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Wednesday, April 02, 2014

Breaking news: Creationist Vincent Torley lies and moves goalposts

Although all types of creationists are anti-science to some degree,1 the Intelligent Design Creationists are unusual because they don't just ignore science, they try to use science to show that science is wrong!

When dealing with the similarities between closely related species, they claim that the similarities (and differences) are due to design and not evolution. They claim that evolution cannot account for the differences between, say, humans and chimps. Only intelligent design can do that.

In an attempt2 to show them that evolution CAN account for the differences between humans and chimps/bonobos, I wrote up a description of how Neutral Theory and random genetic drift produce genomes that differ by 22 million positions if we take the fossil evidence at face value and assume that chimps and humans last shared a common ancestor about 5 million years ago [Why are the human and chimpanzee/bonobo genomes so similar?].

The point is that Intelligent Design Creationists not only have to account for the fixation of 22 million nearly neutral mutations in each lineage but they also have to explain why their designer choose to do it in a way that looks a lot like evolution from a common ancestor. I was hoping to teach them a little bit about evolution along the way since they seem to be stuck in the 1800's.

Vincent Torley was the first one to respond but he followed a typical creationist pattern. Having failed to understand Neutral Theory, population genetics, genomes, and random genetic drift, he falls back on the argument from ignorance and assumes that they must all be wrong [Fixation: the neutral theory’s Achilles’ heel?]. I tried to correct the most obvious misconceptions in that post [A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory].

Now he's back for more. This time Vincent Torley is saying that the discussion was not about whether evolution could account for the differences between chimps and humans but whether it can account for the important adaptive differences. He asks: Can the neutral theory of evolution explain what makes us human?.

No, Vincent, you can't account for all the distinctive differences between humans and chimpanzees by only looking at the fixation of nearly neutral alleles. What ever gave you that idea? Adaptation and natural selection play an important role in the evolution of species.

Let's look at Vincent Torley's recent post to see how he lies and moves the goalposts in order to avoid dealing with the fact that evolution, and not Intelligent Design Creationism, can account for fixation of 22 million nearly neutral alleles in the human genome.

Recall that Vincent Torley wrote a long post about all of his objections to Neutral Theory and random genetic drift [Fixation: the neutral theory’s Achilles’ heel?]. He didn't believe that it could take one million years to fix these neutral mutations in the evolving human population and he expressed doubt that nearly neutral mutations could be fixed at a rate equal to the mutation rate. In fact, he even expressed doubt about the mutation rate.

Now he claims that he was arguing about something entirely different. He says,
When I expressed doubt in a recent post that an accumulation of minor mutations could account for the macroevolutionary transition leading to the emergence of human beings from a primate ancestor, Professor Moran reiterated his position:
I recently wrote up a little description of the differences between the human and chimpanzee/bonobo genomes showing that those differences are perfectly consistent with everything we know about mutation rates and the fixation of alleles in populations [Why are the human and chimpanzee/bonobo genomes so similar?]. In other words, I answered Vincent Torley’s question.
We've shifted back to an earlier discussion about macroevolution where Vincent Torley asked, "Does Professor Larry Moran (or anyone else) understand macroevolution?." I answered that post on March 20th with: What do Intelligent Design Creationists really think about macroevolution?.

One of the claims made by Vincent Torley was that we don't understand macroevolution because there's not enough time for it to occur. (Remember that Torley is a philosopher so it's not surprising that many of his question could be answered by any university student who took a biology course.) He said,
Third, you can’t really claim to understand a mechanism for getting from A to B unless you can demonstrate – at least with back-of-the-envelope calculations – that the mechanism is capable of getting from A to B in the time available. If you are unable to produce the required calculations, then your claim to understand how the process works is tantamount to nothing more than hand-waving. As it turns out, scientific arguments that there’s plenty of time for macroevolution are fundamentally flawed, which means that evolutionary biologists are back at square one.
That's when I replied that I had already answered this question with calculations showing that the evolution of chimps and humans from a common ancestor was consistent with evolution. I did the back-of-the-envelope calculations and showed him that we understand the mechanism for getting from A to B.

