There is no bottom to dumb

If you read through all the comments someone called bornagain77 hijacks the thread to plug some research being touted at www.quantumbrain.org and www.neuroquantology.com for some reason. Very odd.

Oops, sorry, what I was referring to happened on a different thread discussing Paul Davies's article in the Nov 19th issue of Scientific American.

. . . called bornagain77 hijacks the thread . . .

— Jerad Zimmermann

Second, we are not denying that human beings and the human brain are products of evolutionary mechanisms, including natural selection. Only the “creationists” deny this,and we are resolute in our opposition to all forms of creationism. (ref. to footnote 10) (footnote 10) We shall use “creationists” in what follows as a term of art to mean both those committed to the literal truth of the Book of Genesis as well as the proponents of “Intelligent Design.” Intelligent Design is simply creationism for those who have consulted a lawyer and a public relations firm; it has nothing to do with science, since the criticisms of evolutionary biology are without merit and the positing of “intelligent design” as an explanatory hypothesis is on a par, epistemically, with the positing of turtles on whose back the universe rests.

Not that I take it personally, given that their rather silly definition of creationist (literal readers of Genesis and ID advocates) leaves me and many others “off the hook” since we qualify under neither guideline. Geez. Lawyers and journalists arguing about science. A pox on both their houses.

Heddle,

It has come to a point where fear of the almost inevitable quotemining by creationists makes it prudent for authors of even scholarly pieces to add disclaimers. It's unfortunate, but if creationists weren't so obdurately dishonest, it wouldn't be necessary.

"Processes of variation and selection can trivially increase information in the genome. Even Dembski seems to have come to accept this and now he claims that such processes smuggle in information. Of course they do, they transfer information from the environment to the genome."

I'm not even sure that "information" is the correct terminology to use here. It can be a useful metaphor at times (much like "blueprint" for genomes), but I'm not aware of any way it helps illuminate biological questions in a technical way. Even worse, in the wrong hands it can very effectively obscure them. When I see Dembski raise his objections as such, I use the Pauli retort: he's not even wrong. I don't think it's wise for evolution defenders to engage it as if it were a worthy objection.

heddle: And since when do blog-comment level descriptions make it into professional research papers? Do lawyers always write like snarky middle school students? Intelligent Design is simply creationism for those who have consulted a lawyer and a public relations firm. Not very clever, not very original, and totally out of place in a professional document. At this point their writing is on the level of, well, O'Leary's.

What kind of professional writing is that? In context, it reads as if either (a) they think their readers are morons and need a statement of the obvious (nobody with an IQ over 50 would think, at that point in the paper, that they are denying evolutionary biology) or (b) they just decided to sneak in an unnecessary editorial comment.

"Intelligent Design is simply creationism for those who have consulted a lawyer and a public relations firm." Not very clever, not very original, and totally out of place in a professional document. At this point their writing is on the level of, well, O’Leary’s.

I'm not quite sure how to parse the title of this article. Perhaps it should be "...too dumb" instead of "to dumb"?

James Chapman: I'm not quite sure how to parse the title of this article. Perhaps it should be "...too dumb" instead of "to dumb"?

Tyler writes... I’m not even sure that “information” is the correct terminology to use here...

It can be a useful metaphor at times (much like “blueprint” for genomes), but... in the wrong hands it can very effectively obscure {the terms}.

Agree with Tyler (#136065). Any use of the word "information" in a biological context can cause a cringe reflex. Both sides of the IDC/science debate throw it around like some vaguely defined football.

"Real" Shannon) information usually makes little sense in biology. A gene duplication does add Shannon information to a genome, but a point mutation does not--it merely changes the information already there. And losing part of a gene decreases Shannon information, even though it may engender a different function. Yet a biologist (IANAB) would probably think of each of these as adding some kind of "information" to a genome.

Dembski likes to lean on complexity theory, although he distorts it quite a bit. Basically, the complexity of a system is proportional to the informational size of the system relative to the informational size of its simplest description. (And don't forget, Dr Dembski, the Kolmogorov theorem, that a system having maximum complexity is totally random!) So information in the sense of complexity may not be very useful in biology.

Thus, almost all uses of "information" in biology seem to be metaphorical, rather than rigorous or quantifiable. That wouldn't be a problem, except that the IDers treat their metaphorical uses as though they were both quantifiable and rigorous. The question is, can biological science define some sense of "information" that is meaningful and can't be equivocated?

James Chapman (#136088) has trouble parsing "to dumb" because English can noun adjectives so easily. We could transform "dumb" into a real noun by adding "-th," to make "dumbth." This is the method the Olde Englishe used with, e.g., "wide"/"width", "broad"/"breadth", "well"/"wealth", and many others. If you insist on a vowel change as in the other examples, we could say "dembth," which is closer to one of its exemplars.

Re "There is no bottom to dumb"

to? too? two? ;)

Henry

[ID] has nothing to do with science, since the criticisms of evolutionary biology are without merit and the positing of “intelligent design” as an explanatory hypothesis is on a par, epistemically, with the positing of turtles on whose back the universe rests.

Re "The question is, can biological science define some sense of “information” that is meaningful and can’t be equivocated?"

I tend to doubt it, but I'm no expert. I figure if the concept was of any use in biology, biologists would be using it and would have defined it appropriately for that use.

The only use that I see being made of it is political, as a way of increasing confusion about the subject, which by Shannon's definition increases the size of the description, which increases the information content... Wait, that didn't come out right.

Henry

Robert O'Brien:

[ID] has nothing to do with science, since the criticisms of evolutionary biology are without merit and the positing of “intelligent design” as an explanatory hypothesis is on a par, epistemically, with the positing of turtles on whose back the universe rests.

Brian Leiter is a slug, and his above comment, in addition to being gratuitous (as Dr. Heddle points out), is false.

Robert O'Brien:

[ID] has nothing to do with science, since the criticisms of evolutionary biology are without merit and the positing of “intelligent design” as an explanatory hypothesis is on a par, epistemically, with the positing of turtles on whose back the universe rests.

Brian Leiter is a slug, and his above comment, in addition to being gratuitous (as Dr. Heddle points out), is false.

“Real” Shannon) information usually makes little sense in biology. A gene duplication does add Shannon information to a genome, but a point mutation does not–it merely changes the information already there. And losing part of a gene decreases Shannon information, even though it may engender a different function. Yet a biologist (IANAB) would probably think of each of these as adding some kind of “information” to a genome.

Re "A gene duplication does add Shannon information to a genome, but a point mutation does not–it merely changes the information already there."

What if the point mutation is in one of two (or more) exact duplicates of a sequence? In that case what was an exact duplicate is now something different; how does Shannon treat that?

Also, if a point mutation produces a previously nonexistent allele, wouldn't that be an increase in information in the gene pool of the species?

Henry

Stanton: So then please demonstrate why Mr Leiter's opinion is without merit by explaining why Intelligent Design is a science, and show us Intelligent Design's much touted, but never unveiled explanatory power.

PvM: What part is false? That ID has nothing to do with science? That its 'criticisms' of evolutionary biology are without merit, that the positing of ID as an explanatory hypothesis is on par with turtles all the way down? My position is that ID is scientifically without content, its 'criticisms' of evolution especially focused on Darwinian evolution are founded in a misunderstanding of the concept of 'random', and lack in most cases in any merit and certainly have no relevance to ID, and finally ID is not in the business of being an explanatory hypothesis. So perhaps that's the part with which you disagree? The suggestion that ID cannot be a competing explanatory hypothesis?

Should we ever receive signals form an advanced civilization trying to contact us, by calculating the Shannon entropy of the message we could determine how much the civilization is trying to tell us even if we can’t decipher the message. So, applied to DNA, Shannon entropy makes a great explanatory filter to determine how God designs things. For a string consisting of a sequence of letters AGC and T Shannon entropy is a maximum when sequence of these letters is purely random. The Shannon entropy for DNA from a randomly chosen organism is pretty close to this Shannon maximum. So we can conclude that God does his design work by playing dice. Sorry Einstein.

Robert O'Brien: Intelligent Design is not a science in and of itself. However, suggesting evolutionary biology is beyond criticism is false as is equating ID with the belief that the universe rests on the backs of turtles.

I agree with you that Behe’s “flagellum argument” appears to have been successfully refuted (by finding a more primitive structure that features a subset of the proteins contained in the flagellum). I also agree that Dembski has had plenty of time to deliver on his mathematical promises but has yet to do so. So, on those two points, you were right all along and I was wrong. However, I disagree with Leiter (whom I already disdain) that evolutionary biology is beyond criticism and that ID is on the same epistemological footing as the belief that our universe is carried on the backs of turtles.

