My molecular evolution midterm test

My students wrote the midterm test today. Here are the questions. They had to answer the first question and 4 other questions (out of 5). How would you do?

1. What’s the most important new thing about molecular evolution that you have learned in this course so far? Explain your answer by describing your "important new thing."
2. If mutation rates are relatively constant then why does the molecular clock tick at different rates in different proteins?
3. Many evolutionary biologists think that population genetics is the key concept in understanding evolution but biology students often complete several years of courses without ever learning about effective population sizes, mutation rates and the importance of random genetic drift. Why? Is it because population genetics is not a necessary key concept in evolution?
4. Grad students at this university publish a journal called Hypothesis. A few years ago (2005) there was a student who wrote ...
   

   I am a grad student, and long hours at the bench have got me thinking of other things lately, including the idea of marriage. I came up with a few criteria to direct me on my quest for a wife, and near the top of the list was that she needs to know what a gene is. I thought that this would be a reasonable thing to ask for. I like learning about how we and the rest of life work, and knowing how, in a general sense, cells are programmed to do what they do is a pretty good indicator of similar interest. My friends, however, disagreed with me, and on several occasions, as I shared my list, I feared that things were going to get violent. They argued that I will never get married with such a short-sighted and elitist attitude.

   Imagine that you would only seek partners who knew what a gene was. What definition would you require and why?
5. What’s the best evidence that a substantial amount of our genome is junk?
6. Imagine that you are teaching a class and you ask students to calculate a mutation rate in humans based on what they know about biochemistry. What mistakes are they most likely to make and why?

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On moral absolutes and ethical relativism

Last week I commented on whether bigots should be given permission to discriminate against gays just because the bigots belong to a religion that promotes bigotry [The Kansas anti-gay bill]. My opinion is that societies should not tolerate bigotry no matter what motivates people to discriminate. I said ...

I read some newspaper articles, and some blog posts, that stated the obvious. It is totally wrong, all the time, to discriminate against someone based on their sexual preferences. If they use religion as an excuse then they should re-evaluate their religion. There is NEVER a time when an enlightened society should tolerate, let alone legalize, bigotry. I guess it's almost impossible to come out and say this on television, or maybe I'm just watching the wrong channels (mostly FOX and CNN).

What I mean is that enlightened societies will almost always reach a consensus on discrimination against minorities. They will decide that society functions best when all types of discrimination are bad and should not be tolerated.

Muzzled and mad Canadian scientists

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The Kansas anti-gay bill

I'm currently in Los Angeles visiting the grandchildren so I'm a bit more exposed to American culture than normal. I watched several discussions on the Kansas anti-gay bill on television and one thing struck me as highly unusual.

For the sake of non-Americans, let's begin with a description of the bill passed by the Kansas House, which is dominated by Republicans. Here's what Bill 2453 says ...

Notwithstanding any other provision of law, no individual or religious entity shall be required by any governmental entity to do any of the following, if it would be contrary to the sincerely held religious beliefs of the individual or religious entity regarding sex or gender: (a) Provide any services, accommodations, advantages, facilities, goods, or privileges; provide counseling, adoption, foster care and other social services; or provide employment or employment benefits, related to, or related to the celebration of, any marriage, domestic partnership, civil union or similar arrangement; (b) solemnize any marriage, domestic partnership, civil union or similar arrangement; or (c) treat any marriage, domestic partnership, civil union or similar arrangement as valid.

In other words, if you are a bigot then the state will protect you from prosecution as long as you claim that your bigotry is based on religion.

The bill was expected to pass through the Kansas Senate and signed into law by a redneck governor. Fortunately for Kansas, the Republican-dominated senate decided that Kansas should drop out of the competition for most stupid state and they declined to pass the bill [Kansas Senate Comes To It’s Senses And Nixes Extreme Anti-Gay Legislation ].

That's not what I want to talk about. What I witnessed on the American TV channels was a debate over the legality of discrimination of gays. The discussion hinged on whether it was legal for an anti-gay bigot to refuse to serve a gay couple in a restaurant or whether an anti-gay bigot could refuse to bake a wedding cake for a gay couple. Almost everyone I saw on TV agreed that it was perfectly okay for Americans to be anti-gay bigots, especially if their bigotry was related to their belief in God. The only serious question seemed to be whether there were legitimate times when anti-gay bigots could express their bigotry in public.