Torley says,
Now, I am no expert when it comes to mutations. But I do know something about human evolution – I’ve been studying it, on and off, since I was about eleven. So in today’s post, I’d like to explain some of the reasons why I don’t believe that neutral mutations (or nearly neutral ones) have a hope in Hades of accounting for the complexity of the human brain.
I agree with Vincent Torley. The differences in the complexities of chimp and human brains are almost certainly due, in part, to adaptation and fixation of beneficial alleles by natural selection.

Here's what Torley says about me ...
Professor Moran’s view: 22.4 million neutral mutations were what made us human.
That's such a distortion of what I said that it counts as a deliberate attempt to misrepresent my position. In other words, it's a lie.

At no time have I ever denied that natural selection plays a role in the evolution of humans. It would be ridiculous to do that. What I was doing is pointing out that the IDiots have a lot of explaining to do if they are going to account for the differences between chimps and humans because the vast majority of those differences are entirely consistent with the fixation of nearly neutral alleles according to modern evolutionary theory (population genetics). I was also showing them that evolution can account for macroevolution.

Torley makes the case for selection of better brains in the past 300,000 years. He then says,
Readers will recall that one implication of the neutral and near-neutral theories of evolution espoused by Professors Myers and Moran was that new traits should have taken 1,100,000 years to get fixed in the human population, if they were the product of neutral (or near-neutral) mutations. But here we have a biological trait that shaped the course of human history, that did not exist prior to 300,000 years ago!
Is it possible that Vincent Torley is just too stupid to understand the difference between fixing neutral alleles by random genetic drift and fixing beneficial alleles by natural selection? Or, is he deliberately trying to mislead his fellow IDiots by lying about what I meant in my posts?3

Torley concludes with ...
In conclusion: there appear to have been at least four changes in the development of the human brain over the last few million years, which can only be described as beneficial. In addition, the most recent of these changes emerged and fixed itself within the human population far more quickly than allowed for by the neutral theory of evolution. The neutral theory of evolution thus appears to be woefully deficient, as an account of what makes us human.
It's an exaggeration to imply that none of the neutral alleles contribute to what makes us human but I agree with the general idea that Neutral Theory, by itself, can't account for why we are different from chimps.

WARNING: I'm about to post the final sentence from Vincent Torley's latest post. You should turn off your irony meters.
I’d like to close with a short quote from the late John Maynard Keynes. "When my information changes, I alter my conclusions. What do you do, sir?"

BTW, don't read the comments under Torley's post. It can be very depressing. It makes you realize that the level of ignorance we're dealing with is way beyond our ability to fix it with a few posts about evolution. Remember, Uncommon Descent is one of the best blogs on Intelligent Design Creationism. You won't find another where the level of discourse is any better. Where are all the smart ID proponents? Why don't they speak up and correct the mistakes made by their colleagues?

1. Yes, even the Theistic Evolution Creationists.

2, Apparently futile, since the stupidity and bias of the IDiots resists all attempts.

3. Yes, yes, I know. These are not mutually exclusive. He could be both stupid AND a liar.


John Harshman said...

There's a third alternative to "stupid" and "lying": self-deception. People can be quite ingenious, even brilliant, at creative misunderstanding in defense of a core belief. And I think that's much more common than your suggestions. Torley probably isn't lying; he's convinced that he's soundly thrashed you, because he wants very strongly for that to be true.

Anonymous said...

Dr. Moran, I've been following these debates and I was wondering if you could help clarify some things I've wondered about:

1. Perhaps there is also some overlap due to weakly-beneficial mutations, but about what percentage (ball-park) of mutations of the 22 million would you say were fixed by selection vs by drift?

2. Is 22 million the correct number of mutations? Over on the EvoAnth blog, Adam Benton says "Around 80% of the human genome has an equivalent section in the chimp genome. When we compare these sections we find that they’re around 99% similar." 20% of 3 billion is 600 million. If these arose from duplications I think they would be alignable and therefore included in "has an equivalent section in the chimp genome"

colnago80 said...