Does "epistemological footing" here refer to whether there's an observed pattern of evidence that's actually explained by a hypothesis? (If so, ID and the turtle "theory" would seem to both be totally lacking in that regard.)

Henry

Robert O'Brien: I disagree with Leiter (whom I already disdain) that evolutionary biology is beyond criticism

MPW: ID critics aren't saying you're not allowed to criticize evolutionary theory, just that IDists' particular criticisms are bunk. Whether you nonchalantly ignore this simple and obvious distinction because you really don't get it, or because you're engaging in some deliberate but clumsy sleight-of-hand, you should be embarrassed. Somehow I doubt you are.

We shall use “creationists” in what follows as a term of art to mean both those committed to the literal truth of the Book of Genesis as well as the proponents of “Intelligent Design.” Intelligent Design is simply creationism for those who have consulted a lawyer and a public relations firm; it has nothing to do with science, since the criticisms of evolutionary biology are without merit and the positing of “intelligent design” as an explanatory hypothesis is on a par, epistemically, with the positing of turtles on whose back the universe rests. The Intelligent Design Creationists have stated no empirically testable hypothesis, and posit mechanisms that satisfy none of the standard desiderata of scientific theory construction, like ontological parsimony or methodological conservatism.

Robert O'Brien:

We shall use “creationists” in what follows as a term of art to mean both those committed to the literal truth of the Book of Genesis as well as the proponents of “Intelligent Design.” Intelligent Design is simply creationism for those who have consulted a lawyer and a public relations firm; it has nothing to do with science, since the criticisms of evolutionary biology are without merit and the positing of “intelligent design” as an explanatory hypothesis is on a par, epistemically, with the positing of turtles on whose back the universe rests. The Intelligent Design Creationists have stated no empirically testable hypothesis, and posit mechanisms that satisfy none of the standard desiderata of scientific theory construction, like ontological parsimony or methodological conservatism.

The language of the underlined clause suggests there are no legitimate criticisms of evolutionary biology. (Else, it should read: "...its criticisms of evolutionary biology..." or some such.)

SWT: The underlined clause "suggests" no such thing. To say that the criticisms are "without merit" is to say that the criticisms proffered by ID are factually incorrect, not that the criticisms are impermissible in principle.

SWT:I'm still waiting for some ID advocate somewhere to offer a positive argument for ID, or to propose an empirically testable hypothesis using the ID framework.

Intelligent Design is simply creationism for those who have consulted a lawyer and a public relations firm; it has nothing to do with science, since the criticisms of evolutionary biology are without merit and the positing of “intelligent design” as an explanatory hypothesis is on a par, epistemically, with the positing of turtles on whose back the universe rests.

My interest is in seeing holes poked in the common descent hypothesis,

Olorin: "Real" Shannon) information usually makes little sense in biology. A gene duplication does add Shannon information to a genome, but a point mutation does not--it merely changes the information already there. And losing part of a gene decreases Shannon information, even though it may engender a different function. Yet a biologist (IANAB) would probably think of each of these as adding some kind of "information" to a genome. [...] Dembski likes to lean on complexity theory, although he distorts it quite a bit. Basically, the complexity of a system is proportional to the informational size of the system relative to the informational size of its simplest description. (And don't forget, Dr Dembski, the Kolmogorov theorem, that a system having maximum complexity is totally random!) So information in the sense of complexity may not be very useful in biology.

Robert O'Brien:

SWT: The underlined clause "suggests" no such thing. To say that the criticisms are "without merit" is to say that the criticisms proffered by ID are factually incorrect, not that the criticisms are impermissible in principle.

Your bald assertion is nice and all but it does not address Leiter's use of the definite article before "criticisms." Now, it could be that Leiter wields the English language clumsily, which is also consonant with my low opinion of him, but I took the footnote as it is.

Robert O'Brien:

SWT: The underlined clause "suggests" no such thing. To say that the criticisms are "without merit" is to say that the criticisms proffered by ID are factually incorrect, not that the criticisms are impermissible in principle.

Your bald assertion is nice and all but it does not address Leiter's use of the definite article before "criticisms." Now, it could be that Leiter wields the English language clumsily, which is also consonant with my low opinion of him, but I took the footnote as it is.

Olorin: James Chapman (#136088) has trouble parsing "to dumb" because English can noun adjectives so easily. We could transform "dumb" into a real noun by adding "-th," to make "dumbth." This is the method the Olde Englishe used with, e.g., "wide"/"width", "broad"/"breadth", "well"/"wealth", and many others. If you insist on a vowel change as in the other examples, we could say "dembth," which is closer to one of its exemplars.

Robert wrote:

"My interest is in seeing holes poked in the common descent hypothesis, not in offering an empirically falsifiable alternative. I have no problem with leaving it at that and letting people draw their own conclusions from the criticisms."

Great. By all means, poke away. That is what real scientists do every day. So if these holes prove to be areas where evolutionary theory needs some improving, then rigorous hypothesis testing will identify the problems and make the theory that much stronger.

If however your goal is to overthrow the current theory and replace it, then you will fail miserably. Poking holes does not lead to the overthrow of a well established theory. That can only happen if you have something with more predictive and explanatory power to replace it with. ID, as we have seen, has absolutely zero predictive or explanatory power, so it is not a scientific threat to the theory of evolution and never will be.

As a political threat ID might be revived, if the country ever goes backward enough to give fundamentalists control of the government again. But of course that won't require poking any holes or any evidence of any kind. It will just involve explaining away the evidence that already exists or making sure that people remain ignorant of it.

By the way, if you let people draw their own conclusions from your criticisms and your lack of testable alternatives, the only conclusion that can be reasonably drawn is that evoutionary theory is not perfect but that it is the best that science has to offer. No real scientist would discard the most tested theory in the history of science without a viable scientific alternative. You can only play to the ignorant with that strategy. Let me know how that turns out for you.

Robert O'Brien: My interest is in seeing holes poked in the common descent hypothesis

I have no problem with leaving it at that and letting people draw their own conclusions from the criticisms.

. . . My interest is in seeing holes poked in the common descent hypothesis, not in offering an empirically falsifiable alternative. I have no problem with leaving it at that and letting people draw their own conclusions from the criticisms.

Robert O'Brien complains that people supporting the theory of evolution play word games, then proceeds to play a silly word game himself, by trying to make us believe that


    'since the criticisms of evolutionary biology are without merit'


means the same as


    'since criticisms of evolutionary biology are without merit'.


No. The word 'the' tells us quite definitely that specific criticisms of evolutionary biology are the subject. When it is omitted, the subject then becomes generic. Compare 'Flowers have arrived for funerals' with 'The flowers have arrived for the funerals.' (Sorry, when thinking of ID funerals popped into my mind.)

RO'B: If this was not covered in your English courses, you should make a complaint.

. . . My interest is in seeing holes poked in the common descent hypothesis, not in offering an empirically falsifiable alternative. I have no problem with leaving it at that and letting people draw their own conclusions from the criticisms.

Thus neatly illustrating that you have no clue about how science finds stuff out. In science, an incomplete hypothesis is far preferable to no hypothesis at all. If you wish to criticise any specific scientific hypothesis, that’s fine, but it behooves you to propose an alternative, better explanation to replace that which you criticise.

Rolf Aalberg wrote:

"150 years of research has not shown even traces of holes [in the theory of common descent]; the only ‘falsification’ attempts so far being the various flavors of creationism."

Actually, there have been many, many "‘falsification’ attempts" in the last 150 years, starting with Richard Owen's assertion that apes have no hippocampus minor. Even the re-discovery of Mendel's genetic studies was originally touted as an alternative to Darwin's theory. (I never can get my mind around how they thought that.)

The only thing is, all the falsification attempts so far have failed. That's not for want of trying. In the process, many sub-hypotheses have bitten the dust. 75 years ago, all good scientists 'knew' that dinosaurs were slow-moving, cold-blooded, and left no descendants; that cells were full of protoplasm, and so on. When new information proved them wrong, they didn't try to stifle the revolutionary views. On the contrary, they rushed into the new fields, seeing exciting possibilities for their own research.

Criticism is, in fact, the life blood of the scientific enterprise. First-rate scientists try to frame their hypotheses so that they are clear and testable-- so that they can be refuted if they're wrong.

The problem with the ID/creationist movement isn't that they make criticisms of standard science-- it's that they refuse to accept criticisms of their own position, in fact, deliberately making their 'hypothesis' (if you can call it that) so vague that it's useless for scientific prediction. Now, they seem to have given up entirely on even formulating hypotheses, and have retreated to making criticisms of standard science which cannot be refuted because the terms are so vague they convey no real information. This seems to me, frankly, a major step backwards from 'turles all the way down.' At least scientists could mount an expedition to go looking for the turtles.

