From the Biologic Institute, “A Facebook Dialogue”

_{Denyse O'Leary

November 12, 2012

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Ann Gauger posted an amusing facebook dialogue on the blog of the Biologic Institute: “Sometimes it might be a good idea to actually read what ID proponents write before critiquing it.” Click here to read the rest.

Comments

However no one knows how much of a genetic difference exists between chimps and humans
What? This is just sheer nonsense, inherited from desperate creationist poo-flinging to obscure the fact that basically no matter how you measure it, chimps and humans are the two most similar genomes known (unless you count the Neanderthal genome, of course). This isn't just me saying this, go ask Todd Wodd of Bryan College: https://uncommondescent.com/genetics/bryan-college-prof-defends-98-chimp-human-dna-identity/NickMatzke_UD_{November 16, 2012
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Nick, just curious as to your viewpoint:
However, it’s very clear that most of the genetic differences between humans and chimps are just noise and aren’t meaningful — they are just the product of genetic drift, and are in noncoding regions/junk, are synonymous substitutions, etc.
Assuming the above to be true, does this suggest that the differences between humans and chimps do not result primarily from changes in the DNA?Eric Anderson_{November 16, 2012
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Nick @26: I know, I know. I'm giving you a hard time. That's why I threw in the little smiley face. I just think it is funny that we've heard so many claims of absolute certainty about this or that % over the years from everyone from Dawkins on down, how it proves evolution and is a problem for "creationists," etc., and yet the % keeps changing, it is turning out the numbers have often been wildly inflated or are highly questionable in how they are calculated and so on. Of course, "similar" is subjective, so it can be used however one finds it convenient in the particular instance. I presume we can both agree that the exact percentage of identical DNA or even similar DNA does not either prove or disprove a Darwinian or ID origin?Eric Anderson_{November 16, 2012
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Nick:
Science isn’t about complete knowledge, it’s about testing hypotheses.
No one is asking for complete knowledge Nick. We're asking for any knowledge. My request wasn't a request for everything, it was a request for anything. Instead, what we get are shifting explanations and ad hoc rationalizations, and it's hard to think of that as knowledge.
However, it’s very clear that most of the genetic differences between humans and chimps are just noise and aren’t meaningful — they are just the product of genetic drift, and are in noncoding regions/junk, are synonymous substitutions, etc.
Yes. But when we ask about what it takes to get a chimp and a human from a common ancestor, we get tales of drift.Mung_{November 16, 2012
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Unfortunately for Nick there isn't any field nor subfield which can produce positive evidence for his positions' claims.Joe_{November 16, 2012
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Nick Matzke:
Even long before there was any genome sequencing at all, we could tell that human DNA and chimp DNA were highly similar, based on DNA-DNA hybridization experiments.
LoL! Yes similar DNA sequences are similar! However no one knows how much of a genetic difference exists between chimps and humans and no one knows if changes to the genome can account for the transformations possible. IOW it ain't science.Joe_{November 16, 2012
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1. How many and which ones?
It will take hundreds of years to figure this out, heck, we only finished the first genome sequence a little bit ago, and we would have to have a much more thorough understanding of developmental biology, for starters. But using "you don't have complete knowledge" as an argument against evolution would be like using "you don't know what Jesus ate on Thursday, 15 A.D." as an argument against Christianity. Science isn't about complete knowledge, it's about testing hypotheses. However, it's very clear that most of the genetic differences between humans and chimps are just noise and aren't meaningful -- they are just the product of genetic drift, and are in noncoding regions/junk, are synonymous substitutions, etc. To get a sense of how much rarer the "meaningful" changes are, look at the non-synonymous changes in coding DNA:
If you measure nonsynonymous base pair differences within protein coding regions, humans and chimps are 99.75 percent identical (Chimpanzee Sequencing 2005, fig. 9)

2. Wouldn’t the neutral mutations have ridden along and been fixed at the same rate?
A little bit, but not very much. The chromosomes are broken up by crossing-over events every generation, so the blocks that get dragged to fixation during selective sweeps end up pretty small. Actually there are whole subfields of genetics devoted to just the topic of chromosome blocks and their history as they get broken up under selection, drift, and migration. There is all kinds of information about ancestry, selective events, etc. in the size of blocks. There are probably more people that study just this than all the creationist/IDist "experts" put together.NickMatzke_UD_{November 15, 2012
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Hold on just a minute. Here we were being told that 98% (or was it 99% or 97% or whatever last week’s % was?) proved that humans and chimps share a common ancestor. Now you’re saying we don’t really know how similar the genomes are?