I read some newspaper articles, and some blog posts, that stated the obvious. It is totally wrong, all the time, to discriminate against someone based on their sexual preferences. If they use religion as an excuse then they should re-evaluate their religion. There is NEVER a time when an enlightened society should tolerate, let alone legalize, bigotry. I guess it's almost impossible to come out and say this on television, or maybe I'm just watching the wrong channels (mostly FOX and CNN).

I'm reminded of a statement by Winston Churchill about Russia; "Russia is a riddle wrapped in a mystery inside an enigma." That's the way I feel about the United States. There's such a huge difference between Boston and Texas that I wonder how they can both continue to exist in the same country.

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A Darwin Day rap video

An old high school friend of Ms Sandwalk sent me the link to this video by Dirk Murray "Baba" Brinkman, Jr. He is the son of my friend's local MP, Joyce Murray (Liberal, British Columbia).

I hesitated to post in on Darwin Day but now that other blogs have linked to it, I want to use this opportunity to raise two important questions.

1. The video promotes "Darwinism" as the only solution to evolution. This is wrong, but is there value in lying about this for a greater cause? Is it possible to make an effective video like this without distorting the science?
2. I'm very uneasy about promoting Darwin worship, partly for the reason that there's more to evolution than what Darwin wrote in 1859 and partly for the reason that it smacks of religion. What do you think? Should we be pushing "Darwin Day"?

M=

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On the difference between Neutral Theory and random genetic drift

PZ Myers posted an interesting article on The state of modern evolutionary theory may not be what you think it is. He makes the point that there's more to evolution than natural selection.

I think this is an important point but I would not explain it the same way as PZ. He focuses attention on Neutral Theory and the fact that neutral, or nearly neutral, mutations are fixed by random genetic drift. Here's how he describes it ...

First thing you have to know: the revolution is over. Neutral and nearly neutral theory won. The neutral theory states that most of the variation found in evolutionary lineages is a product of random genetic drift. Nearly neutral theory is an expansion of that idea that basically says that even slightly advantageous or deleterious mutations will escape selection — they’ll be overwhelmed by effects dependent on population size. This does not in any way imply that selection is unimportant, but only that most molecular differences will not be a product of adaptive, selective changes.

The debate over adaptationism is a debate over mechanisms of evolution. Random genetic drift is a mechanism of evolution that results in fixation or elimination of alleles independently of natural selection. If there was no such thing as neutral mutations then random genetic drift would still be an important mechanism.

Let's say you have a clearly beneficial mutation with a huge selection coefficient of 0.1 (s = 0.1). Population genetics tells us that the probability of fixation is 2s or, in this case, 20%. That means that the allele will be eliminated from the population 80% of the time. That's random genetic drift. Similarly, some fairly deleterious mutations can sometimes be fixed by random genetic drift.

Random genetic drift is a mechanism of evolution that was discovered and described over 30 years before Neutral Theory came on the scene.

What Neutral Theory tells us is that a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection. The conclusion is inescapable. Random genetic drift is, by far, the dominant mechanism of evolution.

Many people seem to equate Neutral Theory with random genetic drift. They think that random genetic drift is only important when the alleles are neutral (or nearly neutral). Then they use this false equivalency as a way of dismissing random genetic drift because it only deals with "background noise" while natural selection is the mechanism for all the interesting parts of evolution. I think we should work toward correcting this idea by separating the mechanisms of evolution (natural selection, random genetic drift, and others) from the quality of alleles being produced by mutation (beneficial, detrimental, neutral).

The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there's more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don't understand evolution.

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Jesus and Mo Wednesday

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The importance of RNA-Seq and next generation

I want to draw your attention to: Genomics researchers astonished to learn microarrays still exist. I especially like this comment from the author (jovialscientist) ...

In recent years, RNA sequencing (RNA-Seq) has been favoured over microarrays. This new technology, using next-generation sequencing, is slightly more accurate, and nations have recently declared war over which is the best aligner to use.

In a recent poll, 98% of researchers answered "next-generation sequencing" to every single question – even their name, age and job title. The new science of "sequence first, think later" has been coined "nextgenomics".

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The very best argument for the existence of God

The atheists and skeptics had a wonderful time last Friday night. That's because the debate over "Is There a God?" was a tremendous defeat for Roman Catholics who turned out in droves to hear Philip Cleevely make the case for god.

Cleevely's only argument goes like this:

• The world began from nothing.
• That's very mysterious.
• Therefore, god(s) exist.

