Signature in the Cell: self-contradiction and repetition

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Of late the IDists have been complaining about the dearth of reviews by ID skeptics of Stephen Meyer’s book Signature in the Cell. I agree, it would be nice if there were more reviews out there, but (a) the arguments boil down to the same old fallacious “improbability of assembly of functional sequence all at once from scratch by brute chance” creationist argument that dates back to at least the 1960s creation science literature, and (b) the book is tedious and repetitive, basically making the same unsupported assertions again and again in slightly different ways. I.e. information comes from intelligence and is too improbable to explain by chance, therefore intelligence! The actual known origin of the vast majority of genetic “information” – DNA duplication followed by mutation and selection is (1) almost completely ignored by Meyer and (2) directly refutes Meyer’s key claim, which is that the only known explanation of new information is intelligence. So in one sense, there is not a heck of a lot to review in Meyer’s book. If you are a sufficient wonk about the ID debate, there is some interesting stuff about Meyer’s highly revisionist account of his own history and the history of the ID movement, and there is an interesting study to be made of the science that Meyer left out of his book, but that makes for a big project, so it will be awhile before I or someone else get it out there.

But, while reading across the book, you do occasionally come across some examples of truly bizarre argumentation. Here an example which I just posted in response to a Telic Thoughts challenge:

There are many problems with the argument in Signature in the Cell, here is one. Meyer says that “information” – sequence-specific function – is densely concentrated in the DNA genome:

“Thus, far from being dispersed sparsely, haphazardly, and inefficiently within a sea of nonfunctional sequences (one that supposedly accumulated by mutation), functional genetic information is densely concentrated on the DNA molecule.” (p. 461)

“Far from containing a preponderance of “junk” – nonprotein-coding regions that supposedly perform no function – the genome is dominated by sequences rich in functional information.” (p. 461)

Furthermore, says Meyer, not only is this established truth, but it is a prediction of ID theory, and furthermore it was predicted by ID advocates a decade or more ago:

“The genome does display evidence of past viral insertions, deletions, transpositions, and the like, much as digital software copied again and again acumulates errors. Nevertheless, the vast majority of base sequences in the genome, and even the many sequences that do not code for proteins, serve essential biological functions. Genetic signal dwarfs noise, just as design advocates would expect and just as they predicted in the early 1990s.” (p. 461)

However, at numerous places in the book, Meyer notes (correctly) that repetitive sequences have little information:

“Since information and improbability are inversely related, high-probability repeating sequences like ABCABCABCABCABCABC have very little information (either carrying capacity or content). And this makes sense too. Once you have seen the first triad of ABCs, the rest are “redundant”; they convey nothing new. They aren’t informative. Such sequences aren’t complex either. Why? A short algorithm or set of commands could easily generate a long sequence of repeating ABCs, making the sequence compressible.” (p. 107)

Unfortunately for Meyer, he seems to not realize that 40-50% of the human genome (and most animal genomes of similar size) consists of LINEs, SINEs, segmental duplications, and other repeating elements. As documented here: http://www.ncbi.nlm.nih.gov/bookshe[…]mp;part=A642

In other words, there is no way that in “the vast majority” of the genome genetic information is “densely concentrated” – as proven by his own arguments!

QED.

85 Comments

That chart may be a little out of date. Quoth wikipedia:

Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA. In maize, 49-78% of the genome is made up of retrotransposons[1]. In wheat, about 90% of the genome consists of repeated sequences and 68% of transposable elements[2]. In mammals, almost half the genome (45% to 48%) comprises transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons while DNA transposons account for about 2-3%[3].

[…]

1. SanMiguel P, Bennetzen JL (1998). “Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotranposons”. Annals of Botany 82 (Suppl A): 37–44. http://aob.oxfordjournals.org/cgi/r[…]ppl_1/37.pdf.

2. Li W, Zhang P, Fellers JP, Friebe B, Gill BS (November 2004). “Sequence composition, organization, and evolution of the core Triticeae genome”. Plant J. 40 (4): 500–11. doi:10.1111/j.1365-313X.2004.02228.x. PMID 15500466. http://www.blackwell-synergy.com/do[…]2004.02228.x.

3. Lander ES, Linton LM, Birren B, et al. (February 2001). “Initial sequencing and analysis of the human genome”. Nature 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011. http://www.nature.com/nature/journa[…]09860a0.html.

Thanks for that.

So the book is much like the genome, filled with mistakes and repetitive junk.

Trouble is, Meyer is intelligent enough to have made something better. Evolution has the excuse that it lacks rationality and intelligence, hence can only produce something like the genome.

One thing that I think is too missing in these discussions is that the differences between the genome and software–which are in fact considerable–generally are what make the former evolvable.

If he dared to consider that, he’d have to admit that life fits the predictions of evolution, not any entailed design criteria. Which is why he doesn’t.

Glen Davidson

http://tinyurl.com/mxaa3p

Nick and Glen,

What I found rather odd in Meyer’s presentation is his false dichotomy between “experimental” and “historical” sciences, claiming that biology belongs to the latter. Of course he delves into extensive quote mining, citing none other than Stephen Jay Gould to make his case. Of course if this was really true, it wouldn’t account for some of the landmark experiments in evolutionary biology (e. g. Lenski’s and Endler’s) recounted in recent books from Carl Zimmer and Richard Dawkins.

Nick wrote in the post:

the book is tedious and repetitive, basically making the same unsupported assertions again and again in slightly different ways. I.e. information comes from intelligence and is too improbable to explain by chance, therefore intelligence!

