Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research.

Evolution News and Views
EVOLUTION NEWS & VIEWS
 

A Response to Dr. Dawkins' "Information Challenge" (Part 2): Does Gene Duplication Increase Information Content? (Updated)

[Editor's note: This was the second installment of a three-part series. The full article, A Response to Dr. Dawkins' "The Information Challenge", can be read here.]

In Part I, I demonstrated that specified complexity is the appropriate measure of biological complexity. In this section, I will show why merely citing gene duplication does not help one understand how Darwinian evolution can produce new genetic information. Dawkins' main point in his "The Information Challenge" article is that "[n]ew genes arise through various kinds of duplication." So his answer to the creationist question that so upset him is gene duplication. Yet during the actual gene-duplication process, a pre-existing gene is merely copied, and nothing truly new is generated. As Michael Egnor said in response to PZ Myers: "[G]ene duplication is, presumably, not to be taken too seriously. If you count copies as new information, you must have a hard time with plagiarism in your classes. All that the miscreant students would have to say is 'It's just like gene duplication. Plagiarism is new information- you said so on your blog!'"

Duplicating Genes Doesn't Increase Biological Information in Any Important Sense
I now have 2 questions to ask of Darwinists who claim that the mechanism of gene duplication explains how Darwinian evolutionary processes can increase the information content in the genome:

(1) Does gene duplication increase the information content?

(2) Does gene duplication increase the information content?

Asking the question twice obviously does not double the meaningful information conveyed by the question. How many times would the question have to be duplicated before the meaningful information conveyed by the list of duplicated questions is twice that of the original question? The answer is that the mere duplication of a sentence does NOT increase the complex and specified information content in any meaningful way. Imagine that a builder of houses has a blueprint to build a new house, but the blueprint does not contain enough information to build the house to the specifications that the builder desires. Could the builder obtain the needed additional information merely by photocopying the original blueprint? Of course not.

Darwinists Must Give Detailed Accounts of how a Duplicated Gene Acquires its New Function
The Darwinist would probably reply to my objection by saying, "Well, it isn't just gene duplication that increases the genetic information -- such information is increased when gene duplication is coupled with the subsequent evolution of one of the new copies of the gene." Aye, there's the rub.

Darwinists laud the mechanism of gene duplication because they claim it shows how one copy of a gene can perform the original function, freeing up the other copy to mutate, evolve, and acquire a new function. But the new genetic information must somehow be generated during that subsequent evolution of the gene. To explain how Darwinian processes can generate new and meaningful genetic information, Darwinists must provide a detailed account of how a duplicate copy of a gene can evolve into an entirely new gene. But ask Darwinists for details as to how the duplicate copy then starts to perform some new function, and you probably won't get any. At least, Dawkins didn't given us any details (as I explain below) about this in his "The Information Challenge" article, which I am rebutting here.

A recent study in Nature admitted, "Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown." (Ilan Wapinski, Avi Pfeffer, Nir Friedman & Aviv Regev, "Natural history and evolutionary principles of gene duplication in fungi," Nature, Vol. 449:54-61 (September 6, 2007).) Yet the crucial question that must be answered by the gene duplication mechanism is, exactly how does the duplicate copy acquire an entirely new function? Stephen Meyer explains in Proceedings of the Biological Society of Washington that it is difficult to imagine how duplicated genes acquire new functions since they must successfully undergo "neutral evolution" and traverse a random walk in order to acquire a new function:

[N]eo-Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism. According to this scenario, non-coding sections of the genome, or duplicated sections of coding regions, can experience a protracted period of "neutral evolution" (Kimura 1983) during which alterations in nucleotide sequences have no discernible effect on the function of the organism. Eventually, however, a new gene sequence will arise that can code for a novel protein. At that point, natural selection can favor the new gene and its functional protein product, thus securing the preservation and heritability of both.

This scenario has the advantage of allowing the genome to vary through many generations, as mutations "search" the space of possible base sequences. The scenario has an overriding problem, however: the size of the combinatorial space (i.e., the number of possible amino acid sequences) and the extreme rarity and isolation of the functional sequences within that space of possibilities. Since natural selection can do nothing to help generate new functional sequences, but rather can only preserve such sequences once they have arisen, chance alone--random variation--must do the work of information generation--that is, of finding the exceedingly rare functional sequences within the set of combinatorial possibilities. Yet the probability of randomly assembling (or "finding," in the previous sense) a functional sequence is extremely small.

(Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings for the Biological Society of Washington, Vol. 117(2):213-239 (2004).)

