The Sound of Circular Reasoning Exploding

Wow!!

DaveScot, I know that you are a fan of Dr. Davison’s PEH hypothesis dispite the fact that he is a grade ‘A’ putz in a discussion forum. This is the kind of data that one would expect if the PEH were valid. PEH, and the Kruze/Mike Gene hypothesis of “front-loading”, of course are kissing cousins.

I will admit, however, that this data is also consistent with a 6000 year old biosphere.

I mastered arithmetic before I ran out of fingers showing people my age. Within the current NDE paradyme, this doesn’t add up — no way!

The huge question I have on this one is how this data could have been initially brought forth in June, 2004? Has the scientific community been hiding this finding?

I pointed out why knock-out experiments may be ineffective ways to determine function. See: Airplane magnetos, contingency designs, and reasons ID will prevail.

If the function is some sort of backup, contingency, or even artifacts of front-loading, this would favor ID far above neo-Darwinism.

I had commented on this at KCFS and ARN several times. I pointed out repeatedly all the circular reasoning out there in Darwinist circles. I’m glad to see some sane voices finally speak out.

bfase,

You can download the Nature article pdf here: http://www.stanford.edu/class/.....Nature.pdf

In contrast to the New Scientist article, the Nature article does not discuss the significance of nonfunctional genes being conserved.

The article states that 1,243 sequences conserved between human and mouse were deleted. Each segment being at least 100 base pairs and having 70% identity.

“Planning for the future with genomic information is the central tenet of ID front loading hypothesis. Lack of any known means of conserving non-critical genetic information is the major objection lobbed at the front loading hypothesis. Evidently there is a means after all.”

I’m a big fan of front-loading as an avenue of ID research, so these results are especially intriguing. Of course, if these “non-coding” regions of the genome actually turn out to be the location for the front-loaded material, that still doesn’t explain how they are preserved.

If knockout experiments don’t reduce the viability of the organism, then we should expect that random mutations would have substantially altered those portions of the genome. But they haven’t, so there must be some (as yet unknown) mechanism preventing mutations from occurring. I’m not sure what that would be, but I’m also not a genetics researcher.

Sal,

If the function is some sort of backup, contingency, or even artifacts of front-loading, this would favor ID far above neo-Darwinism.

True. How does Darwinism conserve backup or contingency functions?

How does Darwinism conserve backup or contingency functions?

Exactly. Kind of hard to conserve something that’s practically invisible to selection.

Jehu, thanks for the link. This one may be worth buying.

bfast,

It’s free at that link.

I think this is one of the most promising ideas yet. If you could show a future blueprint and uncover the mechanisms to make it unfold, well that would change everything.

““We were quite amazed,” says Rubin”

Darwinists are frequently amazed by the real world.

Jehu, I obvously glossed over your link too quickly, thanks again. Reading the paper hardly suggests that the scientists were shocked at their findings.

Dacook, I did a dilligent search through the annals of NDE predictions, and I did not find this one. In fact, this is solidly negatively predicted by the theory.

Does anybody know off hand when how long ago man and mouse diverged? How random should DNA be if it is submitted to unselected random mutation?

Jehu: ” True. How does Darwinism conserve backup or contingency functions?”

Ah, but you underestimate the truly magical powers of Natural Selection. Does it not seem obvious that those creatures posessing mutations which produce biological systems capable of conserving and maintaining backup and contingency functions will be favoured over those lacking such systems? Why limit the powers of natural selection to only “first order” adaptations?

“How does Darwinism conserve backup or contingency functions?”

I’m not sure this is particularly problematic. In some environments, backups and contingencies are really quite important. The details will vary from case to case, but only under the best possible circumstances will backups and contingencies be “practically invisible to selection.”

“Ah, but you underestimate the truly magical powers of Natural Selection.” Thus it’s called supernatural-selection. Supernatural-selection has the amazing ability to change the DNA just right so it can evolve a new creature while leaving the junk DNA untouch for millions of years.

bFast,

The Nature article plays it off like it is no big deal. But the lead researcher, Edward Rubin, said at the presentation that, ““We were quite amazed.”