(I should hasten to say that I have not more than skimmed the book). Is Meyer relying for this on William Dembski’s Law of Conservation of Complex Specified Information? He should be aware that the LCCSI has been shown by Jeffrey Shallit (in Elsberry and Shallit, p. 27) to be unproven. I have also argued that the LCCSI cannot be proven to apply if we use the same specification (say asking whether the genotype has achieved some high level of fitness) before and after the evolutionary process acts. And to use the LCCSI to show that evolution is ineffective at putting information into the genome, you do have to keep the specification before and after the same). If Meyer is relying on Dembski’s argument, he has built a castle on sand.

Joe I believe he is and he is ignoring all criticisms of Dembski’s work, with the notable exception of an Elsberry and Wilkins paper in Biology and Philosophy, criticism from Pennock, Scott and Branch, claiming that Dembski’s Design Inference does not depend on an “Argument from Ignorance”. After just perusing the bibliography now, one not acquainted with the activities of the Discovery Institute might conclude that there are a few dissenters like Ken Miller, Robert Pennock, Genie Scott and Glenn Branch who enjoy taking potshots at Meyer, his colleagues and their work. This remarkable sense of denial of any meaningful criticism is almost as bad as Behe’s in “The Edge of Evolution”:

Joe Felsenstein said:

Nick wrote in the post:

the book is tedious and repetitive, basically making the same unsupported assertions again and again in slightly different ways. I.e. information comes from intelligence and is too improbable to explain by chance, therefore intelligence!

(I should hasten to say that I have not more than skimmed the book). Is Meyer relying for this on William Dembski’s Law of Conservation of Complex Specified Information? He should be aware that the LCCSI has been shown by Jeffrey Shallit (in Elsberry and Shallit, p. 27) to be unproven. I have also argued that the LCCSI cannot be proven to apply if we use the same specification (say asking whether the genotype has achieved some high level of fitness) before and after the evolutionary process acts. And to use the LCCSI to show that evolution is ineffective at putting information into the genome, you do have to keep the specification before and after the same). If Meyer is relying on Dembski’s argument, he has built a castle on sand.

I might also add that Shallitt’s critiques have been ignored by Meyer in this book (nor is Shallitt referred to at all, even in the book’s extensive footnotes).

Nick Matzke Wrote:

Of late the IDists have been complaining about the dearth of reviews by ID skeptics of Stephen Meyer’s book Signature in the Cell. I agree, it would be nice if there were more reviews out there, but (a) the arguments boil down to the same old fallacious “improbability of assembly of functional sequence all at once from scratch by brute chance” creationist argument that dates back to at least the 1960s creation science literature, and (b) the book is tedious and repetitive, basically making the same unsupported assertions again and again in slightly different ways. …

Looking back over the origins of the misconceptions and misrepresentations from creation “science” that have simply been taken over by ID, I have noticed that the central misconception that keeps popping up is the notion that all atomic and molecular structures come together from a uniform random sampling of atoms and molecules from essentially infinite sample spaces.

Duane Gish was already bludgeoning biology teachers with this misconception back in the late 1960s and 1970s in Kalamazoo, Michigan. After the Institute for Creation “Research” was formed, as I recall, both Gish and Henry Morris were conflating entropy with disorder. Somewhere in that time period they started using the tornado-in-a- junkyard shtick.

I was aware at that time of some of the misconceptions about entropy and the second law of thermodynamics floating around in physics, but chemist Frank L. Lambert appears to have been fighting the battle of these misconceptions in chemistry textbooks for quite some time now; perhaps even longer.

If I understand his historical cataloguing of these misconceptions, I wonder if Gish got his own miseducation from such a textbook, and that reinforced some unfortunate statements about entropy by well-known physicists.

At any rate, the misconceptions were under some control within the physics community as careful instructors made clear distinctions about what was being enumerated in counting available energy microstates.

However, after the political campaign of the creationists got going in earnest, those erroneous memes spread like wildfire; and even scientists who debated creationists fell for them.

Now these misconceptions are standard fare in all ID/creationist literature; and invariably they lead to the erroneous conclusions we see in all the work of Meyer, Dembski, Behe, Abel, and others. They are so predictable that I have often been able to “psych out” the path of their writings before I actually pick up one of their papers or books and slog through it.

And they never correct themselves or retract anything, even after something like 40 years of attempted corrections by the scientific community. It’s getting harder and harder to believe ID/creationists like Meyer don’t know they are screwing up fundamental scientific concepts.

But then, they are pretty wrapped up in themselves.

Yeah, Meyer explicitly relies on Dembski’s specified complexity argument – to the point that, when he tells the history, Meyer sort of says that he co-invented it back in the early 1990s.

However, Dembski really makes 2 different arguments based on 2 different definitions:

1. Definition: Specified complexity is defined as complex (aperiodic) sequence that codes for meaning or function (which defines what is “specified”, according to them). Argument: such sequences are wildly improbable (so improbable as to be impossible, 10^-150) to have arisen through chance or other natural processes (which boil down to chance, according to ID advocates).

2. Definition: Specified complexity is *defined* as a sequence that has a probability of 10^-150 or less under all natural processes. Argument: The existence of these sequences proves evolution doesn’t work. This argument is typically concealed in vast reams of mostly pointless calculation.

Traditionally, Dembski would put forward #1, which is basically the “popular”, but when challenged with counterexamples of e.g. evidence that new genes had originated through natural processes, he or his defenders would switch to #2, and assert that, sure, maybe natural processes produced those genes, but all that means is that those don’t qualify as examples of specified complexity, and thus aren’t actually counterexamples. #2 is obviously just a pointless tautology.

(A similar game is often played with irreducible complexity – sometimes explicitly, as when Dembski invokes IC to head off the possibility that gradual selection-based processes could explain SC. Of course, this sort of manuever makes his entire argument a pointless gloss on IC.)