You do realize, I hope, that one can make a highly accurate statistical estimate based on an incomplete sample...right? That's how polls work, after all. In the case of polls, you have a sample of <0.01% of the population, yet they are accurate. With genomes, we have 90%+. The last stuff to be sequenced is the hardest stuff to sequence, because it is highly repetitive DNA, which is junk and/or low-information structural DNA. Even long before there was any genome sequencing at all, we could tell that human DNA and chimp DNA were highly similar, based on DNA-DNA hybridization experiments.NickMatzke_UD_{November 15, 2012
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Nick:
Neither the human genome nor the chimp genome sequence is actually complete, for various technical reasons. This was particularly true of the chimp genome a few years ago when Coyne’s book was written.
Hold on just a minute. Here we were being told that 98% (or was it 99% or 97% or whatever last week's % was?) proved that humans and chimps share a common ancestor. Now you're saying we don't really know how similar the genomes are? :)Eric Anderson_{November 15, 2012
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Nick:
1. Neutrality is just what happens when s, the selection coefficient, is ~0. Even under neutrality, you will get a bunch of fixation events, even under the very slow rate of fixation under neutrality (about 1.5% divergence over 6 million years). The vast majority of genetic differences between humans and chimps are of this type.
ok, that's what I said. Invoke neutral mutations until they can't do the job on their own. Then invoke something else. 2. Some of the differences (probably a tiny number, perhaps a few thousand or tens of thousands) were indeed promoted by selection, and thus fixed on average much more quickly than the neutral mutations. 1. How many and which ones? 2. Wouldn't the neutral mutations have ridden along and been fixed at the same rate?
1. Even if true, this wouldn’t mean a bunch of new genes on the human line. It could just mean a bunch of losses on the chimpanzee line.
Oh yeah, and if all the above doesn't work invoke lost genes! Flexible theory that. Can use it to "explain" just about anything.Mung_{November 15, 2012
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Nick:
This thread is incredibly silly!
HMM Nick have you ever read evolutionary material? http://sphotos-b.xx.fbcdn.net/hphotos-prn1/23965_368794003215146_1647210664_n.jpgbornagain77_{November 15, 2012
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Nick Matzke:
You guys are trying to play selection off against neutrality, but both clearly exist.
THAT is incredibly silly and bodering on dishonesty.
1. Neutrality is just what happens when s, the selection coefficient, is ~0. Even under neutrality, you will get a bunch of fixation events, even under the very slow rate of fixation under neutrality (about 1.5% divergence over 6 million years). The vast majority of genetic differences between humans and chimps are of this type.
That is the assertion. Of course under a design scenario such a thing would be possible. BTW how many mutations does it take to get an upright biped from a knuckle-walker/ quadraped?
2. Some of the differences (probably a tiny number, perhaps a few thousand or tens of thousands) were indeed promoted by selection, and thus fixed on average much more quickly than the neutral mutations.
Via design or severe bottlenecks. Otherwise all bets are off as evidenced by experiments with fruit flies.
3. Gauger claims that some large proportion of the differences between humans and chimps would have required multiple mutations to happen *before* selection could favor them. If there were a large number of these, there would indeed be not enough time for drift+selection to produce these specific features. But she gives only the vaguest argument that such features exist at all and ignores all the counterarguments that indicate we have no particular reason to think that they are needed (for example, human and chimp DNA sequence is so similar, most regulatory sequences probably only differ by a base pair or two, if at all).
