[asa] more on pseudogenes (was: ID question?)

From: Dehler, Bernie <bernie.dehler@intel.com>
Date: Fri Oct 16 2009 - 10:07:15 EDT

David Clounch said:
"OK, so pseudogenes are one more way molecular biologists make a probabilistic inference that two organisms have a common ancestor. How does this change the situation of the same inference before pseudogenes were discovered? I see nothing especially earth shattering that wasn't already known with functional genes. So I suspect Bernie once again is overclaiming."

It isn't simply a matter of similarity. It is a matter of known genes having real applications in ancestral lifeforms, then seeing non-functional messed-up copies of those same genes in descendent life-forms, that of course now have no function (because they are busted, thus, called pseudogenes).

An interesting quote, regarding the human sense of smell and pseudogenes:

RE: "The Descent of Man: The Concise Edition"
Pg. 22

"The human genome contains 388 working genes for olfactory receptors, and 414 pseudogenes. By contrast, a mouse has 1,037 working genes, and 354 pseudogenes.

  By comparing the human and mouse genomes, scientists have reconstructed the rise and fall of olfactory receptor genes. All of the genes, broken or functional, in both mice and men, originated in an ancestral set of 754 functional genes. Those genes made receptors in the nose of a small mammal that lived approximately 100 million years ago. In the lineage that produced today's mice, many of those original genes were duplicated, and most of those duplicates still work today. In the lineage leading to humans, on the other hand, many more of the ancestral genes became pseudogenes. We carry some new duplicates of the ancestral genes, but far fewer than mice do. Many pseudogenes have disappeared altogether from the human genome"

From: David Clounch [mailto:david.clounch@gmail.com]
Sent: Thursday, October 15, 2009 5:13 PM
To: Dennis Venema
Cc: Ted Davis; asa; Dehler, Bernie
Subject: Re: [asa] ID question?


I would like to quote from wikipedia (admittedly not a good place to quote from, but its handy and I dont think its terribly far off the mark)

Homology is implied by sequence identity between the DNA sequences of the pseudogene and parent gene. After aligning<http://en.wikipedia.org/wiki/Sequence_alignment> the two sequences, the percentage of identical base pairs<http://en.wikipedia.org/wiki/Base_pair> is computed. A high sequence identity (usually between 40% and close to 100%) means that it is highly likely that these two sequences diverged from a common ancestral sequence (are homologous), and highly unlikely that these two sequences were independently created (see typewriting monkeys<http://en.wikipedia.org/wiki/Typewriting_monkeys>).


The key factor to keep in mind is the metric that a protein (remember, coded for by DNA) in two different organisms is sooooooo unlikely to arise twice due to random chance that the inference of common ancestor is reasonable. This is a probabilistic argument. Period.

But probabilistic arguments are the basis for Behe's red-ball versus green-ball billiard game.
I'd like to see Iain Strachan's bayesian analysis of the protein argument versus the pseudogene
argument versus the red-ball argument. One has to look at the numbers. What constitutes a rare likelihood anyway? Again, Bernie has jumped to a conclusion not warranted by his (lack of) demonstration of the numbers.

Let me define some things so I am more clear.

Very very likely, to me, is one part in ten billion parts.

Highly likely, to me, means greater than 1 part in ten to the 35th power parts. (This is an arbitrary boundary). That means you need one trillion moles of organisms to get 1 existent feature. If the likelihood is less than that it isnt high.

Moderate likelihood, to me, is one part in 10 to the 300th power parts.

Unlikely, to me, is one part in ten to the 60,000th power parts. Cosmological inflation is less likely than this (its that highly fine tuned).

Highly likely, to the wikipedia author, seems to be one part in 1000 parts. Thus we aren't even communicating. Do you see why I think the conversation here is all BS (Baloney Saturated)? The analysis is inadequate. One must think like a chemical engineer.

I do apologize for quoting wikipedia.

On Thu, Oct 15, 2009 at 1:22 PM, Dennis Venema <Dennis.Venema@twu.ca<mailto:Dennis.Venema@twu.ca>> wrote:

TED: I agree with you, Bernie: the genetic evidence, esp that coming out of the human genome project, is creating something of a crisis for some in the OEC camp. I also agree with your implicit definition of the OEC/TE division. Referencing my comments above, I add that for many (most?) ID proponents, the genetic evidence is equally capable of producing second thoughts. Their way out of this seems to be to keep pushing the possibility, however remote, that pseudogenes of the kind you have pointed to (vitamin C being a prominent example) really do have functions that will someday be discovered. It is not IMO unscientific to take that strategy, but it does seem more than a bit ad hoc. Copernicus, for example, realized that heliocentrism required the universe to be at least 1000 times bigger in radius than previously thought, since stellar parallax could not be detected in his day. He took the ad hoc response to the observational problem. Most of his contemporaries did the obvious thing: they continued to deny the motion of the earth, and thus the absence of visible parallax was to be expected. The ID proponents in this case are compared with Copernicus -- except that we now know Copernicus was right, and we certainly do not know that the ID proponents are right. They are betting on future knowledge turning out in their favor. By contrast, in their criticisms of Darwinian evolution, they are betting on future knowledge *not* turning out in favor of Darwinian mechanisms that are presently unknown.


A brief comment about pseudogene evidence and parallels to Copernicus: Copernicus was investigating a question at the limits of current technology and could not draw from other lines of evidence. That is not the case here: for pseudogenes, we can see what these sequences do in other organisms (for example the vitellogenin locus I discussed in my ASA talk this summer). We can also see that the pseudogenes are in the right genomic location in different organisms, as common descent would predict (synteny). We can also see that they retain amino acid homology even though most are no longer transcribed or translated (redundancy). Moreover, we can find pseudogenes that strongly suggest adaptation for ways of life the organism no longer uses (again, the vitellogenin gene is a good example: this gene is an egg yolk component in amniotes, but humans are placentals.)

So, Copernicus had to go the ad hoc route for absence of the ability to gather more evidence. Those who deny common descent and give ad hoc appeals to unknown pseudogene functions do so *in the face of several converging lines of evidence* that point to the same conclusion: that humans share ancestry with other forms of life. So, while there are similarities here, there are also significant differences.

The comparison might be more valid at the time when stellar parallax was first measured, providing a second line of evidence for heliocentricity.

my 2 cents.


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