Anyway, back to Meyer: Meyer pretty much relies on the #1 version of specified complexity, equates it to information, and doesn’t get much into the details. I think the Universal Probability Bound is mentioned, but FWIW many of Meyer’s citations are to e.g. Axe’s papers which (allegedly; they actually don’t) show improbabilities on the order of 10^-77 or so which is far from 10^-150.

And yeah Meyer ignores all of the detailed criticism of Dembski which has been published in many places…

The whole line of argumentation that ID predicted function for non-coding DNA in the early 1990s while “Darwinists” stubbornly assumed non-function is completely false historically. The standard assumption based on strict Darwinian principles in the 1970s and at least the early 1980s was that if non-coding sequences did not have a function, natural selection would have gotten rid of them. The selfish DNA hypothesis arose in the early 1980s as a response to the widespread assumptions of function, but even it did not deny the likely cooption of some transposable elements, especially in regulation. Meanwhile, discussions of satellite DNA and other sequences were largely about trying to determine their function, even after the selfish DNA papers. By 1994, there were stories in major journals stating that non-coding DNA was “long thought to have been non-functional but is now turning out to have important roles”. I have done my best to document the actual status of non-coding DNA in the literature since the 1970s here. The dismissal of “junk DNA” never happened in any significant way (and even if it did it could only have been between about 1983-1994), and the reason is that adaptationist assumptions led people to expect functions for any DNA that is so abundant.

(And yes, the fig is way out of date – it was drawn 10 years ago).

Am quoting the following text from my Amazon.com review of “Signature”, which, I believe, demonstrates the poor logic used by Meyer in asserting that Intelligent Design does produce “testable” scientific hypotheses:

So should we accept Meyer’s proposition that Intelligent Design is a valid scientific theory simply because it produces testable hypotheses? What hypotheses? For example, he asserts on Page 489, “Design hypotheses envisioning discrete intelligent action also predict a pattern of fossil evidence showing large discontinuous or ‘quantum’ increases in biological form and information at intervals in the history of life. Advocates of this kind of design hypothesis would expect to see a pattern of sudden appearance of sudden appearance of major forms of life as well as morphological stasis.” Moreover, he claims “…they would also predict a ‘top-down’ pattern of appearance in which large-scale differences in form (‘disparity’ between many separate body plans) emerge suddenly and prior to the occurrence of lower-level (i.e., species and genus) differences in form. Neo-Darwinism and front-loaded hypotheses expect the opposite pattern, a ‘bottom-up’ pattern in which small differences in form accumulate first (differentiating species and genera from each other) and then only much later building to the large-scale differences in form that differentiate higher taxonomic categories such as phyla and classes.”

Granted, life would be a lot simpler for paleontologists and paleobiologists if they heeded Meyer’s most generous advice. We wouldn’t have to worry about long-term persistence of ecological communities replete with morphological stasis of their constituent taxa over considerable spans of geological time or those unfortunate “accidents” known as mass extinctions which have “reshuffled the deck” that is Earth’s biodiversity not just once, but at least seven times over the past five hundred fifty-odd million years. After each of these “accidents” we do see eventual recovery of the Earth’s biosphere via the “bottom-up” pattern that Meyer so clearly disdains. What we don’t see however, is any indication of some Intelligent Designer(s) acting to ensure some kind of restoration of our planet’s biodiversity. All the patterns seen in the fossil record are due to natural laws and processes acting on populations of organisms, not through the direct intervention of Intelligent Designer(s) like Mother Goose, Yahweh or the Klingons.

Meyer also claims that examples of “poor design” in nature merely illustrate that “perfect” designs can “degenerate”. So, hypothetically, I am certain he would assert that the panda’s thumb is the direct consequence of some kind degeneration of an initial “perfect” design.

“I am certain he would assert that the panda’s thumb is the direct consequence of some kind (sic) degeneration of an initial “perfect” design.”

John, he might assert that, but first he’d want you to listen to this podcast about the panda’s thumb (not this website :-) ): http://intelligentdesign.podomatic.[…]_35_14-07_00

Probably after I watch the annual New Year’s Day concert performed each year in Vienna by the Vienna Philharmonic Orchestra. I’d rather listen to superb playing of Strauss waltzes and similar scores than hearing Meyer lying through his teeth, which he seems to do all the time, whether it is in print, in a documentary video (e. g. the newly released “Darwin’s Dilemma) or in an evolution vs. creationism “debate”. Until then, I wish you a most happy new year:

Miranda said:

“I am certain he would assert that the panda’s thumb is the direct consequence of some kind (sic) degeneration of an initial “perfect” design.”

John, he might assert that, but first he’d want you to listen to this podcast about the panda’s thumb (not this website :-) ): http://intelligentdesign.podomatic.[…]_35_14-07_00

Glen Davidson said: So the book is much like the genome, filled with mistakes and repetitive junk.

No, unlike Signature In the Cell, genomes actually have a purpose.

Even if most of the DNA in the human genome has a function, it doesn’t explain why the human genome has 3 billion base pairs, but that the lowly Amoeba dubia has 670 billion base pairs (220 times as many). Listened to Nelson’s podcast, Miranda, I take it you have a bad hangover from last night, and you are trying to spread your misery.

Because the subtitle of the book is “DNA and the evidence for intelligent design”, I skimmed through the book looking for evidence for intelligent design - or just a description of intelligent design, something that one could imagine evidence for.

TR Gregory said:

The whole line of argumentation that ID predicted function for non-coding DNA in the early 1990s while “Darwinists” stubbornly assumed non-function is completely false historically. The standard assumption based on strict Darwinian principles in the 1970s and at least the early 1980s was that if non-coding sequences did not have a function.