My interest is in seeing holes poked in the common descent hypothesis, not in offering an empirically falsifiable alternative. I have no problem with leaving it at that and letting people draw their own conclusions from the criticisms.

that cells were full of protoplasm

The most remarkable conclusion which follows from the foregoing observations is that, in the roots of various plants, cells appearing quite similar and of the same homologous nature yet differ greatly in their contents, as shown by the action on them of certain solutions.

These masses, moreover, display in some cases incessant movements. The process of aggregation is not rarely carried so far that the masses lose the power of movement; nor do they then readily disintegrate when subjected to any deadly influence. From these facts, from other considerations, and more especially from the action of carbonate of ammonia on the chlorophyll-bodies, I am led to believe that the aggregated masses include living protoplasm, to which their power of movement may be attributed.

Well, yes. It took me precisely one guess, and since his complete works are on the net, it wasn't hard to track down.

But, notice, even though Charles Darwin, himself, believed protoplasm was a real thing, that hypothesis was doomed after JD Bernal started doing X-ray crystallography in the 1930's, and discovered proteins had stable crystalline structures.

That, right there, is proof that "Darwinism" isn't a religion.

Identity left as an exercise for the reader

— Wesley R. Elsberry

OK, based on HP's comment it looks like I was wrong there.

Remember that it is not just the mutation but the selection part which affects Shannon information. If a particular mutation has a particular fitness effect it can either disappear of become fixated, in the latter case, Shannon information increases as conserved nucleotides or conserved codons, do in fact contribute to an increase in Shannon information.

... But now we come to natural selection, which reduces the "prior uncertainty" and therefore, in Shannon's sense, contributes information to the gene pool. In every generation, natural selection removes the less successful genes from the gene pool, so the remaining gene pool is a narrower subset. The narrowing is nonrandom, in the direction of improvement, where improvement is defined, in the Darwinian way, as improvement in fitness to survive and reproduce.

Of course the total range of variation is topped up again in every generation by new mutation and other kinds of variation. But it still remains true that natural selection is a narrowing down from an initially wider field of possibilities, including mostly unsuccessful ones, to a narrower field of successful ones. This is analogous to the definition of information with which we began: information is what enables the narrowing down from prior uncertainty (the initial range of possibilities) to later certainty (the "successful" choice among the prior probabilities). According to this analogy, natural selection is by definition a process whereby information is fed into the gene pool of the next generation.

If natural selection feeds information into gene pools, what is the information about? It is about how to survive. Strictly it is about how to survive and reproduce, in the conditions that prevailed when previous generations were alive.

If you want an actual information acquisition analysis done up in terms of Shannon, there's a paper by Kimura in, IIRC, 1961 that does the job.

Natural Selection as the process of accumulating genetic information in adaptive evolution. 1961. Kimura, M.

Daniel Morgan provides the following list

1. Natural selection as the process of accumulating genetic information in adaptive evolution, M. Kimura (1961)
2. Rate of Information Acquisition by a Species subjected to Natural Selection, D.J.C. MacKay
3. Evolution of biological information, T.D. Schneider
4. The fitness value of information, C.T. Bergstrom and M. Lachmann
5. Review of W. Dembski’s No Free Lunch, J. Shallit
6. The Evolution and Understanding of Hierarchical Complexity in Biology from an Algebraic Perspective, C.L. Nehaniv and J.L. Rhodes
7. On the Increase in Complexity in Evolution, P.T. Saunders and M.W. Ho (1976)
8. On the Increase in Complexity in Evolution II: The Relativity of Complexity and the Principle of Minimum Increase, P.T. Saunders and M.W. Ho (1981)

You guys should check out my blog sometime, I have started a series called "Evolution for Creationists" which presents a TON of really good evidence for evolution, with links of course.

http://aigbusted.blogspot.com

-Ryan

As PvM mentioned, I have a few papers you can download on the subject if you're interested: index.

Those claiming that information doesn't apply to biology or that it's "just a metaphor" or that a gene duplication adds information but a point mutation doesn't change information don't understand the subject. It isn't gene duplications or point mutations that add information, it is selection, which adds information to the genome about the environment. There are many facts about the organism produced from a specific genome that are specific to the evolutionary history that produced that genome, facts that make that organism likely to be able to survive in a particular environment. The encoding of facts is subject to information theoretic analysis.

P.S. Please don't feed the trolls, especially that troll.

The only use that I see being made of [information] is political

So while it is true that variation is the engine of the populations genome learning about the environment, it is selection that is the steering wheel.

It isn’t gene duplications or point mutations that add information, it is selection, which adds information to the genome about the environment. There are many facts about the organism produced from a specific genome that are specific to the evolutionary history that produced that genome, facts that make that organism likely to be able to survive in a particular environment. The encoding of facts is subject to information theoretic analysis.

Selection as such has no effect on the raw Shannon information in a given genome. A 3.5 Gbase genome has 7.0 Gbit of raw information, whether it is selected or not. A selected genome may encode more information about the environment, but it has no greater inherent information.

Henry said (136125): “What if the point mutation is in one of two (or more) exact duplicates of a sequence? In that case what was an exact duplicate is now something different; how does Shannon treat that?”

I was probably using the term “point mutation” incorrectly. What I meant was a mere substitution of one amino acid for another. Such substitutions do not increase Shannon information.

Even the basic Shannon measure is slippery. Consider the strings “XFBUR” and “QUEEN”. The first is random, and contains about 5 bits per letter, or 23 bits total. If we know ahead of time that the second string is an English word, for example, “U” almost always follows “Q”, so its info content is very low, maybe 0.1 bit; “after “E” we ask how many words begin with “QUE” and find that the content of the last two letters is very low. This “prior uncertainty” is Torbjorn’s point in 136186. The sense that biologists would use Shannon info would, I think, almost always either involve prior knowledge or refer to encoding something besides raw amino-acid sequences. Each case would require further definition. This leads into—

mad scientist said (136130): “Should we ever receive signals form an advanced civilization trying to contact us, by calculating the Shannon entropy of the message we could determine how much the civilization is trying to tell us even if we can’t decipher the message.”

Au contraire, ms. Only if we had some kind of prior knowledge as to the characteristics of its noodly mind, or made an assumption without evidence. Scientists often assign equiprobable outcomes when they just don’t know—but that’s an assumption from ignorance. Once SETI collectively hit the ceiling when someone discovered an extremely narrow-band signal of absolute regularity from a point source in the sky: fantastically low entropy!. Turned out to be a new kind of supernova. (Yes, I did catch the :-P in your comment, but it’s still a good point.)

Eric said (136153): “There are rigorous mathematical formulations concerning information and complexity. They are not easily adaptable to biology.”

Yes and yes again. Complexity as information is more, uh, complex than Shannon info. For one thing, even its raw quantity depends upon the language in which strings and descriptions are encoded. (Read Greg Chaitin’s AIT book METAMATH! (Pantheon, 2005) Chaitin is an approachable and personable author and teacher.)

Eric redux: “Shannon’s formula indicates that if we can decrease the number of available states, we increase information in the system. This formula does not compare two different systems.”

No and no again. IABAL,* but decreasing the number of states decrease the information; fewer bits are required to describe the system. Comparing the information (or entropy) in different systems is merely the ratio of the numbers of states.

PvM said (136188): “Natural Selection as the process of accumulating genetic information in adaptive evolution.”

As we say in Minnesota: “Yeabut.” Yes, but, without looking at all these references in Daniel Morgan’s list, I’d bet that each of them defines a somewhat different measure of information, or a different referent for the information, or a different something else that makes them incommensurable with each other. This was my original quibble with the use of the term. How can we dispute ID’s equivocation if we can’t define it unambiguously ourselves?

= = = = =

*– IABAL: “I am but a lawyer.”

Use html entities &lt; &gt; for < and >

PvM said (136120): “Remember that it is not just the mutation but the selection part which affects Shannon information.” Selection as such has no effect on the raw Shannon information in a given genome. A 3.5 Gbase genome has 7.0 Gbit of raw information, whether it is selected or not. A selected genome may encode more information about the environment, but it has no greater inherent information.

As we say in Minnesota: “Yeabut.” Yes, but, without looking at all these references in Daniel Morgan’s list, I’d bet that each of them defines a somewhat different measure of information, or a different referent for the information, or a different something else that makes them incommensurable with each other. This was my original quibble with the use of the term. How can we dispute ID’s equivocation if we can’t define it unambiguously ourselves?