Does anybody know off hand when how long ago man and mouse diverged? How random should DNA be if it is submitted to unselected random mutation?

Same question I have been pontificating. To answer that, I have been looking at earlier work by the same lab. Here is something interesting I found from April 2000.

Evolutionary conservation of non-coding DNA sequences that play an important role in regulating gene expression is the key to the success of this study, just as it has been a key to identifying DNA sequences that code for genes across different species.

“If evolution conserved a sequence over the 70-90 million years since mice and humans diverged, it likely has a function,” says Frazer. “Whether its function is to determine the structure of a protein coded for by a gene or to regulate gene expression, we should be able to identify these sequences through mouse to human sequence comparisons.”
…
To search for conserved non-coding sequences (CNSs), Rubin, Frazer, and their colleagues examined a stretch of DNA about a million base-pairs in length from mice and humans that contained the same 23 genes in both species, including three interleukin genes (IL-4, IL-13, and IL-5). Previous studies indicated that these interleukin genes are similarly regulated and that their regulatory sequences may be conserved in mice and humans.

The Berkeley researchers looked for CNSs that were at least 70 percent identical in both species over at least 100 base-pairs. Of the 90 CNSs they identified that met this criteria, the researchers took 15 and did a cross-species sequence analysis which also included DNA from a cow, a dog, a pig, a rabbit, a rat, a chicken, and a fish. Most of these elements were also found to be present in the other mammals, indicating that they most likely have been conserved because they perform an important biological function.

So apparently the researchers at Berkley Labs thought > 100 base pares with at 70% identity was highly conserved enough between mouse and human to predict function. In fact, they found a functioning gene using that method.

“What is unique about our study is that we were lead to the interleukin regulatory element CNS-1 entirely by computational analysis of mouse and human sequences,” says Rubin. “Since we are soon to have the entire genomes of mice and humans sequenced, our study demonstrates one successful strategy of interpreting the sequence information coming from the genome program into meaningful biology.”

http://www.lbl.gov/Science-Art.....model.html

I’ve been calculating with the 70m number myself. That means that the DNA has been experiencing uninhibited genetic drift for 150 million years. I believe that in humans (worse in mice) unused DNA drifts at a rate of about 1% per mil. To get to 30% loss of order, would take 30 million years. By 150 million, the DNA should be as random as a Vegas shoe. 70% conserved requires mechanism, that’s all.

DaveScot, I am well aware that there is all sorts of evidence for an old earth. However, this one falls on the side of supporting a young earth. So far my personal tally is about 846 old, 4 young.

bFast,

I believe that in humans (worse in mice) unused DNA drifts at a rate of about 1% per mil. To get to 30% loss of order, would take 30 million years. By 150 million, the DNA should be as random as a Vegas shoe.

I think that actual drift is a little more than double that, 2.1% per million and according to the Berkley Labs article the seperation between mouse and human is 70 to 90 million is years. So by those estimates you wouldn’t expect any identy of nonconserved genes at all.

See this article

Mutation Rates in Mammalian Genomes

http://www.pnas.org/cgi/reprint/022629899v1.pdf

Funny thing is that article raises another failed Darwnian prediction. Darwinism predicts that there is a correlation between the mutation rate and the generation time because organisms that reproduce faster have more opportunities to produce mutations and organims that reproduce slower have fewer opportunities. In fact, there is no correleation between the mutation rate and generation time.

Therefore, small rate differences seem to exist among lineages, and clearly there are no systematic relationships between the evolutionary rate and generation length. This means that the generation length and physiological differences among diverse groups do not influence the neutral substitution rates significantly, and the evolutionary time is the principal factor dictating the accumulation of neutral mutations.

Hmmm.

