Thursday, December 07, 2006

Neanderthal genome: My testable, falsifiable, risky, common ancestry prediction

As stated on my Why I (a Creationist) Accept Common Ancestry (Not Evolution) page,

[Graphic: click to enlarge: Nuclear DNA: Divergence time from common ancestor of Neanderthals and Homo sapiens, Berkeley University]

I originally held that God separately created basic kinds de novo without actual common ancestry, and argued that the universality of the genetic code and of basic biochemistry was the result of common design, not common descent.

I later realised that this was a fallacy of false dilemma because there are not two, but three possibilities: 1. design without descent (e.g. separate creations); 2. descent without design (e.g. atheistic evolution); and 3. design with descent (e.g. theistic evolution, mediate creation-my position now).

However, well before that, in 1995, I reluctantly had to admit defeat of my then separate creationist position, because of evidence like the vitamin C pseudogene in all higher primates (including monkeys, apes and man) but rarely in other mammals:

"The classic example of a unitary pseudogene is the gene that presumably coded the enzyme L-gulono-γ-lactone oxidase (GLO) in primates. In all mammals besides primates (except guinea pigs), GLO aids in the biosynthesis of Ascorbic acid (vitamin C), but it exists as a disabled gene in humans and other primates." (Pseudogene, Wikipedia).

I had to accept this was the result of common ancestry (i.e. design with descent) on the same principle later stated by Old Earth Creationist Dick Fischer (who also accepts common ancestry) that "It is one thing to suggest that God may have modeled our DNA along the same lines as lower animals .... It is quite another to assert that God also incorporated all the excess nonfunctioning baggage too":

"An examination of the human DNA molecule, the genetic blueprint of man, shows that many of the same sorts of genes and gene sequences are found in lower animals. Some creationists would say this is not surprising. Since man has many of the same physiological functions as lower animals, our DNA naturally would carry comparable information. Thus the argument has been made that any resemblances in DNA mean only that God used similar gene sequences to order similar functions. Although there may be a commonality of design, as the argument goes, that does not prove common descent. ... The case for common design but no common descent becomes suspect when the entire human DNA sequence is analyzed, and copying errors are found in the same places in the DNA of non-humans. In addition to genes that function normally, we have nonfunctioning genes as well, called `pseudogenes.' Our DNA sequence is a complicated set of instructions that appears to have a long history of replications, and therefore contains an abundance of pseudogenes. Humans have pseudogenes incorporated along the entire DNA sequence that can also be found in other animals, i.e., the chimpanzee and gorilla. It is one thing to suggest that God may have modeled our DNA along the same lines as lower animals, such that similarities are due to like genes ordering a protein sequence serving a like function. It is quite another to assert that God also incorporated all the excess nonfunctioning baggage too." (Fischer, D., "The Origins Solution: An Answer in the Creation-Evolution Debate," Fairway Press: Lima OH, 1996, pp.64-65).

Another quote I later found that expressed this same idea was the following by the late paleontologist Colin Patterson, that "in the law courts ... cases of plagiarism or breach of copyright will be settled in the plaintiff's favour if it can be shown that the text (or whatever) is supposed to have been copied contains errors present in the original":

"Darwin could not possibly have predicted that the hereditary material (of which he knew nothing) would turn out to be littered with ... meaningless repeated sequences like the shared Alu sequences in apes and humans ... An interesting argument is that in the law courts (where proof `beyond reasonable doubt' is required), cases of plagiarism or breach of copyright will be settled in the plaintiff's favour if it can be shown that the text (or whatever) is supposed to have been copied contains errors present in the original. Similarly, in tracing the texts of ancient authors, the best evidence that two versions are copies one from another or from the same original is when both contain the same errors. A charming example is an intrusive colon within a phrase in two fourteenth-century texts of Euripides: one colon turned out to be a scrap of straw embedded in the paper, proving that the other text was a later copy. Shared pseudogenes, or shared Alu sequences, may have the same significance - like shared misprints they can have come about only by shared descent." (Patterson, C., "Evolution," [1978], Cornell University Press: Ithaca NY, Second edition, 1999, p.117).

The same assumption is made in reconstructing as near as possible the original Greek text of the New Testament (which our modern translations are based on), that "Those [manuscripts] which share some peculiar feature of spelling or wording, or some common error, are probably related to one another and have a common archetype":