R O'B, in a moment of candor from the ID crowd, writes... You will have to look elsewhere. My interest is in seeing holes poked in the common descent hypothesis, not in offering an empirically falsifiable alternative.

The most common pitfall in defining “information”, or equivalently the entropy, is in defining probabilities. One has to know all the possible scenarios leading to a configuration and what the probabilities of those scenarios are. If one chooses a path leading to a particular configuration that is highly improbable, one can end up with a lot of information where there may be none.

A simple illustration would be the large, thick flat rock perched on top of a relatively slender pillar of rock, often seen in some geological formations. How much “information” is contained in that configuration and what does it tell you?

If one claims that the configuration is so improbable that it could only have occurred because some intelligence put it there, what are you using as the basis for your probability calculation?

You could offer the alternative that a large earthquake launched the slab of rock into the air and it landed perfectly on top of the pillar that just happened to be nearby. However, a more careful investigation shows no evidence of an earthquake.

Relative to that explanation, the probability is extremely low that the rock ended up where it did; therefore it contains a lot of information which must have been put there by some intelligence.

On the other hand, if the configuration could have resulted from differential erosion of the rock due to winds or water (the pillar being somewhat softer than the slab on top), then there is not very much information in that configuration relative to the erosion scenario.

This is where the ID game-playing takes advantage of ignorance and lack of experience.

Mike Elzinga:

My interest is in seeing holes poked in the common descent hypothesis, not in offering an empirically falsifiable alternative. I have no problem with leaving it at that and letting people draw their own conclusions from the criticisms.

It’s one thing to blurt out a statement like this accidentally; it’s quite another to wear it proudly as a badge of some kind of perverse honor.

Mike Elzinga:I don’t believe there have been any reputable scientists in history who have taken this attitude toward understanding the physical universe. It is, however, a common tactic among politically motivated demagogues who find themselves thwarted by more noble people and by loftier ideas and deeper understandings. Their only abilities are to tear down what others have built up, but never to build up or illuminate anything. Any clod can seek to destroy. Creative and inquisitive people build.

Nigel D: So, what substantive, scientific criticisms do you have of the theory of common descent?

Incidentally, I think one of the benefits of shelving the concept of common descent (especially as it concerns the alleged common ancestry of apes and humans) would be a decrease in YEC nonsense, which is a real cause for scientific concern.

For once, Robert O'Brien has hit the doornail on the head (136218). If evolution did not claim that humans are descended from some other form of life, then YEC/OEC/ID/FSM would probably fade into the wallpaper. They'd give us common descent for everything else, but homo sapiens sapiens must remain forever inviolate.

Typically we see an appeal to ignorance to lead to a common designer, although no further details are provided, nor ever will.

Love the quote mining but does Robert actually understand these papers?

That Robert is seriously (?) considering the shelving of the fact of common descent to cater to the needs of some religious people says enough.

Well the informatic discussion here has pretty much taken off without me, but I do have a few comments to leave:

"Yes and yes again. Complexity as information is more, uh, complex than Shannon info. For one thing, even its raw quantity depends upon the language in which strings and descriptions are encoded."

True, but it's also important to note the most interesting result of Kolmogorov-Chaitin measures, which is that they are recursively invariant up to a fixed additive constant independent of the object being described. It's what makes the theory useful.

"Not really, a 3.5Gbase genome has 3.5G * log2(4) or 7GBits of entropy. Information is the reduction in entropy. For instance if selection fixates a single nucleotide then there is a reduction of 2 bits of entropy or alternatively the genome now contains2 bits of information."

I thought that in the Shannon picture an increase in entropy corresponded to an increase in the total information content of an ensemble of messages. Is this a usage exclusive to biology?

PvM: Typically we see an appeal to ignorance to lead to a common designer, although no further details are provided, nor ever will. Love the quote mining but does Robert actually understand these papers? That Robert is seriously (?) considering the shelving of the fact of common descent to cater to the needs of some religious people says enough.

My Molecular Biology teacher told us that a new hypothesis suggests that the reason why humans and chimpanzees are so different morphologically, but so genetically similar is because different introns in the same genes are excised and retained in each species, thus leading to different gene products.

A further point I would like to make is that genetic commonality does not rule out a “common designer.” (Other evidence may militate against that conclusion, but not genetic commonality in and of itself.)

Robert O'Brien: A further point I would like to make is that genetic commonality does not rule out a "common designer."

Selection as such has no effect on the raw Shannon information in a given genome. A 3.5 Gbase genome has 7.0 Gbit of raw information, whether it is selected or not.

Tyler DiP (136222) re PvM (136200): "I thought that in the Shannon picture an increase in entropy corresponded to an increase in the total information content of an ensemble of messages. Is this a usage exclusive to biology?"

Like most biologists, I think PvM visualizes information and entropy backwards. An increase in entropy is an increase in information toute le monde. It's been almost 50 years since Statistical Mechanics 551, but I think that's still correct.

without looking at all these references in Daniel Morgan’s list, I’d bet that each of them defines a somewhat different measure of information, or a different referent for the information, or a different something else that makes them incommensurable with each other.

A further point I would like to make is that genetic commonality does not rule out a “common designer.” (Other evidence may militate against that conclusion, but not genetic commonality in and of itself.)

Olorin: It has been almost 50 years since Statistical Mechanics 551, but I think that's still correct.

Popper's Ghost: "Some people seem to think that 'I’d bet' (even when they wouldn’t) is some sort of argument."

Not an argument. An opinion, extrapolated from the many different usages I've seen so far on this thread.

Popper's Ghost: "Consider a text file and its gzipped equivalent. They contain the same information but one has less than half the bits of the other."

Yeabut only if you have prior knowledge that this relationship exists. My point continues to be that, coming from physics, I see biologists use the term "information" in so many different senses and with so many different referents that it might be hard to accuse the IDologues of equivocation. For example, an earlier comment said that a mutation that has been selected adds information to the genome from the environment. How would you quantify this added information? How do you measure bits of the environment, or bits of the genome corresponding to a certain part of the environment? Sorry, it's bringing on an acute miasma attack.

Ravilyn Sanders:

Robert O'Brien: A further point I would like to make is that genetic commonality does not rule out a "common designer."

Why do you pre-suppose a designer? Why not many designers? Why not 33 million as postulated by some Hindus? So all you can offer as a positive theory for your side is "this particular bit of evidence is not inconsistent with one or more designers who could be intelligent, clumsy, dumb, malicious or stuck-in-a-rut-out-of-new-ideas". All the rest of your intellectual capital will be spent on poking holes on ToE? Do you even begin to understand why ID does not go anywhere?

It’s been almost 50 years since Statistical Mechanics 551

Robert O'Brien: "You must be into your seventies, then. :-)"

Now this may be true, but I'll thank you not to say it in polite company.

information: Information is measured as the decrease in uncertainty of a receiver or molecular machine in going from the before state to the after state. "In spite of this dependence on the coordinate system the entropy concept is as important in the continuous case as the discrete case. This is due to the fact that the derived concepts of information rate and channel capacity depend on the difference of two entropies and this difference does not depend on the coordinate frame, each of the two terms being changed by the same amount." --- Claude Shannon, A Mathematical Theory of Communication, Part III, section 20, number 3

Olorin: Tyler DiP (136222) re PvM (136200): "I thought that in the Shannon picture an increase in entropy corresponded to an increase in the total information content of an ensemble of messages. Is this a usage exclusive to biology?" Like most biologists, I think PvM visualizes information and entropy backwards. An increase in entropy is an increase in information toute le monde. It's been almost 50 years since Statistical Mechanics 551, but I think that's still correct.

If an “intelligent designer” can be inferred, then I equate the designer with God. Moreover, I accept Kurt Gödel’s Ontological Argument as well as Leibniz’s Law, which effectively rules out polytheism as a viable option.

ROB says:

"The authors of PNAS 7708-7713 also calculate the genetic commonality between chimps and humans as 86.7% (accounting for insertions and deletions).

[...]

How, exactly, is my citation a “quote-mine”? Have I misrepresented the authors? No, I have not."

Yes, ROB has. I had fixed up a couple of quotes from the PDF, but Movable Type's software ate them. The bottom line is that the lower sequence identity figure refers only to a portion of the several megabase long MHC region, in which the paper's authors were expecting to find a "large part" of the between-species diversity (from about three gigabases) to be concentrated. Statistics majors are supposed to know that differences between sequences are not necessarily uniformly distributed, right?

"This 1,750,601-bp stretch of DNA, which encompasses the entire class I along with the telomeric part of the MHC class III regions, corresponds to an orthologous 1,870,955 bp of the human HLA region. Sequence analysis confirms the existence of a high degree of sequence similarity between the two species. However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region."

