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

Obviously you didn't understand what I wrote.

On Fri, Oct 16, 2009 at 9:07 AM, Dehler, Bernie <bernie.dehler@intel.com>wrote:

> 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”*
>
>
> http://www.amazon.com/Descent-Man-Concise-Charles-Darwin/dp/0452288886/ref=sr_1_2?ie=UTF8&s=books&qid=1255663893&sr=8-2
>
> 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?
>
>
>
> Dennis,
>
> 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)
>
> [quote]
> 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>
> ).
> [unquote]
>
>
> 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.
>
> 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.
>
>
>
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>
> On Thu, Oct 15, 2009 at 1:22 PM, Dennis Venema <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.
>
> Dennis
>
>
>

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Received on Fri Oct 16 14:11:18 2009