The dismissal of “junk DNA” never happened in any significant way (and even if it did it could only have been between about 1983-1994), and the reason is that adaptationist assumptions led people to expect functions for any DNA that is so abundant.

Thanks, that site of yours has a great collection of quotes from the literature.

Two major groups rejecting the notion of junk DNA were (1) panselectionists among evolutionary biologists (as you have noted), and (2) molecular biologists, many of whom have tended to see the genome as one big machine, with all that extra DNA just waiting to have its function discovered if only more and more grant money could be obtained. In fact population geneticists very early on were worried that there would be too much mutational load if all that extra DNA had function and thus its sequence had to be conserved.

You know the literature – am I summarizing incorrectly?

But there may be even one more way on which ID advocates are fudging the historical record. Where are their scientific predictions that there is no junk DNA? They do frequently assert that there is none, but where in “ID theory” does that “prediction” come from? As far as I can see it comes from theological arguments about what an omniscient deity would do. I cannot see anything in the negative scientific arguments of Dembski and of Behe that speaks to the issue.

Joe wrote:

“But there may be even one more way on which ID advocates are fudging the historical record. Where are their scientific predictions that there is no junk DNA? They do frequently assert that there is none, but where in “ID theory” does that “prediction” come from? As far as I can see it comes from theological arguments about what an omniscient deity would do. I cannot see anything in the negative scientific arguments of Dembski and of Behe that speaks to the issue.”

Precisely. As soon as creationists start making statements about the identity, motives or abilities of the creator, they automatically open themselves up to falsification. This is an especially pernicious problem because they often have no idea of the evidence that is already available. Why they can’t be bothered to do a little research is beyond me (almost).

If they claim that there is no “junk DNA”, then the claim is falsified by present knowledge and the burden of proof is on them to demonstrate a function for every base pair. Without a laboratory, that could be difficult. Of course, even if they can demonstrate this, they would then have to demonstrate the function every vestigial organ as well, since their claim apparently rest on the premise that the creator would not create useless things for no reason.

And of course even this wouldn’t really help the creationist cause, because they would still have to explain all of the other genetic, developmental and morphological patterns that are consistent with common descent and inconsistent with any creation scenario.

Man, no wonder they just throw up their hands, claim they have no idea who the creator is and refuse to make any testable predictions. Every time they do, they get slammed.

Joe Felsenstein said:

But there may be even one more way on which ID advocates are fudging the historical record. Where are their scientific predictions that there is no junk DNA? They do frequently assert that there is none, but where in “ID theory” does that “prediction” come from? As far as I can see it comes from theological arguments about what an omniscient deity would do. I cannot see anything in the negative scientific arguments of Dembski and of Behe that speaks to the issue.

Absolutely right. Maybe they made this “prediction” (read: the same assumption as adaptationists) in their own literature, but I haven’t been able to get a clear explanation from current proponents of why they should expect this. Human design generally includes some imperfections, redundancies, superfluous components, etc., so why should design per se imply no junk DNA? It must be a theological claim, rarely stated explicitly.

This paper: http://www.sciencemag.org/cgi/conte[…]91/5507/1304

Has some very interesting comments, mainly in Table 11. Genome overview.

Percent of human genome that is repeats: 35 Most gene-rich chromosome Chr. 19 (23 genes/Mb) Least gene-rich chromosomes Chr. 13 (5 genes/Mb), Chr. Y (5 genes/Mb)

Looks like that harms Meyer’s case too.

TR Gregory said: Human design generally includes some imperfections, redundancies, superfluous components, etc., so why should design per se imply no junk DNA? It must be a theological claim, rarely stated explicitly.

Until we get a positive description of what “intelligent design” is, the most that we can go on is some analogy with the only design that we know about. The only design that we know anything about uses regularities (and sometimes chance, too). Try to design something without knowing what happens when you do something.

Things are even worse for Meyer than the chart used in this post indicates: there are far less than “~80 000 genes” in the human genome! The number is something closer to 23 000 (although I do not know whether copy numbers of individual genes are taken into account in either figure). To be fair, the chart comes from a book published in 1999, when the number was assumed to be much higher than it turned out to be. Of course, either figure is contrary to Meyer’s claim.

John Kwok, the podcast is not of Meyer.

This is how I characterized their “prediction” regarding “junk DNA” on Coyne’s blog:

But there’s little junk DNA in the genome, just like ID predicts. Cause it predicts, you know, whatever amount it turns out to be.

Or, as I predicted of Meyer’s 12 “ID predictions” in an appendix of his book, these predictions would just be something somebody on the ID side said. How could they be entailed, given that they have no theory?

Needless to say, the “predictions” are indeed just something somebody said, and most rely on the false dichotomy that if evolution (or the infant abiogenesis) doesn’t explain it, Goddidit Designerdidit.

What’s ironic is not even so much that they claim to predict anything, but that they whine piteously whenever we bring up “poor design” (and no, the panda’s thumb apparently isn’t one of them) that we’re doing theology. They didn’t predict “good design” did they? (They didn’t dare.) Except that they claim to have done just that with respect to “junk DNA,” even though they’ll never commit to any criteria, quantities, or characterization of “the designer” (we don’t really say how much it should be, either, because we recognize that too much is unknown to predict, something they won’t admit).

Well, ID hypocrisy is hardly a newly discovered trait.

BTW, why does spell check flag American spellings of words, when this is an American-based site? It likes “characterisation” and “realise”, but not “characterization” and “realize.”

Glen D

http://tinyurl.com/mxaa3p

Glen Davidson said: BTW, why does spell check flag American spellings of words, when this is an American-based site? It likes “characterisation” and “realise”, but not “characterization” and “realize.”

