Rare example of Darwinism seen in action (Deluded Darwinists alert)

EurekAlert ^ | July 31, 2007

[GodGunsGuts]

RIVERSIDE, Calif. – A research team, including UC Riverside biologists, has found experimental evidence that supports a controversial theory of genetic conflict in the reproduction of those animals that support their developing offspring through a placenta.

The conflict has been likened to a “battle of the sexes” or an “arms race” at the molecular level between mothers and fathers. At stake: the fetus’s growth rate and how much that costs the nutrient-supplying mother.

The new research supports the idea of a genetic “arms race” going on between a live-bearing mother and her offspring, assisted by the growth-promoting genes of the father...

[GodGunsGuts]

==The fact that out of over 10,000 pseudogenes in the typical mammalian genome, there are some transcriptinally active ‘pseudogenes’ that do have a function and do not change at the neutral mutation rate tends to reinforce the theory that it is functionality that leads to conservation. An exception that reinforces the rule doesn't contradict my point.

As I have pointed out over and over, according to Balakirev and Ayala "pseudogenes that have been suitably investigated often exhibit functional roles." The key word in that sentence is "often." That seems to indicate that, far from being the exception, functional pseudogenes are quite common and may prove to be the rule (which by the way, Creationists have been predicting all along). I have also demonstrated that supposedly functionless ERVs (such as ERVWE1) are so functional that they have been elevated to the status of an actual gene. In short, your blanket generalizations about pseudogenes and ERVs have been proven false. Finally, the fact that functional ERVs and pseudogenes are preserved is uncontroversial, as it has to do with that aspect of natural selection that is accepted by both camps.

==Why is the Vitamin C Synthase pseudogene (should I say “TRUE pseudogene” from now on?) present at all if not as a relic of evolution?

Simple. It has mutated since it was first created.

==It (Vitamin C Synthase gene) has been shown to have no function, and it changes at the neutral mutation rate. Yet despite this higher mutation rate it shows the SAME disabling frameshift mutation at exactly the same position in primates; yet a different disabling mutation in guinea pigs.

Actually, if you read the following, sent to me by one of my creationist friends, it would appear that the Vitamin C Synthase gene cannot be used as evidence for common descent of primates. Indeed, the best explanation for the same is non-random mutation based on a common mechanism (i.e. "hot spots"), which points to either special creation or directed, non-random saltationism:

There are many deletion and substitution mutations in the LGGLO pseudogene. Although not all, many are indeed shared between humans, chimps, orangutans, and macaques, and also between guinea pigs (all relative to the rat).

What is interesting here is that the sequences of human, chimpanzee, gorilla and orangutan reveals a single nucleotide deletion at position 97 in the coding region of Exon X in all primates. What are the odds that out of over 160 base pairs the same one would be mutated in all these primates by random chance? Pretty slim - right? Is this not then overwhelming evidence of common evolutionary ancestry?

Well, in 2003, the same Japanese group published the complete sequence of the guinea pig LGGLO pseudogene and compared it to that of humans [Inai et al, 2003]. They reported seven shared mutations (substitutions) present in both organisms. Remember now that humans and guinea pigs are thought to have diverged at the time of the common ancestor with rodents. Therefore, a mutational difference between a guinea pig and a rat should not be shared by human with better than random odds. But, this wasn't what was observed. Many mutational differences were shared by humans - including the one at position 97. The probability of the same substitutions in both humans and guinea pigs occurring at the observed number of positions was calculated to be 1.84x10-12 - consistent with mutational hotspots (author's conclusion). Remarkably, the mutational hot spots found in guinea pigs and humans exactly match the mutations that set humans and primates apart from the rat.

How common are these mutational hotspots in Exon X? The data shows that 11 out of 21 positions of exon X are shared and line up as the result of mutational hot spots – that is more than 50 percent. Even the single nucleotide deletion at position 97 is a non-random position. If non-random mutations make up 50-70 percent of the mutations in a DNA sequence they would have dramatic consequences for the molecular evidence of common descent.

I strongly suggest reading the following paper...very eye opening re: common mechanism vs. common descent:

http://www.iscid.org/papers/Borger_SharedMutations_061506.pdf

[GodGunsGuts]

Hi guys, I strongly suggest you read the exchange between allmendream and myself from #161 to the end. I think the so-called ERV and pseudogene “smoking gun” evidence of common descent may be falsified. All the best—GGG

[GodGunsGuts]

In case you’re confused by the terminology:

LGGLO pseudogene = GULO pseudogene = Vitamin C Synthase gene.