Look, folks, there's a definite article to pay attention to!

Seems that Rob is in good company with several other ID proponents who have quote mined the article without really comprehending its claims.
Why is it that ID proponents are often so sloppy in their reading or understanding of scientific research?

Not an argument. An opinion, extrapolated from the many different usages I’ve seen so far on this thread.

Popper’s Ghost: “Consider a text file and its gzipped equivalent. They contain the same information but one has less than half the bits of the other.” Yeabut only if you have prior knowledge that this relationship exists.

I see biologists use the term “information” in so many different senses and with so many different referents that it might be hard to accuse the IDologues of equivocation.

For example, an earlier comment said that a mutation that has been selected adds information to the genome from the environment. How would you quantify this added information? How do you measure bits of the environment, or bits of the genome corresponding to a certain part of the environment?

Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other ({approx}6 million years ago), the molecular basis of traits unique to humans vs. their closest relative, the chimpanzee, is largely unknown. This report describes a large-scale single-contig comparison between human and chimpanzee genomes via the sequence analysis of almost one-half of the immunologically critical MHC. This 1,750,601-bp stretch of DNA, which encompasses the entire class I along with the telomeric part of the MHC class III regions, corresponds to an orthologous 1,870,955 bp of the human HLA region. Sequence analysis confirms the existence of a high degree of sequence similarity between the two species. However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region. This is functionally exemplified by a large deletion of 95 kb between the virtual locations of human MICA and MICB genes, which results in a single hybrid chimpanzee MIC gene, in a segment of the MHC genetically linked to species-specific handling of several viral infections (HIV/SIV, hepatitis B and C) as well as susceptibility to various autoimmune diseases. Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle single-nucleotide substitutions for shaping the recently emerged primate species.

The authors of PNAS 7708-7713 also wrote:

Interestingly, once the indels are taken into account, the above observed 98.6% sequence identity drops to only 86.7% (substitution, 1.4%; indels, 11.9%). This indel-included 86.7% identity may be a better representation of whole-genome sequence similarity between the human and the chimpanzee, as confirmed by a recently published study comparing a number of fragmented chimpanzee sequences with their human counterparts.

Olorin is correct that the concept of information, complexity etc have been poorly defined. Even with the concept of Shannon information, there is some confusion as to the differences between shannon informational entropy and Shannon information, the reduction in entropy.

PvM: In fact, there is a good overview by Richard Hoppe about the Multiple Designers Theory.

Interestingly, once the indels are taken into account, the above observed 98.6% sequence identity drops to only 86.7% (substitution, 1.4%; indels, 11.9%). This indel-included 86.7% identity may be a better representation of whole-genome sequence similarity between the human and the chimpanzee, as confirmed by a recently published study comparing a number of fragmented chimpanzee sequences with their human counterparts.

Nice ad hominem Robert.

P's.G. said (136236): "The important point, which is lost in this confusion about Shannon information is that the genome, via natural selection, encodes information about the environment that allows for reproduction (with modification) of the genome by the organism that the genome builds."

Agree, agree, and yet again agree. But also yet again, can you define such information in a manner that is useful and quantifiable? Suppose Confutatis Maledictis evolves a new opsin that gives it tricolor vision so that it can now spot ripe juju-fruits more easily. How many bits of information has its genome gained? How many bits of environment are encoded? What makes sense in this situation?

Was it Lord Kelvin who said there are only two kinds of science, physics and butterfly collecting? Was he right?

“The chimpanzee is believed to share [approximately] 98.77% nucleotide and [over] 99% amino acid identity with us. [...]

Robert O'Brien said (136249): "The psychologist? Is he your answer to DI’s Medved?"

No. He's our equivalent of Alan Sokal.

Olorin: P's.G. said (136236): "The important point, which is lost in this confusion about Shannon information is that the genome, via natural selection, encodes information about the environment that allows for reproduction (with modification) of the genome by the organism that the genome builds." Agree, agree, and yet again agree. But also yet again, can you define such information in a manner that is useful and quantifiable? Suppose Confutatis Maledictis evolves a new opsin that gives it tricolor vision so that it can now spot ripe juju-fruits more easily. How many bits of information has its genome gained? How many bits of environment are encoded? What makes sense in this situation? Was it Lord Kelvin who said there are only two kinds of science, physics and butterfly collecting? Was he right?

"Olorin is correct that the concept of information, complexity etc have been poorly defined. Even with the concept of Shannon information, there is some confusion as to the differences between shannon informational entropy and Shannon information, the reduction in entropy."

I wouldn't say poorly defined, but it is rather turgid. I pulled down and dusted off a textbook on the subject and information is indeed measured in the reduction in uncertainty. It took a bit to find the actual definition of "information", but it was fun to see Shannon's uncertainty function derived. Thanks for helping to clear up my misconceptions.

Thanks, PvM (136257). Beginning to sound like a brain failure on my part, as P's. G. claims. When physicists or communications wallahs hear the word "information," they want a number, and they want to know how to put a yardstick on it. If that can in fact be nailed down for some appropriate biological entities, then we can say, OK, ID, give us a number for the amount of complex specified information in that there flagellum, and tell us how you measured it. Is this a reasonable kind of thing to ask for in my Christmas stocking?

Tom Schneider uses the concept of Shannon information to detect binding sites

His sequence logos are quite beautiful

Tyler DiPietro said (136222): I thought that in the Shannon picture an increase in entropy corresponded to an increase in the total information content of an ensemble of messages. Is this a usage exclusive to biology?

I’m with you on this. The 3.5 G * log2(4) = 7GBitz is the storage space that would be required on average to store a completely random string of consisting of 3.5 G worth of As, Cs, Gs, and Ts. To store a 3.5 G genome of an organism would require somewhat fewer bits because A, C, G and T generally do not occur with equal frequency and there are repetitive sequences and various correlations that would allow further data compression. But I doubt that the savings in disk space would be very large. I would guess that the savings are so small that genome databases probably don’t employ any data compression. Random mutations will reduce the biases and correlations. So, on average, random mutations will increase the Shannon information (the amount of disk space one would need to store the genome). So, to a creationist’s comment: “Look at all the information contained in a genome.” perhaps a good retort would be: “So what? It would contain even more information if it were truly random.”

Olorin said (136198) “Au contraire, ms. Only if we had some kind of prior knowledge as to the characteristics of its noodly mind, or made an assumption without evidence.”

Actually, I think I am fairly safe on the first statement I made since Shannon entropy does not consider the content of the message or what is in the mind of the sender. Only the probabilities of the arrival of the symbols in which the message is encoded enter in the Shannon entropy formula. In the Shannon entropy context, one should think of “how much the civilization is trying to tell us” as being how much disk storage space is going to be needed to save the message once the data has been maximally compressed. As you caught, the rest of the argument was tongue-in-cheek, taking a common creationist argument to its logical conclusion.

Interestingly, once the indels are taken into account, the above observed 98.6% sequence identity drops to only 86.7% (substitution, 1.4%; indels, 11.9%). This indel-included 86.7% identity may be a better representation of whole-genome sequence similarity between the human and the chimpanzee, as confirmed by a recently published study comparing a number of fragmented chimpanzee sequences with their human counterparts.

The authors of PNAS 7708-7713 also calculate the genetic commonality between chimps and humans as 86.7% (accounting for insertions and deletions).

there are important biomedical (as well as obvious morphological and cognitive) differences between the two species [chimpanzees and humans], which thus far have eluded any molecular explanation within this supposedly 1% diversity range.

Yes. It's that pesky definite article in "the genetic commonality". What they calculated was a figure for a small region. They speculated that their figure might well apply to the whole genome. Then along came the complete chimp genome, and lo and behold, they were wrong in their speculation.

Wesley R. Elsberry: Yes. It's that pesky definite article in "the genetic commonality". What they calculated was a figure for a small region. They speculated that their figure might well apply to the whole genome. Then along came the complete chimp genome, and lo and behold, they were wrong in their speculation.

That is an important update. However, the statements I cited concerning the pronounced differences between human and ape immunobiology still hold.

However, there are important biomedical (as well as obvious morphological and cognitive) differences between the two species, which thus far have eluded any molecular explanation within this supposedly 1% diversity range.

So, to be clear, I apparently misrepresented PNAS 7708-7713 when I paraphrased this excerpt:

The 3.5 G * log2(4) = 7GBitz is the storage space that would be required on average to store a completely random string of consisting of 3.5 G worth of As, Cs, Gs, and Ts.

I am with Tyler DiPietro on this; these definitions of information and complexity as applied to biological systems are rather turgid. That’s not to say that they are necessarily wrong or not useful.

