Saturday, March 22, 2014

An Intelligent Design Creationist explains why chimpanzees and humans are so similar

The genomes of chimpanzees and bonobos are remarkably similar to the human genome. In terms of sequence similarity, they are more than 98% identical in the regions that can be aligned. This, of course, is due to the fact that they descend from a common ancestor in the recent past (about 5 million years ago).

Intelligent Design Creationists don't agree. Many of them do not accent common descent and macroevolution so they make up stories that account for the similarity based on what they think god might have been thinking when he created chimps and humans.

But the scientific evidence for evolution is much stronger than just overall sequence similarity. The number of differences (about 50 million substitutions) corresponds pretty closely with what we expect from evolutionary theory (population genetics) and known mutation rates [Why are the human and chimpanzee/bonobo genomes so similar?]. If the Intelligent Design Creationists are going to dismiss this confirmation of evolutionary theory then they are going to have to be much more inventive.

It's been four weeks since I posted my original calculations and no creationist has responded until now. I mentioned this the other day when I was discussing Vincent Torley's strange views about macroevolution [What do Intelligent Design Creationists really think about macroevolution?].

I guess Torley is embarrassed by the fact that although some of his colleagues pretend to be scientists they didn't dare respond to my post. Torley is a philosopher but he isn't afraid to tackle science questions as we saw in his attempt to refute macroevolution.

Now he thinks he can respond to my post about the evidence that chimps and humans descend from a common ancestor [So, why are the human and chimpanzee/bonobo genomes so similar? A reply to Professor Larry Moran]. This is going to be fun.

Vincent Torley starts off by telling us that he accepts the common ancestry of chimpanzees, bonobos, and humans. He agrees that many Intelligent Design Creationists do not accept common descent, but he's not one of them. Then he explains how the creator made these species so that it looks like evolution.
In his post, Professor Moran (acting as devil’s advocate) proposes the intelligent design hypothesis that “the intelligent designer created a model primate and then tweaked it a little bit to give chimps, humans, orangutans, etc.” However, he argues that this hypothesis fails to explain “the fact that humans are more similar to chimps/bonobos than to gorillas and all three are about the same genetic distance from orangutans.” On the contrary, I think it’s very easy to explain that fact: all one needs to posit is three successive acts of tweaking, over the course of geological time: a first act, which led to the divergence of African great apes from orangutans; a second act, which caused the African great apes to split into two lineages (the line leading to gorillas and the line leading to humans, chimps and bonobos); and finally, a third act, which led humans to split off from the ancestors of chimps and bonobos.

"Why would a Designer do it that way?" you ask. "Why not just make a human being in a single step?" The short answer is that the Designer wasn’t just making human beings, but the entire panoply of life-forms on Earth, including all of the great apes. Successive tweakings would have meant less work on the Designer’s part, whereas a single tweaking causing a simultaneous radiation of orangutans, gorillas, chimps, bonobos and humans from a common ancestor would have necessitated considerable duplication of effort (e.g. inducing identical mutations in different lineages of African great apes), which would have been uneconomical. If we suppose that the Designer operates according to a "minimum effort" principle, then successive tweakings would have been the way to go.
Interesting. One imagines the creator visiting Africa about 15 million years ago and fiddling with the genome of the ape ancestor so that two distinct species are formed. One leads eventually to orangutans and their extinct relatives and the other is the progenitor of the other extant apes and their extinct relatives.

Then the creator gets busy with beetles, or other planets, and lets things evolve on their own for a while, accumulating and fixing alleles at the rate we expect for evolution. Then the creator comes back for a visit about five million years later, having gotten bored with beetles. He (she?) tweaks the genome of some African ape so that a new species arises. The old one is the ancestor of modern gorillas and all the other related species that have gone extinct and the new species becomes the ancestor of chimps, bonobos and humans.

Now the creator turns his attention elsewhere for a few million years as those ape species evolve (insects need attention and his creation on Titan is in peril). Back he (she?) comes about five million years ago to tweak another two species into existence—one that will give rise, by evolution, to several species of Australopithicus, several species of Paranthropus, and several species of Homo (Homo habilis, Homo erectus, Homo heidelbergensis, and Homo sapiens. The other will eventually lead to over-sexed bonobos, the main goal of the exercise, I assume.

I think that what Vincent Torley is saying is that this is all consistent with the data I posted because most of the time these species are evolving just as we would expect. That's why the sequence differences between chimps and humans corresponds to what we expect from evolutionary theory. The reason this is misleading is because it omits the key mutations that god inserted every five million years or so in order to make modern gorillas.

