Signature in the Cell: self-contradiction and repetition

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/reprint/82/suppl_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/doi/abs/10.1111/j.1365-313X.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/journal/v409/n6822/full/409860a0.html.

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!

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).

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. …

— Nick Matzke

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).

TT replies: http://telicthoughts.com/the-signature-in-the-cell-challenge/

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.com/entry/eg/2009-04-29T14_35_14-07_00

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.com/entry/eg/2009-04-29T14_35_14-07_00

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

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.

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.

This paper: http://www.sciencemag.org/cgi/content/full/291/5507/1304

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.

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.

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.

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."

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.

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.

Nick (Matzke) said: 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.

snaxalotl said:

Nick (Matzke) said: 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.

another way of describing what Meyer does, is that he pumps his audience's intuition by giving examples of intended function until they conflate function and intended function reflexively. Then he points to biological examples of function, and says "look: god".

Stephen Meyer demands to know where biological information comes from. Information, he claims, can only come from an intelligence, and the existence of biological information proves that this intelligence exists.

Permit me to make a similar claim. That nature is beautiful, and that beauty springs only from an intelligence. Tonight’s sunset, for example, contained 23.4 milliHelens of beauty.[1] Mindless, naturalistic weather patterns cannot create beauty. Every time we find beauty---in a painting, a symphony, whatever---we find an intelligence that creates it. Therefore, the existence of beauty in nature proves the existence of an intelligence for its origin.

==================
[1] A milliHelen is enough beauty to launch 1 ship.

Olorin wrote:

"Stephen Meyer demands to know where biological information comes from. Information, he claims, can only come from an intelligence, and the existence of biological information proves that this intelligence exists."

Well he can demand whatever he wants, but if he wants to know where information comes from, then why does he claim that it can only come from intelligence? That's just plain crazy. A single example is sufficient to falsify that hypothesis. Intelligence is not required in order to produce information, intelligence is only required in order to interpret information. Why can't he understand this? What is so hard to understand?

Is there information in the color of your urine? What intelligence created that information?

Is there information in your white cell count? What intelligence created that information?

Is there information in the color of a maple leaf? What intelligence created that information?

Is there information in the width of tree rings? What intelligence created that information?

Is there information in the position of SINE insertions in cetacean genomes? What intelligence created that information?

Olorin said: Stephen Meyer demands to know where biological information comes from. Information, he claims, can only come from an intelligence, and the existence of biological information proves that this intelligence exists. Permit me to make a similar claim. That nature is beautiful, and that beauty springs only from an intelligence. Tonight’s sunset, for example, contained 23.4 milliHelens of beauty.[1] Mindless, naturalistic weather patterns cannot create beauty. Every time we find beauty---in a painting, a symphony, whatever---we find an intelligence that creates it. Therefore, the existence of beauty in nature proves the existence of an intelligence for its origin. ================== [1] A milliHelen is enough beauty to launch 1 ship.

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.

Clever, Olorin. Stealing it.

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.

Such principles, which we summarize in a “polar profile”, are useful in explaining newly selected specific RNA binding sites for free amino acids bearing varied side chains charged, neutral polar, aliphatic, and aromatic.

I suggest some cases of "complex specified information", if there is anything which answers this expression:

The close physical relationship which the human body bears to those of chimps and other apes.

Ecological relationships, such as between predator and prey, parasitism.

Changes to the world of life over time, including extinctions and speciations.

Of course, because ID is not a theory, they can shut off discussion whenever they want. But perhaps we can make it abundantly clear that this is what they are doing.

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.

Of course, because ID is not a theory, they can shut off discussion whenever they want. But perhaps we can make it abundantly clear that this is what they are doing.

— TomS

“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)

The genome does display evidence of past viral insertions, deletions, transpositions, and the like, much as digital software copied again and again acumulates errors. [Emphasis mine]

Rich said: From this we can see that not only is Dembski's information theory busted but the entire analogy used by ID is also busted. When life reproduces it does it only once so no iterative decoding there. The genome also accumulates errors and uses these errors to create new functions. A computer program stored on a disc is invariant by design and does not evolve. If the program does change then it is a design flaw. As I stated above one could make the argument that evolution is another way of doing design but that's not what ID argues. By being so violently anti-evolution ID potentially misses the real signature in the cell for a forged one.

Rich wrote:

"A computer program stored on a disc is invariant by design and does not evolve. If the program does change then it is a design flaw. As I stated above one could make the argument that evolution is another way of doing design but that’s not what ID argues. By being so violently anti-evolution ID potentially misses the real signature in the cell for a forged one."

Exactly. If biological systems were in fact designed, (they were not and certainly not intelligently), then they were designed to evolve. At the very best, that makes the entire evolution thing god's idea. Why try to deny this? Why try to place artificial limits on the ability of evolution to generate new features. Are they trying to say that god designed systems to to be suboptimal and to evolve poorly as well? What an incompetent boob.

Mike Elzinga said: When reading ID/creationist books, one gets the distinct impression that, despite their so-called “advanced degrees”, the authors of these books haven’t even mastered 8th grade general science. They don’t even understand what is going on when their eyeglasses fog up.

One way of looking at "intelligent design" is to note that an evolving gene pool does have some of the attributes associated with intelligence. It tries different things, and it "remembers" the things that worked, and emphasizes those that worked well. It lacks things like foresight, keeping track of mistakes to avoid in the future, and ways of redoing features that have undesirable side effects.

Henry

Wheels said: I've only got some entry-level college education about physics and chemistry, but some of the flaws in all the "random chance" arguments against abiogenesis were readily apparent to me and I could explain why they're wrong.

