mutations and information

Evolution was much easier to attack in Darwin’s time, especially since the mechanism of inheritance was not yet known. Since then, evolution by mutation and natural selection has been directly observed both in the lab and the field, and corroborated by genetic studies. As a result, even creationists have been forced to accept that evolution does occur, at least on a small scale. So now, in order to deny macroevolution or common descent, the creationist must argue that the evolution we observe today is not the type of modification that would add up to large-scale morphological change. Perhaps the most commonly used argument today is that mutations do not add “information” to the genome, and that this is required for common descent via mutation and selection. The aim of this paper is to address this general argument, and show that it is not valid.
Since the information argument is considered by creationists to be quite important, and is quite commonly used, it therefore deserves special attention. Phillip E. Johnson is a professor of law, and author of well-known creationist books such as Darwin On Trial. In an interview with the Christian magazine Touchstone, Johnson commented on the argument in question:
“You have said there is no natural explanation for the rise of genetic information. How important is that question in the debate?

PJ: The Wedge of Truth is all about those issues. The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism… Once you get that in the debate, then we will be poised for a metaphysical and intellectual reversal that is every bit as profound as the one with Copernicus.” (5).

Clearly, the argument is one worth addressing. Either it says something very important, or it is misleading those who think it does.
Before addressing the argument, it is important to understand exactly what it implies. It would not refute common descent, because the case for common descent is independent of any specific mechanism. That is, the evidence in support of common descent does not assume the validity of mutation and natural selection as a mechanism for that change (15). Furthermore, the inability to gain information would not prevent all types of macroevolutionary change. For example, it is unclear that the information content of other mammals’ genomes is any less than that of our own. So even if we assume mutations cannot add information to the genome, mutation and natural selection would not be prevented from successfully explaining macroevolutionary changes such as that from early apes to modern humans. So what would the argument tell us, if it were indeed correct? Information theorist David J.C. MacKay says “Evolution has been happening on earth for about the last 109 years. Undeniably, information has been acquired during this process.” (7: p269). This is something that is generally agreed upon. So what the argument would show, if it were correct, is that mutation and selection could never sufficiently account for the descent of all modern species from a common ancestor.
It should be noted at this point, that it is not at all necessary to consider “information” to examine the change of genomic properties in question. What we’re really talking about here is how the complexity of the genome can change. In an article published in Science called The Origins of Genome Complexity,
“The ~100 fully sequenced eubacterial and archaeal genomes contain between 350 and 6000 genes, packed into 0.6 to 7.6 megabases (Mb)… all well-characterized genomes of animals and plants contain more than 13,000 genes in at least 100Mb… Accompanying the increase in gene number in multicellular species is an expansion in the size and number of intragenic spacers (introns) and a dramatic proliferation of mobile genetic elements.” (3: p1401).