Aha - a perfect opportunity for applying the methodology of ID:

Why does spell check do such-and-such?

Because it is intelligently designed.

Does anyone need any more “explanation”?

Yeah, it’s of his YEC colleague Paul Nelson trying to refute Gould’s observation (which IMHO is still valid, if you wish to compare a panda’s thumb with ours). Just heard it and am now looking forward to hearing some really good music courtesy of the Wiener Philharmoniker (Vienna Philharmonic Orchestra) and their New Year’s Day Concert conductor, French conductor Georges Pretre:

Miranda said:

John Kwok, the podcast is not of Meyer.

But there may be even one more way on which ID advocates are fudging the historical record. Where are their scientific predictions that there is no junk DNA? They do frequently assert that there is none, but where in “ID theory” does that “prediction” come from? As far as I can see it comes from theological arguments about what an omniscient deity would do. I cannot see anything in the negative scientific arguments of Dembski and of Behe that speaks to the issue.

Meyer does cite some ID stuff from the 1990s that he says shows they predicted that junk DNA wasn’t junk – I haven’t looked those up to double-check. But yeah, the overall argument is bunkum on so many levels. (1) there is no ID theory in the first place, (2) even we interpret the statement “ID did something somewhere in the Universe” as a theory, that doesn’t tell you anything about junk DNA, (3) what really predicts function for e.g. the noncoding DNA in the human genome is “God specially created humans relatively recently, and He wouldn’t have put in a bunch of low-information junk sequence, because we know (somehow) that he’s a neat guy” – but ID “officially” denies that they are talking about God, that they make any such assumptions, or that they deny common ancestry, even though they clearly do.

Only after all this do we get to my point, (4), repetitive DNA shows that Meyer can’t be right about information density anyway, on his own arguments. But yeah, I wouldn’t take #4 to be a falsification or test of “ID”, “ID” as officially presented is untestable and not science.

It is some kind of test of #3, though, which has some validity when made explicit.

My biggest point, though, is that #4 is strong evidence for proposition #5:

(5) The ID movement and its leading proponents, and fans, are clueless, can’t think critically, can’t detect or correct simple errors, and generally are completely intellectually bankrupt.

But there may be even one more way on which ID advocates are fudging the historical record. Where are their scientific predictions that there is no junk DNA? They do frequently assert that there is none, but where in “ID theory” does that “prediction” come from? As far as I can see it comes from theological arguments about what an omniscient deity would do. I cannot see anything in the negative scientific arguments of Dembski and of Behe that speaks to the issue.

Meyer does cite some ID stuff from the 1990s that he says shows they predicted that junk DNA wasn’t junk – I haven’t looked those up to double-check. But yeah, the overall argument is bunkum on so many levels. (1) there is no ID theory in the first place, (2) even we interpret the statement “ID did something somewhere in the Universe” as a theory, that doesn’t tell you anything about junk DNA, (3) what really predicts function for e.g. the noncoding DNA in the human genome is “God specially created humans relatively recently, and He wouldn’t have put in a bunch of low-information junk sequence, because we know (somehow) that he’s a neat guy” – but ID “officially” denies that they are talking about God, that they make any such assumptions, or that they deny common ancestry, even though they clearly do.

Only after all this do we get to my point, (4), repetitive DNA shows that Meyer can’t be right about information density anyway, on his own arguments. But yeah, I wouldn’t take #4 to be a falsification or test of “ID”, “ID” as officially presented is untestable and not science.

It is some kind of test of #3, though, which has some validity when made explicit.

My biggest point, though, is that #4 is strong evidence for proposition #5:

(5) The ID movement and its leading proponents, and fans, are clueless, can’t think critically, can’t detect or correct simple errors, and generally are completely intellectually bankrupt.

Yes, Bilbo, we know you can always save your “design” by saying “that’s the way he did it.”

As it makes actual sense only via evolution, why is it not better to say that “God made a universe in which such an arrangement would evolve?” Or, if you’re not concerned about God, just say that such an arrangement is explicable in this universe due to evolution, without reference to God.

Glen D http://tinyurl.com/mxaa3p

Bilbo said:

Even if all 20 amino acids are attracted to their appropriate codons, it doesn’t show that intelligent design hasn’t been at work. Afterall, the way it currently happens is that an aminoacyl-tRNA-synthetase first binds the amino acid, then binds it to the opposite end of the tRNA, furthest from the codon. Not exactly the way we would expect it to work. Why wouldn’t the amino acids just bind to their codons on the mRNA? Why the need for two intermediate components – the synthetase and the tRNA? Is it possible that a designer, noticing the attraction between the amino acids and their codons, and knowing that would increase the likelihood of the amino acids being the right neighborhood, designed the synthetases and tRNAs accordingly?

The amino acids cannot bind to the codons because then the codons could not bind to the anticodons.

The point is that if the system were intelligently designed from scratch, there is no reason whatsoever why there should be any correspondence between the tRNA structure and the codons. If however, the system evolved from a much simpler beginning, then such nonrandom associations would be expected. The presence of aminoacyl-tRNA-synthetases means that the affinity may no longer be required. This is strong evidence that the system has evolved rather than being designed.

Of course the designer could have done it this way for some unknowable reason or possibly to fool us. But the fact that these observations are completely congruent with all other evidence once again points directly to evolution rather than design.

Gary Hurd said:

Arthur Hunt said:

A review that cuts the heart out of Meyer’s book. A snippet from the abstract:

“Accordingly, there was likely a stereochemical era during evolution of the genetic code, relying on chemical interactions between amino acids and the tertiary structures of RNA binding sites.”

