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Is Eugenie Scott an Atheist?

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This question was posed in one of the earlier threads on this blog. According to the following article, “Scott describes herself as atheist but does not discount the importance of spirituality.” Scott never asked the San Francisco Chronicle to retract this designation of atheism.

EUGENIE SCOTT
Berkeley scientist leads fight to stop teaching of creationism
Monica Lam, Special to The Chronicle
Friday, February 7, 2003
©2003 San Francisco Chronicle | Feedback

URL: http://www.sfgate.com/cgi-bin/article.cgi?file=/chronicle/archive/2003/02/07/EB75914.DTL

One morning in September, Eugenie Scott of Berkeley got a long-distance phone call from an alarmed parent in Cobb County, Ga. The board of education there was considering allowing creationism to be taught side-by-side with evolution as an alternative, scientific theory on human origins.

Scott sat at her desk, beneath a portrait of Charles Darwin in an office littered with books about evolution, models of hominid skulls and a map of the human genome, and typed up a speech she has delivered many times before. While students’ religious views should be respected, she wrote, schools should allow only science to be taught in science classes.

Two hours before the board’s vote, Scott e-mailed the speech to the parent to deliver to the board. But that board had already put disclaimers against evolution in the science textbooks, saying “evolution is a theory, not a fact” and that it should be “critically considered.”

Scott, the director of the National Center for Science Education in Oakland, has been fighting this particular battle for more than 15 years, and it has taken her around the country — from small towns in California to the deep South.

Her opponents are parents, politicians and even teachers who want creationism — the belief that God created human beings as literally described in the Bible — taught in public schools. This despite the fact that the U.S. Supreme Court has issued numerous decisions disallowing the teaching of creationism in public schools because it is a religious view and would violate the separation of church and state.

Scott’s work often takes her into the Bible Belt — the Midwest and the South — but closer to home, a recent conference in San Francisco on “intelligent design” attracted 200 college students and adults. Here Scott was confronted by the relatively new attack on evolution: scientists looking for scientific evidence to prove creationism is true.

While organizers insisted that the conference was about science — creation science — not religion, almost all the speakers were creationists. The intelligent design theory says that life on Earth is so complex and intricate that only an intelligent entity could have designed it.

“What we call creation science makes no reference to the Bible,” said Duane Gish, vice president of the Institute for Creation Research in San Diego.

“It says there are two possible explanations for the origin of the universe and living things: theistic, supernatural creation by an intelligent being, or nontheistic, mechanistic evolutionary theory that posits no goal and no purpose in the evolutionary process. We just happen to be here.”

“I think what bothers me so much of the time,” Scott said, “is they take the data and theory and distort it. They must know they’re distorting.”

But intelligent design theory has gained a lot of momentum, Scott said, because it allows religion, labeled as science, to sneak into schools through the back door.

But another opponent, Phillip Johnson, a Jefferson E. Peyser professor of law, emeritus at UC Berkeley’s Boalt Hall School of Law and author of “Darwin on Trial,” said Darwinism is all about religion.

“Its (evolution’s) impact is cultural,” he said. “It’s impact is it puts God out of reality. I am not bringing religion into the sacred precinct of science. The biologists are already neck deep in religion.”

The Ohio Board of Education recently considered including intelligent design theory in the science curriculum, but after a long debate voted against it. Scott and the National Center for Science Education advised the opponents of the proposal and counts it as another victory. However, Johnson also considers it a victory because the ruling did not exclude teaching intelligent design.

Don Kennedy, a Stanford University biology professor and editor in chief of the journal Science, said Scott has been effective because she’s knowledgeable about evolutionary theory.

“She’s the central force in contesting creationist claims by bringing good science to bear,” he said.

Scott grew up in Wisconsin and studied physical anthropology. She first heard of creationism in 1971, when she was a graduate student and, fascinated by what she thought was a rarity, started collecting literature and information on the movement.

Later, while teaching physical anthropology at the University of Kentucky in 1980, she led her first successful battle, blocking a Kentucky school board from including creationism in the curriculum.