However, what I see beginning to happening in this discussion is the exploitation of technical jargon by creationists to bamboozle the public. The creationists don’t know what any of this stuff means; they just have to get a complicated discussion going to make it appear that they are on top of the game.

If I may offer a suggestion; it may perhaps be better to translate the basic ideas into something simpler that the lurkers here can grasp.

Years ago I took some cues from Richard Feynman and Victor Weiskopf about explaining complicated ideas to the public and to non-specialists (both of these physicists were masters at explaining complicated ideas in simple terms).

The most important (and most difficult) idea is to shed the equations. Next, find some simple systems that capture the essence of what you are trying to explain, find simple words that describe the phenomena, and then introduce the technical words later.

It was one of the hardest things I had to learn, but eventually I developed the ability to explain complicated ideas to young high schools students. The payoff was worth it, and I learned to understand the physics better. There is a strong temptation on the part of physicists to start writing down equations, and I am certainly no exception; but that has to be fought.

I think what the public and the lurkers here would appreciate most is to see attempts to bring these ideas into sharper focus using simpler steps.

I have used many of these ideas in my research with no problems, but I am still not comfortable with the ways they are being used in much of the literature, especially as it relates to biology. Signal and information processing is a rich and well developed field (e.g., Donald Knuth has written a whole series of books on this), but the physics, chemistry and biology of living systems are what are being discussed. Burying these ideas in the jargon of signal and information processing is not going to help the public.

I think we all need to learn these educational techniques, and begin attaching the information aspects to it in a more gentle fashion (if that is even necessary). I'm not afraid of Dembski.

Just a suggestion.

Following Mike Elzinga above, I'd like to amend my initial position here. What I said initially was actually true, in that I wasn't aware of specific technical instances where information theory has been successfully applied to biology. I was only aware of the trivial point that you could apply an informatic measure to the genome, but now it has been pointed out to me that it has been applied in non-trivial and (at least potentially) illuminating in fruitful ways. But I'd still like to emphasize that a lot of the discussion of "information" in a biological context seems very general and that only "gives a leg up" to the IDers (to use Mike's phraseology). It would help to narrow the field a bit and stress the technical nature of the applications in contrast to the intuitive or metaphorical ways it is often used. Just a thought.

Referring to "important biomedical" differences between chimpanzees and humans, Robert O'Brien mentions "HIV (progression to AIDS)."

Robert, did you not follow the Open Letters thread by Ian Musgrave regarding Abbie Smith's challenge to Michael Behe? The whole issue was that Smith presented proof that HIV has mutated from SIV. (Simian IV.) There is no particular reason to think a priori that apes and people are very different in their susceptability to AIDS, since humans are being infected by a different virus.

"The language of the underlined clause suggests there are no legitimate criticisms of evolutionary biology. (Else, it should read: “…its criticisms of evolutionary biology…” or some such.)

[...]

The authors of PNAS 7708-7713 also calculate the genetic commonality between chimps and humans as 86.7% (accounting for insertions and deletions).

[...]

That is an important update. However, the statements I cited concerning the pronounced differences between human and ape immunobiology still hold."

ROB didn't introduce his quotes as having a meaning restricted to immunobiology ("immunobiology" being notable by its absence in ROB's own phrasing until his latest claim). Nor does his "common designer" argument make much sense within a context where science is pinpointing where most of the differences between chimp and human have accumulated, rather than the obvious reading of ROB's comments as establishing a lower whole genome genetic commonality than was previously thought. The point that if sequence diversity is not uniformly distributed, then one should expect to discover regions with higher (and lower) sequence diversity was cleanly avoided, even though that point is something that one would also have expected to be best appreciated (and perhaps expressed) by the statistics maven in the discussion.

So, is ROB a "slug", or just "clumsy with the language"? Or is it possible that one can argue for a bit more charity all around? Sowing, reaping, and all that?

My interest is in seeing holes poked in the common descent hypothesis, not in offering an empirically falsifiable alternative. I have no problem with leaving it at that and letting people draw their own conclusions from the criticisms.

Wesley R. Elsberry: ROB didn't introduce his quotes as having a meaning restricted to immunobiology ("immunobiology" being notable by its absence in ROB's own phrasing until his latest claim). Nor does his "common designer" argument make much sense within a context where science is pinpointing where most of the differences between chimp and human have accumulated, rather than the obvious reading of ROB's comments as establishing a lower whole genome genetic commonality than was previously thought.

Wesley R. Elsberry:The point that if sequence diversity is not uniformly distributed, then one should expect to discover regions with higher (and lower) sequence diversity was cleanly avoided, even though that point is something that one would also have expected to be best appreciated (and perhaps expressed) by the statistics maven in the discussion.

The authors of PNAS 7708-7713 also calculate the genetic commonality between chimps and humans as 86.7% (accounting for insertions and deletions).

While I am knowledgeable concerning distribution theory, I did not have occasion to study the underlying sequence data myself. Thus, when the authors suggested that the region they observed was representative, I accepted their calculation.

So use of the definite article definitely means something when someone else does it, but not when ROB does it?

I think I'm catching on...

Robert O'Brien: If an "intelligent designer" can be inferred, then I equate the designer with God. Moreover, I accept Kurt Gödel's Ontological Argument as well as Leibniz's Law, which effectively rules out polytheism as a viable option.

Well hey, we do science because we refuse to accept the word of those who say that some things just can't be discovered.

They do ID because they refuse to accept the word of those who say that there is no bottom to dumb. If anyone can find it, the IDists can.

So there's a kind of balance between us after all. Trouble is, dumb really doesn't know the difference between science and plumbing the depths of ignorance and stupidity.

Glen D
http://tinyurl.com/2kxyc7

ravilyn sanders:

Robert O'Brien: If an "intelligent designer" can be inferred, then I equate the designer with God. Moreover, I accept Kurt Gödel's Ontological Argument as well as Leibniz's Law, which effectively rules out polytheism as a viable option.

Robert O'Brien, I really don't think you follow either the onotological [sic] argument or the Leibnitz's [sic] law. You read somewhere that these two arguments prove that polytheism is not a viable option. And you, warning pun ahead, faithfully quote them from your quote/link bank. Let me see if you can show using these two references, a. There is less then ONE invisible pink unicorns in the universe. b. There is more than ONE chimpanzee in the jungles. These philosophical treatises proving this part of this religion or that essence of that cult are all essentially stretchable socks. They can be stretched to prove/disprove anything you want. All it requires is credulity, aka faith.

It really was refreshing to see Robert O'Brien respond to Nigel D.'s request for "substantive, scientific criticisms" with, well, substantive, scientific criticisms.

As I understand it, however, his three points were:

1.) "There are important biomedical (as well as obvious morphological and cognitive) differences between the two species, which thus far have eluded any molecular explanation within this supposedly 1% diversity range."

To which Richard Simons responded:

"Chimpanzee DNA was sequenced what, two years ago? It seems to me it’s a bit premature to complain that the biochemical differences are not yet fully explained."

2.) [Chimpanzees and humans have] "differential handling of a number of infectious agents, e.g., HIV (progression to AIDS), late complications of hepatitis B and C, as well as susceptibility to Plasmodium falciparum, which are of utmost public health importance."

As I pointed out above, Abbie Smith has offered conclusive evidence that HIV has mutated from SIV (simian IV.) Thus, differences in reactions to infections will, at least in some cases, indicate mutations in the infectious agents, rather than intrinsic differences between apes and humans.

3.) The paper PNAS 7708-7713 gave a lower-than expected correlation between chimpanzee and human genomes.

Wesley R. Elsberry offered a refutation, which O'Brien has apparently accepted.

As I said at the beginning, it was a pleasant surprise to have someone from the ID camp offer a true, scientific argument. Unfortunately, the hallmark of true science is that it can be refuted. As far as I can see, all of O'Brien's arguments either have been refuted, or are currently active areas of research, but with plausible hypotheses well within the limits of modern evolutionary theory.

Robert O'Brien: If you cannot apprehend Gödel's Ontological Argument or Leibniz's Law then just say so.

Re "Prove that there is more than one chimpanzee in the jungle."

That's documented in pretty much any Tarzan movie.

Q.E.D.

Henry

Henry J: Re "Prove that there is more than one chimpanzee in the jungle." That's documented in pretty much any Tarzan movie. Q.E.D. Henry

Variation is the fuel, selection is the engine, and the environment is the steering wheel.

it may perhaps be better to translate the basic ideas into something simpler

The chimpanzee is believed to share [approximately] 98.77% nucleotide and >99% amino acid identity with us. However, there are important biomedical (as well as obvious morphological and cognitive) differences between the two species, which thus far have eluded any molecular explanation within this supposedly 1% diversity range. Among these are our differential handling of a number of infectious agents, e.g., HIV (progression to AIDS), late complications of hepatitis B and C, as well as susceptibility to Plasmodium falciparum, which are of utmost public health importance” (PNAS 7708-7713).