I'm just sitting here reading this and laughing at the temerity of a philosopher like Torley trying to argue issues in biology with a veteran biologist like Prof. Moran, much like the recent debate where theological philosopher William Lane Craig tried to argue issues in cosmology with astrophysicist Sean Carroll. Torley and Craig were fighting way above their weight class.

Mark said...

It's possible Torley graduated, with a degree in evolutionary biology, from the University of Wikipedia...he's an alum with Jenny McCarthy.

colnago80 said...

I am reminded of a comment made during the OJ Simpson trial by one of the cable commentors to the effect that it is bad cross examination technique to try to argue with a technical expert on the witness stand. Torley and Craig should follow that advice.

John Harshman said...

It isn't Torley's profession that's the problem, nor is it his lack of a degree in evolutionary biology. It's his personal ignorance. There are plenty of people with fancy degrees in biology and jobs in the field who are ignorant of what Larry is talking about and there are plenty of people with neither who are knowledgable. Don't fall into an argument over credentials. You should be paying attention to the arguments themselves.

Now, Torley has displayed copious ignorance of biology. That's the point. How he gained all that ignorance is irrelevant.

Piotr Gąsiorowski said...

I'm trying hard to understand Torley's line of reasoning. He's probably somehow got it into his head that according to Larry Moran nearly neutral theory has defeated and completely replaced adaptationism, and that according to this radically new view of evolution (attributed to a straw man he insists on calling Professor Larry Moran) random drift is the only mechanism of evolutionary change (including adaptation). As far as those people and their mental powers are concerned, the evolution of the human brain over millions of years has been a bloody waste of time.

John Harshman said...

I suspect a lot of that would be due to deletions in the chimp lineage. If the common ancestor had a sequence and the chimp ancestor lost it, that would be a bit that had no equivalent sequence in the chimp.

But when Benton says "equivalent", are you sure he's counting both orthologs and paralogs?

Anonymous said...

Based on the language I assumed he was including paralogs. I added a comment on his blog asking for more information, which is still awaiting moderation.

Losses would require that the chimpanzee lose 600 million bases in 6 million years? Doesn't that seem like an alarming rate? Isn't the chimpanzee genome still something like 13% bigger than ours today?

John Harshman said...

I can't say what he means. We'll see.

I don't say that all the differences are due to deletions in the chimp lineage, just that a lot of them might be. There are about 5 million indels between chimps and humans in the easily alignable portions of the genome. I've seen estimates that the average indel size is around 1kb. Of course some of those are insertions and some are deletions in the human lineage. Let's say a quarter are the deletions we want. That gives 125 million bases lost by the chimp. Not 600 million, but certainly a significant percentage.

Notice, however, that these numbers come from alignments. Big indels that result in major alignment problems aren't being counted, and may account for a lot of the difference. (Or may not. Who knows?) A multiple alignment of chimp, human, gorilla, and orangutan assemblies might help.

Note also that a huge amount of deletion doesn't result in any change in genome size if it's balanced by a similarly huge amount of insertion. And we know that levels of insertion and deletion, though not equal, aren't enormously different either.

Faizal Ali said...

That's not so much a third alternative, as it is a combination of the two. :)

Anonymous said...

If there are 5 million indels in the easily alignable regons at an average size of 1kb, that would make 500 million bases from those indels. I think this number is way too high, since "The difference between the two genomes is actually not ∼1%, but ∼4%—comprising ∼35 million single nucleotide differences and ∼90 Mb of insertions and deletions." Am I missing anything here?

As for insertions, wouldn't a 1kb insertion come from existing sequences and then be align-able?

To skip to the chase, how many mutations total do you think separate humans and chimps, and what type of mutations were they? Dr. Moran, I would like your perspective here too if you have time.

Anonymous said...

Sorry, that should be 5 billion, not 500 million. It obviously can't be 5 billion so I'm wondering where the numbers are off.

John Harshman said...

Am I missing anything here?