A quick google to find others talking about this research revealed this: http://www.planetark.com/daily...../story.htm

In this Reuters story, the fact that the mice could live without the DNA was written about, the fact that there were significant portions of the mouse DNA that was conserved in humans was just not mentioned. This report presents the study as being very supportive of NDE. So far, other than what has been presented here, this is the only discussion I have found on this study.

Ops, another good link — again, datad back to 2004. This link again ignores the challenge presented to NDE by this paper, only presenting the fact that chunks of DNA are removable. What makes it even more interesting is that the author challenges Dembski to explain the findings. Well, Dembski and crew have been a bit slow at explaining, but the explanation is a doozie.

http://evolutionblog.blogspot......-junk.html

Another link, again from 2004: http://www.i-sis.org.uk/AUEI.php

At least this paper brings out the issue very clearly. Let me point out, however, that the scientists avoided the untraconserved (99-100%) sections of the genome when they did their cutting. The “highly conserved” (average 70%) sections still very well should have shown some implementation in the phenotype so that natural selection could conserve them.

It is my view that this finding should be as significant to evolutionary biology as the Michelson-Morley experiment was to the theory of “ether”. The evolutionary biology community should be in an absolute quandry in response to these findings. This should be front page news in my local paper. But we can’t just bring down a religious icon, just because it wears the cloke of science, can we?

Folks, I’m a little confused about this… I’m a newcomer to UD and I have relatively little knowledge of the specifics of genetics and so forth, but I am a fervent supporter of ID and want to learn more. Perhaps someone can help me out…

I understand that NDE would predict junk DNA. And I also understand that ID would predict that so-called junk DNA would turn out to have function. And I also understand that, bit by bit, functions are being uncovered in non-coding DNA. What I don’t understand is that this experiment seems to me to have demonstrated that non-coding regions really DON’T have function. But you folks are interpreting this as a resounding win for ID. As much as I’d relish a any victory for ID, I can’t see how this is a win. Seems like a loss. Seems like if it was a win, the removal of the non-coding regions would have yielded mice that, for example, were born dead and were turned inside out. Something like that, you get the idea.

Honestly, I want ID to win as much as the next guy, but I don’t get this. I’m sure I’m missing something. Can someone enlighten me?

Thank you!

TRoutMac

TRoutMac - I believe the significance is the fact that the DNA sections removed code for function but are unused by the mice. The section may show up in other organisims DNA and posses function but in a mouse they do nothing. This would support a front loaded system because the mouse is carrying around DNA sections that would be used in later evolved generations as it adapted.

I could be way off but this my interpration. It is great to see others seeking to understand the issues better and speaking up about it.

TRoutMac,

Darwinism predicts that only DNA with function will be conserved. If the DNA has no function it will mutate at a rate of 2.2 x 10^-9 per base per year. So, according to Darwinism, after 70 - 90 million years, sequences without function should not have any homology. But they do.

This panspermia article makes a related point.

http://panspermia.org/nongenseq.htm

TRoutMac, the issue here is that if DNA does not implement in an organism’s phenotype (it’s body with all of its complexity) then natural selection, which selects by phenotype alone, cannot select for it. Therefore, any DNA that doesn’t implement in the phenotype should be subject to any random mutation that happens along. It should experience the full force of genetic drift. Therefore when significant chunks of DNA are similar between a man and a mouse, NDE requires that the DNA implement in the phenotype.

As to, hey we have proved that this is “true junk”, which has not been predicted by ID, well, “true junk” status has surely not been established. Is this DNA remnant from the original organism that was “programmed” to become all the variety that we see? If so there should be echoes in the DNA, echoes that look exactly like what we are seeing. Is this DNA actually capable of producing phenotype effects, but it is not seen as such because of redundant code? Well, redundancy certainly has been seen in the simplest organisms, but it is really hard to find when there is gazillions of DNA to consider.

Peter Borger, on Brainstorms, shows why redundancy is absolutely unsupportable within the NDE framework. His case is very strong. However redundancy is easily supported within an ID framework.

A very light look at this data would see it as anti-ID, but a closer look is anything but. It is damning to the neo-Darwinian evolutionary hypothesis.