[allmendream]

If, when speaking of the rule that things denser than water sink and things less dense than water float, I say “wood floats and rock sinks”; it doesn’t argue against the rule when you demonstrate that pumice (a rock) will float and Ironwood will sink. No, both are exceptions that prove the rule.

Both the transcriptionally active pseudogene you mention and the ERV ‘gene’ have function and are conserved; this makes them exceptional in that most pseudogenes and ERV’s do not have a function and are not conserved.

The opinion of Balakirev and Ayala has not been confirmed. The pseudogenes that have been ‘suitably’ investigated for function have been ones that have been shown to be conserved. In the specific case of the human Vitamin C synthase gene, no function has been shown, the same type of function is impossible as it produces a truncated transcript (the STOP codon), and it has been seen to change at the neutral mutation rate.

[allmendream]

In the next example we see that of the chickens 51 retroposed pseudogenes (compared to 15,000 in mammalian genome) 36 are clearly pseudogenes (not transcribed, frameshift, STOP codon), and of the 15 only 8 show conservation are are likely to serve a function. This ratio of functionality would probably be even less in mammals who have active Line-1 elements. Once again conservation is tied to function.

http://www.nature.com/nature/journal/v432/n7018/full/nature03154.html;jsessionid=C279A286BEA0F619ED2D5E7AB7FE2711

Only 51 duplicates of protein-coding genes probably formed by retroposition (that is, exhibiting loss of introns)51 were identified in the chicken genome, in contrast to the more than 15,000 cases observed in mammalian genomes3, 52. In mammals, the ancient LINE1 (L1) transposable element is responsible for the origin of most if not all retroposed (pseudo) genes53. Although birds host their own LINE-like elements (chicken repeat 1 (CR1); see below)54, the reverse transcriptase encoded by these elements is unlikely to copy polyadenylated mRNAs55, probably explaining the paucity of processed pseudogenes in chicken. Within the set of 51 (Supplementary Table S4), 36 clearly represent pseudogenes, because their former coding regions are disabled by alterations (including frameshifts and premature stop codons) that preclude protein function. Among the remaining 15 elements, eight show strong evidence for selective constraint (Supplementary Table S4) and therefore may represent functional retroposed genes. We found no clear bias towards either particular gene families or chromosomal locations for the retrocopies (Supplementary Table S4).

http://www.nature.com/nature/journal/v432/n7018/full/nature03154.html;jsessionid=C279A286BEA0F619ED2D5E7AB7FE2711

[GodGunsGuts]

==If, when speaking of the rule that things denser than water sink and things less dense than water float, I say “wood floats and rock sinks”; it doesn’t argue against the rule when you demonstrate that pumice (a rock) will float and Ironwood will sink. No, both are exceptions that prove the rule.

Not a good analogy. We are comparing pseudogenes to pseudogenes, ERVs to ERVs. You would have to demonstrate a difference analogous to sinking wood and floating rocks. You have not.

==Both the transcriptionally active pseudogene you mention and the ERV ‘gene’ have function and are conserved; this makes them exceptional in that most pseudogenes and ERV’s do not have a function and are not conserved.

You have not demonstrated this either. You said that pseudogenes have no function. I have demonstrated that pseudogenes that have been “properly investigated” are proving to be functional. This means that the neo-Darwinian assumption that “junk DNA” have no function is now in doubt, and that we now have good reasons to expect that other so-called “junk DNA” will also prove to be functional.

==The opinion of Balakirev and Ayala has not been confirmed. The pseudogenes that have been ‘suitably’ investigated for function have been ones that have been shown to be conserved. In the specific case of the human Vitamin C synthase gene, no function has been shown, the same type of function is impossible as it produces a truncated transcript (the STOP codon), and it has been seen to change at the neutral mutation rate.

But as I have already shown, the study of the non-functioning Vitamin C Sythase gene/Gulo gene/LGGLO gene suggests a common mechanism rather than common descent. Moreover (again, as already mentioned), “the mutational hot spots found in guinea pigs and humans exactly match the mutations that set humans and primates apart from the rat.”