In 1987, Scott was hired as the founding director of the nonprofit National Center for Science Education, the only national organization dedicated to “defending the teaching of evolution in public schools.”

In 2001, Scott’s organization recorded incidents in 43 school districts and five state boards of education in which the teaching of evolution was challenged. Legislation promoting the teaching of creationism was introduced in eight state legislatures and in the U.S. Senate, according to the center.

“She’s a front-line soldier in this war,” said Al Janulaw, a retired schoolteacher and spokesman for the California Science Teachers Association. “She’s everywhere in the country fixing things.” The association, a membership organization of K-12 and university educators, gave Scott its Margaret Nicholson Distinguished Service Award in 2002.

Scott gave up her career as a scientist to pursue activism because she says she sees science as fundamental to a proper education.

“You can’t really be scientifically literate if you don’t understand evolution,” Scott said. “And you can’t be an educated member of society if you don’t understand science.”

Scott describes herself as atheist but does not discount the importance of spirituality.

“Science is a limited way of knowing, looking at just the natural world and natural causes,” she said. “There are a lot of ways human beings understand the universe — through literature, theology, aesthetics, art or music.”

One of Scott’s biggest victories was in Kansas. In 1999, the Kansas State Board of Education voted to remove evolution from the testing standards, generating national headlines and prompting a campaign to preserve the standards. The grass-roots group, Kansas Citizens for Science, called on Scott for advice.

“We’d never been through this before,” said Liz Craig, who helped lead KCFS’ effort. Scott provided reference materials, people to contact and a shoulder to cry on, Craig said.

Scott also traveled to Kansas for several speaking engagements. In her earnest, soft-spoken voice, she tried to explain to parents and teachers that science and evolution are not anti-religion. “Students don’t have to accept evolution,” Scott frequently has said. “But they should learn it — as it is understood by scientists.”

Two years later, a new board was elected, and it restored evolution to the school standards.

The Kansas fight drew national attention to Scott’s work and brought in additional funding. With a spacious, loft-style office on 40th Street in Oakland, NCSE’s annual budget is $500,000, and Scott recently received a raise in her salary to $70,000.

Hanging next to photos of her husband and daughter are awards and cards from scientists and teachers around the country expressing their gratitude.

In 2002, she received a public service award from the National Science Board, which governs the National Science Foundation, to go along with the CSTA honor.

Still, there are many smaller conflicts that are beyond her reach, many of which involve individual students. In the spring, a seventh-grader in Edmond, Okla., was branded “Monkey Girl” by her classmates because she wanted to learn about evolution.

NCSE wrote a letter on the girl’s behalf, asking the principal and the teacher to respect her request and to curb the peer harassment, but to no avail. The family eventually moved to another school district.

Over the years, Scott has found her fight to be much less about science and more about politics. “I learned very early on that it’s necessary but not sufficient for scientists to go to school board meetings and say, ‘We shouldn’t be teaching creationism,’ ” Scott said. “Being right doesn’t mean it’ll pass.

“Public schools are where the next generation of leaders are educated and where cultural exchange will take place,” Scott said. And Scott will be there, fighting to ensure that students are taught evolution.

It’s scientific For more information on the National Center for Science Education, visit www.ncseweb.org or contact Eugenie Scott at 420 40th St., Suite 2, Oakland, CA 94609-2509; (510) 601-7203; ncseoffice@ncseweb.org.