Probably. It may be that the average indel size has been very poorly estimated in my source, or it may have been talking about some other population of indels. If we take the estimate you have, then we account for only 24Mb of the difference by chimp-lineage deletions in aligned sequences.

As for insertions, wouldn't a 1kb insertion come from existing sequences and then be align-able?

Maybe. Depends on what you mean by "alignable". An alu insertion could certainly be aligned to other alu insertions in different parts of the genome. But is that what alignment means here? And any newly inserted retroviruses would not come from within the genome.

I think there are about 40 million mutations, total. There are some that haven't been counted, but I think they make up a very small proportion of that total. Those would be huge indels, inversions, other chromosomal rearrangements, new retroviral insertions, and perhaps something else I'm not thinking of. But I think there could be a few thousand of those at most. Point mutations and indels account for the ovewhelming majority of events.

Bill said...

Torley claims to have been studying evolution since he was 11. That's only two years ago! Give the guy a break.

Larry Moran said...

joecorder asks,

To skip to the chase, how many mutations total do you think separate humans and chimps, and what type of mutations were they? Dr. Moran, I would like your perspective here too if you have time.

See: What's the Difference Between a Human and Chimpanzee?

Updated numbers suggest 44 million point mutations and something like 2 million insertions/deletions for a grand total of 46 million mutations.

We don't know how many of those were beneficial (adaptive) leading to ways in which modern chimps are better adapted than the common ancestor. (Same for humans.) My guess would be only a few thousand in each lineage.

You have to keep in mind that the human genome sequence only covers about 2.9 billion base pairs out of a total length of 3.2 billion [How Much of Our Genome Is Sequenced?]. There are over 350 gaps in the sequence that can't be filled in because they consist mostly of repetitive sequences.

Even less of the chimpanzee genome is contained in contiguous, well-annotated scaffolds. We're working with what we've got. You have to be skeptical of some of the SNP results and especially of the indels.

Nevertheless, it's remarkable that the differences between the human and chimp genome agree so nicely with what we expect from our understanding of evolution.

I don't know if they agree with Intelligent Design Creationism because none of the IDiots have described their explanation of the data. They spend most of their time questioning the data, which suggests that they find it very troubling.

I think they're a little bit worried about a designer who would spend so much time making neutral mutations in junk DNA. Such a designer doesn't seem very intelligent.

Diogenes said...

Joecoder7, I think Joe Felsenstein could answer your question as well as Larry, if he shows up.

The whole truth said...

Torley said:

"In conclusion: there appear to have been at least four changes in the development of the human brain over the last few million years, which can only be described as beneficial. In addition, the most recent of these changes emerged and fixed itself within the human population far more quickly than allowed for by the neutral theory of evolution."

I've sworn off going to the UD site but II'm wondering if Torley said what the "at least four changes" were/are, and especially "the most recent of these changes"?

As far as "can only be described as beneficial" is concerned, that's highly debatable, especially when considering changes that enabled humans to conjure up gods, spirits, angels, demons, heaven/hell, astrology, palm reading, 'holy' books, and all the other woo that pervades most of our species and societies.

One of the things that comes to my mind when I see or hear religious people pushing their god(s) is: Why do they need to speak for an allegedly powerful, supernatural being? Why can't the so-called 'God' speak for itself? Why does the 'God' need sales people, especially if the 'God' is omnipotent, omniscient, and omnipresent? And if they're speaking for the same 'God', and they're basing their beliefs on the same 'holy' book, why don't those religious people believe and say exactly the same things? After all, 'God's word' should be exactly the same to every human, and especially to everyone who believes in and worships that so-called 'God'.

colnago80 said...

Re John Harshman

Let me expand on my comment to further explain what I meant to say. Prof Moran has specialized in evolutionary biology and keeps up with the literature in the subject. Further, based on his education, background, and interests, he is fully capable of understanding the literature on the subject. He does this for a living. Not so Torley. Similarly, Sean Carroll has the necessary background in cosmology and astrophysics which he does for a living. Not so Craig.