Thus if random mutation is correct, the analysis of the Vitamin C Synthase/GULO/LGGLO pseudogene suggests that the guinea pig is much closely related to humans than it is to rats! So the so-called “smoking gun” of common descent turns out to be one of the best examples AGAINST common descent...Unless, of course, you are positing that guinea pigs are indeed more closely related to humans than to rats!!!

[GodGunsGuts]

Unfortunately, I have to go to work. To be continued...

[Alamo-Girl]

Thanks for the ping!

[AndyTheBear]

no ultimate meaning in life exists

Then why would an evolved creature need there to be one?

If evolution could make the eye work in the vast majority of us, certainly it could have weeded out delusions of the numinous.

[betty boop]

Taking your advice GGG, I've been following along this conversation you are having with allmendream and others. I'm enjoying it so much! Thank you! and also thank you for the valuable links.

It seems the issue we are grappling with here finds resolution either in natural selection or natural purpose (functionality). (Or is it maybe both? -- i.e., are they complementarities in Niels Bohr's sense?)

We know that historically, Darwin's theory has had no truck with "teleology," or the theory that nature (and the universe) is purposeful in any way, shape, or form. That is, directed in such a way as to achieve goals, or fulfill ends.

Since I believe that nature, the living universe, expresses purpose at all levels, it has long seemed to me that there is no such thing as "junk DNA," now called by the currently fashionable moniker, "pseudogene." It seems to me such terms are "cop-outs," placemarkers denoting something that we do not (yet) know of or understand.

But really, I'm just taking it all in, and plan to be silent, leaving the issue to you and allmendream....

I'm grateful to you both for the opportunity to be an attentive, interested bystander!

[allmendream]

Glad you are enjoying the exchange.

Science itself is unable to ascribe motive or purpose to the universe because it it immeasurable, like beauty or music. That isn’t to say it is not without value. I too ascribe purpose to this miraculous universe and unlimited admiration of the rules by which it is governed; but I know it is philosophical or theological not scientific.

The concept of “junk” DNA has been exactly that, a place-marker awaiting further study. It is often spoken with the scare quotes. There are a lot of non-gene elements that have obvious function in transcription control and DNA packaging, still others are obviously mutated copies of other genes ‘psuedogenes’ or a mutated copy of a viral genome ‘ERV’s’ or staggered repeats. In all cases functionality is clearly tied to increased conservation between related species, and non-functionality is tied to decreased conservation and change is at the neutral mutation rate.

Indeed there was a recent study that called into question the assumption that a particular repeat element (a different type of “junk” DNA) had no function, however they did not show any function for this repeat, they just indicated that it ‘stood out from the crowd’ in regards to conservation between species. Most pseudogenes and ERV’s and repeat elements will change at the neutral mutation rate, but these repeat elements showed some conservation indicating that they might have a function (showing the predictive power of the theory). If it turns out that they do show a function for this particular repeat element (and I eagerly await the finding that would once again confirm the predictive power of the theory of neutral mutation and common descent), it will not show that all repeat elements have a function, only indicate that the ones that show conservation is a good place to look.

[allmendream]

In the analogy:

Rule: “denser than water sinks. less dense than water floats”

Rule: “functional DNA shows high conservation between related species. nonfunctional DNA shows lower conservation and changes at the neutral mutation rate.”

General Observation: “Wood floats. Rocks sink.”

General Observation: “Genes are conserved. Pseudogenes and ERV’s change between species is at the neutral rate.”

Exceptions that Reinforce the Rule: “Pumice is a stone that floats (it is less dense than water). Ironwood is a wood that sinks (it is more dense).”

Exceptions that Reinforce the Rule: “A Pseudogene shown to have a transcript with a function shows conservation between related species. A ERV “gene” has a function and also shows conservation.”

[betty boop]

If it turns out that they do show a function for this particular repeat element (and I eagerly await the finding that would once again confirm the predictive power of the theory of neutral mutation and common descent), it will not show that all repeat elements have a function, only indicate that the ones that show conservation is a good place to look.

Then by all means we should go look! And then I'd say, just "let the evidence speak for itself."

The problem is, evidence never can speak for itself: It has to be interpreted by human observers in order to have any meaning at all. In short, people who agree about the evidence can nonetheless draw different conclusions....