Earth to Nick, YOU are ignoring the fact that no one has any idea how many mutations it would take nor to what chromosomes they would have to occur, in order to do the job. You have no idea if the transformations required are even possible via genetic changes. So please stop with your bloviations already.Joe_{November 15, 2012
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This thread is incredibly silly! You guys are trying to play selection off against neutrality, but both clearly exist. Let me outline what actual mainstream evolutionary theory would assert: 1. Neutrality is just what happens when s, the selection coefficient, is ~0. Even under neutrality, you will get a bunch of fixation events, even under the very slow rate of fixation under neutrality (about 1.5% divergence over 6 million years). The vast majority of genetic differences between humans and chimps are of this type. 2. Some of the differences (probably a tiny number, perhaps a few thousand or tens of thousands) were indeed promoted by selection, and thus fixed on average much more quickly than the neutral mutations. 3. Gauger claims that some large proportion of the differences between humans and chimps would have required multiple mutations to happen *before* selection could favor them. If there were a large number of these, there would indeed be not enough time for drift+selection to produce these specific features. But she gives only the vaguest argument that such features exist at all and ignores all the counterarguments that indicate we have no particular reason to think that they are needed (for example, human and chimp DNA sequence is so similar, most regulatory sequences probably only differ by a base pair or two, if at all). Worse, much of the discussion here and elsewhere gets 1, 2, and 3 confused, and you get assertions like 1.5% divergence couldn't have happened, because drift is too slow because of #3, or whatever. Random other comment on this line from Jerry Coyne's book: "More than 6 percent of genes found in humans simply aren’t found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps." Any serious usage of this number would require consideration of the following: 1. Even if true, this wouldn't mean a bunch of new genes on the human line. It could just mean a bunch of losses on the chimpanzee line. E.g. we already know that hundreds of genes for smelling and taste receptors have been gradually lost as primates became more specialized on vision compared to nocturnal, rodentlike ancestors. 2. Computer programs that find genes in genomes have a nonzero error rate, because ORFs (open reading frames) can be created by chance mutation (all you need is for a mutation to produce a start codon from a different codon). Not all ORFs are actual genes that get expressed and do something, although on rare occasions in evolution they might (emphasize might) be the beginning of a new gene. Furthermore, sequencing errors can produce fake ORFs if a base is misread so that it looks like a start codon. Sequencing error rates and mutation rates are low, but when there are 3,000,000,000+ nucleotides you are looking at, unlikely things happen all the time. 3. Neither the human genome nor the chimp genome sequence is actually complete, for various technical reasons. This was particularly true of the chimp genome a few years ago when Coyne's book was written.NickMatzke_UD_{November 15, 2012
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PaV:
Well, they want to invoke BOTH neutral evolution and positive selection as working at the same time, with neutral evolution coming up with all these ‘mutations’ and then positive selection promoting the ‘beneficial’ mutations to ‘fixation’.
Not quite. They want to invoke whatever is required to save the phenomena. So if invoking onlyy neutral mutations will do so, invoke only neutral mutations. If invoking neutral mutations and beneficial mutations, invoke both, and argue that the rate of fixation is the same as the neutral mutation rate. If that doesn't work, toss in some deleterious mutations, convergence, hgt, and symbiosis or whatever else seems even remotely possible. And blame Joe for being a math denier.Mung_{November 14, 2012
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Towards the end, my latest post should read: "Just as the chimps are doomed to typing gibberish, so, too the process wd400 and others are clinging to cannot possibly . . . ." Sorry for not proofreading this.PaV_{November 14, 2012
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Eric Anderson: I just posted something at the other thread. Hopefully it might illuminate some matters. Eric, you wrote:
The real fundamental issue that Nick (and wd400 on the other thread) have with Gauger’s approach is that they think no specific mutations are required to get from organism A to B, because, ya see, evolution is just a contingent process and anything goes. So we don’t need to explain how a functional specified string of information arose in DNA, the thinking goes, because anything could have happened. It was just one of many random possibilities. Therefore, there is nothing to explain.