So much for Meyer’s idea that the genetic code is a designed, arbitrary mapping. So much for all 600+ pages of his book, based as it is on something that is contradicted by experimental evidence.

Freaking great article. Thanks for the link Arthur.

And thanks for the kind remark, Gary. I decided to expand on the subject - just goes to show what a little bit of encouragement can lead to.

Bilbo said:

Even if all 20 amino acids are attracted to their appropriate codons, it doesn’t show that intelligent design hasn’t been at work. Afterall, the way it currently happens is that an aminoacyl-tRNA-synthetase first binds the amino acid, then binds it to the opposite end of the tRNA, furthest from the codon. Not exactly the way we would expect it to work.

Bilbo, Yarus and his colleagues are careful to point out that the current translation system we see today is almost certainly NOT what it was like at the time the genetic code was developing.

Why wouldn’t the amino acids just bind to their codons on the mRNA? Why the need for two intermediate components – the synthetase and the tRNA?

That would be a better question for ID proponents to have to explain, if you ask me. What if the designer had a Rube Goldberg kind of approach to design? Then any weird setup would be acceptable.

Is it possible that a designer, noticing the attraction between the amino acids and their codons, and knowing that would increase the likelihood of the amino acids being the right neighborhood, designed the synthetases and tRNAs accordingly?

Anything is possible, with a designer whose nature, capabilities, and intent are completely unknown.

Dave Lovell said:

…Error free copying is impossible…

probably true, but a relevant point is that in the digital domain you can reduce the error rate below any arbitrarily specified amount with appropriate design. in the real world an error rate that is insignificant compared to other considerations (eg a higher probability of a chaos demon appearing as a coincidence of quantum fluctuations and killing everyone in the office) might reasonably be described as zero. this would be analogous to the difference in certainty between a logical fact and a scientific fact

saxalotl said:

Dave Lovell said:

…Error free copying is impossible…

probably true, but a relevant point is that in the digital domain you can reduce the error rate below any arbitrarily specified amount with appropriate design. in the real world an error rate that is insignificant compared to other considerations (eg a higher probability of a chaos demon appearing as a coincidence of quantum fluctuations and killing everyone in the office) might reasonably be described as zero. this would be analogous to the difference in certainty between a logical fact and a scientific fact

Also note that you can look at the encoding and from it you can infer that error-free copying is a design goal. If you look at how the genome copies you can infer the exact opposite. When a RAID system has multiple copies the number of copies is fixed. The genome on the other hand has copy number variation. (If the ID folks were really thinking they would have not insisted that the genome is mostly functional because the less dense the genome is the more robust it is to copying errors.) The fact you have multiple copies and such things as heat shock proteins and other chaperones that allow life to tolerate a bad copy but nothing is done to minimize the bad copies until there is a copy that is so bad that it causes the life to not be able to reproduce as well as its peers.

Error-free copying is assumed in anti-virus software. If it sees the operating system change it assumes that the change was not intended by the designer. The software then looks for the “signature” of the virus and then reverts the operating system back to its original state. What happens to life when the analogous thing happens? In humans, endogenous retroviruses occupy about 1% of the genome, in total constituting ~30,000 different retroviruses embedded in each person’s genomic DNA (Sverdlov 2000). There are at least seven different known instances of common retrogene insertions between chimps and humans. So, life copies these pieces presumably not intended by the designer along common descent. Maybe if life is designed to tolerate these virus infections that they are just inactivated, but no. It seems that a ERV helped in the function of the placenta in mammals. Here the env gene of the retrovirus was co-opted to allow the embryo to implant in the placenta without it being rejected as “foreign”.

This brings me back to my original point. We have “non-intended” code in our genomes that nevertheless produces an important function. If this is designed you need a designer that not only controls the encoding of the genome but also controls contingent viral infections. The only such designer must be God with a capital G. If life is designed it’s designed in such a way that to make an analogy with the kind of design I do is to make a category error like Meyer did in his book.

But this causes a problem to ID because such an ID theory would be blatantly unconstitutional to teach in the public schools and it uncovers that ID is not “just science”. I happen to believe that there is such a God but I do not desire to impose my religious beliefs in high school science classes other than maybe let the students know that people such as myself exist and that people who believe that evolution is completely purposeless also exist. It is the wonder of the scientific method that we can work side-by-side to advance scientific knowledge. Note that this is precisely what the NAS did when publishing on Evolution and Creationism.

Bilbo said: Even if all 20 amino acids are attracted to their appropriate codons, it doesn’t show that intelligent design hasn’t been at work. … Why wouldn’t the amino acids just bind to their codons on the mRNA?

The paper does not show that, say, isoleucine simply preferentially “binds to” a isolated AUU codon. In fact, a staple of creationist literature is that it was shown long ago there are no preferences at that simplistic level, thus allegedly no ‘code evolution’ possible.

Instead this paper (and its refs) shows that, for example, random RNA sequences at least 22 nt long, with a UAUU motif somewhere internally, will coil up and collectively form a pocket that often preferentially binds isoleucine. In Fig. 7a, the presence of the entire surrounding ‘DRT’ is required for binding, not just the codon/anticodon. Instead this constant association eventually, thru a succession of events outlined in Part IV, results in the trailing AUU becoming a Ile codon, and the leading UAU an anticodon to the current AUA Ile codon. This is not the simplistic 1:1 AA-to-codons-on-a-string m-RNA in ribosome of Fig. 7c. (In fact Ile had all 4 AUx codons assigned until AUG was captured by Met much later.)

Is it possible that a designer, noticing the attraction between the amino acids and their codons, and knowing that would increase the likelihood of the amino acids being the right neighborhood, designed the synthetases and tRNAs accordingly?