There are a number of species of plants in eastern North America (including skunk cabbage) of which populations are also found in a certain area in eastern Asia. These widely separated populations on two different continents are not only morphologically indistinguishable, but apparently also fully fertile with each other, even though they must have been isolated from each other for 6 - 8 million years. The American botanist Asa Gray called this fact to Darwin’s attention. [See Darwiniana (1876) by Asa Gray, pp. 181-186.]
…
[Living fossils are] species of animals and plants that have not visibly changed in more than 100 million years. This includes the horseshoe crab (Limulus; Triassic), the
fairy shrimp (Triops), and the lampshell (Lingula; Silurian). Equally long-lived have been found among the plants: Gingko (dating to the Jurassic), [etc.] … The complete standstill or stasis of an evolutionary lineage for scores, if not hundreds, of millions of years is very puzzling. How can it be explained? In the case of living fossils, all the species with which it had been associated 100 or 200 million years ago had either changed drastically since that time or had become extinct… To explain why the underlying basic genotype was so successful in living fossils and other slowly evolving lineages requires a better understanding of development than is so far available.

(Ernst Mayr, What Evolution Is: Except When It Isn’t (2001), pp. 186, 195.)

And now this. Are the DNA error correction mechanisms enormously better than generally believed, or what? (”Mutations? What mutations?”)
—————

…If awareness of anomaly plays a role in the emergence of new sorts of phenomena, it should surprise no one that a similar but more profound awareness is prerequisite to all acceptable changes of theory. On this point historical evidence is, I think, entirely unequivocal. …Copernicus…Newton…wave theory…thermodynamics…quantum mechanics… In all these cases except that of Newton the awareness of anomaly had lasted so long and penetrated so deep that one can appropriately describe the fields affected as in a state of growing crisis. Because it demands large-scale paradigm destruction and major shifts in the problems and techniques of normal science, the emergence of new theories is generally preceded by a period of pronounced professional insecurity. As one might expect, that insecurity is generated by the persistent failure of the puzzles of normal science to come out as they should.

(Thomas S. Kuhn, The Structure of Scientific Revolutions (1962), pp. 67-68.)

Jehu, thanks for the panspermia link. I would love to find that these “ultra-conserved” DNA segments prove to be “not essetial”.

BTW, where have the evolutionist loud-mouths gone? C’mon you guys, please explain to us why this evidence is no big deal. I dare yea!

bFast,

Jehu, thanks for the panspermia link. I would love to find that these “ultra-conserved” DNA segments prove to be “not essetial”.

At least some of most likely regulate gene expression, I am not sure if that would make them “essential” Even in the megabase gene deletion experiment we have been talking about, one of the sequences did have a function of regulating gene expression. Apparently the absence of the gene didn’t effect the mouse’s health and therefore it is hard to argue it is “essential” or even say for sure that it provides a selective benefit.

That does raise another issue. How do these genes regulate gene expression? What is the code they use? Is it different than the code of the central dogma? Is there a second code DNA for gene regulation as opposed to gene expression?

I find this very interesting:

A newly observed class of genomic elements of unknown function are 100% conserved, with no insertions or deletions, among the human, rat and mouse genomes. There are over 5,000 such segments longer than 100 base-pairs, and 481 longer than 200 bp. Many of them are also present in the chicken and dog genomes, at 95% and 99% identity, respectively. Many of them are also found in fish. They are widely distributed across the human genome, sometimes overlapping with the exons of genes for RNA processing, sometimes in introns or near regulatory genes, and sometimes far from any gene. The international team who discovered them calls the 481 longest ones “ultraconserved elements.”

http://panspermia.org/whatsne33.htm#040507

Patrick,

I’d still like to see these mice tested for notable loss of instinctual behavior. Many tests were run but from what I’ve read it’s not bee directly addressed.

What would be the hypothesis for instinct genes from mice being conserved in humans?

“Does anybody know off hand when how long ago man and mouse diverged? How random should DNA be if it is submitted to unselected random mutation?”