I agree with you completely here. I've been thinking about this type of argument being made by wd400, Nick, Elizabeth Liddle, and others. It seems to me that what they're arguing comes down to Dawkins' "Me Thinks It Is a Weasel" model. What do I mean? Well, they want to invoke BOTH neutral evolution and positive selection as working at the same time, with neutral evolution coming up with all these 'mutations' and then positive selection promoting the 'beneficial' mutations to 'fixation'. This is almost exactly like Dawkin's and his chimps. He says for these chimps, typing away madly at their typewriters, to arrive at the phrase "Me Thinks It Is a Weasel" in an entirely 'random' manner would take forever. But, if, every time they struck a correct letter within the phrase this letter was kept (equivalent to positive selection 'fixing' a particular mutation), then in no time at all would the chimps arrive at the target phrase. But even Dawkins has to admit that this isn't how 'natural selection' works, because NS doesn't 'know' what the final target will be. So he considers this not to be a good analogy, or model, for how NS works. Here, what is happening, is this: wd400 is saying: "You don't know what the 'target phrase' looks like either. It could be "Me Thinks It Is a Weasel", or it could be "No Thanks if it wheezes" or "Me Stinks like a Weasel," etc. And the assumption behind all of this is that some kind of final target phrase will eventually arise. Well, getting back to Dawkins and his chimps, if we are no longer concerned about what the final target phrase is--i.e., if it isn't known in advance--then it hardly matters what the chimps type. Anything could be the 'final target phrase'. But the process so described is nothing more than a random number generator. I can't write anything here and be able to communicate unless there were a protocol for how the English language is used. To effect meaning, rules must be employed. Likewise, a process that contains no known rules cannot possibly generate meaning. Just as the chimps are doomed to typing gibberish, so, too, the process wd400 are clinging cannot possibly erect a system capable of interacting with itself. I think it's like going to the movies for the Darwinists: i.e., "suspension of disbelief." In their 'movie' the chimps come up with "Me Thinks It Is a Weasel" on the first try. And, as we all know, 'movies' don't lie.PaV_{November 14, 2012
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OT: "Is The Material World All There Is?" William Lane Craig, St Andrews 2012 - video http://www.youtube.com/watch?v=hOwe2TxisB8 video description: In September 2012, during his visit to The University of St Andrews in Scotland, Dr William Lane Craig delivered a lecture entitled "Is The Material World All There Is?" followed by audience Q&A. In this lecture Dr Craig outlined seven reasons to think that the material world is not all there is but, quite to the contrary, that the material world contains "signposts of transcendence" pointing towards the truth of Christianity.bornagain77_{November 13, 2012
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I've been been doubling up with laughter recently at references to 'enchanters', 'wizards' and the like, being summoned by various kings in the O.T., such as Nebuchadnezzar, before being obliged to summon one or other of the Hebrew prophets, to get the truth. I couldn't help thinking (implicitly) of the sovereignty of today's corporations and (explicitly) of their own court 'enchanters' and 'wizards'. And of course, your good selves, our own 'bona fide' scientific oracles.Axel_{November 13, 2012
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semi related: Complex Tool Discovery Argues for Early Human Smarts By Stephanie Pappas – Wed, Nov 7, 2012 Excerpt: One potential sign of complex thought would be an elaborately produced artifact that would have required capabilities such as language to pass along the technique to future generations.,,, Continuity of history These artifacts were discovered over the course of nine years at a site known as Pinnacle Point, in a storm-prone area with a temperate climate like San Francisco's. Initially, Marean found many artifacts and fossil bones on the beach. Then, one day, a storm exposed deposits of these materials from a cave higher up. So far the researchers have found sediments about 45 feet (14 meters) deep containing artifacts and fossils dating from approximately 50,000 to 90,000 years ago. "As an archaeologist and scientist, it is a privilege to work on a site that preserves a near-perfect layered sequence capturing almost 50,000 years of human prehistory," said researcher Kyle Brown at the University of Cape Town, South Africa. "Our team has done a remarkable job of identifying some of the subtle but important clues to just how innovative these early humans on the south coast were." The scientists uncovered thin blades of stone, known as microliths, each about 1.2 inches (3 centimeters) long at most. These were blunted along one edge so they could be glued onto slots carved in wood or bone. The stone used to produce these blades, silcrete (quartz grains cemented by silica), was carefully treated with heat to make it easier to shape. These microliths could have found use as the earliest known arrowheads. However, researchers suggest they were more likely incorporated into spear-hurling devices known as atlatls. These spear-throwers were essentially sticks with spurs or cups to hold the projectile. Swinging the atlatl provided leverage to increase the distance and killing power of the hurled dart or spear. The microliths may have served as spurs in these atlatls. [See images of the ancient tools] "They are parts of a complex composite weapon," Marean said. Past research suggested microlithic technology appeared briefly between 60,000 and 65,000 years ago. "Eleven thousand years of continuity is, in reality, an almost unimaginable time span for people to consistently make tools the same way," Marean said. "This is certainly not a flickering pattern." Moreover, heat treatment of stone was seen at Pinnacle Point about 160,000 years ago, suggesting people there mastered this complex technique for nearly 100,000 years. http://news.yahoo.com/complex-tool-discovery-argues-early-human-smarts-181913070.htmlbornagain77_{November 13, 2012
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The fantastical storyline is that neutral mutations silently accumulate until, one happy day in an explosion of creativity, they come together to do something wonderful.
