allowed himself to be deluded by what is actually infantile nonsense wrapped in jargon. And increasingly, ordinary people are realizing this -- which is why Jerry Coyne bemoans the fact that intelligent business people refuse to accept this proofs of evolution, anymore than they do the claims of the JW's at their door.
Stanton · 26 July 2009
AJ, I would ask you if you had EVIDENCE to support your prattling about PZ claiming to have supernatural powers or about how Charles Darwin was allegedly trying to falsify God and the Book of Genesis, but, you're nothing but a bullshitting creationist who lies and slanders for Christ, and who uses his alleged faith in God as an aegis for his own ignorance and bigotry.
And since you've repeatedly demonstrated that you have been lying out of your sanctimonious ass when you claimed to be searching for "truth," please do us a favor and go away.
stevaroni · 26 July 2009
Stanton · 26 July 2009
Dan · 26 July 2009
Stanton · 26 July 2009
eric · 27 July 2009
DS · 27 July 2009
AJ wrote:
"I suppose it comes down to what you prefer to believe in – God, or the fortuitous accumulation of random DNA copying errors."
I suppose you are completely wrong, since many people happily believe in both.
"One final comment – Darwin was not seeking Truth, but desperately pursuing a personal agenda. He didn’t want Genesis to be true."
Wrong again. Darwin desperately wanted not to offend his family or religious people. That is why he waited so long to publish. You have been told that this was not true before. You should really get your facts straight.
Congratulations for at least trying to read a paper. But really, if you don't have access to data bases it will be impossible for you to accurately access even a small portion of the evidence for modern evolutionary theory. Why not just trust the experts who do this for a living? Now if you have any actual evidence that gene duplications did not occur or that they could not produce the hox gene complexes, then maybe we could discuss that. If not, the "I don't want to belive it" routine isn't going to work here. As I said before, you are prerfectly free to believe anything you want, but you aren't going to convince anyone with an argument from incredulity, especially when you have demonstrated your utter unfamiliarity with the evidence.
fnxtr · 27 July 2009
DS · 27 July 2009
AJ,
Why don't you just go to the web page I provided and look at the figures from the paper that are reproduced there? Why don't you give us your explanation for the patterns observed? Why don't you explain what exactly you think it is that prevents this type of system from evolving? Why don't you state exactly what evidence you require in order to convince you? Why don't you tell us exactly what mechanisms you think are speculative and what alternatives you propose? Why don't you tell us how this evidence is compatible with your idea of separate origins? Why don't you give us the details of exactly how many origins, when where and how they were produced? Why don't you explain to us why every animal, despite their vast differences in morphology, has exactly the same kind of hox genes? Until you at least attempt to do this, I must reiterate my objection to your blatant double standard.
AJ · 28 July 2009
OK this is my last post – so thanks to those who have corresponded. Here are my conclusions.
If you accept the evolution scenario, then I can see how logical the descent with modification concept is. If you believe organisms evolved then it is logical to do the best you can to fit the facts to the theory – and on a common-sense basis, the fact that man resembles an ape would fit well with the theory. Likewise, arranging the flora and fauna of the paeleozoic and mesozoic into trees of descent, from simple to complex also makes good sense. It convinced the Greeks.
Of course, the theory predicts an infinite range of failed intermediate forms that are missing. But I understand how most dead organisms do not get fossilized, which again seems a reasonable point. More recently, computerixed cladistics programs, looking for common design elements, have been used to generate intermediate forms. And again that seems a logical thing to do if you accept the basic theory of evolution as your compass.
Darwin, with his genius as a biologist, was convinced – and until recently, so was Derek Hough, who called it the “most seductive” theory in all science. It does actually fit the facts pretty well – which is clearly why so many intelligent thinking people accept it.
Clearly, the facts are open to alternative explanations (e.g. punctuated equilibrium). Choices are usually made. And it is interesting, as Dawkins points out, that those choices often depend on a person’s upbringing.
Furthermore, I think evolutionists are confirmed in their beliefs by the unscientific, and I believe un-scriptural, claims of so many “creationists” -- e.g. that the earth is just six thousand years old, and that Noah’s flood created most of the earth’s sedimentary rock strata. Many Christians hold such beliefs but I find them untenable.
However, with a personal agenda different to Darwin's, I find Buckland’s ideas abou the prehisoric world and the modernized G-Theory idea from “the Darwin Delusion” more convincing. It does, of course, posit God as the creator, which atheists will find unacceptable. That is their choice, and I do not condemn them, Darwin or Dawkins for it – nor do I think does God or the Bible, despite what many creationists would claim bases on “quote mining” the Bible to suit their personal beliefs.
Finally that paper has arrived, and it is nice to read an authoritative source rather than information filtered through journalists.
There is little point in me “quote mining” scores of phrases to make the point that this interesting paper is simply attempting to solve obscure problems by extrapolating what has recently been discovered about gene technology, and the variation that is now ongoing in plants and animals, backwards zillions of years to try to create a logical model of how Hox genes might have been formed initially and then evolved greater complexity. In my opinion, they are pursuing the end of the evolutionary rainbow. But it is the way science works, trying to think creatively, hypothesizing and suggesting further lines of inquiry needed.
The nub of he problem is the starting point. If Darwin had taken the Genesis kinds as the set of common ancestors, no problem -- which is why his friend Rev Charles Kingsley saw no problem at first. It seems odd that even Karl L. thought the organisms in his day were generally identical with the Genesis forms. Darwin realized different and this seems to have been regarded as a great revelation. He then pushed things further.
Abuse me in you want. I hope you will not. Best wishes, AJ.
Stanton · 28 July 2009
So, AJ never had anything substantial to say after all, and still doesn't have the backbone to realize that his so-called "quest for truth" is nothing but reaffirming his own prejudices and maligning people who do not share his ignorance. And then there's the persecuted martyr complex, despite the fact that he was the one who initiated hostilities to begin with.
Don't let the door hit you on your way out, AJ.
eric · 28 July 2009
DS · 28 July 2009
AJ,
So, I guess you really haven't learned anything. Fine by me. You really should stop using the same old tired creationist lies that have already been demonstrated to be fradulent though.
You are perfectly free to believe anything you want, however, you really can't honestly say that you have examined the evidence for evolution if all you have done is tried to read one paper. I have listed dozens of references for you to read. How do you know that the information that you want is not in them? I also note that you have completely failed to even attempt to answer any of my questions. Once again, you can believe anything you choose, but you are not going to convince anyone that what your believe is correct if you refuse to state what you believe.
You seem to think that all conclusions in science are somehow constrained by preconceived notions. I can assure you that many scientists have found results exactly opposite to what they expected. Somehow you cannot seem to grasp that people who are intellectually honest can be persuaded by the evidence. Once you are familiar with the evidence you will have earned the right to an opinion. Until then, have a good life.
stevaroni · 28 July 2009
stevaroni · 28 July 2009
Stanton · 28 July 2009
Stanton · 28 July 2009
Henry J · 28 July 2009
Dan · 29 July 2009
Stanton · 29 July 2009
eric · 29 July 2009
Ben Young · 19 January 2010
My discovery of your blog came just right in time! I am asking your permission to quote some things here, I need to show its irony, mathematically.