Obviously, since Evolution is true, the experiment does not cast doubt on Evolution, but merely shows that mice and men are very closely related. All those progressively evolving images of fish to ape to man should probably now be fish to cows to whales to cows to ape to mice to man.

(The extra “cows” is not a typo, by the way.)

Thank you late_model, Jehu and bFast for the explanations. I understand it much better now. Turns out I made the same mistake the Darwinists made with regard to this “junk DNA”, which is that I jumped to the conclusion that just because we can’t see a function NOW, that we will never find a function, or that there never will be a function. You would think I’d know better. And I understand better that this non-coding DNA should have deteriorated into honest-to-goodness junk by now and that because it remains unchanged, the mutations are not happening, which runs counter to NDE theory.

Pretty amazing. Am I really out of line to think that within ten years Darwinism will be yesterday’s papers? It really seems like these folks are on the slippery slope, ’specially when the best arguments they make are as ridiculous as that article by Jack Woodall about the large blue butterfly. Funny stuff!

Thanks again!

TRoutMac

Dave,
I guess your argument is biased. Caging mice for experimental work requires maintaining constant housing conditions (e.g. temperature, humidity, food, day night cycles). In addition, breeding normally is carried out in specific genetic backgrounds (e.g. Balb/c, C57BL/6 or 129SV) and researchers make some effort to prevent genetic drift I their colonies. Thus, lack of phenotypic consequences in mouse mutants doesn’t mean that a sequence is not functional.
E.g. the IL-10 knockout mouse lives happily if it is kept under pathogen free conditions. However, if kept under less rigid hygienic conditions it will develop gut inflammation similar to Crohn’s disease in man. In addition severity of the disease depends on the genetic background and the sex of the effected animals.
Since Animal houses cannot provide the several magnitudes higher variability of the natural habitat, since there is no free choice in breeding for caged animals and allele frequencies are fixed in mouse colonies it is hardly never possible to prove that a sequence doesn’t any function, irrespective if your investigating coding or non-coding sequences.

Douglas, “Obviously, since Evolution is true, the experiment does not cast doubt on Evolution, but merely shows that mice and men are very closely related.”

You may read back in post 2 that I mention that these findings are consistent with a young earth. I’m still an old earther on acounta all that other evidence flyin’ in from everywhere.

However, even if this were to challenge the age question, the real question being asked here is whether the NDE paradyme can support this data. If we are going to look at what NDE says “should” happen, we must begin with NDE’s expected timetable.

Jehu, “Even in the megabase gene deletion experiment we have been talking about, one of the sequences did have a function of regulating gene expression.” Please expound.

What I really want to see is a mouse where one of the “untra-conserved” non-coding segments is knocked out. If you can knock out the ultra-conserved stuff too, it’ll just be more nails in the ‘ol coffin.

TRoutMac

Am I really out of line to think that within ten years Darwinism will be yesterday’s papers?

That’s how I see it. I am still somewhat puzzled that this data has been around for a year and a half and it hasn’t made the front page of the Washington Post. There is only one explanation that I can find — the halls of biological science are not filled with enough honest scientists who are prepared to admit that their foundational theory, their “fact”, is toast!

BTW, after googling this article I have found nobody who has even ventured an explanation. The scientific community MUST come up with an explantion, or yell UNCLE!

This was certainly a surprising result, and clearly makes everyone examine in more detail the assumption that conservation implies function. It should first be noted that the study did identify significant changes in the expression patterns of two genes near the deleted DNA, in the brain and in the heart. They also did show that one of the most conserved elements in the deleted regions does act as an expression enhancer element. Perhaps partially for these reasons, the authors were careful to note that “It is possible—even likely—that the animals carrying the megabase-long genomic deletions do harbour abnormalities undetected in our assays, which might affect their fitness in some other timescale or setting than those assayed in this study.”

This is not to say that it was anything less than very surprising that the mice did fine against a large battery of tests; that is, after all, why Nature published it. It certainly makes genomicists and evolutionary biologists raise their eyebrows, but it hasn’t made them run for the hills.