Comments
"But, we know that the vast majority of synonymous sites do not have a specific, conserved function." Uh huh. And a couple years ago you knew that coding genes controlled everything. Knowing is sometimes a fleeting thing, ain't it?DaveScot
November 16, 2005
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"It might simply be the case that there is no better data." Indeed, quite possible. It may be the case that laboratories populations have different mutation rates than in the wild, etc... I guess the main point I'm trying to make is that synonymous sites lacking function is not an argument from ignorance. The most pausimonious explanation for the observed patterns of synonymous substitution rates is that the sites are evolving neutrally. Of course, this parsimonious explanation is not necessarily the truth, only the most reasonable hypothesis that exists at the moment that explains patterns of rate variation. In this case function is an unnecessary additional parameter, and it is removed by Occam's razor. *But* if synonymous sites do have some function, we actually know quite a lot about what sort of function it would be (just from the sequence data). This function would have to exert the same (low) pressure on the vast majority of synonymous codons across the genome (and also the same pressure on many stretches of non-coding DNA). There could be something akin to genomic formatting going on having to do with AT, GC biases, or something of that nature, something specific to the genome, rather than a particular gene. Or, it could also be the case that there is another small subset (cannot be too much more than 1%) besides splice site enhancers that do very particular functions. But, we know that the vast majority of synonymous sites do not have a specific, conserved function.cambion
November 16, 2005
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"What we really need is some better data on the rate of spontaneous mutations…." It might simply be the case that there is no better data. I think you're trying to find patterns in chaos - the genomic equivalent of connecting the dots on star charts to find outlines of familiar objects. There are too many unknown variables effecting mutation rates and no tractible way of eliminating their effects to see what, if anything, is left over. Of course I could be wrong. Stranger things have happened than me being wrong... ;-)DaveScot
November 16, 2005
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What we really need is some better data on the rate of spontaneous mutations...cambion
November 15, 2005
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"f the effects of synonymous substitutions are subtle then they are likely not going to rise above a factor of 2 noise level due to selection pressure." Looks like we might be getting closer to agreement. Assuming that the factor of 2 reflects the true difference (rather than experimental noise) between rates of spontaneous mutation and rates of synonymous substitution, then the most pausimonious explanation would be *very* low-level selection acting at the same strength across synonymous sites and many other non-coding regions. They key here is that function cannot vary across sites...cambion
November 15, 2005
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cambion "Their rates of evolution are just too similar to one another (and to ancestral repeat sequences and to the rate of spontaneous mutation) to suggest otherwise." Wasn't what you deemed "similar" a factor of 2 difference? If the effects of synonymous substitutions are subtle then they are likely not going to rise above a factor of 2 noise level due to selection pressure.DaveScot
November 15, 2005
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cambion: "If Design == Function -> homology data points to common descent If Design > Function -> homology data could give either conclusion" You got it. Now, just to address the earlier discussion of PE: (Letting alone that NS+RV does not have the power that Darwin attributed to it:) In The Origin, Darwin specifically argued against isolation being necessary, and thought that any evolution that occured due to isolation would be inconsequential, since organisms evolved in larger populations would be more robust and eliminate those evolved in smaller populations. Based on analogy with human populations (big fish in little school; small fish in big school), this assumption of his seems completely logical. But the fossil record (still) clearly violates what Darwin said should be there if his theory was correct. As for PE as a patch: Isolation may tend to cause organisms to become smaller or larger (to make do with sparse food - eat less, or eat more and store it up when the opportunity presents itself). But develop new functions? That allow them to wipe out their ancestral species? And that's how all evolution occurs (since the fossil record is inexplicable otherwise)? It's a shame that it's so often misunderstood or misrepresented by creationists; there's no need to misunderstand or misrepresent PE to think that it's an unconvincing attempt to rescue a semblance of Darwin's theory from his own predictions.jay
November 15, 2005
