Odd fly uncovers evolution secret [speciation]

BBC News ^ | 20 April 2005 | Staff

[DannyTN]

Here's an article recaping opinions from several Creationist PHD's in Geology that answers many of your questions about tracks and burrowings. Below it, I'll quote some key excerpts.

FootprintsInStone

On Burrowings

"Modern marine and terrestrial organisms are 'biological bulldozers' which so thoroughly rework and burrow recent sediments that stratification is often completely homogenized...The intensity of burrowing in sediments on land and under the sea causes us to ask a fundamental question. How could any laminae be preserved in the strata record if sediment accumulates very slowly and is in contact with burrowing organisms for so long? Some evolutionists proposed that the deep-burrowing activity of organisms had not yet evolved when most Grand Canyon strata were deposited. (Thayer, 1979) However, this opinion was strongly challenged by more recent investigators who document deep-burrow structures even in Cambrian strata. (Miller; Sheehan, 1984)." [Austin, p. 31]

On raindrop impressions

"Related to animal tracks that have been thus preserved are the many instances of preservation of ancient ripple marks or raindrop impressions. But that such ephemeral markings could have been preserved in such great numbers and in such perfection is truly a remarkable phenomenon and one for which there is little if any modern parallel. It is a matter of common experience that impressions of this sort in soft mud or sand are very quickly obliterated. It seems clear that the only way in which such prints could be preserved as fossils is by means of some chemical action permitting rapid lithification [rockification] and some aqueous action permitting rapid burial. Some sudden and catastrophic action is again necessary for any reasonable explanation of the phenomena.

On Tracks

However, the Flood didn't overrun the entire earth immediately after the ark door was sealed. We shouldn't expect all land animals and birds to get wiped out by the first encroachments of ocean water on the land. They wouldn't be as vigorous as later inundations. The Flood waters ebbed and flowed, increasing in height day by day until finally the land was submerged. Prior to that time, the deposition of marine layers over land layers would not prevent animals from running, walking, slithering or flying across the topmost layers later on. Indeed, most animals would try to escape the Flood by heading for higher ground, and animals living at higher elevations prior to the Flood would also have been spared. These would later be able to make their tracks in the mud left from earlier wave deposits.

[Ichneumon]

Please explain how all the items for evolution to occur occured first, in the correct sequence at second, the correct place and third, at the necessary time.

I'll be glad to, just as soon as you define the terms "the items for evolution to occur", "the correct sequence", "correct place", and "necessary time", as you are using them in this query.

At the moment, your question is incredibly vague, and appears to be built upon several faulty premises.

[From many - one.]

That's right, it was an inversion, a type of "rearrangement."

IOW a beneficial mutation and one that did not diminish the information.

That's how it works. The issue was your assumption that mutations cause a loss of information.

This was an example of one that doesn't.

[Ichneumon]

[You have no idea of the difficulties inherent in the "not enough time" (6-10 thousand years) hypothesis in explaining the world we see. No doubt this is a conscious decision on your own part not to know some things.]

The only difficulty would be for you because it would involve God.

Horse manure. The difficulties are enormous, and have nothing to do with a god or the lack thereof.

First, there are literally thousands of observations in geology that are inconsistent with the possibility that they were all formed within the timespan of only a few thousand years.

Another problem is that the biodiversity of humans, for example, is orders of magnitude greater than that which could arise in only a few thousand years from a starting genepool of either one man and one woman (using the Adam/Eve scenario) or one man and four women (using the Noah scenario).

There are more shark teeth in the sediments of the ocean than could possibly be produced by a even a ridiculously large overpopulation of sharks in only a few thousand years.

Etc. etc. etc.

[Ichneumon]

The article was interesting, but it did not prove that information is added, just rearranged.

Adding information:

Koch, AL: Evolution of antibiotic resistance gene function. Microbiol Rev 1981, 45:355378.

Velkov, VV: Gene amplification in prokaryotic and eukaryotic systems. Genetika 1982, 18:529543.

Romero, D & Palacios, R: Gene amplification and genomic plasticity in prokaryotes. Annu Rev Genet 1997, 31:91111.

Stark, GR & Wahl, GM: Gene amplification. Annu Rev Biochem 1984, 53:447491.

Reinbothe, S, Ortel, B, & Parthier, B: Overproduction by gene amplification of the multifunctional arom protein confers glyphosate tolerance to a plastid-free mutant of Euglena gracilis. Mol Gen Genet 1993, 239:416424.

Gottesman, MM, Hrycyna, CA, Schoenlein, PV, Germann, UA, & Pastan, I: Genetic analysis of the multidrug transporter. Annu Rev Genet 1995, 29:607649.

Schwab, M: Oncogene amplification in solid tumors. Semin Cancer Biol 1999, 9:319325.

Widholm, JM, Chinnala, AR, Ryu, JH, Song, HS, Eggett, T, & Brotherton, JE: Glyphosate selection of gene amplification in suspension cultures of three plant species. Physiol Plant 2001, 112:540545.