That is because, in sprite of a few surprises like this one, the NDE prediction that conserved sequences are functional has largely held up, and has proven to be a tremendously powerful heuristic for discovering new mammalian biology. Just a few recent examples that come to mind were the discovery of an RNA gene expressed in brain based on its accelerated evolution in the human lineage compared to other vertebrates (Pollard & Haussler, 2006), the identification of a conserved enhancer mechanism and its evolutionary origins (Bejerano & Haussler, 2006), and the demonstration that many of the “ultraconserved” elements act as enhancer elements during embryonic development (Pennacchio & Rubin, 2006).

One nice thing about this story is that the same PI (Rubin) has published on both sides of the story, this study openly questioning the function of conserved elements and several others demonstrating them. It shows that there’s at least one prominent scientist who keeps an open mind towards dogmatic questions

GeoMor, you said,

This was certainly a surprising result, and clearly makes everyone examine in more detail the assumption that conservation implies function. It should first be noted that the study did identify significant changes in the expression patterns of two genes near the deleted DNA, in the brain and in the heart.

The article does not say the changes were significant, it says they were “detectable.” Only 2 of 108 samples (12 tissues for 9 genes) had any difference in gene expression. The article does not conclude that is evidence of causality. It is true, that out of 1,243 sequences they found one sequence that reproducibly drove B - galactosidase expression in mammary glands and abdominal muscle tissue. However, there is no evidence that this function is enough to provide selective benefit.

This is not to say that it was anything less than very surprising that the mice did fine against a large battery of tests; that is, after all, why Nature published it. It certainly makes genomicists and evolutionary biologists raise their eyebrows, but it hasn’t made them run for the hills.

That is because, in sprite of a few surprises like this one, the NDE prediction that conserved sequences are functional has largely held up, and has proven to be a tremendously powerful heuristic for discovering new mammalian biology.

It is not news that many conserved sequences have function or that looking for conserved sequences is a way of finding functional sequences. That has already been pointed out in this thread. What is news is that nonfuncting sequences are conserved. Natural selection has no mechanism for conserving sequences without function. That is the point.

That piece of “junk” removed might have a function that was just not tested under the described conditions.
To immediatley conclude that this is prove for genetic planning for the future is premature. that does not help convicing people of the idea of ID.

darth314,

That piece of “junk” removed might have a function that was just not tested under the described conditions.

It is possible. But the conclusion of the paper was that they did not have function. They expected to find function and made a significant effort to find function but could not. It has been over 2 years since the paper was published and I can’t find any evidence that anybody has even suggested a function. The over 200 mice they produced showed not phenotypic effects. So I see no real evidence that the sequences provide selective benefit.

To immediatley conclude that this is prove for genetic planning for the future is premature. that does not help convicing people of the idea of ID

Nobody is concluding that it is proof of planning for the future. But do you have a hypothesis of how and why natural selection would conserve all of these sequences that have no function?

| What is news is that nonfuncting sequences are conserved.

The paper demonstrates that a mouse with only about 99.9% of its genome does not show major abnormalities in its development, physiology or lifespan in the laboratory environment. It is true that, based on sequence conservation in the deleted regions, many biologists may have expected such gross effects to be visible, and that’s why it was a surprising result. But while we, as optimists, may have expected this, NDE does not imply it.

You are basically correct that “Natural selection has no mechanism for conserving sequences without function”. The nonfunctionality of these sequences has not been proven, and NDE’s prediction very bluntly remains that they are functional, despite the evident fact that they are not essential. NDE’s only prediction based on sequence conservation is that they must confer some “sufficient” selective advantage to the species (as you have noted).

So why have there not been massive efforts to search for the more subtle function that NDE predicts these sequences must have? Well, we are still sequencing genomes just to identify all the conserved sequence in mammalian genomes, let alone track down what every last bit does. The question will be addressed eventually. In the meantime, it will certainly fester, and it is not inappropriate to point this out. There is an interesting puzzle here, but not some massive problem. No one is running from the principle that “conservation implies function” because it has proven so scientifically fruitful in understanding how our genomes operate and evolve.