There is, of course, no evidence that Torley's scenario is true and no evidence that a creator exists. I thank Vincent Torley for showing us just how ridiculous the Intelligent Design Creationist movement has become if this is the best they can do.
Professor Moran makes the remarkable claim that 130 mutations are fixed in the human population, in each generation. Here are a few reasons why I’m doubtful, even after reading his posts on the subject (see here, here and here):

(a) most mutations will be lost due to drift, so a mutation will have to appear many times before it gets fixed in the population;
(b) necessarily, the mutation rate will always be much greater than the fixation rate;
(c) nearly neutral mutations cannot be fixed except by a bottleneck.

I owe the above points to a skeptical biologist who kindly offered me some advice about fixation. As I’m not a scientist, I shall pursue the matter no further. Instead, I’d like to invite other readers to weigh in. Is Professor Moran’s figure credible?
A classic argument from ignorance. Vincent Torley doesn't understand evolution (population genetics) therefore he's "doubtful" of any result that he can't understand even though it seems consistent with the scenario he proposes above.
Professor Moran is also assuming that chimps and humans diverged a little over five million years ago. He might like to read the online articles, What is the human mutation rate? (November 4, 2010) and A longer timescale for human evolution (August 10, 2012), by paleoanthropologist John Hawks, who places the human-chimp divergence at about ten million years ago, but I’ll let that pass for now.
It's possible that our estimate of the human mutation rate is off by a factor of two (i.e. 70 per generation instead of 130 per generation) [see Theme: Mutation for a thorough discussion1). Personally, I doubt it but if it turns out to be the case then chimps and humans may have diverged ten million years ago. It would then still be true that the differences between chimps and humans is what we expect if they evolved from a common ancestor at a slower mutation rate.
I shall also overlook the fact that Professor Moran severely underestimates the genetic differences between humans and chimps. As Jon Cohen explains in an article in Science (Vol. 316, 29 June 2007) titled, Relative Differences: The Myth of 1%, these differences include "35 million base-pair changes, 5 million indels in each species, and 689 extra genes in humans," although he adds that many of these may have no functional meaning, and he points out that many of the extra genes in human beings are probably the result of duplication. Cohen comments: "Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene networks, and the very structure of chromosomes confound any quantification of ‘humanness’ versus ‘chimpness.’" Indeed, Professor Moran himself acknowledges in another post that "[t]here are about 90 million base pair differences as insertion and deletions (Margues-Bonet et al., 2009)," but he goes on to add that the indels (insertions and deletions) “may only represent 90,000 mutational events if the average length of an insertion/deletion is 1kb (1000 bp)." Still, 90,000 is a pretty small number, compared to his estimate of 22.4 million mutations that have occurred in the human line.
There have been plenty of insertions, deletions, and chromosomal rearrangements in the lineages leading to chimps and humans. If you want to count a deletion of 1000bp as 1000 differences then be my guest. It doesn't change the fact that we can examine the rate of single nucleotide substitutions as a close proxy for the total number of mutations and arrive at a figure that's remarkably close to that predicted by evolutionary theory.

Counting the deletion as 1000 separate mutation events events doesn't make any sense, even for a creationist.
I could also point out that the claim made by Professor Moran that the DNA of humans and chimps is 98.6% identical in areas where it can be aligned is misleading, taken on its own: what it overlooks is the fact that, as creationist geneticist Jeffrey Tomkins (who obtained his Ph.D. from Clemson University) has recently demonstrated, the chromosomes of chimpanzees display "an overall genome average of only 70 percent similarity to human chromosomes" (Human and Chimp DNA–Nearly Identical, Acts & Facts 43 (2)).
The claim that the human and chimp genomes are only 70% similar in overall sequence is too silly too waste time on. Besides, as I already explained, it's the rate of substitution in the regions that can be aligned that has to be explained. Why is this rate so similar to what evolutionary theory predicts?
I might add (h/t StephenB) that Professor Moran has overlooked the fact that humans have 23 pairs of chromosomes, whereas chimpanzees (and other great apes) have 24. However, Dr. Jeffrey Tomkins has published an article titled, Alleged Human Chromosome 2 "Fusion Site" Encodes an Active DNA Binding Domain Inside a Complex and Highly Expressed Gene—Negating Fusion (Answers Research Journal 6 (2013):367–375). Allow me to quote from the abstract:
Irrelevant. (And boring.)
Leaving aside these points, the real flaw in Professor Moran’s analysis is that he assumes that the essential differences between humans and chimpanzees reside in the 22.4 million-plus mutations – for the most part, neutral or near-neutral – that have occurred in the human line since our ancestors split off from chimpanzees. This is where I must respectfully disagree with him.
I assumed no such thing. I'm just asking creationists to account for the fact that there's powerful evidence of evolution in the sequence comparisons. It's not just the overall similarity but the number of differences that support an evolutionary explanation.