Otto, E, Young, JE, & Maroni, G: Structure and expression of a tandem duplication of the Drosophila metallothionein gene. Proc Natl Acad Sci USA 1986, 83:60256029.

Maroni, G, Wise, J, Young, JE, & Otto, E: Metallothionein gene duplications and metal tolerance in natural populations of Drosophila melanogaster. Genetics 1987, 117:739744.

Kondratyeva, TF, Muntyan, LN, & Karvaiko, GI: Zinc-resistant and arsenic-resistant strains of Thiobacillus ferrooxidans have increased copy numbers of chromosomal resistance genes. Microbiology 1995, 141:11571162.

Tohoyama, H, Shiraishi, E, Amano, S, Inouhe, M, Joho, M, & Murayama, T: Amplification of a gene for metallothionein by tandem repeat in a strain of cadmium-resistant yeast cells. FEMS Microbiol Lett 1996, 136:269273.

Sonti, RV & Roth, JR: Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources. Genetics 1989, 123:1928.

Brown, CJ, Todd, KM, & Rosenzweig, RF: Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol Biol Evol 1998, 15:931942.

Hastings, PJ, Bull, HJ, Klump, JR, & Rosenberg, SM: Adaptive amplification: an inducible chromosomal instability mechanism. Cell 2000, 103:723731.

Tabashnik, BE: Implications of gene amplification for evolution and management of insecticide resistance. J Econ Entomol 1990, 83:11701176.

Lenormand, T, Guillemaud, T, Bourguet, D, & Raymond, M: Appearance and sweep of a gene duplication: adaptive response and potential for new functions in the mosquito Culex pipiens. Evolution 1998, 52:17051712.

Guillemaud, T, Raymond, M, Tsagkarakou, A, Bernard, C, Rochard, P, & Pasteur, N: Quantitative variation and selection of esterase gene amplification in Culex pipiens. Heredity 1999, 83:8799.

[bert]

Great piece. The Crea's should commit it all to memory.

[DannyTN]

You are obviously uncomfortable with me agreeing with Patrick Henry that the Intelligent Designer has an Intelligent Eraser.

[From many - one.]

Here's one that shows just how hard it is to end up with less information.

Every line in the chart represents a viable dog and/or wolf:

http://www.kc.net/~wolf2dog/wayne1.htm

[aMorePerfectUnion]

 

 

 

Welcome to the HARD Science of Evolution!

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

An Advanced Scientific Spectrum Qualifier Analysis

of this post reveals the following qualifiers used to

buttress the claims of evolution:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

"... speculate... may... think... may...theory...

It is thought... apparent... may...  they speculate

...might...  believe...  could... "

 

 

__12__   TOTAL

 

 

Yes! By including LESS than 15 qualifiers, this article
remains in competition for the title of
Best HARD Evolution Post of 2005 on FreeRepublic!!!!!

[From many - one.]

More, not less.

In the hard sciences we qualify everything. That's because at any moment a datum could show up that changes the perspective.

That's kind of what science is all about. Effects have causes and we are going to do our best to figure them out. If it means dumping mountains of past work...so be it.

[CharlesWayneCT]

I am waiting for the Human Genome Project to do a similar complete genetic mapping on our nearest neighbor, the chimp, and then to show how they can, by sucessive change of genetic material equivalent to what might be expected by random mutation, work their way back from each current organism to a common genetic ancester -- and then to show that each step of the way represents a viable living organism.

I think that would be a pretty good validation of historical record.

In general, the fact of reuse of large amounts of genetic material is nothing more than something "consistant with" an evolutionary historical hypothesis, and in no way proves it or makes it scientific. It is just another level of the forensic-type science where, when we do a DNA test and find results much different than expected, it doesn't change in any way the "theory of evolution", but has a large effect on the historical evolution hypothesis.

I believe that just happened recently, some discovery was found to be much less of a difference with our modern genetic makeup than was "predicted" by the hypothesis.

As a believer in the non-scientific theory of creation, it makes sense to me that a creator would from time to time use common genetic material to implement common function. It is just as possible that, as a being of great capability, the creator might from time to time find different ways to implement the same function.

This is analogous to computer programming. If you look at a lot of computer programs, you will find common code. This does not suggest that one program "evolved" into another, or even that one programmer extended the one program into the other. It could be that the same programmer wrote both, or that somebody wrote a snippet of code and published it and others used it. It is not predictive to determining the history of a piece of code.

It is also common in looking at code to find that two programs which have the same function don't use the same code, even if they are written by the same programmer.

BTW, if you want to claim that your hypothesis of an evolutionary history for origins is more elegant than my creation theory, or has the attribute of not requiring a mythical higher being, I will not dispute the point. On the other hand, you would be hard-pressed to disprove my unscientific hypothesis of history that says a creator made it the way it is, since for any observation you make I can simply modify my hypothesis to fit the new observation (much like the evolution historical hypothesis is modified whenever new information is found).