GeoMor

The paper demonstrates that a mouse with only about 99.9% of its genome does not show major abnormalities in its development, physiology or lifespan in the laboratory environment.

You are mischaracterizing the results. The paper showed that after the deletion of 1,243 conserved sequences of at least 100 base pairs in over 200 mice, there was no evidence of the deletions causing any phenotypic difference between the modified mice and the wild type.

You are basically correct that “Natural selection has no mechanism for conserving sequences without function”

“Basically correct”? As if to imply there are exceptions? Are you aware of any exceptions? Is it not absolutely correct?

The nonfunctionality of these sequences has not been proven, and NDE’s prediction very bluntly remains that they are functional, despite the evident fact that they are not essential.

The evident fact is that they have no function at all, save one sequence that has a function that does not appear to be essential. If you think these sequences have a function, please indicate where the investigators could have looked for function and they did not. It seems to me they were very thorough, doing 108 tissue samples for gene expression.

NDE’s only prediction based on sequence conservation is that they must confer some “sufficient” selective advantage to the species (as you have noted).

Of course, some function is not enough, it must confer a selective benefit. However, the conclusion of the authors of the paper in question was that the 1,242 of those sequences did not have a function, much less a selective benefit.

There is an interesting puzzle here, but not some massive problem. No one is running from the principle that “conservation implies function” because it has proven so scientifically fruitful in understanding how our genomes operate and evolve.

Under NDE conservation has to do better than “imply” function, it has to guarantee it because NDE predicts that sequence without function will not be conserved.

Me: “Obviously, since Evolution is true, the experiment does not cast doubt on Evolution, but merely shows that mice and men are very closely related.”

bFast: “You may read back in post 2 that I mention that these findings are consistent with a young earth. I’m still an old earther on acounta all that other evidence flyin’ in from everywhere.”

I saw where you mentioned that about a young Earth. (We’ll convert you, yet, so be ready.) And, my post was more directed at those who subscribe to Neo-Darwinian Theory. Although, now that you mention it, I thought I had noticed some buzzing noises - I guess I assumed they were mosquitos.

GeoMor:

No one is running from the principle that “conservation implies function” because it has proven so scientifically fruitful in understanding how our genomes operate and evolve.

As I posted on another thread, I think it’s possible that “evolutionists” are running away from it. Prof. Allan MacNeil, for example, has said something to the effect: “The Modern Synthesis is dead. Long live evo-devo.” Conserved sequence=essential function is certainly part of the Modern Synthesis. It seems that maybe some scientists see what I saw in reading the article two years ago: Darwinism (Modern Synthesis) is dead. Only the “obits” haven’t carried the news. Not yet, anyway.

The deleted sequences were not ultraconserved. They explicitly avoided deleting ultraconserved sequences. The deleted sequences fall into a category of conserved sequences less than “ultra”

DaveScot, let me keep this discussion painfully honest, after all we’ve got ‘em this time, and we don’t need to bungle it.

The original publication, link in post #4 says:

Together, the two selected regions contain 1,243 human–mouse
conserved non-coding elements (more than 100 base pairs (bp),
70% identity), also similar to genome averages, whereas no ultraconserved
elements9 or sequences conserved to fish (more than
100 bp, 70% identity) are present.

If 70% conserved is the average, I’m still very interested to know how conserved the most conserved region is.

DaveScot, perhaps the scientists in question suspect the answer such additional research would yield/confirm, and don’t want to face it. Many people who suspect thier cherished spouses are unfaithful will go to great lengths to avoid knowing for certain. So too might it be for a cherished belief.