So far, the only "reasonable" thing that Vincent Torley has said is that he agrees that most of the changes are due to evolution but that god tweaked a few other spots every five million years in order to make sure that bonobos appeared on his favorite planet. (Although he clearly liked beetles better.)
These [orphan genes] are the genes that I’m really interested in. Can a neutral theory of evolution, such as the one espoused by Professor Moran, account for their origin?
That's a discussion for another time. We first need to prove that all potential orphan genes are really functioning genes and we're quite a long way from that. If they aren't, then Neutral Theory is a good foundation for explaining the origin of things that look like functional genes but aren't.

The rest of Torley's post is about what creationists think of species. I don't feel the need to discuss it. He concludes with ...
I shall stop there for today. In conclusion, I’d like to point out that Professor Moran nowhere addressed the problem of the origin of orphan genes in his reply, so he didn’t really answer the first argument in my previous post, which was that we cannot claim to understand macroevolution until we ascertain the origin of the hundreds of chemically unique proteins and orphan genes that characterize each species.
I didn't discuss orphan genes because it's irrelevant to either of the points I was making. It has nothing to do with the question of human/chimp sequence similarity and it has nothing to do with the abundant evidence in support of macroevolution.

Besides, I don't accept his premise that there are hundreds of unique genes that characterize each species.
To Professor Moran’s credit, he did attempt to answer my second argument (why is there so much stasis in the fossil record?), by suggesting that even large populations will still change slowly in their diversity, as new alleles increase in frequency and old ones are lost, but that morphological change is “more likely to occur during speciation events when the new daughter population (species) is quite small and rapid fixation of rare alleles is more likely.” But as I argued previously, why, during the times of environmental upheaval described by Professor Prothero, don’t we see a diversification of niches? Why don’t species branch off? Why do we instead see morphological stasis persisting for millions of years? That remains an unsolved mystery.
Nope, it's not a mystery.
Finally, it seems to me that Professor Moran has solved the “time” question (my third argument) only in a trivial sense: he has calculated that the requisite number of mutations separating humans and chimps could have gotten fixed in the human line. I have to say I found his claim that in the last five million years, 22.4 million mutations have become fixed in the lineage leading to human beings, utterly astonishing. But even supposing that this figure is correct, what it overlooks is that the mutations accounting for the essential differences between humans and chimps aren’t your ordinary, run-of-the-mill mutations. Many of them seem to have involved orphan genes, which means that until we can explain how these genes arise, we lack an adequate account of macroevolution.
In other words, Vincent Torley is "astonished" that the differences between the genome sequences of chimps and humans correspond to what we would expect if they evolved from a common ancestor.

Why am I not surprised that a creationist doesn't understand evolution?


1. Vincent Torley could have read this as well.

58 comments :

  1. For single-base substitutions, Torley did not need to construct any elaborate explanation at all. He agrees that there has been common descent. So that explains why aligned regions of human genomes are so similar to those of chimpanzees. Why go to the trouble of asserting that a Designer is called for, to explain why these aligned regions are so similar? The Designer does not improve the fit of those data.

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    1. Hi Joe, I think there is a simple explanation to your question;

      http://assets.amuniversal.com/6bf962e05f63012ee3c100163e41dd5b

      ;-)

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  2. So let me get this straight. Vicent Torley is postulating that his designer simply went out of his way to design all the great apes to look like they evolved from a common ancestor through the expected average mutation rates.

    Or in other words, we have the observed fact that mutations happen.
    We have the observed fact that genetic drift happens.
    We have the observed fact that natural selection happens,
    We have the observed fact that the genetic distances, and the pattern of similarities between humans and the other great apes, forms a twin nested hierarchy that implies common descent through the expected average mutation and fixation rates.

    - therefore an unobserved supernatural god did it over millions of years with divine magic.

    Why, exactly, is the designer here going out of it's way to design things with this ludicrous method that looks exactly like no designer participated at all?

    Of course, all of this also curiously ignores that it is an ad-hoc rationalization observations that imply evolution. The kind of design Vincent Torley postulates here is patently unfalsifiable, it is compatible with any concievable observation. He can simply sit down and allow himself infinite wiggleroom by saying that "the designer then designed things to be exactly the way they are by intentionally mimicking an evolutionary mechanism". There's no actual predictions made here, it's all just after the fact rationalizations of evolutionary patterns.

    What the fuck is the matter with these people if they can convice themselves that this is a rational, acceptable alternative?

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  3. If Torley after all these years, and he's been an IDiot for many, many years, STILL doesn't understand the basics of the theory of evolution (and, face it, you can take an 18-year old high school graduate and get him up to speed on the theory, and more, in four years or less, so what's Torley's problem?), then Torley is either stupid or his religious delusion makes him appear stupid. I suppose, according to Torley, that the Intelligent Designer could have tweaked Torley's genes to be delusional and appear stupid, or vice versa.