MET - Miraculous Evolutionary TransitionsMung_{November 13, 2012
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PaV @7: This relates directly to what we have been discussing on the other thread: https://uncommondescent.com/news/is-there-enough-time-for-humans-to-have-evolved-from-apes-dr-ann-gauger-answers/ A bit painful to wade through 100 comments, but the upshot is this: Neutral mutations get "fixed" in the population at a high rate (i.e., the overall mutation rate) because we are not talking about any particular mutation. Any mutation at any point whether or not it has anything to do with forming any functional system gets added to the aggregate number of mutations in the lineage over time. It is really a definitional issue: (i) the kind of fixation Nick is talking about is really just the accumulation of mutations from generation to generation over time; (ii) this is quite different from selection acting to fix a particular beneficial mutation in a relatively-contemporaneous population. This is a legitimate use of the concept of fixation; just took me a bit to parse through and figure out that two separate processes were being called by the same name, but I understand what Nick and wd400 are saying on that front. The real problem with the neutral mutations idea is not whether neutral mutations aggregate from one generation to the next over time -- they do. The real problem is that this accumulation of mutations over time does absolutely nothing to solve the issue of how we get functional complex specified information in DNA or in biology generally. The fantastical storyline is that neutral mutations silently accumulate until, one happy day in an explosion of creativity, they come together to do something wonderful. The real fundamental issue that Nick (and wd400 on the other thread) have with Gauger's approach is that they think no specific mutations are required to get from organism A to B, because, ya see, evolution is just a contingent process and anything goes. So we don't need to explain how a functional specified string of information arose in DNA, the thinking goes, because anything could have happened. It was just one of many random possibilities. Therefore, there is nothing to explain. This is another manifestation of what I will now term the Great Evolutionary Explanation,* namely: Stuff Happens. So the real issue is whether any coordinated mutations are required to get from organism A to B. From an engineering and biological standpoint it is quite obvious that significant coordination is required at some point along the path. Nick and wd400 appear to want to deny this. Check out, in particular, comments #47 and #99 on the other thread. ----- * Otherwise known as "GEE" as in "gee-whiz"!Eric Anderson_{November 13, 2012
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PaV:
Nick, what do you mean about neutral mutations fixing at “much higher rates”? I would think that ‘neutral’ mutations would fix at much lower rates than mutations affected by positive selection.