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DaveScot, I think you misunderstand me... Natural selection acting as a purely stabilizing force (i.e. not creating anyting at all) will lower the observed rates of evolution of DNA sequences. Sequences that are more important will change more slowly than sequences that are less important. This can be seen when comparing the rate of change of DNA polymerase vs. some less vital enzyme. However, the observed rates at which synonymous sites change (see points #2 - #4 above) strongly suggests that the vast majority have no function. Their rates of evolution are just too similar to one another (and to ancestral repeat sequences and to the rate of spontaneous mutation) to suggest otherwise. We don't need to know all classes of biological function to make this assessment. If synonymous sites had 'any' function whatsoever, they would NOT show the rates of evolution that they do. Well, actually, if they have some function, it must be that the function is independent of the base pairs used among synonymous sites. And in this case, we would still observe 'neutral' evolution among synonymous sites, as mutations would appear that 'neutral' in the eyes of natural selection.cambion
November 15, 2005
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cambion "quite certain that synonymous sites lacking function >> synonymous sites with function" This implies that every possible function has been identified. There may be entire classes of functionality that have been missed by experiment. There's simply too much that is still unknown to make the kind of claims you're making. Let's take immune function as an example of something likely overlooked by synonymous substitution. Skin graft acceptance/rejection is an easy case to study. http://www.uvm.edu/~jdavison/davison-manifesto.html#variability
The gynogenetic offspring from a common mother are also interesting from the point of view of semi-meiosis as a device for generating genetic diversity. Frogs, like mammals, have evolved immune systems and will reject a skin transplant from a genetically different donor. Gynogenetically produced siblings reject skin transplants from one another. They also reject skin transplants from their common mother because none of them have all of her genes. In fact they each have exactly one half (qualitatively) of her total genetic constitution, the other half having been eliminated in the first polar body. The mother will, however, accept a skin transplant from any of her gynogenetic progeny because none of them have any genes that are not hers (Nace and Richards 1969).
So tell me, would a synonymous site substitution change the immune response in the above experiments? How was modified immune function ruled out in the experiments you use to conclude that synonymous substitutions have no effect other than splice site recognition? As I said before, code comparison operations that fail because of a synonymous substitution could (and almost certainly do) extend beyond splice site recognition. Mobile elements for instance glom onto sequence specific sites on the DNA molecule and the function of these mobile elements is just a complete mystery but it's reasonable to conclude there is *some* function behind them. Just a few years ago it was the consensus that coding genes do everything. Now the consensus is that there is a whole bunch of biological function that is not under the control of coding genes.DaveScot
November 15, 2005
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Should be: (note* that ET does not rely in the least on Haeckel's work).cambion
November 15, 2005
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mentok, "You can say that PE doesn’t postulate “short time frames” and “large mutations” or rapid mutations, all you want. You’re just playing with semantics..." I'd suggest you read the primary literature on the subject... Other straw man attacks from darwinismrefuted.com: 1. Attacking abiogenesis and then saying it has 'refuted' evolution. You can see this in their discussion of thermodynamics. They say: "The theory of evolution says that disordered, dispersed, and lifeless atoms and molecules spontaneously came together over time, in a particular order, to form extremely complex molecules such as proteins, DNA, and RNA..." The theory of evolution says nothing of the sort... 2. They refer to the overall genetic similarity of human and chimp as 95%, and then contrast this with a genetic homology (what percent of 'genes' have matches, not base pairs) of 75% between human and nematode. They say: how can 6 million year separate be 5% and a 530 million year separation be 25%. Another straw man attack. 3. "What used to be called the "recapitulation theory" has long been eliminated from scientific literature, but it is still being presented as a scientific reality by some evolutionist publications." They attack Haeckel, and justly so, but seem to rely on a sort of guild by association scenario with modern evolution theory (not that ET does not rely in the least on Haeckel's work). I'd that's just few examples. These sorts of straw man attacks makes me think that darwinismrefuted.com may have some sort of agenda to push. Maybe...cambion
November 15, 2005
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jay, I understand your point much better now. You kind of put me on the defensive before with the accusation of "unscientific opinion." I agree that my assessment of molecular homology depends on an assumption of function being the only thing that is important. This assumption may or may not be valid, and whether or not it's valid determines whether 'my' point is itself valid. However, science makes assumptions all the time, just because there are assumptions doesn't make something unscientific. I thinkk we're in agreement: If Design == Function -> homology data points to common descent If Design > Function -> homology data could give either conclusioncambion