By the way, it is no sin that many biologists don't know much about evolutionary biology. Before he was inveigled by his students into debating Henry Morris, Ken Miller admitted that he didn't really know much about the subject either. As someone whose PhD is in elementary particle physics, I don't know much about solid state physics. Most physical chemists don't know much about organic chemistry. It's not required to do their jobs.

Diogenes said...

Torley is one of the smarter IDers. That's damning with faint praise, it's true.

In the infamous MathGrrl thread at Uncommon Descent, where MathGrrl asked the IDiots how to compute the change in Dembski's "Complex Specified Information" for the simplest conceivable genetic changes, Torley was the only one with the balls to actually do a computation. His math was all f*&@ed up (he thought genes were about 100,000 bps long) but at least he immediately computed that gene duplication vastly increases Dembski's "Complex Specified Information."

At least Torley, for a brief moment, conceded that natural processes can increase Dembski's CSI. Which would normally mean that ID is dead dead dead.

Then he took it back, naturally. A few days later Torley wrote another post where he basically invoked the usual ID circular-logic fraud-- since gene duplication is a natural process that increases Dembski's CSI, and that's the answer they don't want, therefore Dembski's CSI just shouldn't be computed for gene duplication events. It's like you're doing a double blind test on a pill that's said to cure cancer. Uh-oh, you find the same number of patients who took your pill got cancer as the control group. That's easy to fix-- just say the pill doesn't work on people who will later get cancer. Problem solved! Torley's take-it-back post is entitled, and I kid you not, "Why there’s no such thing as a CSI Scanner." Uh-- we know why, Vince. Every time you give us a real equation for CSI, we can show by simple f&%$ing math that natural processes increase it enormously. So you damn well better not give us an equation, you ID frauds.

Torley is also unusual among IDiots in that, in the MathGrrl thread, he admitted that Dembski's CSI is based on a "probability" calculation in which the "probability" is never the actual probability of the evolutionary path under consideration, but is instead the fake probability of a totally unrelated process-- the random scrambling of all parts-- which I call the tornado probability. Dembski himself almost never admits that his CSI calculation for all natural processes is based always on tornado probability and never on the probability of real evolutionary pathways (Richard Wein got him to admit it once, sort of, but mostly Dembski obfuscates and BS's, which is one of the reasons why none of the IDiots know how to compute CSI. Dembski doesn't want them to know how.)

The other IDiots, though they brag and boast they are smarter than the world's scientists, can't do long division. Multiplication troubles almost all of them.

Look at their reaction to Larry's ultra-simplified math. Larry tried to dumb neutral evolution down to simple multiplication and IDiots like Sal Cordova can't understand the math. Of multiplication. Multi-f%^&ing-cation. It isn't even frikkin calculus. How the hell should we communicate with these people? Hand puppets? But every UDite think he's Galileo.

Joe Felsenstein said...

I can show up but as Larry knows the empirical data better than I, I'll leave it to him. Most of the differences between human and chimp genomes would represent neutral mutations, either point mutations or insertions/deletions. There will be about 30 million of these. As for selected changes (mostly advantageous but some accidentally-fixed deleterious changes too) they must be many fewer, but there isn't an easy method to assess how many there are.

Let's put the whole discussion in perpective -- it is not about whether Larry or us commenters can completely account for human evolution. No one knows enough to claim to do that. Rather, it is about assessing creationist and ID-ist claims that there is some valid argument that shows that human evolution by the natural forces of evolution (including mutation, genetic drift and natural selection) is impossible.

Joe Felsenstein said...

Diogenes: at the time of the MathGrrl thread, most everyone thought that Dembski's assertion was that the observation of CSI was how one decided that natural processes could not produce an adaptation.

So it seemed very relevant to find out whether natural processes could increase SI, and ultimately make it into CSI. ID-ists usually tried to show that this couldn't happen, and they argued that Dembski's Law of Conservation of Complex Specified Information prevented it from happening.

But since then, Demsbki has clarified that this was not his argument. Instead, to declare the presence of CSI, you first had to show that natural processes could not have brought about that amount of SI. In other words, you first had to rule out natural processes, and then and only then could you declare that CSI was present.