What he means is that mutations that do nothing towards evolving a proto-human into a human are far more prevalent than ones that do, therefore, mutations that do nothing will become fixed at a higher rate than a mutation that never happens. It's simple math.Mung_{November 13, 2012
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"Neutral evolution" as an engine for productive evolutionary change is such a joke. 1. Anyone who thinks that adding random changes to a massive database can be anything but net deleterious over time needs to have their head examined. It doesn't even pass the laugh test. 2. As others have pointed out, adding new material costs resources in terms of maintenance, replication, etc. 3. Most importantly, it does precisely nothing to help explain functional complex specified information in DNA. The only thing neutral mutations are supposed to do is provide more genetic material to work with. But we don't need no stinkin' new genetic material -- sheesh, we've already got 90% of the genome that is pure junk; how much more do we need to work with!? :) The neutral mutations idea, boiled down, is this: getting a bunch of beneficial mutations to arise is way too improbable, so instead we'll get a bunch of random, unrelated neutral mutations to arise and then at some glorious moment in time light will break through the mists of darkness and . . . wait for it . . . the neutral mutations suddenly poof into an information-rich sequence that performs a beneficial function. It is all so clear. Ya, see, (i) having a bunch of unrelated, random mutations suddenly poof into a beneficial, information-rich sequence is *way* more likely than (ii) having a bunch of unrelated, random mutations slowly form a beneficial, information-rich sequence over time. Yeah, that's the ticket!Eric Anderson_{November 13, 2012
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"Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle." - John Sanford - Genetic Entropy and The Mystery of The Genome - pg. 21 - Inventor of the 'Gene Gun' Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt:,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.htmlbornagain77_{November 13, 2012
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Nick Matzke, Your entire position is all about fooling people as you don't have any evidence to support its claims. You don't know how many mutations it takes to get an upright biped from a knuckle-walker/ quadraped. You don't even know if any amount of mutational accumulation can do the job required. BTW Nick, no one knows how fast or slow neutral mutations take to become fixed. No one knows how long it takes beneficial mutations to become fixed.Joe_{November 13, 2012
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To go well above my allotted two cents worth, 'neutral' mutations are a joke as far as the evidence, and theoretical considerations, are concerned: Majestic Ascent: Berlinski on Darwin on Trial - David Berlinski - November 2011 Excerpt: The publication in 1983 of Motoo Kimura's The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura's theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. "A critique of neo-Darwinism," the Dutch biologist Gert Korthof boasted, "can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science." By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian. http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html Ann Gauger on genetic drift - August 2012 Excerpt: The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter. https://uncommondescent.com/evolution/ann-gauger-on-genetic-drift/ Here is a Completely Different Way of Doing Science - Cornelius Hunter PhD. - April 2012 Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon. Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding. Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place. http://darwins-god.blogspot.com/2012/04/here-is-completely-different-way-of.html Thou Shalt Not Put Evolutionary Theory to a Test - Douglas Axe - July 18, 2012 Excerpt: "For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be 'neutral'). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years). My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they're in the position of insisting that something is a scientific fact without having the faintest idea how it even could be." Doug Axe PhD. http://www.evolutionnews.org/2012/07/thou_shalt_not062351.html Michael Behe on the theory of constructive neutral evolution - February 2012 Excerpt: I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. - Michael Behe https://uncommondescent.com/evolution/michael-behe-on-the-theory-of-constructive-neutral-evolution/ Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory - 2008 Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue. Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation.. http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf Oxford University Admits Darwinism's Shaky Math Foundation - May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html related notes: Haldane's Dilemma Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift - creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors - it surely would have killed us. Since Haldane's dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation - but has obtained identical results. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 159-160 Kimura's Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most 'evolution' must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom's (neo-Darwinism's) very validity. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 161 - 162 A graph featuring 'Kimura's Distribution' is shown in the following video: Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086bornagain77_{November 13, 2012
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Nick Matzke: (2) Even the source they cite, Durrett and Schmidt 2007, notes that they are only talking about one very specific sort of change, and most of the changes between humans and chimps were neutral (and thus fix at much higher rates, basically equal to the mutation rate), . . . Nick, what do you mean about neutral mutations fixing at "much higher rates"? I would think that 'neutral' mutations would fix at much lower rates than mutations affected by positive selection.PaV_{November 13, 2012