November 15, 2005
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DaveScot, You make a good point... Teaches me to overstate my case. The statistical analysis that show that 'all' synonymous sites evolve at the same rate, do not have 100% statistical power. The statistics are consistent with each and every synonymous site evolving at the same rate, as well as consistent with the vast majority of synonymous sites evolving at the same rate. The latter is probably the case due to splice site enhancers. Although also possible are other synonymous site functions (you could imagine signals to tell the cell where to take the mRNA and such). So, it is quite possible (and indeed likely) that some synonymous sites have function. However, it is quite certain that synonymous sites lacking function >> synonymous sites with function.cambion
November 15, 2005
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cambion: "If synonymous sites are indeed functionless (all available evidence points to this - see above post), then it follows that I can make the exact same organism in terms of structure, function, behavior, etc. with any ‘isometric’ combination of synonymous codons. From a design perspective, it doesn’t matter what synonymous sites you use. How, exactly, is this an 'unscientific opinion'?" I understood. No explanation needed. It's unscientific because you are assuming what the designer would or would not do for something that isn't constrained. That's an artistic call. "You accuse me of an “unscientific opinion” and then go on to state that the designer could have made things the way they are for “artistic reasons?” Obviously, your designer can do whatever he (it) wants to do, so why bother talking about science…" You're the one who raised the artistic critique. But that is the nature of designers. Within some constraints, they often can do whatever they want to do. And if a phenomenon is actually due to a designer, then to assume that it's not and attempt to force fit it into some pre-conceived notion of material causes will lead to the wrong conclusion. It seems that what you are really saying is that if it's not a material explanation, then it's not science. My point is simply to keep an open mind. I don't rule out neutral evolution or common descent. "This is exactly what common descent is NOT doing. It does not assume a functional (or “artistic”) explanation…" Your are misunderstanding what I said. The requirement for function tends to constrain things, and not to allow artistic license.jay
November 15, 2005
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cambion
1. Synonymous sites have no observed function (expect for the 1% involved in splice site recognition). 2. Synonymous sites evolve at characteristic rate, which is the same among genes and between synonymous sites within a gene. If they have some function it must exert the same influence on each and every synonymous site.
These two points contradict each other. If synonymous changes effect splice site recognition (which is the code comparison I talked at length about) then by definition all synonymous sites cannot have exactly the same influence. Back to the drawing board with you.DaveScot
November 15, 2005
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cambion Evolutionary changes take place instantaneously in a single individual. To say otherwise is to deny descent with modification. Surely you're not doing that. The time-frame argument is thus not about evolutionary change but about enough evolutionary change so that a new species is created. This can almost certainly occur as saltation by way of chromosomal reorganization.DaveScot
November 15, 2005
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cambion you don't know what you are talking about and Talk Origins is useless as they don't either. Saltation is a red herring in your argument as the author of that article did not equate PE with Saltation, he said it was a modified form of it, and it is. You can say that PE doesn't postulate "short time frames" and "large mutations" or rapid mutations, all you want. You're just playing with semantics and claiming that the author of that book was attacking a straw man. That's a straw man attack by you. Anyone can do some reading and see for themselves, if you disagree, well, good luck with that..I can't debate someone who is unable to debate in a straightforward and honest way. I'm through debating you because you are consistently trying to word juggle or mischaracterize or use some other fallacious rhetoric in your futile quest to prove ID wrong at any cost (without even knowing what it really teaches nor what evolution really teaches).mentok
November 15, 2005