The insertion of a higher being or external cause clearly puts my hypothesis outside the bounds of science, but I've never advocated teaching creation or intelligent design in science class as a scientific theory.

Did I wave my hands sufficiently for you?

[From many - one.]

As a scientist I, for one, have never had a problem with Creationists-by-Faith.

On the other hand there are those wo post either in ignorance or by design, specious to outright false arguments against evolution. I try to counter those when I have time.

My personal view is that God was not writing either a biology text or a cosmology...He was speaking to the people of the time in the language of the time and to try to read more into Genesis than that is a form of hubris. Again, my personal view, and not meant to offend.

[Stark_GOP]

Here's one that shows just how hard it is to end up with less information.

Every line in the chart represents a viable dog and/or wolf:
---
You should have mentioned insects.
Good thing it is hard to end up with LESS information.
The point you need to confirm is that you can end up with MORE information.

[From many - one.]

Easy. Polyploidy, common in ferns (Dryopteris spp) and other plants (Solidago canadensis complex) etc.

Duplication of segments of chromosomes
Duplication of whole chromosomes.

And so on.

[Stark_GOP]

Easy. Polyploidy, common in ferns (Dryopteris spp) and other plants (Solidago canadensis complex) etc.

Duplication of segments of chromosomes
Duplication of whole chromosomes.

And so on.
---
Sorry, but you didn't answer my post.
I know that DNA is very adapt at making copies of itself.
Your knowledge is vast, but you are using it to try to dazzle me and avoid my request.

[Ichneumon]

Here's an article recaping opinions from several Creationist PHD's in Geology

Nice try.

Henry Morris does not have a "PhD in Geology". He has a PhD in Hydraulic Engineering.

Jon Covey does not have a "PhD in Geology". He is a certified "Medical Technologist".

Anita Millen does not have a "PhD in Geology". She is a physician.

Leonard Brand does not have a "PhD in Geology". He has a PhD in Ecology and Evolutionary Biology.

Harold Coffin does not have a "PhD in Geology". He has a PhD in Zoology.

Robert Brown does not have a "PhD in Geology". He has a PhD in Biology.

Arial Roth does not have a "PhD in Geology". He has a PhD in Zoology.

Steve Austin (author of your first quote) actually *does* have a PhD in Geology, but all by himself he does not qualify as "several Creationist PHD's in Geology", and two of your three quotes aren't by geologists at all, contrary to the impression you're trying to give.

that answers many of your questions about tracks and burrowings.

No it doesn't. Hand-wavings and straw-man evasions do not answer the questions that were posed.

Below it, I'll quote some key excerpts.

On Burrowings

"Modern marine and terrestrial organisms are 'biological bulldozers' which so thoroughly rework and burrow recent sediments that stratification is often completely homogenized...

"Often", not always. It critically depends upon the nature and depth of the strata and the number and kind of the burrowers. However, watch Austin's sleight-of-hand as he attempts to mislead the reader into turning "often" into "always":

The intensity of burrowing in sediments on land and under the sea causes us to ask a fundamental question. How could any laminae be preserved in the strata record if sediment accumulates very slowly and is in contact with burrowing organisms for so long?

Because "often" is not "always". In order for Austin to express mock surprise that "any laminae" could be "preserved in the strata record", he has to pretend that he doesn't know that while some soils are "often" well-churned by burrowers (such as my garden bed after years of earthworm activity), many others aren't (such layers of sediments too deep for their depth to be fully "bulldozed" by animals of various types, those rapidly covered by floods, landslides, etc., and those in areas where burrowers live but are not highly abundant enough to work over every cubic inch of sediment, etc. etc. etc.)

For example, although there are many lake-bed burrowers, annual laminae (layers) which have been laid down over the years (and actually OBSERVED being laid down gradually) remain mostly undisturbed and neatly layered, so obviously the presence of burrowers is no real impediment to the formation and continued existence of neatly layered sediments. I don't know how in the hell creationist Dr. Austin could have a PhD in Geology and *not* be fully aware of this, so the most likely explanation for his "forgetting" to mention this fact which torpedoes his "point" in the above paragraph is that he's just being purposely dishonest. But then what else would we expect from the guy who submitted dishonestly prepared samples to a radiometric dating laboratory in order to dishonestly try to discredit the accuracy of radiometric dating?

Also note Austin's straw-man ploy: He asks how layering could be preserved "if sediment accumulates very slowly and is in contact with burrowing organisms for so long". Actually there are *two* straw-men tricks in this sentence. The first is that (as Austin well knowns, he's just pretending he doesn't) sediments are not always laid down "very slowly". While the *average* deposition rate is quite slow, the deposition rate of any *given* layer can be quite fast, due to sandstorms, flooding, landslides, rapid erosion, etc. No real-world geologist (as opposed to the cartoon-version the creationists describe which don't actually exist) believes that the geologic column was built up exclusively gradually. Austin knows this, he just pretends he doesn't.