— Robert O'Brien

The authors of PNAS 7708-7713 also calculate the genetic commonality between chimps and humans as 86.7% (accounting for insertions and deletions).

A further point I would like to make is that genetic commonality does not rule out a “common designer.” (Other evidence may militate against that conclusion, but not genetic commonality in and of itself.)

The relative after selection

If an “intelligent designer” can be inferred, then I equate the designer with God.

— Bobert O'Brien

Moreover, I accept Kurt Gödel’s Ontological Argument as well as Leibniz’s Law, which effectively rules out polytheism as a viable option.

Eight, so you accept Id as a religious proposition, not a scientific one.

— Nigel D

That is an important update. However, the statements I cited concerning the pronounced differences between human and ape immunobiology still hold.

— Robert O'Brien

Nigel D: ...[S]o you accept ID as a religious proposition, not a scientific one.

Nigel D:

Moreover, I accept Kurt Gödel’s Ontological Argument as well as Leibniz’s Law, which effectively rules out polytheism as a viable option.

So you support your argument by reference to philosophy only, not to any actual real-world evidence. In fact, even a casual glance at the two links you supplied for these arguments has enabled me to pick holes in your logic.

Nigel D: First, I disagree with some of the definitions and axioms proposed to support Gödel's ontological argument.

Nigel D:The argument itself can only succeed if one accepts all of the definitions and axioms upon which it is based.

Nigel D: For a start, any God that proposes some of the so-called justice that is in the Old Testament is far from a positive thing. Therefore, if one accepts the Biblical God as being God-like, the entire ontological argument is blown out of the water. The Biblical God demonstrably has negative properties (e.g. killing every firstborn son, no matter how guilty or innocent; that does not sound very just to me).

Nigel D: Second, Leibniz's Law applies only to real objects and real entities, and anything that obeys natural laws. To any entities that are omnipotent, it need not apply. So your argument against polytheism is almost as weak as your arguments against evolutionary theory.

Nigel D:

That is an important update. However, the statements I cited concerning the pronounced differences between human and ape immunobiology still hold.

— Robert O'Brien

Maybe so, but certainly not as an answer to my question "[W]hat substantive, scientific criticisms do you have of the theory of common descent?", which is the context in which you first quoted from that paper. Thus, I ask again, Robert: what substantive, scientific criticisms do you have of the theory of common descent?

First, I disagree with some of the definitions and axioms proposed to support Gödel’s ontological argument.

First, I disagree with some of the definitions and axioms proposed to support Gödel’s ontological argument.

— Nigel D

That is your only avenue of attack.

It seems rather pointless to post the same rebuttal to Robert O'Brien for the third time--

But, Robert, the whole point of Abbie Smith's challenge Michael Behe was that HIV, an infectious agent, has mutated from S(imian)IV. Differences in immunology don't necessarily imply substantial differences between apes and people. They are at least as likely to be the result of mutations in the infectious agents as in the mammals.

The psychologist? Is he your answer to DI’s Medved?

that's like saying science needs an "answer" to any remaining flat earthers out there.

you keep seeming to imply that the larger body of scientists gives a flying f*ck what anybody in the DI has to say to begin with.

if that's what you think, you're more deranged than anyone has previously considered.

...and that's saying a lot.

I'll go along with Ichthyic. Not only do the majority of scientists neither know nor care what the DI has to say, they think it is a complete waste of time to bother with creationists and IDers.

ID is certainly not empirical science.

ID is certainly not empirical science.

(O_o)

or is it

:o

or should it be like a yawn?

wait, how does one express a yawn in ASCII?

hoary puccoon: It seems rather pointless to post the same rebuttal to Robert O'Brien for the third time-- But, Robert, the whole point of Abbie Smith's challenge Michael Behe was that HIV, an infectious agent, has mutated from S(imian)IV. Differences in immunology don't necessarily imply substantial differences between apes and people. They are at least as likely to be the result of mutations in the infectious agents as in the mammals.

Richard Simons: I'll go along with Ichthyic. Not only do the majority of scientists neither know nor care what the DI has to say, they think it is a complete waste of time to bother with creationists and IDers.

And yet, a great deal of time and energy is spent by the people here opposing it. I guess they are aberrant.

crunch the numbers sometime for this site and UD.

tell me just how much interest they really generate, then answer your own question, dumbass.

btw, aberrant is best applied when speaking of yourself, there, RO. I know it's tough when your whole life is nothing but projection after projection, but here's a clue:

how many people do you think are interested in what YOU have to say, given the number of comments on your own site?

as far as your idiotic argumentation re: common descent is concerned, i suppose you also think that the fact that chimps have more body hair than humans is also indicative of a lack of common descent?

idiot.

why is it that you bother to even post again, since nobody responds to you on your own blog, and the only responses you get here merely point out what an ignoramus you appear to be based on what you post?

is this some weird form of xian self-flagellation on your part?

oh wait, now I get it, RO is trying to show us that there really IS a bottom to dumb.

Who said anything about the Old Testament conception of God?

— Robert O'Brien

Leibniz’s Law applies just as well to the God-like being in Gödel’s argument.

As far as I am concerned, the differences in immunobiology between apes and humans is a mark against the common descent hypothesis (specific to the alleged common ancestry of apes and humans). It may not be fatal to common descent, but it certainly does not help your case (quite the opposite, in fact).

— Robert O'Brien

Differences in immunology don’t necessarily imply substantial differences between apes and people. They are at least as likely to be the result of mutations in the infectious agents as in the mammals.

The whole point of Abbie Smith's and Ian Musgrave's challenging of Behe was that HIV is substantially different from SIV.

Presumably, at some point a human was infected with SIV.(This is not surprising. The polio virus, for instance, infects both chimps and people, with the same effect.) We don't know at all that the person who was first infected got AIDS. But he or she passed on the infectious agent. At some later point, the virus mutated into a more toxic form. So, now, being infected by HIV eventually results in AIDS. Being infected by SIV doesn't. Could a human be infected with SIV, and never get AIDS? I don't know. The fact is, very few people come into enough contact with apes to exchange blood. So each virus is spread almost exclusively within species.

There may be minor differences between chimps and people in their vulnerability to HIV or SIV. But the very fact that the infection jumped from apes to people shows the similarly of their cell chemistry. SIV and HIV, on the other hand, now have substantial differences, as Abbie Smith demonstrated. Given the choice of these two hypotheses:

1. Humans get AIDS and apes don't because the immunodeficiency virus found in humans leads to AIDS and the one found in simians doesn't. Or--

2. Humans get AIDS and apes don't because humans are a different special creation from apes;

I know which hypothesis I'd choose.

Of course, the fact that minor genetic differences can have substantial effects on vulnerability to the toxin is also true. I read somewhere that some gay men with one particular allele didn't seem to get infected with HIV, although they engaged in risky sex. Does that make them ANOTHER special creation, or what?

Humans get AIDS and apes don’t because the immunodeficiency virus found in humans leads to AIDS and the one found in simians doesn’t.

If an “intelligent designer” can be inferred, then I equate the designer with God.

Moreover, I accept Kurt Gödel’s Ontological Argument

On Gödel's theoretical assumptions, we can show that any set which conforms to (1) - (6) is such that the property of having as essential properties just those properties which are in that set is exemplified. Gödel wants us to conclude that there is just one intuitive, theologically interesting set of properties which is such that the property of having as essential properties just the properties in that set is exemplified. But, on the one hand, what reason do we have to think that there is any theologically interesting set of properties which conforms to the Gödelian specification? And, on the other hand, what reason do we have to deny that, if there is one set of theologically interesting set of properties which conforms to the Gödelian specification, then there are many theologically threatening sets of properties which also conform to that specification? In particular, there is some reason to think that the Gödelian ontological argument goes through just as well — or just as badly — with respect to other sets of properties (and in ways which are damaging to the original argument). Suppose that there is some set of independent properties {I, G1, G2, …} which can be used to generate the set of positive properties by closure under entailment and "necessitation". ("Independence" means: no one of the properties in the set is entailed by all the rest. "Necessitation" means: if P is in the set, then so is necessarily having P. I is the property of having as essential properties just those properties which are in the set. G1, G2, … are further properties, of which we require at least two.) Consider any proper subset of the set {G1, G2, …} — {H1, H2, …}, say — and define a new generating set {I*, H1, H2, …}, which I* is the property of having as essential properties just those properties which are in the newly generated set. A "proof" parallel to that offered by Gödel "establishes" that there is a being which has as essential properties just those properties in this new set. If there are as few as 7 independent properties in the original generating set, then we shall be able to establish the existence of 720 distinct"God-like" creatures by the kind of argument which Gödel offers. (The creatures are distinct because each has a different set of essential properties.) Even if the above considerations are sufficient to cast doubt on the credentials of Gödel's "proof", they do not pinpoint where the "proof" goes wrong. If we accept that the role of Axioms 1, 2, 4, and 6 is really just to constrain the notion of "positive property" in the right way — or, in other words, if we suppose that Axioms 1, 2, 4, and 6 are "analytic truths" about "positive properties" — then there is good reason for opponents of the "proof" to be sceptical about Axioms 3 and 5. Kant would not have been happy with Axiom 5; and there is at least some reason to think that whether the property of being God-like is "positive" ought to depend upon whether or not there is a God-like being.

as well as Leibniz’s Law, which effectively rules out polytheism as a viable option.