    However, snark aside, what Torley and all the IDiots fail to account for is that all life on the planet is evolving at the same time - animals, plants, bugs, fish, etc. Simultaneously. You can't just "tweak" a single critter, you have to "tweak" everything.

    Torley ignores a perfectly rational and explainable mechanism that a child could understand to account for the diversity of life only to find a day job for his favorite deity. Then he has the hubris, I'd call it blasphemy (!) to speculate on the motives of his unknown and unknown favorite deity. I've been around creationists for a long time and I'm still amazed that thinking adults, and I'm using the phrase graciously, can ignore the obvious in preference to their childish nonsense.

    Sorry, but I don't buy Torley's "I'm only a philosopher" routine any more.

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  4. Torley seems a pleasant chap. But after a couple of exchanges I get the feeling that arguments make a similar impression upon him as your body upon bathwater.

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  5. "If we suppose that the Designer operates according to a minimum effort principle, then successive tweakings would have been the way to go."

    Your god is all powerful. He can do whatever he wants. Ergo, the assumption is false.

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    1. Apparently Torley's god is omnipotent but very, very lazy.

      And the reason that Torley's designer waited so long between tweaking sessions is that it was oh so busy agonizing over the proper uses of human genitals eventually to be revealed to an obscure tribe of middle eastern nomadic goat herders with a bent for genocide, slavery, misogyny and homophobia.

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    2. It baffles me when the creationists go on about 'common designer' as if the Creator would have functioned like some human design team.

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  6. I'm a little confused here. Torley says that he accepts the premise that apes and humans had a common ancestor. He then turns around and cites a creationist article that claims that the fusion of ape chromosomes 12 and 13 to form human chromosome 2 didn't happen and presumably that the structures in the middle of chromosome 2 aren't telomeres. If he accepts common descent, why is he citing the paper denying that the fusion occurred?

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    1. This is a guy who believes that his god has the mutually exclusive qualities of omnipotence and omniscience.

      He can handle the relatively trivial (in comparison) inconsistencies in his article without even breaking into a sweat.

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    2. As I ask below: if creationists really think "common design implies common designer" why do they always lie to make the design seem less common, and never try to make it look more common?

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    3. ...why do they always lie to make the design seem less common, and never try to make it look more common?

      That's a good question. Conservation of features noted by a creationist just makes perfect sense, until an evolutionary biologist mentions these same features at which time they must be declared not real.

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    4. Yes, Torley makes that very mistake in his article. He starts from saying the 98% similarity is simply evidence that The Designer wanted to work most efficiently. But then he says the similarity is only 70%. Well, then why would this Efficient Intelligent Designer waste all the time and effort to create an additional 28% of dissimilarity, when He could have achieved the creation of a new species with just a very strategically placed 2% difference?

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  7. Torley: "However, Dr. Jeffrey Tomkins has published an article titled, Alleged Human Chromosome 2 "Fusion Site" Encodes an Active DNA Binding Domain Inside a Complex and Highly Expressed Gene—Negating Fusion (Answers Research Journal 6 (2013):367–375). "

    Larry makes the mistake of calling this irrelevant. Instead of saying "irrelevant", he should have been checking the facts. Since a creationist said something relevant-- and since all creationist arguments are either factually false or redefinitions of the scientific method-- you should have known this claim is factually false. And it is.

    Tomkins' alleged coding gene at the fusion site was already checked and debunked by Ken Miller, FSM bless him, who showed the gene in question was thousands of base pairs from the fusion site.

    Larry calls Ken Miller a creationist, but Miller double checks his facts.

    Torley and Tomkins should retract.

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    1. Tomkins' alleged coding gene at the fusion site was already checked and debunked by Ken Miller

      Do you have a link to Miller's debunking of Tomkin's claims?

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    2. ShadiZ1:

      Chris Mooney got it from Ken Miller

      But that's just wrong, according to Miller. The fusion site is "more than 1,300 bases away from the gene," he says, based on a review of major gene databanks. "These increasingly desperate efforts to 'debunk' the chromosome 2 story have failed before, and they've failed this time, too," Miller concludes. "Once again, we can see that the story of human evolution is written not only in the language of bones and fossils, but in the far more eloquent script of the human genome."