And it seems to me there is a vast difference in the results that can obtain from different "initial conditions" or presuppositions. This is what different human observers bring to the party, differently, presumably according to their own best lights.

There is a huge difference of presupposition between the assumption of a common ancestor at the root of biological evolution/speciation, the assumption of neutral mutation and common descent; and the assumption of a principle that serves as a "guide to the system" of biological life -- in a dynamic, living universe, as elaborated in Genesis 1.

The thought has struck me that we can agree all day long on the evidence before us, and still disagree on what it all means.

I am heartened to see in you a total recognition of the splendor and glory of the universe. I assume that you recognize that there is no way that such a production could have been assembled by blind chance.

Thank you so very much for your astute, able, and insightful contributions to this thread, allmendream!

Now, please just allow me to be a "fly on the wall" for a duration....

[Coyoteman]

There is a huge difference of presupposition between the assumption of a common ancestor at the root of biological evolution/speciation, the assumption of neutral mutation and common descent; and the assumption of a principle that serves as a "guide to the system" of biological life -- in a dynamic, living universe, as elaborated in Genesis 1.

The thought has struck me that we can agree all day long on the evidence before us, and still disagree on what it all means.

You are saying that all interpretations are of equal value. I do not agree. That way lies madness!

I know this is contrary to the new age, touchy-feelie, postmodern, multicultural, preserve-self-esteem-at-all-costs way of thinking, but that's the sad fact of how things really are. Some interpretations are absolutely worthless.

[Alamo-Girl]

Thank you so much for your beautiful essay-posts, dearest sister in Christ! I too am enjoying the sidebar.

There is a huge difference of presupposition between the assumption of a common ancestor at the root of biological evolution/speciation, the assumption of neutral mutation and common descent; and the assumption of a principle that serves as a "guide to the system" of biological life -- in a dynamic, living universe, as elaborated in Genesis 1.

The thought has struck me that we can agree all day long on the evidence before us, and still disagree on what it all means.

So very true. Of course, I agree with your perception of cosmos - that it has a First Cause and a Final Cause. And we call Him Alpha and Omega, Jesus Christ.

And it is certainly true that people - including scientists - will often look at the same evidence and disagree on what it means. The angry debates in the historical sciences (e.g. archeology) are legend. LOL!

[allmendream]

Absolutely not by blind chance. Randomness in mutation no more precludes a role for the author of creation than randomness in quantum mechanics. We are miraculous creations, but just as I think the heavens and the earth were created under the observance of natural laws, I think mankind was created from “dust” by the laws of nature that the lawgiver set in place.

Ok. Fly on the wall. ;)

[BlueDragon]

"...people - including scientists - will often look at the same evidence and disagree on what it means. The angry debates in the historical sciences (e.g. archeology) are legend. LOL!"

Ben reading some back issues of Biblical Archaeology Review, have you?

I'm only kidding around here, mentioning that particular publication, but I do remember there being some long running, heated exchanges, back about ten years or so. I haven't kept up with it, much at all since then.
For the lurkers here, I'll add that these disputes that I'm referring to where not concerning matters of theology, or disputes of a 'religious' nature, but were instead, between those that held mainly 'secularist historian' viewpoints.

[BlueDragon]

woops, spelled “Been”, not with only one “e”. I really wasn’t asking about anyone named “Ben”, there, AG.

[Alamo-Girl]

The Biblical Archeology Review is a great example. Thank you, BlueDragon!

Some of the behavior became embarrassing, IMHO - unlike the scholar disputes over where exactly the temple was located.

[BlueDragon]

"I think mankind was created from “dust” by the laws of nature that the lawgiver set in place."

Has it ever, sort of jumped out at 'ya, that if "mankind" really has been tens of thousands of years, if not much longer, not too far from being in his near-to-present-day, genetic "form", why is that we don't see much of the remains of civilizations, going back more than something less than six thousand years?

Old campfires, maybe, possibly dated to be being older than six thousand, and some cave paintings, called older...but nothing much significant, like buildings or cities, and certainly not "writings" exhibiting developed language usage.

Now don't get me wrong here...I'm certainly not saying that the earth, or "man" [be it some form or hominid?] has only existed for 6 thou...
but something changed, about that far back, and the animal we know of as being "man', began to behave quite differently than before. Or so the archaeological evidence suggests, anyway...