"The special character of the New Testament has given rise to special types of errors over and above those which are common in all manuscript copying. ... The study of these witnesses to the original text and the restoration by their means of the original text as nearly as it can be determined belong to the science of Textual Criticism. This is not, of course, a science which has to do specially with the New Testament or the Bible as a whole; it makes its contribution to all kinds of literature. In English literature it is a very necessary science in the study of the works of Shakespeare and the determining of his original text by the comparative study of the early editions. There are four principal stages in the work of the textual critic. First, he makes a study of such individual manuscripts as are available to him, correcting obvious slips and taking cognizance of what appear to be scribal alterations, whether accidental or deliberate. Next, he arranges these manuscripts in groups. Those which share some peculiar feature of spelling or wording, or some common error, are probably related to one another and have a common archetype. There are different ways of grouping manuscripts, according as their evident relation to one another is more or less close. Those whose mutual relation can be fairly precisely established are said to constitute a family. But a number of separate families, while they are diverse from one another in many respects, may have a sufficient number of significant features in common to suggest that they all represent one rather early textual type. In the third place. when the arranging of manuscripts in groups leads to the establishment of an archetype for each of the groups which have been distinguished, these archetypes themselves are subjected to comparative study in the hope that it may be possible to reconstruct a provisional archetype from which the archetypes themselves are descended; if this is achieved, then we have arrived as closely as we can to the autographic text." (Bruce, F.F., "The Books and the Parchments: Some Chapters on the Transmission of the Bible," [1950], Pickering & Inglis: London, Third Edition, 1963, pp.178-179)

In a debate on a forum I used to be on, with a separate creationist who agreed with Cornelius (George) Hunter's view that "the creator formed the species out of nothing" (my emphasis):

"Here I will briefly summarize four very different approaches. Ex nihilo and de novo creation mean the creator formed the species out of nothing, or out of nonliving matter, respectively. The species were not formed as derivatives from preexisting species. This is the most interventionist of all approaches, and there has been substantial religious feeling against it for this reason. Many feel that God would not be so involved with the details of creation. The fact that the world is not always harmonious has served to increase the opposition. Despite its metaphysical opposition, I believe this approach continues to provide the best empirically-based and parsimonious explanation for the origin of species .. Indeed, though the evaluation of scientific evidence is ultimately subjective, I believe it supports ex nihilo creation better than the other approaches." (Hunter, C.G., "Darwin's Proof: The Triumph of Religion Over Science," Brazos Press: Grand Rapids MI, 2003, pp.124-125. Emphasis original)

I made then a testable, falsifiable prediction that same Endogenous Retroviral Sequences (ERVS) found in apes and man, e.g.:

"The human endogenous retrovirus type II (HERVII) family of HERV genomes has been found by Southern blot analysis to be characteristic of humans, apes, and Old World monkeys. New World monkeys and prosimians lack HERVII proviral genomes. Cellular DNAs of humans, common chimpanzees, gorillas, and orangutans, but not lesser ape lar gibbons, appear to contain the HERVII-related HLM-2 proviral genome integrated at the same site (HLM-2 maps to human chromosome 1). This suggests that the ancestral HERVII retrovirus(es) entered the genomes of Old World anthropoids by infection after the divergence of New World monkeys (platyrrhines) but before the evolutionary radiation of large hominoids." (Mariani-Costantini, R., Horn, T.M. & Callahan, R., "Ancestry of a human endogenous retrovirus family," Journal of Virolology, Vol. 63, No. 11, November, 1989, pp.4982-4985)

will also be found in Neanderthal nuclear DNA (i.e. not mitochondrial DNA) when that part of its genome is sequenced (see "Neanderthal yields nuclear DNA," BBC, 16 May 2006, and more recently, (Fox, M., "Neanderthal DNA shows we're quite separate," ABC/Reuters, 16 November 2006), which as far as I am aware it has not yet been.

But (from memory) the separate creationist (and indeed no other separate creationist on the forum) was willing to make a similar testable, falsifiable prediction that the same ERVS would not be found in Neanderthal nuclear DNA that are found in apes and Homo sapiens nuclear DNA.

From memory I did not include the vitamin C pseudogene because the debate was not about that. But, again assuming that that part of the Neanderthal nuclear DNA has not yet been sequenced and published, I will here now add it to my earlier prediction.

I hereby publicly make a testable, falsifiable, risky (see `tagline' quote), prediction that the same: 1) endogenous retroviral sequences (ERVS) found in apes and Homo sapiens; and 2) vitamin C pseudogene found in primates (including monkeys, apes and Homo sapiens); will both also be found in Neanderthal nuclear DNA, when those sections of its genome are sequenced (if they have been, I am not aware of it and I would appreciate a link to the relevant journal article, etc).

I invite any separate creationist who denies that apes, Neanderthals and Homo sapiens share a common ancestor, and is willing to identify him/herself, to make in the comments of this post (anonymous comments will be rejected), the alternative testable, falsifiable, risky, prediction that the same: 1) endogenous retroviral sequences (ERVS) found in apes and Homo sapiens; and 2) vitamin C pseudogene found in primates (including monkeys, apes and Homo sapiens) will not also be found in Neanderthal nuclear DNA, when those sections of its genome are sequenced.

Stephen E. Jones, BSc (Biol).