The second straw-man trick is in the phrase, "in contact with burrowing organisms for so long". Um, *how* long exactly? Again, Austin tries to mislead the reader into presuming that this means that as every allegedly microscopically thin layer (false, see above) is added to the geologic column, it lays there on the surface for long spans of time before the next one arrives. Nonsense. Clearly there will be countless cases where deposition was rapid, and/or one surface will be soon overlaid by another. I don't know how the creationist readership of this pap can be so gullible, but anyone who watches the news (or lives in California...) should know that landslides, mudslides, tsunamis, earthquakes, sandstorms, floods, etc. can and do frequently bury the current landscape with a new layer of mud, silt, sand, or dirt.

Furthermore, while it's probably true that animal burrows will seldom be found in those areas which *do* happen to experience nothing but slow, gradual sedimentation for long periods of time, there are ways in which burrows can *still* be preserved (albeit less often than in areas of sudden coverage). For example, a particularly deep animal burrow might experience a cave-in, preserving the burrow several feet under the surface, and be unlikely to be re-excavated by another animal even in the long time it takes for another few feet of sediment eventually accumulates and puts it beyond reach of any further disturbance.

Another method is a change in climate (again, even in a slow-deposition region) which causes the region to be abandoned by a deep-burrower species (leaving their burrows abandoned as well), and replaced by more shallow-burrowing replacements more comfortable in the new climate. The shallow-burrowing activity will soon collapse the upper sections of the older deep burrows, preserving them in the strata to be discovered by geologists eons later.

And so on.

Again, Austin must already know this material. Why is he misrepresenting it? And why do his readers lap it up despite its obvious holes (no pun intended)?

Some evolutionists proposed that the deep-burrowing activity of organisms had not yet evolved when most Grand Canyon strata were deposited. (Thayer, 1979) However, this opinion was strongly challenged by more recent investigators who document deep-burrow structures even in Cambrian strata. (Miller; Sheehan, 1984)." [Austin, p. 31]

Straw man -- even if deep-burrowers existed from the very start, that would not invalidate the many methods by which burrows would still be preserved in the strata, although that's the impression Austin *wants* the reader to draw...

Furthermore, Austin "forgets" to mention that many parts of the geologic column have *multiple* layers of burrows *overlaying* each other in *widely* vertically separated layers. This shoots the whole "they musta been buried in The One Big Flood" theory all to hell, and yet again points unmistakably to the "many layers laid down over each other separated by long periods of time" scenario...

On raindrop impressions

"Related to animal tracks that have been thus preserved are the many instances of preservation of ancient ripple marks or raindrop impressions. But that such ephemeral markings could have been preserved in such great numbers and in such perfection is truly a remarkable phenomenon and one for which there is little if any modern parallel.

Horse manure.

It is a matter of common experience that impressions of this sort in soft mud or sand are very quickly obliterated.

Usually, yeah. Not always, and that's the point the author of this quote (Morris) is trying to sweep under the rug. Even today you can sometimes see raindrop (or other delicate impressions) being buried without destruction by blowing sands, for example, I've seen this happen myself at the beach. And clearly a similar process preserved the many raindrop impressions "fossilized" in the Coconino strata in the Grand Canyon, among other places. Is there some reason Morris is trying to pretend that these things don't actually happen? Other than the reason that he's lying in order to try to con his audience, I mean...

It seems clear that the only way in which such prints could be preserved as fossils is by means of some chemical action permitting rapid lithification [rockification] and some aqueous action permitting rapid burial.

ROFL! Yeah, sure, the "only" way...

Some sudden and catastrophic action is again necessary for any reasonable explanation of the phenomena.

Complete twaddle. On the contrary, a "sudden and catostropic action" would be almost certain to wash away the delicate raindrop impressions, as would any "rapid" kind of "some chemical action" (unspecified -- Morris is waving his hands very frantically here) which would obviously necessitate some "chemical" being flushed through the sands at a fast clip, again destroying the delicate impressions. Nice try.

And YET AGAIN, we see the spectacle of a creationist "forgetting" to remind his audience that such impressions are frequently found *overlaid* veritically, with one layer of raindrop impressions appearing several feet *above* another. I'd just *love* to know how this "sudden and catostropic action" could "suddenly" preserve raindrops on a sandy surface, *then* allow a few more feet (containing *multiple* layers itself) of new sediment to be stacked on top, then *more* raindrops to delicately impress themselves upon this new, smooth, non-turbulent surface, and then *again* be "suddenly and catostrophically" preserved in some [wave hands here] manner, then *more* layers, then *more* raindrops, etc. Nice try. Do the creationists even *think* before they write this pap?