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mentok, I'm sorry, I thought that I had actually backed up my claim. I've previously pointed out darwinismrefuted.com's statements of: “This theory was actually a modified form of the “Hopeful Monster” theory put forward by the German paleontologist Otto Schindewolf in the 1930s.” “According to this viewpoint, evolutionary changes take place in short time frames and in very restricted populations-that is, the equilibrium is divided into separate periods or, in other words, “punctuated.” Because the population is very small, large mutations are chosen by natural selection and thus enable a new species to emerge.” These statements push the idea that PE means both "short time frames" and "large mutations." Notably, darwinismrefuted.com goes on to "disprove" the fact that large mutations can be beneficial, in effect, attacking a straw man. However, I also previously posted a link to TalkOrigins posting on PE (http://www.talkorigins.org/faqs/punc-eq.html). Here is an excerpt: “PE is by no means either synonymous with “saltationism”, nor did Gould’s essay on Richard Goldschmidt “link” PE with Goldschmidt’s “hopeful monster” conjecture. Gould wrote an article that has caused much confusion. “Return of the hopeful monsters” sought to point out that a hatchet job had been done on some of the concepts that Richard Goldschmidt had formulated. The discussion of systemic mutations as mutations which affect rate or timing of development has caused many people to assume that Gould was somehow linking PE to this concept. A close reading of the article shows this to not be the case.” “Gould and Eldredge did not specify any particular genetic mechanism for PE. PE does not require large scale mutations.” "Short time frames" and "large mutations" are not part of PE. It's quite aggrevating to me, that they would misrespresent the theory to such a large degree (although I have to admit it makes their rhetorical argument sound better...)cambion
November 14, 2005
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cambion simply claiming it is wrong and then asking me to repond to your claim is putting the cart before the horse. Since you claim they are wrong the onus is on you present a point by point rebutall and prove you are right. At least that's the preferred methond of debate.mentok
November 14, 2005
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mentok, I would love to hear a response to darwinismrefuted.com's (quite possibly deliberate) misrepresentation of the theory of punctuated equilbrium.cambion
November 14, 2005
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Bombadill, Was my explanation of common descent vs. common design clear enough? Please let me know if there is anything I wasn't conveying properly...cambion
November 14, 2005
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jay, You say that my suggestion that “it just doesn’t matter from a design perspective…” is "an unscientific opinion." If synonymous sites are indeed functionless (all available evidence points to this - see above post), then it follows that I can make the exact same organism in terms of structure, function, behavior, etc. with any 'isometric' combination of synonymous codons. From a design perspective, it doesn't matter what synonymous sites you use. How, exactly, is this an "unscientific opinion"? You then go on to say: "Why wouldn’t (or couldn’t) the intelligent designer for, say, artistic reasons, make nonfunctional details similar on similar species?" You accuse me of an "unscientific opinion" and then go on to state that the designer could have made things the way they are for "artistic reasons?" Obviously, your designer can do whatever he (it) wants to do, so why bother talking about science... "Apart from philosophical grounds, why assume that everything must have a functional explanation?" This is exactly what common descent is NOT doing. It does not assume a functional (or "artistic") explanation...cambion
November 14, 2005
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So annoying, none of my comments want to take... ----------------- DaveScot, In response to possible functions of synonymous sites... I don't want to get into this too much again (as I remember our first discussion ended on a rather sour note). However, I would like to back my self up. The argument is more complete than: "molecular biology observes no function in synonymous sites, therefore there is none." Instead, we have the following pieces of evidence: 1. Synonymous sites have no observed function (expect for the 1% involved in splice site recognition). 2. Synonymous sites evolve at characteristic rate, which is the same among genes and between synonymous sites within a gene. If they have some function it must exert the same influence on each and every synonymous site. Note that this is not the way it works with protein-coding changes. We see different rates between genes and among genes for these sites (which we know are functional). 3. This rate of evolution is the exact same (0.46-0.47 changes per site between mouse and human) for synonymous sites and ancestral sequence repeats. Now, to posit some function it must exert the same influence in both classes of putative functionless sites. 4. This rate of evolution is very close to the observed rate of spontaneous mutation. This match is perfectly predicted by population genetic theory. 5. The site frequency spectum of synonymous polymorphisms (how many polymorphisms are at X% frequency in the population) corresponds quite nicely to population genetic predictions for sites undergoing neutral evolution. There certainly can be pieces of noncoding DNA performing functions that we have no idea exist. However, I think it's pretty well settled that synonymous sites are not among these.cambion
November 14, 2005
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DaveScot, In response to possible functions of synonymous sites... I don't want to get into this too much again (as I remember our first discussion ended on a rather sour note). However, I would like to back my self up. The argument is more complete than: "molecular biology observes no function in synonymous sites, therefore there is none." Instead, we have the following pieces of evidence: 1. Synonymous sites have no observed function (expect for the cambion
