Vincent Torley tries to understand fixation

I'm having an interesting discussion with some creationists. They claimed that the differences between the sequences of the human and chimpanzee genomes could not be explained by evolution. Therefore, it had to be due to design.

I wrote up a little post showing that there were about 44 million differences and that they could be accounted for by our understanding of population genetics and Neutral Theory. What his means is that the creationist explanation has to account for the fact that the vast majority of differences look like what we would expect if most of them were neutral and population genetics is correct. It's not good enough to simply invoke design and magic to explain the differences, you have to account for all the data.

Vincent Torley attempted to understand modern evolution theory. Some of these concepts were quite new to him because he doesn't have much of a biology background. We've had an exchange of posts were he expressed his astonishment and I try to explain evolution. You can find the links at: Vincent Torley apologizes and claims that he is not a liar.

I was thinking that this exchange would wind down but I was wrong. Vincent Torley is having second thoughts about accepting my explanation of Neutral Theory, population genetics, and mutation rates. He posted those second thoughts yesterday at: A Short Post on Fixation. My apologies if this is getting boring for Sandwalk readers but I feel an obligation to try and teach creationists about evolution, if for no other reason than being able to say that I tried.

Why does Stephen H. Webb use the word "Darwinism"?

We know why the IDiots use the words "Darwinist" and "Darwinism" to describe evolutionary biologists and modern evolutionary theory. There are three main reasons.

1. They want their flocks to believe that modern scientists worship Charles Darwin and his 150 year-old theory so that when they discredit him—as they are constantly trying to do—it reflects on evolution.
2. They want to link modern evolutionary biology to social Darwinism and it's easier to do so if they refer to evolutionary biologists as Darwinists.
3. They are too stupid to realize that there's a lot more to modern evolutionary biology than natural selection.

Every time you challenge creationists on this point they find some way to defend their use of Darwinism rather than just say "evolutionary biology" or "modern evolutionary theory." There's a reason for this (see above).

Stephen H. Webb is the latest example. Apparently his use of "Darwinism" was challenged so he wrote a blog post on Evolution News & Views (sic) defending it The Strange Mental World of Darwinian Fundamentalists. I hope you appreciate the irony in the title.

Why is Adobe Reader such bad software that it needs to be fixed every few weeks?

I run Adobe Reader on about six different devices so I see that annoying "update required" notice far too often. I've just given in and updated to version 11.0.03 but when I went to the website I saw that you can download version 11.0.06. I assume that means I'm going to be prompted to update three more times in the near future.

None of the other programs I run are so flaky that that the manufacturer needs to issue updates on a regular basis. What's wrong with Adobe? Why can't they get it right after all these years?

I think I may know part of the answer. If you aren't careful when you update the Adobe software it will automatically install "McAffe Security Scan Plus" on your computer. This will screw up a lot of other programs so you must be sure to uncheck the box. I wonder if the purpose of these frequent "updates" isn't to sneak McAffee software on to your computer—and maybe some other things as well?

Oops! I almost forgot. Flash Player is also pretty bad software that needs frequent fixing. I wonder who makes it?

Stop bundling McAfee in Flash updater!
Why Adobe is recommending McAfee security scan during flash player installation?
Adobe Reader installing McAfee Security Scan Plus Scareware
Why does Adobe require DAILY updates? Are they just trying to push McAfee on everyone?
Adobe Please Stop Including Bloatware Like McAfee Security Scan and Toolbars With Free Downloads
Trust Nobody – Especially Adobe and McAfee

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Jonathan Wells proves that life must have been created by gods

This YouTube video is described as "The most ignorant 82 seconds you'll ever see." I don't know about that. I been around IDiots for quite a long time. It may not be the "most ignorant" but it's surely in the top ten.

Remember, this is the best they've got. Really. Trust me on this.

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University rules and regulations

Today is the last day of classes at the University of Toronto and I have to submit a copy of the final exam to the Examination Supervisor. Actually, I have to submit a copy for each student PLUS 11 extra copies AND the "original." They have to be in two separate sealed packages with specified labels on the outside.

There's a set of rules and regulations that must be followed, including specific formatting rules. Some of the rules make sense and some don't.

Rule #12 is interesting. Here's what it says ...

Instructors and departmental offices should take stringent measures to prevent unauthorized persons from having access to the examinations. NO COPY OF AN EXAMINATION IS TO BE KEPT IN THE DEPARTMENT BEFORE THE FINAL EXAMINATION IS WRITTEN. This applies to electronic storage as well as to flash drives/usb key and paper copies.