Again, the clear and obvious explanation for these observations is that raindrops landed on the sandy surface of an arid region, and then baked to a fragile crust by the Sun (again, you can see this happen on the beach when the conditions are good), only to be covered by fine blowing sand, then later (perhaps much later, no rush) after more sand has accumulated, more raindrops manage to get preserved, etc., over many hundreds or thousands of years, scores of independent layers (many with raindrop or animal track impressions) end up stacked like a sandy layer cake, eventually to be lithified by time and pressure (of subsequent layers) to be someday discovered by geologists.

On Tracks

However, the Flood didn't overrun the entire earth immediately after the ark door was sealed. We shouldn't expect all land animals and birds to get wiped out by the first encroachments of ocean water on the land. They wouldn't be as vigorous as later inundations. The Flood waters ebbed and flowed, increasing in height day by day until finally the land was submerged. Prior to that time, the deposition of marine layers over land layers would not prevent animals from running, walking, slithering or flying across the topmost layers later on. Indeed, most animals would try to escape the Flood by heading for higher ground, and animals living at higher elevations prior to the Flood would also have been spared. These would later be able to make their tracks in the mud left from earlier wave deposits.

That's a sweet fairy tale and all, but again it "forgets" to mention -- or even try to explain -- how and why tracks are found *LAYERED* through the geologic column, and not just on the "one" geologic horizon which was allegedly the surface of the planet at the time the Flood(tm) hit.

How, exactly, do burrows, tracks, raindrops, etc. get preserved on *multiple* layers (and often displaying different climates) which are *vertically stacked* through the geologic column if they're done by *one* big-ol' flood, eh?

I can't believe there are people who lap this stuff up uncritically.

And I can't believe that you haven't yet taken our advice to try to learn some *science*, from *science* sources, instead of filling your head with just this sort of "pay no attention to that man behind the curtain -- or all that other evidence which torpedoes our lame-ass attempt to explain just this *one* thing we're focusing on right now" nonsense.

Creationist sources are almost without exception misinformation and propaganda. Your heros are lying to you (sometimes directly, sometimes by omission). Why do you keep trying to fill your head with it? Afraid some actual knowledge might sneak in otherwise and challenge your cherished preconceptions?

[PatrickHenry]

[Thunderous applause!]

[From many - one.]

Wrong. You started out advocating the notion that mutations diminish the information in the genome.

I demonstrated that was not so, which you more or less acknowledged.

Then you wanted examples of increasing the information by mutation.

I mentioned a couple of items that I remember teaching in a basic college biology class. If it happens you didn't learn it, why not try google? Or ask politely?

[Ichneumon]

I am waiting for the Human Genome Project to do a similar complete genetic mapping on our nearest neighbor, the chimp,

Already been done.

and then to show how they can, by sucessive change of genetic material equivalent to what might be expected by random mutation, work their way back from each current organism to a common genetic ancester

That's already been done on a piecemeal basis as well.

A few quick examples:

Accelerated Evolution of the ASPM Gene Controlling Brain Size Begins Prior to Human Brain Expansion

Abstract: Primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by global reduction in cerebral cortical volume. The microcephalic brain has a volume comparable to that of early hominids, raising the possibility that some MCPH genes may have been evolutionary targets in the expansion of the cerebral cortex in mammals and especially primates. Mutations in ASPM, which encodes the human homologue of a fly protein essential for spindle function, are the most common known cause of MCPH. Here we have isolated large genomic clones containing the complete ASPM gene, including promoter regions and introns, from chimpanzee, gorilla, orangutan, and rhesus macaque by transformation-associated recombination cloning in yeast. We have sequenced these clones and show that whereas much of the sequence of ASPM is substantially conserved among primates, specific segments are subject to high Ka/Ks ratios (nonsynonymous/synonymous DNA changes) consistent with strong positive selection for evolutionary change. The ASPM gene sequence shows accelerated evolution in the African hominoid clade, and this precedes hominid brain expansion by several million years. Gorilla and human lineages show particularly accelerated evolution in the IQ domain of ASPM. Moreover, ASPM regions under positive selection in primates are also the most highly diverged regions between primates and nonprimate mammals. We report the first direct application of TAR cloning technology to the study of human evolution. Our data suggest that evolutionary selection of specific segments of the ASPM sequence strongly relates to differences in cerebral cortical size.