      [“This Picture Has Creationists Terrified", Chris Mooney, Mother Jones, Feb. 4, 2014]

      FWIW, here is Tomkins naming the gene:

      In this report, it is also shown that the purported fusion site (read in the minus strand orientation) is a functional DNA binding domain inside the first intron of the DDX11L2 regulatory RNA helicase gene, which encodes several transcript variants expressed in at least 255 different cell and/or tissue types. [Alleged Human Chromosome 2 “Fusion Site” Encodes an Active DNA Binding Domain Inside a Complex and Highly Expressed Gene—Negating Fusion. by Jeffrey P. Tomkins. Answers Research Journal. October 16, 2013. ]

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    3. Dr. Kenneth Miller admitted he was wrong about the alleged Human Chromosome #2 "end-to-end Telomere fusion".
      See link: http://www.evolutionnews.org/2014/08/youre_welcome_d089381.html
      Quote from this site: Dr. Kenneth Miller admitted the mistake to Tomkins: “in this transcript, the fusion site ("end-to-end Telomere fusion") is in the middle of the first [gene] exon as you note.” (exons contain part of the code for RNA)

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    4. If you are correct then I'm sure Diogenes will apologize for insulting me. If you are wrong then you can expect a rant.

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    5. First question: is it supposed to be an intron (per Diogenes citing Tomkins) or an exon (per Mark citing ENV citing, apparently, Miller)? Second question: what are the primary sources here? Where did Miller make the claim and where did he retract the claim?

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    6. You can watch the interview here that gives all the details,
      https://www.youtube.com/watch?v=jZoto0nyHho

      This link is where Dr. Miller said Dr. Tomkins was wrong.
      http://www.motherjones.com/politics/2014/01/bill-nye-creationism-evolution

      This link points out that later after corresponding with Dr, Tomkins, Dr. Miller admitted he was wrong.
      http://www.theblaze.com/contributions/defenders-of-the-evolutionary-consensus-could-benefit-from-more-fact-checking-2/

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    7. Mark: I know I am more than a year later, but I thought it'd be important to add this:

      http://www.rationalskepticism.org/creationism/casey-luskin-lies-about-ken-miller-on-chromosome-2-t50094.html

      Ken Miller seems to have admitted nothing.

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  8. Larry: "The claim [by Jeffrey Tomkins] that the human and chimp genomes are only 70% similar in overall sequence is too silly too waste time on."

    On the contrary, hard numbers should be the first things we debunk.

    I think Torley is referring to some shit published years back by Tomkins and the profoundly dishonest non-scientist, Jerry Bergman. IIRC they cooked the numbers by assuming that all bits that can't be sequenced or aligned are 100% different between human and chimp (bullshit) and counting duplicated DNA as 100% different between human and chimp.

    The work of Tomkins and Bergman needs exposure as the creationist hoax it is.

    BTW: if creationists really think "common design implies common designer" why do they always lie to make the design seem less common, and never try to make it look more common?

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    1. I think Torley is referring to some shit published years back by Tomkins and the profoundly dishonest non-scientist, Jerry Bergman. IIRC they cooked the numbers by assuming that all bits that can't be sequenced or aligned are 100% different between human and chimp (bullshit) and counting duplicated DNA as 100% different between human and chimp.

      The work of Tomkins and Bergman needs exposure as the creationist hoax it is.


      It's more recent (at least in current iteration), from last year:

      http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome

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    2. How much similarity is required in order for sequences to be aligned? If I recall Tomkins tried varying lengths of sequences in the range of a few hundred bases.

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  9. Torley: "If we suppose that the Designer operates according to a "minimum effort" principle, then"

    Then your Designer did not create the universe, with its superclusters of galaxies that have 100 billion stars each.

    If there's one thing the universe is not, it's not economical.

    There are three different species of louse specific to the human species. There are many human-specific diseases and STD's and parasites designed by his Designer. There are hundreds of species of the parasitic fungus cordyceps, each specific to one species of insect host, who lives in horrible pain and whose mind is taken over by the parasite to alter the insect's behavior to the fungus' advantage. How economical is that?

    How economical is malaria? Guinea worm? River blindness? Schistosoma? The botfly? Sacculina?

    Just another sttempt to evade the scientific method. The mind boggles.

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  10. Professor Moran makes the remarkable claim that 130 mutations are fixed in the human population, in each generation.

    Had Prof. Moran really claimed such a thing, it would indeed be remarkable. Torley doesn't even understand what "fixed in the population" means.

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    1. Yeah... I'm sure everyone here knows where you got this info from... ;)

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    2. Why are you so stupid ty huju?

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    3. Well, 130 mutations would be fixed in the human population each generation if the population were not increasing at a high rate.

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    4. And many more than that would be fixed during any prehistoric bottleneck. There's a lot of a difference between "per generation" (averaged out over 5 million years or so, which is what Professor Moran actually said) and "in each generation".

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    5. I think the point is that, given a stable population and enough time for equilibration, the neutral fixation rate equals the neutral mutation rate, which is what Torley refuses to accept.

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    6. @John Harshman,

      This is pretty elementary stuff. You can read about it in any evolution textbook. Why do the IDiots have such a hard time understanding evolution? Surely there must be some of them who get it and can explain it to the others?

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    7. Torley: I owe the above points to a skeptical biologist who kindly offered me some advice about fixation.