Those of you who know me well will be able to imagine how much effort I have taken to erase everything from my hard drive and the automated backup drive attached to my computers. They will understand exactly how difficult it was for me to check my flash drive to make sure that no copy of the exam was stored there or in dropbox. They'll also know just how scrupulous I've been about not having a copy of my exam anywhere in my files. They can imagine that I've stored a copy safely at home so I can print out a version the day after the exam is written and put if back on my desktop hard drive.

I wonder how many of my colleagues will follow this rule? What do you think the penalty is if you don't?

Thank the gods for bureaucrats.

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What does "liberal arts education" mean in the 21st century?

The President of the University of Toronto recently published an article about undergraduate education. I questioned whether my university really is committed to the ideals of undergraduate education (critical thinking etc.) [Does the University of Toronto really care about undergraduate education?]. The answer, IMHO, is "no."

Now I want to bring up something else from the article by President Meric Gertler. It's not a major point—more like a motherhood throwaway line—but I think it raises an interesting question. Gertler said,

U of T reaffirms the value of a broad liberal arts education at the undergraduate level, and we are working to help our graduates extract the full benefit from that education.

I suppose there are as many definitions of "liberal arts education" as there are teachers but I think we can agree on a few points. A "liberal arts education" does not put much emphasis on math and science courses. In fact, I'm pretty sure that there are many who would be happy with a "liberal arts education" that didn't include a single math or science course.

I think that there are some extremely important humanities courses that every student should take. Philosophy (logic and reasoning) is the most obvious one but there's also history and maybe even sociology. I think university students should be familiar with great literature and many other topics in the humanities programs. But I also think that every single university student needs to take (and pass) some math and science courses in order to call themselves university-educated.

This is the 21st century. Surely we can agree that science is at least as important as "liberal arts"? Maybe we should be talking about a "broad science and humanities" education as the important value that we are trying to achieve?¹

I'm not sure where that leaves the thousands of students who are getting degrees in commerce and business. Perhaps we should admit that those undergraduate programs, like engineering, are not really education programs. They are job training programs.

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1. I'm not talking about "astronomy for poets" and other watered-down science courses. Humanities majors should take the same courses that science majors take just as science majors take the same courses that humanities students take.

Does the University of Toronto really care about undergraduate education?

My university, the University of Toronto (Toronto, Canada), is huge. We have 60,000 undergraduates making it one of the biggest universities in North America. You'd think that undergraduate education should be a very high priority.

The university publishes an online "newspaper" called the Bulletin every Tuesday and Thursday. It's basically a PR ploy to advertise everything that's great about the University of Toronto. There was a time in the past when the Bulletin had editorials that were critical of university practice and policies but I haven't seen anything like that in years.

The latest issue has a link to an article by the President of the University, Meric Gertler. The title of the article is: Job Ready: U of T is developing new programs to help students succeed after graduation. I want to discuss two things in that article. The first is whether the university really is committed to the goals of undergraduate education (this post). The second is What does "liberal arts education" mean in the 21st century?.

Vincent Torley apologizes and claims that he is not a liar

I was very upset when Vincent Torley suggested that I attributed all of the evolution of chimpanzees and humans to the fixation of nearly neutral alleles by random genetic drift. He tried to convince his audience that I was rejecting natural selection as a component of that evolution. I corrected him at: Breaking news: Creationist Vincent Torley lies and moves goalposts.

When he said, "Professor Moran’s view: 22.4 million neutral mutations were what made us human," I concluded that this was so ridiculous that it had to be a deliberate misrepresentation, i.e. a lie.

Later on in the post I admitted that there was another possibility, he may just be stupid and not a liar.

He has now posted an "update" on his original post: Can the neutral theory of evolution explain what makes us human?. Here's what he says ....

How did the zebra get its stripes?

A couple of years ago I posted an article on How Did the Zebra Get Its Stripes?.

I pointed out that this wasn't a Rudyard Kipling story but that many of the explanations had strong ties to just-so stories. I noted that everyone just assumed that there had to be an adaptive explanation for zebra stripes so they kept looking and looking. Every time one of the adaptive explanations was ruled out, they invented another one.

The best explanation back in 2012 was that zebra stripes evolved to protect zebras from horseflies and there was some experimental support for the idea that horseflies tended to avoid stripes. However, there was no evidence that avoiding some horseflies actually conferred enough selective advantage to drive the evolution of stripes.

Now we have a press release that announces the final solution: Scientists solve the riddle of zebras' stripes.

Why zebras have black and white stripes is a question that has intrigued scientists and spectators for centuries. A research team led by the University of California, Davis, has now examined this riddle systematically. Their answer is published April 1 in the online journal Nature Communications.

The scientists found that biting flies, including horseflies and tsetse flies, are the evolutionary driver for zebra's stripes. Experimental work had previously shown that such flies tend to avoid black-and-white striped surfaces, but many other hypotheses for zebra stripes have been proposed since Alfred Russel Wallace and Charles Darwin debated the problem 120 years ago.