November 14, 2005
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cambion: "it just doesn’t matter from a design perspective..." That's an unscientific opinion. "The null hypothesis given by common design would be equivelent levels of synonymous similarity between all mammalian species." Human designers make non-functional details similar on similar designed things all the time. Why wouldn't (or couldn't) the intelligent designer for, say, artistic reasons, make nonfunctional details similar on similar species? "The observed patterns of correspondence provide an excellent indication of patterns of common ancestry. It is possible that a designer is just trying to fool us, but there is no functional reason for finding these patterns." Why assume common ancestry? If not, then why assume devious intent on the part of the designer? Apart from philosophical grounds, why assume that everything must have a functional explanation? "[The] design...prediction [is that] morphologically similar species and morphologically dissimilar species should have the same level of differences regarding ribosome sequence...Plants and animals have the most differences between their conserved genes, and mammals have the least." Species with the most functional similarity having most similarity in functional coding. What a surprise. "Let me restate one thing. This only shows common descent. It is hypothetically possible that neutral evolution has been occuring for many millions of years, resulting in these patterns, while all functional differences were created by an intelligent agent and not natural selection." Even the assumptions of common descent and neutral evolution aren't necessary...except from a materialist mindset.jay
November 14, 2005
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Another good example of synonymous code handling is the common practice of converting all uppercase ASCII characters to lower case before comparing. Thus a password "PASSWORD" and "password" are identical in function. Just don't rely on that that where the password parser is case sensitive. There are a plethora of parsers operating on DNA sequences in the cell. Undoubtedly many of these are still uncharacterized. So just because a ribosome doesn't seem to care which of several redundant codons is used for an amino acid doesn't mean that other parsing mechanisms ignore the difference.DaveScot
November 14, 2005
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"except in some rare circumstances having to do the splice site recognition" I think that's a bit misleading. It seems to imply that we know everything there is to know about splicing mechanisms and that's pretty far from true. It was only in the past year or two that we realized the huge shortfall in expected number of coding human genes was because most of the proteins human cells can produce are the result of tRNA splicing. God only knows what all is going on. Mobile elements, for instance, are hopping around the genome like grease in a hot skillet. It's extremely premature to bound the effects that so-called synonymous mutations can have. There are analogous situations in many human devised codes where such changes have non-obvious effects. The majority of the non-obvious effects are when code comparisons are made and otherwise identical code sequences pop up as not identical, where the mismatch causes process changes further down the line. For instance, it is common programming practice to strip certain "white space" characters from a string before parsing. Yahoo's message boards for instance have spam filters that count the occurence of URLs and one that's repeated too many times throughout their system is deemed spam and all posts containing the URL are deleted. I found a charming way to defeat the filter. The filter doesn't strip ASCII carriage returns and line feeds before doing the comparison and updating the URL counts. So I append a CR or LF escape sequence to rejected URLs in my posts get around it. I can do this and still have a hotlink posted because the software that processes hotlinks does, unlike the spam filter, strip CR & LF characters before parsing. Now suppose there are cellular functions where a synonymous mutation that doesn't alter an expressed protein actually does alter things like frequency of expression, splicing, mobile elements that are glomming onto certain sequences by exact match, etc.DaveScot
November 14, 2005
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10:53 AM
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"I bet they don’t add up to 100%." That would be quite exciting to somehow show that... It would be quite a contribution...cambion
November 14, 2005
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"what proportion of genetic differences can be attributed to natural selection and what proportion can be solely attributed to drift" I bet they don't add up to 100%. ;-)DaveScot
November 14, 2005
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Let me restate one thing. This only shows common descent. It is hypothetically possible that neutral evolution has been occuring for many millions of years, resulting in these patterns, while all functional differences were created by an intelligent agent and not natural selection.cambion
November 14, 2005
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