      The "sceptical biologists" among them apparently don't get it.

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    8. No other kind has an opinion worth listening to, for the 'true sceptic'.

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  11. Dino-genes,

    Why don't tell off this "blind chance" that created the universe and slowdown the speed of the expansion and the acceleration a bit.... I personally think that when you do that, the effects of macroevolution will be finally visible; they will just pop up like mushrooms.. lol

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  12. This one is a perfect example where the believers of macroevolution can prove their claims.... They can go to the lab and manipulate the genome of a chimpanzee a bit and see if it loses interest in bananas first... Then... "...he might find the missionary positioning a bit more "evolutionary"...

    I'm sure with the human and chimpanzee genomes being almost identical, some of the proponents of macroevolution can believe that chimpanzees will go through an evolutionary process themselves.... and become.... at least self-aware-humans...
    I personally think that It's about time for the chimpanzees who will take over the universities... to become more than self-aware...

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    1. that chimpanzees will go through an evolutionary process themselves....

      Chimpanzees, like any other species, are undergoing evolution.


      ...and become.... at least self-aware-humans...

      Why should they become "at least self-aware humans"?


      I personally think that It's about time for the chimpanzees who will take over the universities... to become more than self-aware...

      They already took over the Discovery Institute.

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    2. Go back to school and don't stink the world with bacalaha....

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  13. " Successive tweakings would have meant less work on the Designer’s part." .

    Why would the amount of work matter to the Omnipotent One?

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  14. "If we suppose that the Designer operates according to a minimum effort principle"

    We may therefore propose that he has done sod all?

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  15. If Vincent Torley ever goes through the comments:

    Recent paper reporting de novo gene synthesis from non-coding DNA:

    http://www.sciencemag.org/content/343/6172/769

    Reviews on the evolutionary origin of orphan genes:

    http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0024601/full

    http://www.nature.com/nrg/journal/v12/n10/full/nrg3053.html

    Orphan genes are not magically created by the creator, Mr. Torley.

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    1. Of course, now the creationist "argument" becomes: "See? The 'Designer' created junk DNA to allow orphan genes to arise."

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  16. If in fact Torley's principle of the "economical" creator were his actual hypothesis, he would be trying to prove that *no* miracles, or a minimum number, occurred throughout evolution. The most economical creator is one who does *no* miracles. Surely a philosopher should see this.

    Instead, he attempts to *maximize* the number of miracles required by falsely shrinking the similarity between humans and chimps to 70% (if there were a lower number, even 0%, he would grab that too) and buying into a "coding gene" supposedly at the fusion site of chromosome 2. Anything to maximize miracles.

    This is why I define pseudoscience in terms of an opposition between the predictions which logically follow from a hypothesis, and the alleged predictions claimed by the authority figures in a pseudoscience movement. IDers say "common design implies common designer", then they cook the books to make the designer appear far *more uncommon* than it really is. They speak of minimizing the miracles of an "economical" creator, then they fake the numbers in order to *maximize* the number of miracles he did. Surely an honest man would recognize this opposition between the claimed hypothesis and predictions from authority figures.

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  17. Quest said: I'm sure with the human and chimpanzee genomes being almost identical, some of the proponents of macroevolution can believe that chimpanzees will go through an evolutionary process themselves.... and become.... at least self-aware-humans...
    I personally think that It's about time for the chimpanzees who will take over the universities... to become more than self-aware...


    Forever clueless.

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  18. Curious how totally absent all the usual IDiots are from this thread. The only one stupid enough was Quest.

    A declaration of complete defeat.

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    1. Rumrocket,

      I take it as complement... :)

      BTW: Any news from those hydrothermal vents...? Did any life form appear there yet...? lol

      Also, I have mentioned it before; What Larry and others believe had happened with mutations leading to macroevolution turned out to be a total fiasco with fruit fly lab experiments... Therefore, your speculations that random mutations can lead to major changes are a species is totally unfounded.... As usual...

      Same applies to the bacteria lab experiments by Lenski or something...
      I looked at all the literature regarding those experiments...It's bullshit... No new metabolic pathway evolved... Bacteria is still bacteria an it is not about to fly out of the tube or turn into a fly... Dream on...lol

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    2. Bla bla bla, seen god supernaturally create an organism with magic yet? No. Oh well...

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  19. Is it a FACT that likeness of men and primates is oNLY explained from common descent??
    why not a creator giving man the best body on earth within the spectrum of a common biological framework.
    hOWEVER i'm just showing if its ONLY by lines of reasoning then another line cancels out evolutionists line.
    Or rather lines of reasoning are not genetic scientific evidence.
    The other stuuf likewise is well within a common design also.
    is there genetic evidence for man/primate common descent??