Sounds like old news to me. And I'm still not convinced that you need an adaptive explanation.

Here's the paper ...

Caro, T., Izzo, A., Reiner Jr, R.C., Walker, H. and Stankowich, T. (2014) The function of zebra stripes. Nature Communications 5, Article number: 3535 [doi: 10.1038/ncomms4535]

Despite over a century of interest, the function of zebra stripes has never been examined systematically. Here we match variation in striping of equid species and subspecies to geographic range overlap of environmental variables in multifactor models controlling for phylogeny to simultaneously test the five major explanations for this infamous colouration. For subspecies, there are significant associations between our proxy for tabanid biting fly annoyance and most striping measures (facial and neck stripe number, flank and rump striping, leg stripe intensity and shadow striping), and between belly stripe number and tsetse fly distribution, several of which are replicated at the species level. Conversely, there is no consistent support for camouflage, predator avoidance, heat management or social interaction hypotheses. Susceptibility to ectoparasite attack is discussed in relation to short coat hair, disease transmission and blood loss. A solution to the riddle of zebra stripes, discussed by Wallace and Darwin, is at hand.

I'm betting that in five years there will be papers examining the SIX major adaptive explanations and five of them will be ruled out in favor of the latest one.

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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?].

A creationist tries to understand genetic load

Apparently there are some creationists who are slightly embarrassed that they don't understand evolution. First, there was Vincent Torley who made an attempt to understand population genetics (from the 1920s and 1930s) and Neutral Theory, which is only 45 years old. You can read his attempt at: Fixation: the neutral theory’s Achilles’ heel?. See my attempt to correct his errors at: A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory.

I appear to have been partially successful because if you scroll down to the bottom of Vincent Torley's post you'll see an "update" that pretty much refutes his entire post.

The comments on Torley's post reveal that there are very few creationists who have ever heard of population genetics and Neutral Theory. Now that they've been exposed, their response is to reject it because they don't understand it. Salvador Cordova (scordova) pops up in those comments to explain that modern evolutionary theory is all wrong because of "unfixing." Apparently, evolutionary biologists have missed something important that only creationists can see. This happens a lot.

Sal is so proud of himself that he puts up another post at Uncommon Descent: Fixation rate, what about breaking rate?. One gets the impression that some of the creationists are a bit worried.

The irony is that the vast majority of creationists will have absolutely no idea what Cordova is talking about. To them, it's like he's speaking gibberish. In this case, it means that the average IDiot isn't even posting comments under Cordova's post because they don't know what to say. This is all news to them.

So, what is the great discovery that refutes population genetics and Neutral Theory? It's got something to do with the idea that for neutral alleles the rate of fixation is equal to the mutation rate. Cordova agrees with the math but thinks it is "flawed from a functional standpoint." Why? Because ...

Ok, so let’s do an experiment. Let’s subject bacteria or plants or any organism to radiation and thus increase the mutation rate mutation rate by a factor of 1 million or 1 billion. Do you think the above formula will still hold? We tried it in the lab, it killed the plants, and at some point rather than speeding evolution we are doing sterilization.

Cordova is correct. An organism will die if you subject it to massive amounts of radiation. This blast doesn't have much to do with mutation rate but later on Cordova comes closer to a serious discussion of evolutionary theory.

Here's what upsets him ...

... even with moderate rates of mutation per individual per generation, genetic deterioration will happen. Further, this claim is reinforced by the work of Nobel Prize winner Hermann Muller who said a deleterious mutation rate of even 0.5 per individual per generation would be sufficient to eventually terminate humanity. So the simple model I present is actually more generous than Muller’s. Current estimates of the number of bad mutations are well over 1.0 per human per individual. There could be hundreds, perhaps thousands of bad mutations per individual per generation according to John Sanford. Larry Moran estimates 56-160 mutations per individual per generation. Using Larry’s low figure of 56 and generously granting that only about 11% of those are bad, we end up with 6 bad mutation per individual per generation, 6 times more than the cartoon model presented, and 12 times more than Muller’s figure that ensures the eventual end of the human race.

He's talking about genetic load although he goes out of his way to avoid using that term.

Sal Cordova is correct that if the deleterious mutation rate is too high, the species will go extinct. We don't know the exact minimum number of deleterious mutations that have to happen per generation in order to cause a problem. It's probably less than two (2). It's probably not as low as 0.5. It should be no more than 1 or 2 deleterious mutations per generation.

Genetic load arguments have been around for over forty years [Non-Darwinian Evolution in 1969: The Case for Junk DNA]. Back then, they were used to explain that most of our genome is junk and mutations in that part of the genome have no effect. We now know that those arguments were correct and 90% of our genome is junk.