So, it turns out, the presence of CSI does not rule out natural processes, it is just a label you slap on after you have, by some other means, ruled them out. On short, the presence of CSI adds nothing of interest to the argument. And showing that CSI cannot be brought about by natural forces is trivial -- it's defined as that way. So we can basically forget about CSI as an important quantity for a Design Inference.

Les said...

Upton Sinclair wrote: "It is difficult to get a man to understand something when his salary depends upon his not understanding it." Substitute "belief system" for "salary" and you have Intelligent Design Creationists.

Anonymous said...

Thanks to the three of you for your replies. The estimates were 30, 40, and 46 million mutations, with Dr. Moran suggesting 2 million indels. If we take EvoAnth's ~600 million bases would make the average indel size 300 bases? While keeping in mind the unknowns Dr. Moran mentioned above.

Taking "a few thousand in each lineage" compared to ~30-46 million total, that would mean about one out of ten thousand mutations fixed during primate evolution are adaptive, and the rest are neutral or deleterious?

Diogenes said...

Oh no, Stephen Meyer of the DiscoTute makes something like $92K per year IIRC. Some of them are quite well paid. People like Casey Luskin and David Klinghoffer would have no other jobs if not for their cushy, secure jobs at the DiscoTute, with travel expenses to fly around the country and lobby far right-wing politicians. Maybe they started out believing it, but when it's been your career for several years, you've got no other options for paying the rent.

Anonymous said...


Don't hide.... this is not going to change your "religion".. You lost....
Your shitty science is just as good as garbage... You , liked LM have spent your life trying to find a way around the obvious.... Larry doesn't give a shit about that, but you might unofficially of course...

Faizal Ali said...

Now, Torley has displayed copious ignorance of biology. That's the point. How he gained all that ignorance is irrelevant.

I'd always understood philosophy to be the discipline that best understood logic and how to form a rational argument. In which case. Torley has shown he is incompetent in his own field.

Faizal Ali said...

I wonder why neither Torley nor any of his fellow IDiots have been discomfitted by the fact that they are now arguing in favour of Darwinism.

John Harshman said...

...neutral or slightly deleterious, i.e. nearly neutral.

John Harshman said...

colnago80. I reiterate: it isn't Larry's degree or any claims to keep up with the literature that tell us Larry knows the subject; it's what he says, which demonstrates that he knows. It isn't Torley's lack of a degree or anything about the literature (has he even said whether he does or doesn't read it?) that tell us he doesn't know; it's what he says, which demonstrates his ignorant. These supposed credentials you mentioned are irrelevant. Credentials are nothing; actions are everything.

Corneel said...

Yes, I too believe this is the case. Here is how Vincent Torley puts it himself in his update:
What I do think is that they, like most human beings, are prone to ideological bias against viewpoints which they find profoundly uncongenial, and that in attempting to discredit these viewpoints, they are liable to be swayed by emotion rather than reason.
...except that he was talking about evolutionary biologists rather than self-reflecting.

Larry Moran said...

Where does he say that? I can't find it.

Piotr Gąsiorowski said...

The last paragraph of the "Update":

Corneel said...

Mind: The "update" is in the beginning of the text, not at the end.

Piotr Gąsiorowski said...

Larry: BTW, don't read the comments under Torley's post. It can be very depressing.

It can be quite amusing too. The following could be part of a Monty Python sketch:


Mung April 2, 2014 at 6:22 pm

1. Are there good reasons to think that there have been muutations/genes that have been positively selected in the human lineage or is this just evolutionists making stuff up?



MungApril 2, 2014 at 6:23 pm

1. Are there good reasons to think that there have been muutations/genes that have been positively selected in the human lineage or is this just evolutionists making stuff up?

I mean Yes.

colnago80 said...

Re John Harshman

I am afraid that you and I are just going to have to agree to disagree on this subject, hopefully not disagreeably.

Diogenes said...

Dung is one of the dumber IDiots, and that is really saying something, but he really thinks he's sharp. With his wit and a butter knife, he could cut butter.