No one is claiming this list to be exhaustive of the differences in genomes, but it is interesting to note that these types of changes do indeed occur.
There are a few ways that gene number can be increased, including “Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling” (6). Another mechanism is duplication mutation. It is estimated that 15,000 of the 40,000 genes in the human genome were acquired in this way (12). In this type of mutation, we get a second copy of some functional gene. Although this new gene will initially be the same as the gene it was copied from, “Preservation of both members of a duplicate pair can be promoted when one member of the pair acquires a beneficial mutation at the expense of an original essential function retained by the other (neofunctionalization).” (3: p1401). So, subsequent mutation of the new gene can result in a novel gene, while preserving the increased total number of genes. For example, from the pancreatic ribonuclease gene (RNASE1) in a leaf-eating monkey, a duplication and subsequent mutation resulted in a second gene (RNASE1B), which functions differently than its parent gene (11). Other examples abound in the primary literature, as an online search of the PubMed database will show.
Introns are non-coding sections of DNA that occur within a gene. Introns are found between exons, which code for functional domains of the protein corresponding to the gene. The size of an intron can be increased by an insertion mutation. Introns are non-coding, so changing an intron in this way may not affect the protein produced by the gene at all. There is not much certainty about how new introns are introduced, but among other theories, there is evidence for the insertion of new introns in certain genes. For example, there is evidence for the insertion of an intron into the sex-determining gene, SRY, of dasyurid marsupials. The scientists who determined this say “[their] data demonstrate that introns may be inserted as spliced units within a developmentally crucial gene without disrupting its function.” (10: p1653). The total number of introns in the genome can also be increased by duplication of genes with introns.
It is also interesting to note that a multicellular form of the green alga, Chlorella vulgaris, has evolved in the lab from the usual unicellular form (2).
So we have seen specific examples of the type of change that occurred during the evolution of modern species from our prokaryotic ancestors. We will now examine whether information theory has any implications for this problem.
By this point, an important question should be coming to mind. What is “information”, exactly? The intuitive meaning is obvious, but to talk about changes in information content, we need a formal, quantifiable definition. This question deserves special attention, because the validity of the information argument is dependant on how we define evolution. Unfortunately, our question has no simple answer. The information content of something depends on how information is defined, and there is no one right way to do that. A definition may be useful in answering one question, but meaningless to another. In his book Information Theory, Inference, and Learning Algorithms, MacKay poses the question of why some organisms reproduce sexually, rather than asexually. By MacKay’s model, asexually reproducing populations can gain 1 bit of information per generation, while the number of bits that a sexually reproducing population can accumulate is up to the square root of the size of the genome (7: p269). However, creationists are unlikely to define information the way MacKay did in his example.
Unfortunately, most creationists use the term “information” without explicitly stating what information is. This is often the main strength of the information argument for creationists. Without a formal definition of information, we can’t really say what type of change in the genome would represent increased information and in turn, it is then difficult to provide an example of such a change by mutation. One should be weary of any argument involving “information” content where the term is not explicitly defined.
Even without a strict definition of information, something can be said about the information argument. There is no shortage of creationist claims that certain mutations represent a loss of information. This exposes a problem with the information argument, because for any mutation, the opposite mutation is also possible, and in many cases, equally likely. So if a mutation can result in a loss of information, then surely the opposite mutation would mean a gain of information; if information can be lost, it can certainly be gained as well.
Dr. Lee Spetner has been more cooperative than other creationists in defining information. In an online exchange with Dr. Edward E. Max, Spetner says “I thought it rather obvious that a mutation that destroys the functionality of a gene (such as a repressor gene) is a loss of information. I also thought it rather obvious that a mutation that reduces the specificity of an enzyme is also a loss of information.” (13). This gives us an idea of what is considered to be a gain of information. If the loss of gene functionality is a loss of information, surely gaining a new functional gene would be a gain of information. An example of this has already been provided, but there are others that are of interest. For example, a frame shift mutation in a Japanese bacterium gave it the ability to digest nylon waste (16). Since the bacteria did not previously have this ability, this is a new biological function, and thus represents an increase in information. Spetner agrees, but contends that the mutation was not a random occurrence (14). Creationist organization Answers in Genesis claims that because the gene is on a plasmid, it has likely always existed, and was just transferred to the bacteria from another strain (1). However, nylon is an artificial compound that did not exist until it was invented in the 30’s, and bacteria with the gene require nylon to survive. The gene, therefore, could not have existed before the 30’s. This example is especially interesting in that the nylon digesting ability has given these bacteria an entirely new ecological niche to inhabit. One in which they have no competition but each other!

A well-known, good example of increased protein specificity is the evolution of a mutant version of a protein called Apolipoprotein AI (Apo-AI) in a small Italian community. The new version of the protein, Apo-AIM (the M is for Milano) is associated with reduced risk of arteriosclerosis, heart attack, and stroke.
“Apo-AI is a lipid-binding protein and is the major component of High Density Lipoprotein (HDL) particles, which play an important role in removing cholesterol from cells. Subsequent detailed research of the Apo-AIM mutation has demonstrated that it has improved biological function that directly contributes to lowering the incidence of cardiovascular disease in the individuals carrying it.” (8).

It works by actively stimulating cholesterol removal from cells (8). It also prevents some of the inflammatory damage of arteriosclerosis because of its antioxidant ability (8). Incidentally, the antioxidant ability is a new biological function, not possessed by the original Apo-AI protein (8). It has been shown that “Apo-AIM is 1) of a more complex tertiary structure 2) more stable and 3) activates cholesterol efflux more effectively than Apo-AI. Furthermore, Apo-AIM has an antioxidant activity not present in Apo-AI that is sequence and substrate specific.” (8). The mutation therefore represents increased specificity, and consequently is an increase in information by Spetner’s standards.

sorry, it's longer than 15,000 characters, so i'm gonna have to post the rest in a second post...

This is one of the best explanations of this I've seen here. You should consider sending it to Talk.Origins--my one suggestion if you do is that you not use Talk.Origins as a source, since they would probably prefer that their articles refer to the primary material.

Someone should keep track of this essay so we can bump it each time creationists use their "no new information" argument.

The average person reads the first 64 words of any article / letter before losing interest.

Check out any newspaper and count the number of words you read of each article. Honestly

You read the whole newspaper?
Wow.

Journalists try to make the first paragraph comprehensive, slightly larger print, and about 64 words long. This is the average number of words a person reads of each article which catches their eye.