The Inconvenient Truth for Dawkins: At best, the mechanism of gene duplication shows how a hiker can get to the foot of a hiking trail, but never explains how the hiker finds the peak of the mountain, while doing a random, blindfolded walk. We don't need to know that genes can make copies of themselves; we need to know how the duplicate gene evolves, step-by-step, into an entirely new gene.

Mistaking Similarity as Evidence for Common Descent, and then Mistaking Common Descent as Evidence for Darwinian Evolution
Rather than giving a step-by-step mutational account of how a duplicated gene acquires a new function, Dawkins' article substitutes bland evidence of sequence identity between different genes as evidence for Darwinian evolution by gene duplication. Dawkins gives the example of the evolution of various globin genes that he claims arose via gene duplication. His evidence is that "[c]areful letter-by-letter analysis shows that these different kinds of globin genes are literally cousins of each other, literally members of a family." Of course the "[c]areful letter-by-letter analysis" simply means finding amino acid sequences that are similar or identical between two different proteins. David Swift explains that such claims of relationship "are inferred solely on the basis of assuming a common ancestry and then deriving a route of polypeptide evolution, typically the most parsimonious one, to fit the known present day amino acid sequences and consistent with the observed pattern of conserved amino acids." (David Swift, Evolution Under the Microscope, pg. 165 (Leighton Academic Press, 2002), emphasis in original.) At best, such sequence identity demonstrates common ancestry (if one ignores the possibility of common design), but it does not demonstrate Darwinian evolution. Michael Behe easily rebutted the over-extrapolation from sequence-similarity to Darwinian evolution in both Darwin's Black Box and The Edge of Evolution:

"Although useful for determining lines of descent ... comparing sequences cannot show how a complex biochemical system achieved its function--the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter. ... Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?" (Michael Behe, Darwin's Black Box, pgs. 175-176.)

"[M]odern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation." (Michael Behe, The Edge of Evolution, pg. 95.)

Darwinists like Dawkins continue to make the mistake cited by Behe and Swift. (In fact, if you read the aforementioned "Natural history and evolutionary principles of gene duplication in fungi" article, you'll find it gives only anecdotal or circumstantial evidence of evolution by gene duplication, not directly observed evidence, and there certainly aren't any detailed step-by-step models for how the genes evolved.)

The Dangerous Road Faced by Duplicated Genes
If a duplicated gene cannot successfully traverse its random walk, it may die. As Lynch and Conery found, "the vast majority of gene duplicates are silenced within a few million years." (Lynch & Conery, "The Evolutionary Fate and Consequence of Duplicate Genes," Science Vol. 290:1151-1155 (Nov 10, 2000).) Does Richard Dawkins give a step-by-step mutational account of how globin genes evolved from one another while remaining functional at all times, such that the duplicate copies were never "silenced," terminating their evolution? Of course not. Dawkins has not demonstrated how Darwinian evolution can take a duplicated gene and evolve it into a new gene. The problem for Dawkins is that duplicating a gene may increase your amount of Shannon information, but it does not increase the amount of specified complexity in any non-trivial sense. To explain how one gene can turn into another, Dawkins must explain how new specified and complex information can enter the genome, and give a step-by-step mutational account of the origin of some gene via gene duplication. Dawkins has provided none of this.

To understand this point, consider the following sentence (with spaces removed):

METHINKSDAWKINSDOTHPROTESTTOOMUCH
If we merely consider the Shannon information of the 33 letters (not counting spaces) in the sentence, then it has about 155 bits of Shannon Information. Now we duplicate it, like what happens in a gene duplication event:
METHINKSDAWKINSDOTHPROTESTTOOMUCHMETHINKSDAWKINSDOTHPROTESTTOOMUCH
The amount of Shannon information has now doubled (~310 bits), but we have seen no non-trivial increase in the amount of specified complexity. Still, Dawkins thinks gene duplication is the answer, and that "[i]t is by these, and similar means, that genome sizes can increase in evolution."

[Update Note: The Shannon information in the doubled-string is twice the Shannon information in the shorter string if the shorter string does nothing to predict the sequence of the doubled-string. By granting this assumption, we are able to increase the Shannon information in the genome, even though this is a trivial informational increase that does not provide a meaningful increase in the specified complexity. The key questions are (a) what process is generating the new sequence, and (b) to what extent does that process predict the new sequence? In this sense, duplicating a gene would predict that the duplicate gene would be an identical copy of the original gene. From this standpoint, gene duplication actually does NOTHING to increase the Shannon information in the genome because you can predict the sequence of the new stretch of the DNA with a Probability of 1 (where Log (1) = 0), leading to an increase in the Shannon information of 0 bits. In this sense, the Shannon information in the doubled-string is not increased at all from the original, shorter string, as it remains 155 bits. Keep in mind that it is Dawkins who raised the issue of increasing Shannon information in the genome via gene duplication. Viewed in this fashion, Dawkins' claim that gene duplication can increase the Shannon information is even more dubious: if gene duplication predicts that you will have an identical copy of the original gene, then gene duplication not only fails to increase the specified and complex information, it also fails to increase the Shannon information in the genome!]