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    1. why not a creator giving man the best body on earth

      Then how come there are undeveloped breasts (nipples) on guys, Robert, that are subject to breast cancer? A creator would have to be either a doofus or very evil to design that intentionally.

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    2. is there genetic evidence for man/primate common descent?

      Yes, of course there is. How long have you been doing this?

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    3. Allan Miller. ARE YOU SURE/ I've never seen any yet. Really!

      judmare
      No death before the fall and so cancer. Ape males have nipples, i think, and so would we on the same blueprint.

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    4. Robert,

      YES I'M SURE. That you haven't seen any does not surprise me, as you look at all evidence with eyes tight shut.

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  20. Quest, you are clueless. That's the reason you are unable to discriminate between two different subejcts:
    A: How did life originate on Earth?
    B: What is the cause of the changes in life forms since the beginning 4 billion years?

    And to make it clear that you are entirely off target: There is no rule that a species shall "evolve". Species exist in synergy with their environment. Variations only have effect when they lead to a change in ratios of alleles within a population.

    The effect of one powerful environmental factor, geographic isolation, can be observed anywhere you look at life on the planet. What do you propose is the cause?

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  21. IMHO, Torley gave up in the first few paragraphs of his piece. The primary evidence for the fact of evolution is concordance of similarities, i.e., we see a hierarchical structuring of similarities and differences. This was not anticipated under the special creation theory. Under special creation, we should see one giant star phylogeny. When this was not observed, creationists fell back on the idea that different species were created from a smaller number of "types." The expectation from this modified idea is that there will be, not a single star phylogeny, but 1 star phylogeny for each type.

    Torley simply retro-fits creationism to match phylogeny, proposing a creator that creates types and subtypes and further subtypes, for the sake of efficiency. Otherwise, he explains, the creator would have to give the same mutations to many different lineages. But this just begs the question-- does the creator *have to* give the same mutations to different lineages?

    Previously, the creator was attributed with various properties such as omniscience and wisdom that, along with the divine record in the bible, guided the construction of creationist theory. I don't remember the creator's "efficiency" being mentioned in the bible or invoked previously in creationist theory.

    Again, by conceding that a hierarchical pattern of concordance is perfectly explained by a modified creationist theory, Torley is simply revealing that the theory has no substance and can be adjusted at will by attributing ad hoc properties to the creator, so that the creator tends to make things that look like they evolved.

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  22. Concerning the fused chromosome: Well so far we have J Tompkins stating and writing in an article that the fusion site is in the middle of a functioning gene and we have Ken Miller stating that this is not true. However, Dr. Tompkins said that a particular data set was omitted in Miller's analysis and when it was included, Miller admitted that Tompkins was right. Then we have Larry Moran saying it is irrelevant. So who is correct? And Tompkins states that he has it in writing - in an email, that Ken Miller admitted he was wrong.
    Here is an excerpt from EvolutionNews.org.
    "When challenged privately, Dr. Miller conceded that the fusion point was only far away from the gene when one excludes results from a genomic database called "refseq." When refseq is included, a longer gene transcript is found -- produced by a section of DNA that includes the fusion site.
    Miller admitted the mistake to Tomkins: "In this transcript, the fusion site is in the middle of the first [gene] exon as you note."

    Mooney apparently wanted to give the impression that the "fusion site" is useless junk DNA, produced by random evolutionary mutations. The evidence suggests otherwise -- it's an important, functional gene.
    http://www.evolutionnews.org/2014/08/youre_welcome_d089381.html
    My money is on Tompkins. :) Maybe Professor Moran will comment further?

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    1. Hello Kristen,

      *Concerning the fused chromosome: Well so far we have J Tompkins stating and writing in an article that the fusion site is in the middle of a functioning gene and we have Ken Miller stating that this is not true.*

      It's not, the gene in question, DDX11L2 is a sub-telomeric pseudo gene, and coincidentally every DDX gene not on sex chromosome is sub-telomeric, I made a list:

      DDX11L1: 1p36.33, sub-telomeric
      DDX11L3: 3q29, sub-telomeric
      DDX11L4: 6p25.3, sub-telomeric
      DDX11L5: 9p24.3, sub-telomeric
      DDX11L6: 9q34.3, sub-telomeric
      DDX11L7: 11p15.5, sub-telomeric
      DDX11L8: 12p13.33, sub-telomeric
      DDX11L9: 15q26.3, sub-telomeric
      DDX11L10: 16p33.3, sub-telomeric
      DDX11L11:17p13.3, sub-telomeric
      DDX11L12: 19p13.3, sub-telomeric
      DDX11L13: 20p13, sub-telomeric
      DDX11L14: 20q13.3, sub-telomeric
      DDX11L17: 2q37.3, sub-telomeric

      If anything the DDX11L2 gene doesn't negate fusion but affirms it.