Since the different chemical tendencies of elements are generally taught in high school by the latest, I don’t see how anybody with a degree in science or mathematics can possibly make the “random chance” argument for anything to do with the chemistry of life, but cdesign proponentsists make these arguments all the time.

Since the different chemical tendencies of elements are generally taught in high school by the latest,

Henry J said: One way of looking at "intelligent design" is to note that an evolving gene pool does have some of the attributes associated with intelligence.

Olorin said: Show a creationist a few systems that exhibit novel behavior, yet demonstrably have no central controller, no overall guiding principle separate from the system itself. Could his dogma survive that? At least, without peals of laughter from his audience.

Wheels said: I like the RAID analogy; it shows how real design is different than "Intelligent Design." Think I'll add that explanation to my list of how ID is useless compared to sciences that use design inferences (SETI and archeology).

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.

Rich said: While RAID systems are used for a high-reliability disk farms for most uses is uncompetitive. The reason why digital has won over analog is that you can copy the information over and over again and not lose anything.

What this means is a digital system does not accumulate errors because the errors are removed in each read/write cycle.

But life does not have a read channel. It just makes copies and accumulates errors just a Meyer noted.

Sorry if I sounded at all confrontational Rich, I really liked your comment.

I'm a biologist and someone has to stick up for the absolutely mindboggling awesomeness of the nano-machines that compose us all.

I know a bit about this computer stuff, and Matt is essentially correct. What he left out (he may assume we all know it) is that it is much easier to detect errors than to correct errors. Disk storage technology has a block of data associated with each sector containing a lot of information about what's in that sector. From this, it's vanishingly unlikely that a copying (or reading) error will go undetected. Not zero, of course, but very small. Problem is, recovering the original requires full redundency of both the data and the metadata describing it (to know which copy is wrong). In cases where the metadata says BOTH are wrong, it's still possible to compare the two, and where differences are found, attempt all permutations of reconstructing one from the other and recreating the resulting metadata until the metadata match. And even still, it's theoretically possible for error to creep in, because certain pairs of bit-swaps produce identical metadata, though the underlying data is clearly now wrong.

The RAM involved in making copies between disks is generally not a problem for a couple of reasons. Modern RAM has one or two error identifying and correcting bits (and repeated errors in the same RAM cells cause modern systems to disable banks containing such cells), and multiple disk-compares where mismatches are found can statistically eliminate RAM as the culprit. Again not a zero probability of error, just very very small.

BUT except in the most extraordinary circumstances, none of these attempts to restore original data after errors are detected, are actually done. The philosophy is, such errors are so extremely infrequent, and the "retry" option so effective on the rare occasions when errors are detected, that we can just live with the current low error rate. The rate of physical media errors (on disks or in RAM) is MUCH smaller than the error rate introduced by logic errors in programs (which can be extremely subtle, involving multiple programs simultaneously interacting with incompletely understood hardware, and dependent on the data themselves, etc.)

DS said: Olorin wrote: "Stephen Meyer demands to know where biological information comes from. Information, he claims, can only come from an intelligence, and the existence of biological information proves that this intelligence exists." Well he can demand whatever he wants, but if he wants to know where information comes from, then why does he claim that it can only come from intelligence? That's just plain crazy. A single example is sufficient to falsify that hypothesis. Intelligence is not required in order to produce information, intelligence is only required in order to interpret information. Why can't he understand this? What is so hard to understand? Is there information in the color of your urine? What intelligence created that information? Is there information in your white cell count? What intelligence created that information? Is there information in the color of a maple leaf? What intelligence created that information? Is there information in the width of tree rings? What intelligence created that information? Is there information in the position of SINE insertions in cetacean genomes? What intelligence created that information?

Matt Ackerman said:

Rich said: While RAID systems are used for a high-reliability disk farms for most uses is uncompetitive. The reason why digital has won over analog is that you can copy the information over and over again and not lose anything.

and

What this means is a digital system does not accumulate errors because the errors are removed in each read/write cycle.

Actually: no. While you are correct that digital information can make error free copies, the fact that information is digital does not guarantee that error free copies are made. Meyers really is right when he states that digital information copied again and again has some rate of error accumulation. With an analog system the probability of making a perfect copy is exactly zero. With any digital system the probability is strictly less than one. While my knowledge of computers is somewhat limited ...

But life does not have a read channel. It just makes copies and accumulates errors just a Meyer noted.

Well, I don't really know what a read channel is, so I can't say that life has something exactly analogous to a read channel, however, our cells certainly do maintain redundant copies of genetic information and use those redundant copies to correct errors that are detected in any one given copy of the information. Each living thing has minimally two copies of each gene, since DNA is kept in a double helix. Most living things have four or more copies, and these copies really are used to correct errors in other copies of genes. I don't see how this is a drastically different situation than in RAID arrays, if I am understanding your analogy correctly. Granted, if certain specific errors are introduced in two copies of information simultaneously the cell might not be able to detect the error, but the same should be true of the RAID array as well. Anyway, I can pour beer all over my cells and they will continue copying information just fine. I'd like to see your fancy dancy RAID arrays pull that one off. ;)

Rich said: Nick, it's interesting how ID proponents speak on subjects they don't have a clue. Whether it's speaking about biology when they don't know biology or climatology when they don't know climatology. Now it's telling me who has been designing computers and hard drives for over a quarter century how they are designed! Both of the responses are woefully ignorant as I will show shortly. ...

Sylvilagus 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.

Would someone please offer a translation and/or clarification of the significance of this finding for Meyer's argument? I am interested but the material is way outside my knowledge base. Thanks.

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?

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?

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.

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?

Dave Lovell said: ...Error free copying is impossible...

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

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?

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?

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?

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

— DS

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?

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 ‘ .......

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

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.

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.

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.

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

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.

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