I understand that HIV and SIV are different. But if chips cannot contract HIV and AIDS, then they’ve got a significant genetic difference from humans in at least this respect, right? Which is O’Brien’s point. And if both species DO contract AIDS from the same agent, what’s the issue here anyway?

the differences in immunobiology between apes and humans is a mark against the common descent hypothesis (specific to the alleged common ancestry of apes and humans)

Human T cells respond much more robustly than chimpanzee cells do, a disparity that could be explained by the absence of human T cell Siglecs. The explanation for this human-specific evolutionary loss of Siglecs is currently unknown. The UCSD scientists speculate that this may have been due to a selective pressure by a microbe that once drove human ancestors to require a high level of T cell activation. Another possibility is that this phenotype was secondarily acquired, during the adjustment to the human-specific loss of the sialic acid Neu5Gc some three million years ago, and that the phenotype has been carried by all humans ever since. The study raises warning flags about the stimulatory and potentially destructive potential of the absence of Siglec molecules in human T cells, compared to chimpanzees and other nonhuman primate counterparts. This may explain some major differences in susceptibility to certain diseases between humans and great apes. One example is the lack of progression to AIDS in the great majority of chimpanzees infected with HIV virus. It could also account for the rarity of T-cell mediated liver damage, such as chronic active hepatitis, cirrhosis and cancer, following Hepatitis B or C infection in chimpanzees. In addition, several other common human T cell-mediated diseases, including bronchial asthma, rheumatoid arthritis and type 1 diabetes, have, so far, not been reported in chimpanzees or other great apes.

“The good news is that the loss of this brake system is not permanent, as we still have the Siglec genes in our genomes, and do continue to express them in other blood cell types,”

“The chimpanzee is believed to share [approximately] 98.77% nucleotide and >99% amino acid identity with us. However, there are important biomedical (as well as obvious morphological and cognitive) differences between the two species, which thus far have eluded any molecular explanation within this supposedly 1% diversity range. Among these are our differential handling of a number of infectious agents, e.g., HIV (progression to AIDS), late complications of hepatitis B and C, as well as susceptibility to Plasmodium falciparum, which are of utmost public health importance” (PNAS 7708-7713).

Referring to “important biomedical” differences between chimpanzees and humans, Robert O’Brien mentions “HIV (progression to AIDS).” Robert, did you not follow the Open Letters thread by Ian Musgrave regarding Abbie Smith’s challenge to Michael Behe? The whole issue was that Smith presented proof that HIV has mutated from SIV. (Simian IV.) There is no particular reason to think a priori that apes and people are very different in their susceptability to AIDS, since humans are being infected by a different virus.

OK, I think I follow this now. Humans were capable of being hosts to SIV. SIV subsequently mutated to HIV in humans. Chimps are also perfectly capable of contracting HIV. (Which implies that the Simian and Human prefixes apply to where the form originated, rather than which species is susceptible.) So we're talking about two different viruses here. AND, the HIV form develops to AIDS in humans, but not in chimps, due to immunological differences between the species. So with respect to AIDS, both the virus, and the hosts, have mutated significantly from their prior forms. All of which points strongly to common descent.

Humans were capable of being hosts to SIV. SIV subsequently mutated to HIV in humans. Chimps are also perfectly capable of contracting HIV. (Which implies that the Simian and Human prefixes apply to where the form originated, rather than which species is susceptible.)

All of which points strongly to common descent.

All of which points strongly to common descent.

As I understand it, SIV doesn’t infect humans, and HIV-1 doesn’t infect chimps (but HIV-2 does).

Flint-- I hope you won't be too affected by Popper's Ghost's extreme hostility to me. I have no idea what it's based on.

Another way I could have made the same point would have been to mention avian flu, which occasionally jumps from birds to people. In that case, it's obvious that the host organisms are very different, so the ability to crossover must be due to mutations in the infectious agent. So Robert O'Brien's point isn't valid because: first, a large difference in susceptability doesn't necessarily mean a large genetic difference between the host animals. Second, a large difference in susceptability may be due to a different, more virulent strain of the infectious agent in one of the host animals. In neither case would the hypothesis of common descent be threatened, of course.

Flint– I hope you won’t be too affected by Popper’s Ghost’s extreme hostility to me. I have no idea what it’s based on.

So Robert O’Brien’s point isn’t valid because: first, a large difference in susceptability doesn’t necessarily mean a large genetic difference between the host animals

Second, a large difference in susceptability may be due to a different, more virulent strain of the infectious agent in one of the host animals.

Popper's Ghost:

Moreover, I accept Kurt Gödel’s Ontological Argument

I would simply point out that axiom 5 is erroneous -- as Russell pointed out, existence is not a property (it would be an odd sort of property that everything has and nothing lacks), and thus neither is necessary existence.

Popper's Ghost: (When we say in mathematics that a solution to some problem necessarily exists, what we mean is that the set of solutions is necessarily non-empty; it's a statement about the solution set, not about the solution, which we haven't even identified. All claims about existence can be reformulated as statements about set inclusion -- e.g., the set of unicorns is empty).

Popper's Ghost:

as well as Leibniz’s Law, which effectively rules out polytheism as a viable option.

Since polytheism posits the existence of gods with different attributes, it isn't incompatible with Leibniz's Law (which itself isn't necessarily true, as O'B's own reference notes). And if the claim is that Gödel's argument establishes all the properties of god and thus all gods must be identical (but that claim is false: "If there are as few as 7 independent properties in the original generating set, then we shall be able to establish the existence of 720 distinct 'God-like' creatures by the kind of argument which Gödel offers. (The creatures are distinct because each has a different set of essential properties.)"), it must be noted that "intelligent designer" is not a property attributed to god by Gödel's argument.

I hope you won’t be too affected by Popper’s Ghost’s extreme hostility to me. I have no idea what it’s based on.

So Robert O’Brien’s point isn’t valid because: first, a large difference in susceptability doesn’t necessarily mean a large genetic difference between the host animals.

Second, a large difference in susceptability may be due to a different, more virulent strain of the infectious agent in one of the host animals.

Popper's Ghost: As for O'B's larger "point":

the differences in immunobiology between apes and humans is a mark against the common descent hypothesis (specific to the alleged common ancestry of apes and humans)

it is of course nonsense. It's like saying that the differences between the pre-Aguillard and post-Aguillard versions of "Of Pandas and People" are a mark against the hypothesis that one was derived from the other. Close examination of the nature of the differences, in context, show that that is the furthest thing from the truth.

Argument by analogy is known as the weakest form of argumentation for good reason. There is no analogy between an inanimate, lifeless book that was changed by the direct intervention of intelligent agents and the evolution of two mammals that allegedly share a common ancestor.

leave it to RO to entirely MISS the point of the analogy, which was an analysis of RO's level of logic by metaphor, and was entirely apt.

yuppers, keep on showin' us the bottom 'o that barrel there, RO.

you always provide us with edifyin' posts, even if they don't communicate what you intend (er, not that anybody can ever figure what you intend from what you write anyway).

Argument by analogy is known as the weakest form of argumentation for good reason.

There is no analogy between an inanimate, lifeless book that was changed by the direct intervention of intelligent agents and the evolution of two mammals that allegedly share a common ancestor.

leave it to RO to entirely MISS the point of the analogy, which was an analysis of RO’s level of logic by metaphor, and was entirely apt.

As far as I can see, this is the posture he adopts as a matter of policy and persona. He often makes valid points, but makes a fetish out of belligerant intolerance while doing so.

In this case, fighting past the usual pile of gratuituous insults

Popper's Ghost: You once again prove yourself to be a foul hypocritical asshole.