The designer could make any synthetases and thus any code desired. Why would It care about affinities only exemplified in longer chained random RNA libraries?

John wrote:

“The designer could make any synthetases and thus any code desired. Why would It care about affinities only exemplified in longer chained random RNA libraries?”

This is exactly the point. The affinities do not falsify a designer hypothesis. The designer could presumably do just about anything. That hypothesis is not falsifiable. However, the affinities are exactly what one would expect if the current system actually evolved from a simpler preexisting system. Coincidence? A wise man once said:

“I believe in coincidences, I just don’t trust them”

And, once again, I was right.

I was just thinking about the information content in genomes and wondering, can’t the simple process of recombination increase information as well? Any individual undergoing meiosis can potentially produce many different haplotypes – presumably different from the haplotypes that came from either of that individual’s parents. Wouldn’t this count as an increase in “information?” Has Meyer or Dembski addressed this, or is it too simplistic a criticism? Maybe someone here at PT has already dealt with this?

ps. I know that is on a different scale than the RNA-codon discussion, but isn’t it still an increase in information without the requirement of intelligence?

DS Wrote:

The designer could presumably do just about anything. That hypothesis is not falsifiable.

So why do critics of ID/creationism spend 99+% of their time arguing “no designer needed for that,” which only gives the pseudoscientist opponent more “gaps” to play with and/or more quotes to mine? Why” is it so rare to hear one of us reply with “OK, so what exactly do you think the designer(s) did and when did he/she/it/they do it?

A skilled Gish-galloper can find an almost unlimited supply of cool sound bites to promote unreasonable doubt of evolution, but how many ways can they say “it’s not our job to connect dots” without eventually making it clear to all but the most hopelessly deluded audiences (who don’t need anti-evolution activists anyway) that they are playing games, and know that they don’t have a prayer against evolution.

Herbert Spencer “The Development Hypothesis”

Originally published in The Leader, March 20, 1852. Reprinted, slightly modified, in: Essays: Scientific, Political, and Speculative. Library Edition, containing Seven Essays not before republished, and various other Additions (London: Williams and Norgate, 1891). Vol. 1

Online at:

http://oll.libertyfund.org/?option=[…]mp;Itemid=27

If they have formed a definite conception of the process, let them tell us how a new species is constructed, and how it makes its appearance. Is it thrown down from the clouds? or must we hold to the notion that it struggles up out of the ground? Do its limbs and viscera rush together from all the points of the compass? or must we receive the old Hebrew idea, that God takes clay and moulds a new creature? If they say that a new creature is produced in none of these modes, which are too absurd to be believed, then they are required to describe the mode in which a new creature may be produced—a mode which does not seem absurd; and such a mode they will find that they neither have conceived nor can conceive.

Should the believers in special creations consider it unfair thus to call upon them to describe how special creations take place, I reply that this is far less than they demand from the supporters of the Development Hypothesis. They are merely asked to point out a conceivable mode.

Ninety five percent of comments of critics of Stephen Meyer’s book (signature in the cell) are having same wording like: ‘ Repetitive junk - Creationist argument - argument from ignorance - making castle from the sand “etc. Permit me to ask those scholars and experts on evolution: What are you people giving us NEW since 150 years on natural selection? Except cursing, naming and denying us. I will tell you something: What is going to happen to the Darwinism, say within 10-15 years? The theory will disappear like other several theories like ‘ Socialism - Communism-Marxism ‘ because your Charlie built a hundred storey building, one hundred fifty year ago, but forget to make its foundation and ground floor!

AJ

a.j.baaqail said:

Permit me to ask those scholars and experts on evolution: What are you people giving us NEW since 150 years on natural selection?

How long have you got, and are you prepared to listen?

What are you giving us NEW since 6000 years on creationism?

and also:

What is going to happen to the Darwinism, say within 10-15 years? The theory will disappear like other several theories like‘ Socialism - Communism-Marxism ‘ .……

Can you promise us that? When are you personally going to stop using a term with no scientific meaning? MET is the best current understanding of how life developed on the this planet, not a political manifesto or moral code.

I wouldn’t want to put you to the effort of actually thinking about this, AJ, but could it be that Meyer actually is making the same false argument over and over, that he really is saying that if he doesn’t know how it happened, it couldn’t have happened, and maybe it’s possible that his entire premise is based on sand, just like the experts say? I mean, it’s a wild idea, but it could just be right.

And something new in the last 150 years, you ask? Like, oh, the 4.5 billion year history of the Earth demonstrated and documented, you mean? Or population genetics? Or DNA? Or about a dozen observed speciations? Or radiographic dating? Or the K-T event? Or maybe a hundred transitionals that Darwin never heard of? Or at least five or six different hominid species that aren’t modern humans, and aren’t modern apes either, being bipedal, with larger brains and different teeth. Stuff like that, you mean?

Foundations and ground floor? Being science, they’re made of evidence, AJ. Maybe you’ve heard the word? Now all you have to do is to work out what it means.

Oh, and one more thing. The Theory of Evolution isn’t going to disappear. It’s too well-established now - established by the evidence of which you are so sadly and shamefully ignorant. Sadly, ignorance won’t disappear either, so long as there are rogues like Meyer to promote it to fools. But don’t expect us to do anything but snicker at you when you show it.

a.j.baaqail said:

Ninety five percent of comments of critics of Stephen Meyer’s book (signature in the cell) are having same wording like: ‘ Repetitive junk - Creationist argument - argument from ignorance - making castle from the sand “etc. Permit me to ask those scholars and experts on evolution: What are you people giving us NEW since 150 years on natural selection? Except cursing, naming and denying us. I will tell you something: What is going to happen to the Darwinism, say within 10-15 years? The theory will disappear like other several theories like ‘ Socialism - Communism-Marxism ‘ because your Charlie built a hundred storey building, one hundred fifty year ago, but forget to make its foundation and ground floor!