The paper indicates that some of the conserved sequences were conserved in frog genomes as well. Does this mean that we are talking about hundreds of millions of years of conservation, not just 70-90 million years? I’d like to see knockout experiments on frogs using the relevant sequences.

bfast,

For the record, the article defines ultra conserved as being conserved across mamamals and fish. However there were some large sequencs, conserved amongst birds, mammals, and frogs with 90% identity.

From the article:

From the MU19 desert we picked five human-mouse conserved elements representing the most conserved sequences between these species (more than 180 bp, 90% identity ) for the in vivo assay. The ten elements chosen from desert MMU3 ( more than 400 bp, 90% identity ) included all five sequences that are conserved across humans, rodents, chicken and frog , and five that are conserved across humans, rodents and chicken only.

It should be noted that from those 15 sequences they found a small function in one of the sequences. I have mentioned that function twice before in this thread already and suffice it to say there is no indication it provides selective benefit.

bFast,

So these sequences are even more conserved between mice and men than even protein coding genes.

It appears to me that they have a different code than the protein expressing “central dogma” genes, this code does not have the alternative spellings that are acceptable in the “central dogma.”

I should also point out that function in gene regulation has been demonstrated for many of these CNG’s.

Sabre, that’s how I see it.

Chunkdz, if the thing is found in frogs, we’re dealing with a mear 500 million years (250M ancestor to frog, 250M ancestor to mouse.) But 140m, 500m in this case it doesn’t make a hair of a difference — 20m might help. Douglas chimes in — how ’bout 6000!

DaveScot, they’re realin’ and a wrigglin’ — or at least they should be.

No wonder Modern Evo Synthesis is being superceeded.

Hmmm, along with Vole info posted here before(by Gil?)…
http://www.medicalnewstoday.co.....wsid=51906

This is turning into a conspiracy against science!

Monthy Python was right all along, our world was build by mice!

“If mice and men had a common ancestor many millions of years ago and they still have highly conserved DNA in common, the story follows that all the conserved DNA must have an important survival value.”

Or perhaps (gasp) common descend is a crock, and some designer(s) came up with all the body plans, and shared various components from a “library”, and the “junk” just happened to be in the library as filler, etc.

Think OOP.

Boy would I love to toy with that library. Seems like it would be fun populating a planet with variouos lifeforms that interact. Hmm, I wonder if the “angels” (read: extraterrestial brainiacs) did that on this planet? Seems I read in the Talmud that this is exactly what happened. Hmm.

…and if they haven’t been productive you’re going to be demoted to lurker status.

I resemble that remark.

[moderator] smartass

Just as NDE theory has morphed to account for all situations - evolution is gradual, except when it’s rapid or static - I suspect the theory will just morph again without ever admitting defeat.

Maybe they’ll call it the “New and Improved NDE Theory (now with twice the dogma)”, or perhaps “NDE Theory v12.0″.

Lurker, cut the defeatest attitude, we’ve got ‘em tight with this one. Function must be found or preservation happens dispite no natural selection. That’s all.

Their best response to this one is to shut up ‘an hope it goes away.

Lurker:

As I posted earlier, I think that the (no longer Darwinists) evolutionists have moved onto “evo-devo” (Allen MacNeil), and will probably say (as did MacNeil) that the trick is in how all of this genetic stuff “develops” over time and how they need a theory of developmental biology. The next step is to simply say that Darwin talked about the importance of “embryology”, and that’s what “evo-devo” is all about anyways.

And they’ll simply go on their merry way……..

PaV, there is bunches of evolutinary biology that is not challenged by these findings. Evo-Devo, particularly is not a very RM+NS bound topic. There is nothing about these findings that challenges common descent.

These findings only address one core issue — the role of random mutation and natural selection in evolution. The problem with this core issue is that the only alternative even close to the table is, well, telic.

DaveScot, back in post #47, you suggested the possibility of “horizontal DNA flow” explaining these findings. If this were so, then the “preserved” data would not present the phylogenic tree. This could be checked easily enough. If in these regions, the chimp and the human are more highly preserved than the mouse and human, (throw in a couple of other test points, a dog maybe, for good measure) and this possibility would be ruled out.