      *However, Dr. Tompkins said that a particular data set was omitted in Miller's analysis and when it was included, Miller admitted that Tompkins was right.*

      This is false but I'll get to that in a minute.

      *Then we have Larry Moran saying it is irrelevant. So who is correct? And Tompkins states that he has it in writing - in an email, that Ken Miller admitted he was wrong.
      Here is an excerpt from EvolutionNews.org.
      "When challenged privately, Dr. Miller conceded that the fusion point was only far away from the gene when one excludes results from a genomic database called "refseq." When refseq is included, a longer gene transcript is found -- produced by a section of DNA that includes the fusion site.
      Miller admitted the mistake to Tomkins: "In this transcript, the fusion site is in the middle of the first [gene] exon as you note."*

      This is utterly false not only can you email, Miller yourself but you can go to rationalskepticism.com and see an email from Miller in which he says he never said Tomkins was right. I'll post an email he sent to me asking about this.

      *Mooney apparently wanted to give the impression that the "fusion site" is useless junk DNA, produced by random evolutionary mutations. The evidence suggests otherwise -- it's an important, functional gene.*

      Also wrong, the low levels of transcript suggest DDX11L2 is a pseudo gene. That and it has no known function.

      *My money is on Tompkins. :)*

      Hope you didn't bet too much

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    2. *Then we have Larry Moran saying it is irrelevant. So who is correct? And Tompkins states that he has it in writing - in an email, that Ken Miller admitted he was wrong. 
      Here is an excerpt from EvolutionNews.org.
      "When challenged privately, Dr. Miller conceded that the fusion point was only far away from the gene when one excludes results from a genomic database called "refseq." When refseq is included, a longer gene transcript is found -- produced by a section of DNA that includes the fusion site.
      Miller admitted the mistake to Tomkins: "In this transcript, the fusion site is in the middle of the first [gene] exon as you note."*

      Here are 2 emails from Ken Miller (one sent to me) in which he basically says Tomkins is a fucking liar,

      Here's the email he sent to me:  [I have no idea what Luskin wrote, so I don't know whether it was a misquote, a distortion, or a falsehood.  I'd leave that to you to judge.  However, when I was quoted in a Chris Mooney piece about chromosome 2, Tomkins wrote me out of the blue stating I was wrong about the DDX11L2 gene.  He claimed it was a highly transcribed gene that spanned the alleged fusion site, and therefore the fusion hypothesis was falsified.]

       [I wrote back explaining that Tomkins' claim was nonsense. The available genome databases actually show that DDX11L2 (which is a pseudogene!) is off to one side of the fusion site. Now, there is a single entry in one of the databases reporting a transcript of that pseudogene that does indeed span the fusion site. All that shows is that sometimes RNA polymerase does not stop at the actual end of this pseudogene, producing a longer RNA transcript. This is a common observation for many genes and pseudogenes where variable length transcripts are reported.  But what Tomkins ignored (and I pointed out to him) was that this pseudogene was part of a family of related DDX11 pseudogenes found in many places on the human genome.  And, with the exception of DDX11L2, guess where all of them are located?  Right next to telomeres. All of them!]

        [So, the presence of this pseudogene on chromosome 2 actually confirms that the alleged fusion site is genuine, since it contains an additional marker indicating that it once was a telomere.  And there's one more thing. Right next to every member of the DDX11 family is another gene, transcribed in the opposite direction, abbreviated "WILD."  That is also true of the chromosome 2 site, further confirming the sequences at that region as the remnants of a true telomere, which is exactly what one would expect for the fusion event.]

        [So, if Luskin actually claimed I had "admitted" that Tomkins was right about the fusion site, then his claim was the exact opposite of what I wrote to Tomkins, and the exact opposite of the genetic facts.]

        [If this were the case, it would be nothing new for Luskin.  During the Kitzmiller v. Dover trial in 2005, every time there was a recess Luskin would stand in the lobby of the courtroom loudly proclaiming to journalists how well that day's events were going for "intelligent design."  He did this day after day.  And yet, we all know that the trial proved to be a disaster for the ID movement, despite his best efforts to spin it otherwise.]

         [Apparently, the Luskin spin machine is still in gear.]

            [Sincerely,]

               [Ken]

      Here is another email Ken sent to someone named itsdemtitans and you can read that here: http://www.rationalskepticism.org/creationism/casey-luskin-lies-about-ken-miller-on-chromosome-2-t50094.html

      *Mooney apparently wanted to give the impression that the "fusion site" is useless junk DNA, produced by random evolutionary mutations. The evidence suggests otherwise-- it's an important, functional gene.*

      Wrong as I explained above, the evidence suggests it's a sub-telomeric pseudogene. If you put your money on Tomkins, I hope you didn't bet too much.

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