Identification of paralogous HERV-K LTRs on human chromosomes 3, 4, 7 and 11 in regions containing clusters of olfactory receptor genes

Abstract: A locus harboring a human endogenous retroviral LTR (long terminal repeat) was mapped on the short arm of human chromosome 7 (7p22), and its evolutionary history was investigated. Sequences of two human genome fragments that were homologous to the LTR-flanking sequences were found in human genome databases: (1) an LTR-containing DNA fragment from region 3p13 of the human genome, which includes clusters of olfactory receptor genes and pseudogenes; and (2) a fragment of region 21q22.1 lacking LTR sequences. PCR analysis demonstrated that LTRs with highly homologous flanking sequences could be found in the genomes of human, chimp, gorilla, and orangutan, but were absent from the genomes of gibbon and New World monkeys. A PCR assay with a primer set corresponding to the sequence from human Chr 3 allowed us to detect LTR-containing paralogous sequences on human chromosomes 3, 4, 7, and 11. The divergence times for the LTR-flanking sequences on chromosomes 3 and 7, and the paralogous sequence on chromosome 21, were evaluated and used to reconstruct the order of duplication events and retroviral insertions. (1) An initial duplication event that occurred 14-17 Mya and before LTR insertion - produced two loci, one corresponding to that located on Chr 21, while the second was the ancestor of the loci on chromosomes 3 and 7. (2) Insertion of the LTR (most probably as a provirus) into this ancestral locus took place 13 Mya. (3) Duplication of the LTR-containing ancestral locus occurred 11 Mya, forming the paralogous modern loci on Chr 3 and 7.

Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux

Abstract: The enzyme glutamate dehydrogenase (GDH) is important for recycling the chief excitatory neurotransmitter, glutamate, during neurotransmission. Human GDH exists in housekeeping and brain-specific isotypes encoded by the genes GLUD1 and GLUD2, respectively. Here we show that GLUD2 originated by retroposition from GLUD1 in the hominoid ancestor less than 23 million years ago. The amino acid changes responsible for the unique brain-specific properties of the enzyme derived from GLUD2 occurred during a period of positive selection after the duplication event.

A uniquely human consequence of domain-specific functional adaptation in a sialic acid–binding receptor

Abstract: Most mammalian cell surfaces display two major sialic acids (Sias), N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). Humans lack Neu5Gc due to a mutation in CMP-Neu5Ac hydroxylase, which occurred after evolutionary divergence from great apes. We describe an apparent consequence of human Neu5Gc loss: domain-specific functional adaptation of Siglec-9, a member of the family of sialic acid–binding receptors of innate immune cells designated the CD33-related Siglecs (CD33rSiglecs). Binding studies on recombinant human Siglec-9 show recognition of both Neu5Ac and Neu5Gc. In striking contrast, chimpanzee and gorilla Siglec-9 strongly prefer binding Neu5Gc. Simultaneous probing of multiple endogenous CD33rSiglecs on circulating blood cells of human, chimp, or gorilla suggests that the binding differences observed for Siglec-9 are representative of multiple CD33rSiglecs. We conclude that Neu5Ac-binding ability of at least some human CD33rSiglecs is a derived state selected for following loss of Neu5Gc in the hominid lineage. These data also indicate that endogenous Sias (rather than surface Sias of bacterial pathogens) are the functional ligands of CD33rSiglecs and suggest that the endogenous Sia landscape is the major factor directing evolution of CD33rSiglec binding specificity. Exon-1-encoded Sia-recognizing domains of human and ape Siglec-9 share only 93–95% amino acid identity. In contrast, the immediately adjacent intron and exon 2 have the 98–100% identity typically observed among these species. Together, our findings suggest ongoing adaptive evolution specific to the Sia-binding domain, possibly of an episodic nature. Such domain-specific divergences should also be considered in upcoming comparisons of human and chimpanzee genomes.

Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution

Abstract: Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.

Sequence Variation Within the Fragile X Locus

Abstract: The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To understand the nature and pattern of variation and linkage disequilibrium comprising this history, we present a study of ~31 kb spanning an ~70 kb region of FMR1, sequenced in a sample of 20 humans (worldwide sample) and four great apes (chimp, bonobo, and gorilla). Twenty-five polymorphic sites and two insertion/deletions, distributed in 11 unique haplotypes, were identified among humans. Africans are the only geographic group that do not share any haplotypes with other groups. Parsimony analysis reveals two main clades and suggests that the four major human geographic groups are distributed throughout the phylogenetic tree and within each major clade. An African sample appears to be most closely related to the common ancestor shared with the three other geographic groups. Nucleotide diversity, [pi], for this sample is 2.63 ± 6.28 × 10^-4. The mutation rate, [mu], is 6.48 × 10^-10 per base pair per year, giving an ancestral population size of ~6200 and a time to the most recent common ancestor of ~320,000 ± 72,000 per base pair per year. Linkage disequilibrium (LD) at the FMR1 locus, evaluated by conventional LD analysis and by the length of segment shared between any two chromosomes, is extensive across the region.

Structural and evolutionary analysis of the two chimpanzee alpha-globin mRNAs

Abstract: Two distinct alpha-globin mRNAs were detected in chimpanzee reticulocyte mRNA using a primer extension assay. DNA copies of these two mRNAs were cloned in the bacterial plasmid pBR322, and their sequence was determined. The two alpha-globin mRNAs have obvious structural homology to the two human alpha-globin mRNAs, alpha 1 and alpha 2. Comparison of the two chimpanzee alpha-globin mRNAs to each other and to their corresponding human counterparts revealed evidence of a recent gene conversion in the human alpha-globin complex and a marked heterogeneity in the rate of structural divergence within the alpha-globin gene.

Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages

Abstract: Alu elements are primate-specific members of the SINE (short interspersed element) retroposon family, which comprise 10% of the human genome. Here we report the first chromosomal-level comparison examining the Alu retroposition dynamics following the divergence of humans and chimpanzees. We find a twofold increase in Alu insertions in humans in comparison to the common chimpanzee (Pan troglodytes). The genomic diversity (polymorphism for presence or absence of the Alu insertion) associated with these inserts indicates that, analogous to recent nucleotide diversity studies, the level of chimpanzee Alu diversity is 1.7 times higher than that of humans. Evolutionarily recent Alu subfamily structure differs markedly between the human and chimpanzee lineages, with the major human subfamilies remaining largely inactive in the chimpanzee lineage. We propose a population-based model to account for the observed fluctuation in Alu retroposition rates across primate taxa.

Adaptive Evolution of MRG, a Neuron-Specific Gene Family Implicated in Nociception

Abstract: The MRG gene family (also known as SNSR) belongs to the G-protein-coupled receptor (GPCR) superfamily, is expressed specifically in nociceptive neurons, and is implicated in the modulation of nociception. Here, we show that K_a/K_s (the ratio between nonsynonymous and synonymous substitution rates) displays distinct profiles along the coding regions of MRG, with peaks (K_a/K_s > 1) corresponding to extracellular domains, and valleys (K_a/K_s < 1) corresponding to transmembrane and cytoplasmic domains. The extracellular domains are also characterized by a significant excess of radical amino acid changes. Statistical analysis shows that positive selection is by far the most suitable model to account for the nucleotide substitution patterns in MRG. Together, these results demonstrate that the extracellular domains of the MRG receptor family, which presumably partake in ligand binding, have experienced strong positive selection. Such selection is likely directed at altering the sensitivity and/or selectivity of nociceptive neurons to aversive stimuli. Thus, our finding suggests pain perception as an aspect of the nervous system that may have experienced a surprising level of adaptive evolution.

-- and then to show that each step of the way represents a viable living organism.

This is routinely done by producing, say, mice which have a particular human gene. This is typically done to isolate the particular effects of the gene for study, but the fact that this doesn't kill the mouse also shows that the genetic differences between humans and chimps -- or even humans and mice -- do not result in nonviability. For that matter, the genetic differences between chimps and humans are so small that it would be extremely surprising if any one -- or any combination -- of changes between the two species caused nonviability.

I think that would be a pretty good validation of historical record.

And it is.

In general, the fact of reuse of large amounts of genetic material is nothing more than something "consistant with" an evolutionary historical hypothesis, and in no way proves it or makes it scientific. It is just another level of the forensic-type science where, when we do a DNA test and find results much different than expected, it doesn't change in any way the "theory of evolution", but has a large effect on the historical evolution hypothesis.

You're missing the point -- although we're occasionally surprised by the DNA implications for a particular evolutionary history (i.e., which species diverged from which ancestors when), we have not yet *ever* been surprised by finding a genetic difference between species which was *not* entirely compatible with evolutionary origins. And we *would* very quickly and very obviously find such discordance between the contents of the DNA and evolutionary theory if, in fact, the DNA of modern living things was *not* the result of evolutionary processes.

It's nothing as simple as just "reuse of large amounts of genetic material" which provides support for evolution, it's the very specific *kinds* and exact *patterns* of DNA which support an evolutionary origin to the exclusion of alternative hypotheses (except for the ad hoc one which postulates that some designer *purposely* crafted our DNA in order to *fake* an evolutionary origin).

I believe that just happened recently, some discovery was found to be much less of a difference with our modern genetic makeup than was "predicted" by the hypothesis.

Could you be more vague?

As a believer in the non-scientific theory of creation, it makes sense to me that a creator would from time to time use common genetic material to implement common function. It is just as possible that, as a being of great capability, the creator might from time to time find different ways to implement the same function. This is analogous to computer programming. If you look at a lot of computer programs, you will find common code. This does not suggest that one program "evolved" into another, or even that one programmer extended the one program into the other. It could be that the same programmer wrote both, or that somebody wrote a snippet of code and published it and others used it. It is not predictive to determining the history of a piece of code. It is also common in looking at code to find that two programs which have the same function don't use the same code, even if they are written by the same programmer.

That's a common argument, but it doesn't stand up to close examination. I've written thousands of computer programs, *and* produced code via genetic algorithms (aka "evolutionary computing"). No one could possibly mistake the one type of program for the other. The results are vastly different in form and character, and each contains features which clearly distinguish it from the other.