Imagine that there are 130 new mutations per generation. Since only 10% of our genome is functional DNA, this means that only 13 of these mutations occur in DNA that has a biological function. We know that in a typical coding region about 25% of all mutations are seriously detrimental so if all the functional region of the genome were coding region that would mean 3.25 detrimental mutations per generation.¹ However, less than 2% of our genome encodes protein. The remaining functional regions are much less constrained so they can tolerate more mutations. It's likely that there are fewer than 2 detrimental mutations per generation and this is an acceptable genetic load.

All of this information is readily available in textbooks and scientific papers. It's basic evolutionary theory and facts about the human genome.

Cordova is correct to raise the point about genetic load but he is quite wrong in his calculation.

Still, we seem to be making a bit of progress because at least the creationists are talking about evolutionary theory from the 100 years after Darwin died.

Better late than never. Now all they have to do is get the facts right and they'll be ready to move into the 21st century.

Lynch, M. (2010) Rate, molecular spectrum, and consequences of human mutation. Proceedings of the National Academy of Sciences 107, 961-968. [doi: 10.1073/pnas.0912629107]

Keightley, P.D. (2012) Rates and fitness consequences of new mutations in humans. Genetics 190, 295-304. [doi: 10.1534/genetics.111.134668]

Kondrashov, A.S. (2002) Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human mutation 21, 12-27. [doi: 10.1002/humu.10147]

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1. Estimates of the percentage of deleterious mutations in coding regions are all over the map. I figure that most distantly related genes are only 30% identical in amino acid sequence. Some mutations in the conserved amino acid codons will be synonymous. But even if this value is 50% instead of 25%, the total number of deleterious mutations in coding regions would only be 50% × 2% × 130 = 1.3 deleterious mutations.

A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory

I know I've said this before, but I continue to be astonished at the ignorance of creationists. Those who oppose evolution most vehemently don't understand it in spite of the fact that they are convinced it has to be wrong.

This is most obvious with the Intelligent Design Creationists because they like to use science-sounding jargon to convince us that they know what they are talking about. They claim that they can refute evolutionary biology using scientific evidence. Instead they just reveal their ignorance.

They've been doing it for decades in spite of the fact that many people have tried to educate them. I don't get it.

Recently, I tried to explain how the difference between the chimpanzee and human genomes is consistent with what we know about population genetics, mutation rates, and Neutral Theory. I was aware of the fact that this stuff would all be news to most Intelligent Design Creationists but it was still an opportunity to try, once again, to teach them about modern evolutionary theory.

Monday's Molecule #235

Last week's molecule [Monday's Molecule #234] was insect juvenile hormone. The winners are Frank Schmidt and Raul Félix de Sousa (still an undergraduate?). They live in foreign countries so they won't be coming to lunch.

This week's molecule (right) is very common. You have to identify the entire molecule including the specific polynucleotide. Emphasis is on the word "specific"—there's only one possibility. I'm betting that there won't be very many correct answers for this one.

Email your answer to me at: Monday's Molecule #235. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

God's not dead

God's not dead is a movie that's gaining some notoriety in the USA. Here's a synopsis ...

Present-day college freshman and devout Christian, Josh Wheaton (Shane Harper), finds his faith challenged on his first day of Philosophy class by the dogmatic and argumentative Professor Radisson (Kevin Sorbo). Radisson assigns him a daunting task: if Josh will not admit that "God Is Dead," he must prove God's existence by presenting well-researched, intellectual arguments and evidence over the course of the semester, and engage Radisson in a head-to-head debate in front of the class. GOD'S NOT DEAD weaves together multiple stories of faith, doubt and disbelief, culminating in a dramatic call to action.

I haven't seen the movie (yet) but I'm guessing that the 18 year-old Christian student wins the debate against his "dogmatic" professor.

This sort of thing happens quite a bit in the movies. It's pretty rare to find a university professor portrayed as a good person, or even a smart person who knows their stuff. If you are one of those university students who watch the movie and are convinced that you can win a debate with a professor on the subject "Do gods exist?" then please contact me and we'll set up a time and place for you to make the attempt. I'm pretty sure I can find a smart professor at most major universities.

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Science education and indigenous knowledge

Yesterday afternoon I attended a forum on Science and Mathematics teaching in Ontario schools. It was put on by The Centre for Science, Mathematics and Technology (SMT) Education at the Ontario Institute for Studies in Education (OISE) at the University of Toronto (Toronto, Canada).

OISE is one of the places responsible for training teachers in Ontario. It offers advanced degrees (Masters. Ph.D.) in education. I thought this might be a good opportunity to network with the people responsible for teaching science in our high schools.

Here's a description of the forum ...