"Popper saw that a theory that appears to explain everything actually explains nothing. If wages fell this was because the capitalists were exploiting the workers, as Marx predicted they would, and If wages rose this was because the capitalists were trying to save a rotten system with bribery, which was also what Marxism predicted. A psychoanalyst could explain why a man would commit murder- or, with equal facility, why the same man would sacrifice his own life to save another. According to Popper, however, a theory with genuine explanatory power makes risky predictions, which exclude most possible outcomes. Success in prediction is impressive only to the extent that failure was a real possibility." (Johnson, P.E., "Darwin on Trial," [1991], InterVarsity Press: Downers Grove IL, Second Edition, 1993, p.148).

4 comments:

Steve said...

Hi
Because we share some alleged ERV's with chimps. It is thus suggested as proof for our common descent, that we both must have originated from a specie that was infected by this virus. The first problem with this argument is that it's hard to tell what an ERV is when you meet one. It doesn't come with a tag attached saying: "This is an ERV". It could be that some genes which we expect to be ERV's aren't ERV's but something completely different, or it could even be junk genes, byproduct. That is because a virus will rarely be embedded in it's complete form. To explain this, let my use a simplified example. Imagine a woman who has a flu and the virus gets embedded and passed on to a fertilized egg cell. This is of course unlikely because the common flu virus is usually not located near the ovaries, but indulge me for the sake of argument and simplicity. The child would have a flu in every single cell of his body. His cells would constantly reproduce this virus, and spread it throughout it's body. You can imagine this fetus doesn't have a fighting chance from the start on. No, for an ERV to be passed down trough generations, it has to be rendered harmless first. So how do you recognize it as a virus after this rendition to harmless junk then?

A second problem of the argument, is it's slippery slope. What if both chimps and humans were infected by the virus, and both got ERV's in a similar fashion? After all, given their similar physiology, that seems reasonable enough right? Well the reply from evolutionists is, that the ERV is specific in a certain locus (place on the genes) and it is improbable for both chimps and humans to create an ERV at the exact same spot. However, I disagree. There is a recent discovery at the university of Pennsylvania US that shows a human DNA-associated protein that would dictate where on the DNA AIDS is to be inserted. The protein called LEDGF would travel along with the retrovirus in it's mantel and then modulate where in the human genome the virus is inserted. So if retroviruses can be locus specific, then loci-specific ERV's is no longer a problem for creationists. It is then a matter of simple causality. Not only similar results by common design; but also similar results by similar processes of viruses become endogenous.

Stephen E. Jones said...

Steve

Thanks for your comments.

>it's hard to tell what an ERV is when you meet one ...

Have you any references from the scientific literature to back this up?

That is, it is *impossible* to tell the difference between an ERV (endogenous retrovirus) sequence and "something completely different"?

>the reply from evolutionists is ...

I am not an evolutionist. I am a *creationist* who accepts the evidence for universal common ancestry.

>... a recent discovery ... a human DNA-associated protein that would dictate where on the DNA AIDS is to be inserted.

Have you any references from the scientific literature which says *an ERV* must start at the same locus in both chimps and humans (itself evidence of common ancestry that there *are* the same loci in both species!)?

Stephen E. Jones

Steve said...

> ... Have you any references from the scientific literature to back this up?

Not directly no. To be honest I'm not an expert on the field of ERV's I'm simply questioning, how do you tell an embedded virus from just any other part of DNA? Well I imagine that
A) By comparison to known viruses
B) Because the function of the genes are typical to viruses.
There are some ERV's like the Phoenix virus that have been proven as ERV trough method (A). But to do the same for a million old virus, would be nearly impossible, because we simply don't have any samples of ancient viruses to compare to as far as I am aware of. In the case of method (B), that is of course subject to interpretation and highly debatable.

> ..I am not an evolutionist. I am a *creationist* who accepts the evidence for universal common ancestry.

Yes I got that from reading your blog. I didn't intend to attack you directly, this was simply a copy paste from my own website. Sorry if some parts were inappropriate :)

> ..Have you any references from the scientific literature which says *an ERV* must start at the same locus in both chimps and humans (itself evidence of common ancestry that there *are* the same loci in both species!)?

No, I haven't. It would also be very troublesome to collect such evidence because these ERV's are mostly ancient viruses and viruses tend to constantly change dramatically, so it would be impossible to know exactly how the ancient virus worked. However, since we know there are proteins today which do this in current retrovirus we can't exclude the same would have happened in the past. The mere plausibility of this possibility is sufficient to render the argument of ERV's inconclusive. If those who believe in common ancestry wish to prove their viewpoint by use of ERV's, the burden of evidence (or in this case counter-evidence) is with them.

(sorry if this is a double post, I didn't seem to get confirmation for the first submittion, so I'm posting it again just to be safe)

Stephen E. Jones said...

Steve

>> ... Have you any references from the scientific literature to back this up?

>Not directly no. ...

>> ..Have you any references from the scientific literature which says *an ERV* must start at the same locus in both chimps and humans (itself evidence of common ancestry that there *are* the same loci in both species!)?

>No, I haven't. ...

Then I am not interested in discussing it further.

Stephen E. Jones