AJ

Well A. J. let’s see, how about a short list just off the top of my head:

Punctuated equilibrium

Neutral theory

Hox genes

Evo Devo

Interference RNA

Transposition

SINE insertions

Cladistics

Well, you get the idea. The list goes on and on. In fact, over one million publications is peer reviewed journals contain quite a bit of new information, even entirely new fields of study. Your turn. Name one new idea in creationism in the last one hundred and fifty years. Not made up worthless crap like “complex specified information”, not tired old recycled “intelligent design” nonsense, something actually new. See Meyer is just making the same tired old argument over and over, no one buys it.

As for the demise of evolutionary theory, all I have to say is WATERLOO, WATERLOO!!! Just keep screaming it until you can’t talk anymore. Evolution will still be around long after humans have evolved enough to realize that it is true.

DS said:

As for the demise of evolutionary theory, all I have to say is WATERLOO, WATERLOO!!! Just keep screaming it until you can’t talk anymore. Evolution will still be around long after humans have evolved enough to realize that it is true.

People have been screaming this about evolution for the last 149 years. One would think that these people would realize that making false predictions won’t change the future. But…

P.S.

Let’s not forget such favorites as:

Endosymbiosis

Lateral gene transfer

Molecular population genetics

RNA World Hypothesis

See A.J. the thing is that ignorance of every major discovery in the last one hundred and fifty years is not evidence against evolution. It is only evidence against ignorance.

Still waitin for your list lad.

a.j.baaqail said:

Ninety five percent of comments of critics of Stephen Meyer’s book (signature in the cell) are having same wording like: ‘ Repetitive junk - Creationist argument - argument from ignorance - making castle from the sand “etc.

Alright. Here’s a new argument.

Meyer spends hundreds of pages talking about the “specified information content” of the genome and how it’s so meaningful and important, but in all that time never defines his terms and never tells us how to go measure it.

Now, why might that be, AJ?

Why has ID, after 30 years of “research” never told us how to actually go measure the most important variable in the ID universe?

I would note that science, on the other hand has used the intervening 30 years to years, to decode and publish the entire human genome, and the entire genomes of hundreds of creatures, and to more or less double the number of known transitional forms for dinosaur-to-bird, land-animal-to-whale, fish to-to-amphibian and, of course, ape-to-man.

a.j.baaqail said:

Ninety five percent of comments of critics of Stephen Meyer’s book (signature in the cell) are having same wording like: ‘ Repetitive junk - Creationist argument - argument from ignorance - making castle from the sand “etc.

Yeah, and ninety five percent of the comments of critics of the TV show “The Bachelor” have some wording like “banal crap”.

So?

When a huge majority of serious reviewers call your product crap it should tell you something.

Still waitin A.J. You are getting further and further behind here. Do you really want me to post another hundred examples before you can think of one?

Don’t ask questions you don’t want answered dude.

SINE insertions

That won’t help; the guy will still go off on a tangent.

It seems to me that Dr. Robert Shapiro’s (certainly not a friend of ID theory) stinging criticism of pre-biotic synthesis, upon which the entire RNA First scenario depends, is right on the money. All of these experiments, including those of Joyce and Lincoln, Sutherland, and Szostak, depend on the genius of the experimenter and the advanced technology of the respective laboratories to succeed. To me, this does not offer much insight into how life could have started by itself in a pre-biotic soup 3.6 billion odd years ago. Dr. Graham Cairns Smith and Sir Fred Hoyle were also extremely critical of the techniques of pre-biotic synthesis to help us understand how life started by a purely naturalistic process. At the very least, the sharp criticisms of scientists of this stature should evoke a little bit of humility in discussing the origin of life.

If Stuart Kaufmann can state without reservation that we do not know how life started, I don’t why other people who certainly are far below his level of expertise and knowledge cannot say the same thing.

There is currently an “Origin of Life Prize” being offered for a million dollars for someone who can present a “highly plausible” explanation for the genetic material needed for life to exist and evolve. So far nobody has won it. That would mean that, at least in the eyes of the sponsors, there does not exist a highly plausible explanation for the origin of DNA. I don’t know if Meyer is right or not about an intelligent designer, but there certainly is nothing unreasonable in considering such an option. I get the feeling from reading some of the comments on this site, that people are afraid of such a possibility.

I also do not understand the “junk DNA” argument. Everyone agrees that DNA is a highly sophisticated digitally encrypted code which contains the instructions to build a living cell. Szostak himself says that “even the simplest bacterium teems with molecular contraptions that would be the envy of any nanotechnologist”. From everything I have read it seems that what goes on in the simplest cell is enough to make your head swim. It seems to me that the “junk DNA” argument is not that DNA does not exhibit design, but that it exhibits “poor design” or “design that leaves something to be desired”, or it is not put together in a way that we would have liked to see it. Toyota screwed up on its cars, but no one would conclude from that fact that the Toyota Prius was not the product of intelligent designers.

It seems to me that an honest person should at the very least give some sort of consideration to Meyer’s ideas. In the meantime it seems clear that nobody really knows how life did start.

All of these experiments, including those of Joyce and Lincoln, Sutherland, and Szostak, depend on the genius of the experimenter and the advanced technology of the respective laboratories to succeed.

So, if I interpret your argument correctly, you’re saying that if an experiment is clever than it can’t have anything to say about natural processes. Have I got that right? Fascinating.

Btw, citing Fred Hoyle is not exactly convincing.

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This page contains a single entry by Nick Matzke published on December 31, 2009 4:26 PM.

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