Similarly, the evolutionary character of DNA is clear and distinctive. The hallmarks of evolution go far beyond mere "reuse of code". For example, it contains features that no sane designer would ever use (such as silent codon differences which vary in exact evolutionary patterns -- it's as if you, as a programmer, randomly changed characters in the variable names in source used in common between all your programs, while having no effect on the compiled code, *and* did it in a way that falsely implied an evolutionary relationship between all the programs you wrote...) Furthermore, a designer has *vastly* more design options to him than *just* the ones which could result from evolutionary processes, and yet "oddly" enough, such structures are not found in DNA -- if there's a designer, why would he restrict himself in that way? *I* certainly don't write my programs in only those ways that could have been produced by genetic algorithms...

BTW, if you want to claim that your hypothesis of an evolutionary history for origins is more elegant than my creation theory, or has the attribute of not requiring a mythical higher being, I will not dispute the point.

Okay.

On the other hand, you would be hard-pressed to disprove my unscientific hypothesis of history that says a creator made it the way it is, since for any observation you make I can simply modify my hypothesis to fit the new observation (much like the evolution historical hypothesis is modified whenever new information is found).

No, not "much like" the way that evolution is modified to fit the evidence. Yours example is just an attempt to "explain" things ad hoc by saying, "well I guess the designer wanted to do it that way, whether it makes sense to design that way or not." Evolutionary scenarios, on the other hand, have to make *sense* and actually be workable.

The insertion of a higher being or external cause clearly puts my hypothesis outside the bounds of science,

Not by itself, no. Science is perfectly capable of studying the products of humanity, for example, (or the behavior of humanity, such as sociology and economics), and could do similarly with a "higher being" or an advanced alien race that may have designed us, etc.

What does put the "intelligent design" movement out of the realm of science, however, is their refusal to actually make any testable hypotheses about the alleged design process.

A recent post on the "talk.origins" newsgroup by poster "Stephen J." said it very well. I'm not saying that this describes your own view, just that your comment about "non-scientific" design concepts reminded me of a good point I'd like to share:

A "natural process" is one that acts according to its own nature; that is, it has certain capabilities, and certain constraints. It will, under appropriate conditions, produce certain effects and be unable to produce other, contrary effects. And, in order to serve as an explanation, the nature of the process must be discoverable: research must be able to uncover regular patterns to its behavior and infer the rules according to which it operates. One can discover natural processes, understand something about how they work, and predict their likely effects under at least some conditions.

[...]

The second difficulty is that ID proponents and creationists, especially, have had a bad run, these last two centuries, with predictions based on the creation model, so they are especially leary of positing anything testable about the nature of the Designer or the mechanisms of creation. For purposes of ID, "supernatural" means "please don't try to check my logic here."

As noted above, "non-natural" seems to mean "acting in ways beyond human comprehension or prediction." A "non-natural" cause cannot be said to be more likely to produce one outcome than another. You can explain shared pseudogenes in humans and chimps in terms of inheritance from a common ancestor, but could not, in such terms, plausibly explain pseudogenes shared by humans and dogs, but not by nonhuman primates. But you could "explain" either, or the absence of either, equally well by invoking the ineffable whim of a Designer of unknown motives, methods, and design philosophy.

You cannot, of course, make any sort of testable predictions about the work of such a Designer, which is why ID proponents wish to establish ID by excluding all "natural" explanations. But of course there can be discoverable and humanly understandable explanations that have not yet actually been discovered or understood, so merely excluding known natural causes does not establish a "non-natural" cause, merely (at best) an unknown cause. IDers could, in principle, posit testable hypotheses about a Designer (even one of powers exceeding what we currently regard as the laws of nature) constrained by particular motives and methods, but that would risk having their hypotheses falsified by those tests; it is better, from their standpoint, to use gaps in current understanding as excuses for demanding that "explanations" that explain nothing and cannot be tested be admitted to science.

but I've never advocated teaching creation or intelligent design in science class as a scientific theory.

We agree on that, anway.

Did I wave my hands sufficiently for you?

I've seen more vigorous hand-waving. ;-) Actually, that was a pretty good post, thanks.

[DannyTN]

Get a life.

Your diatribe consists mostly of putting strawmen in Austin's mouth and then knocking down those strawmen by showing that a lack of burrowings could be explained by floods or landslides or rapid burial. Well, CONGRATULATIONS, that was the whole point! The lack of burrowings is good evidence that it was not slow deposition.

Also don't believe everything you read on TalkOrigins, some of it's not credible, especially when they post attacks on Creation scientists by people without adequate credentials who have no support for their claims.

Answering Austin's critics

Response to Chris Stassen taking him to task for making unsupportable and vague claims

AIG takes Glenn Morton another frequent Talk Origins writer to task for sloppy sloppy work

Also, You failed to mention Henry Morris's PHD had a minor in Geology. And you completely left out Geologist Kurt Howard, but then he only has a masters, not a PHD. But thanks anyway for posting yet another list of PHD's who believe in Creation and don't buy the bunk put out by evo's.