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This study just came out: Study suggests humans are slowly but surely losing intellectual and emotional abilities - November 12, 2012 Excerpt: "Human intelligence and behavior require optimal functioning of a large number of genes, which requires enormous evolutionary pressures to maintain. A provocative hypothesis published in a recent set of Science and Society pieces published in the Cell Press journal Trends in Genetics suggests that we are losing our intellectual and emotional capabilities because the intricate web of genes endowing us with our brain power is particularly susceptible to mutations and that these mutations are not being selected against in our modern society." http://medicalxpress.com/news/2012-11-humans-slowly-surely-intellectual-emotional.html#jCp A few related notes: If Modern Humans Are So Smart, Why Are Our Brains Shrinking? - January 20, 2011 Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.” “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,, He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.” http://discovermagazine.com/2010/sep/25-modern-humans-smart-why-brain-shrinking Genetic Entropy - Dr. John Sanford - Evolution vs. Reality - video (Notes in description) http://vimeo.com/35088933 Stark Differences Between Human and Chimp Brains - Brian Thomas, M.S. - Oct. 5, 2012 Excerpt: The researchers used a new technique to peer in unprecedented detail at the methylation patterns of human and chimp DNA that they harvested from brain tissue of three cadavers of each species. They compared only those DNA sequences already known to have basically the same genes, ignoring the vast majority of DNA. If humans and chimps are close relatives, then they should have similar DNA methylation patterns in the areas of chromosomes that they have in common such as similar gene sequences.2 However, this team found major differences. In particular, human and chimp DNA methylation patterns, called "methylomes," were very different between the two species’ brain tissue. The data statistically indicated that "major principal components separate humans and chimpanzees," according to their report in American Journal of Human Genetics.1,3 A second observation is that the very genes that were differently methylated "exhibit striking associations with several disorders, including neurological and psychological disorders and cancers."1 These data show that methylation patterns in many cases can tolerate very little disruption, thus presenting another impossible hurdle for the evolutionary model to overcome. If humans evolved from chimpanzee-like creatures, then some unknown evolutionary process must have altered their methylomes. But since methylomes apparently cannot tolerate that much alteration, then the evolutionary story must be in error. Human and chimp species-specific and irreducibly complex methylomes refute human evolution.,,, (Zeng, J. et al. 2012. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. American Journal of Human Genetics. 91 (3):455-465.) http://www.icr.org/article/7067/ Of note: This following study, in which the functional role of unique ORFan genes were analyzed, the (Darwinian) researchers were 'very shocked' and 'taken aback' by what they found; New Genes, New Brain - October 2011 Excerpt: “This is one of the first studies to look at the role of completely novel genes” in primate brain development,,, A bevy of genes known to be active during human fetal and infant development first appeared at the same time that the prefrontal cortex,,, Finally, 54 of the 280 genes found to be unique to humans were also highly expressed in the developing prefrontal cortex,,,, “We were very shocked that there were that many new genes that were upregulated in this part of the brain,” said Long, who added that he was also taken aback by synchronicity of the origin of the genes and the development of novel brain structures.,,, (From the PLoS article, author’s summary: We found these genes are scattered across the whole genome, demonstrating that they are generated by many independent events,,, Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination,,) http://the-scientist.com/2011/10/19/new-genes-new-brain/ Darwin's mistake: explaining the discontinuity between human and nonhuman minds. - 2008 Excerpt: Over the last quarter century, the dominant tendency in comparative cognitive psychology has been to emphasize the similarities between human and nonhuman minds and to downplay the differences as "one of degree and not of kind" (Darwin 1871).,,, To wit, there is a significant discontinuity in the degree to which human and nonhuman animals are able to approximate the higher-order, systematic, relational capabilities of a physical symbol system (PSS) (Newell 1980). We show that this symbolic-relational discontinuity pervades nearly every domain of cognition and runs much deeper than even the spectacular scaffolding provided by language or culture alone can explain,,, http://www.ncbi.nlm.nih.gov/pubmed/18479531 "Nothing in evolution can account for the soul of man. The difference between man and the other animals is unbridgeable. Mathematics is alone sufficient to prove in man the possession of a faculty unexistent in other creatures. Then you have music and the artistic faculty. No, the soul was a separate creation." - Alfred Russell Wallace, New Thoughts on Evolution, 1910 of note: Human brain has more switches than all computers on Earth - November 2010 Excerpt: They found that the brain's complexity is beyond anything they'd imagined, almost to the point of being beyond belief, says Stephen Smith, a professor of molecular and cellular physiology and senior author of the paper describing the study: ...One synapse, by itself, is more like a microprocessor--with both memory-storage and information-processing elements--than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth. http://news.cnet.com/8301-27083_3-20023112-247.htmlbornagain77_{November 13, 2012
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Nick:
...most of the changes between humans and chimps were neutral (and thus fix at much higher rates, basically equal to the mutation rate)...
Are you saying that there was no 'selection' at all going on during either lineage after the alleged split? If there was selection, does that really have no effect on the rate of fixation of a neutral mutation?Mung_{November 12, 2012
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You are not an accident Nick! http://2.bp.blogspot.com/-U_oFWHPHGt4/TrQT3sTnjqI/AAAAAAAAAlY/5VH3MmWGgb4/s1600/Rickwarrencoffee.jpegbornagain77_{November 12, 2012
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