But we aren't trying to simply change the "genome siz[e]," and thereby change the Shannon information. We're trying to construct something functionally new. Thus, imagine that one duplicate copy of the original sentence evolves into a new sentence of the same length:

BUTIMSUREDAWKINSBELIEVESHEISRIGHT
A Darwinian theorist would find that both sentences contain the word "Dawkins," and thus share a 21% sequence identity. They would then infer that both sentences evolved from that common ancestor via Darwinian evolution. They would conclude that a duplicated version of the sentence "METHINKSDAWKINSDOTHPROTESTTOOMUCH" has evolved into "BUTIMSUREDAWKINSBELIEVESHEISRIGHT".

David Swift explains that finding such similarities is not enough to justify the claim that Darwinian evolution has produced the observed pattern: "[F]or family trees to be credible, most if not all of the putative ancestral sequences must be functional; but this presents a major stumbling block in the production by divergence of proteins with different functions. To get from one set of conserved amino acids to another is either an unlikely big jump, or the intermediates must have biological activity; but the latter seems unlikely because it contradicts what we know about conserved amino acids." (Pg. 166). Thus, in order for Darwinists to convince me that Darwinian evolution can produce new information, at minimum I need to see a step-by-step mutational account of how they can take the sentence:

"METHINKSDAWKINSDOTHPROTESTTOOMUCH"
and evolve it into:
"BUTIMSUREDAWKINSBELIEVESHEISRIGHT"
by changing the first sentence one letter at a time, and having it always retain some comprehensible English meaning along each small step of its evolution. Telling me that you can duplicate the sentence does NOT answer the question posed in the video, "Can you give an example of a genetic mutation or evolutionary process that can be seen to increase the information in the genome?" As Michael Behe requested over ten years ago in Darwin's Black Box, what is required is a "detailed, scientific [explanation of] how mutation and natural selection could build" the sentence. (Behe, Darwin's Black Box, pg. 176.)

Don't Blame Natural Selection: It's Just Acting upon What Mutations Provide
It's worth noting that Dawkins finally claims that it is natural selection that "feeds information into gene pools" by selecting for mutations that help organisms survive. Thus, Dawkins would argue that the information in the environment is transferred into the genome of the organism. Fair enough. But Dawkins isn't telling the most important part of this story. We all know that mutations must provide the raw fuel upon which natural selection can act. As Gilbert, Opitz, and Raff write:

The Modern Synthesis is a remarkable achievement. However, starting in the 1970s, many biologists began questioning its adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern only the survival of the fittest, not the arrival of the fittest. As Goodwin (1995) points out, "the origin of species -- Darwin's problem -- remains unsolved.

(Scott Gilbert, John Opitz, and Rudolf Raff (1996) "Resynthesizing Evolutionary and Developmental Biology," Developmental Biology 173, 1996, pg. 361.)

Natural selection can (given the right population circumstances, etc.) preserve traits that confer a survival advantage, and it is very effective at weeding out traits that are disadvantageous. But natural selection can only act upon what mutations provide. Thus, we can't account for the survival of particular mutations until we account for the arrival of particular mutations. We cannot account for the increase in information content of genomes until we consider how random mutations produce the raw fuel that natural selection can preserve.

My Information Challenge Reiterated:
So here is my "Information Challenge": For the sake of the argument, I will grant that every stage of the evolutionary pathway I requested above will survive, and thus I'll give natural selection every possible benefit of the doubt. What I need is a step-by-step mutation account of how one sentence evolved into the other wherein the sentence remains functional -- i.e., it has comprehensible English meaning -- at all stages of its evolution. In short, I request to see how:

"METHINKSDAWKINSDOTHPROTESTTOOMUCH"
can evolve into:
"BUTIMSUREDAWKINSBELIEVESHEISRIGHT"
by changing the first sentence one letter at a time, and having it always retain some comprehensible English meaning along each small step of its evolution. This seems like a reasonable request, as it is not highly different from what Darwinists are telling me can happen in nature.

How would Dawkins reply? Would he get angry and complain that this is "the kind of question only a creationist would ask"? Or would he dodge the question like he did in his "The Information Challenge" article? Personally, I'd like to see an answer to the question.