Justin Trottier did a very good job for the skeptic point of view. In particular, he made it very clear that he was NOT defending the proposition that gods do not exist. That's not what he means by atheism. He made it very clear that the burden of proof was on those making the extraordinary claim (god exists). He had to do this because rather than provide evidence for the existence of god(s), Cleevely kept trying to show that materialism.naturalism could not prove the nonexistence of gods.

I'm pretty sure that Cleevely didn't get it. I think he is committed to the idea that atheism means the denial of god(s) and he couldn't wrap his mind around the idea that he might be wrong.

The other point he (Cleevley) was trying to make was that science absolutely requires "something" in order to work. Since the universe began from "nothing" that means that it's beyond science. Again, this is an argument about the possible limitations of science but it says absolutely nothing at all about the case for the existence of god(s).

I think that most of the audience, even the Christians, realized that the priest was avoiding the question. As I said, Justin did an excellent job of steering the debate back to the main topic whenever possible. Near the end of the debate, Justin pointed out that Phillip Cleevely had not made much of a case and that the only evidence he had presented was not much more than philosophical babble. Justin didn't go on about this—just the right amount of harsh criticism—but it had to be said.

I'm pretty sure I wouldn't have been so kind.

Two other issues came up. Cleevely demanded that Justin explain where morality came from and where rational thought came from. Justin did a pretty good job but added that we don't have all the answers. He then assumed that Cleevely did have the answers but it turns out that Cleevely was not making the case for god based on the origin of morality or rationality. He said that those topics were too complicated—maybe they could be covered in another debate. The point of his questions was to show that science doesn't have all the answers. The implication is that because science doesn't have all the answers then god exists but Cleevely was clever enough (or stupid enough?) to avoid saying this.

Finally, Cleevely is an ordained priest and the moderator kept referring to him as "Father" whereas Justin was addressed as "Justin." There was a big difference between the respect that the moderator showed for Father Cleevely and for atheist Justin Trottier.

I imagine that it's impossible to avoid "Father" in a debate sponsored by Roman Catholics. His opponent should have been addressed as "Mr. Trottier."

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Is There a God? Find out tonight!

There are still a few tickets available. Email me ASAP.

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Why is a brain surgeon afraid of evolution?

Michael Egnor is a brain surgeon who doesn't like evolution. Egnor isn't a scientist so why does it matter so much to him?

Listen to this podcast where Casey Luskin interviews Michael Egnor: Dr. Michael Egnor on Debating Intelligent Design. You may want to turn off your irony meter.

Egnor is afraid of evolution for exactly the right reasons. It's because evolution (and science) threaten his worldview. Science tells us that we don't have free will—at least not the kind of free will that Christians demand. Science tells us that there's no such thing as moral absolutes that are dictated by god(s). Science is materialistic and it may be the only valid way of knowing.

No wonder he's scared. Michael Egnor is a Roman Catholic and he knows that evolution threatens his religion.

You'll probably enjoy hearing Egnor and Luskin talk about atheist blogs and about the high quality of science writing on Evolution News & Views. Casey Luskin (lawyer) and Michael Engor (physician) are responsible for some of that high quality science writing.

David Klinghoffer really likes the podcasts. Here's his review at: Listening to Neurosurgeon Michael Egnor on the Brain and Intelligent Design, Rubik's Cube and Jerry Coyne's Blog.

I've exchanged many emails with brain surgeon and ENV contributor Dr. Michael Egnor, but I had never actually heard his voice till now. It's a good voice, which is vital for a physician, mellow yet authoritative, with the correct pitch and timbre. Egnor's stellar academic and medical background aside, I've often thought that, if you had no other information about a healthcare provider, what you don't want is a doctor with the wrong kind of voice.

Now you can hear Egnor as I just did in this fascinating new series of podcasts in which he is interviewed by Casey Luskin. Their themes include evidence of intelligent design in the complexity of the brain, but no less so in the simplest creature, a bacterium. Dr. Egnor compares that design to the solution of a Rubik's Cube. It doesn't happen by chance.

Egnor also talks about the unusual window that Jerry Coyne provides into the mind of a materialist, which is why his name comes up here often. Coyne, unlike many Darwin apologists, doesn't self-censor. You don't have to wonder: What does he really think about, for example, personal responsibility. Because he tells you! Whatever else Coyne may be, he's no weasel. For that, Egnor expresses his gratitude and -- yes, appropriately.

I'm disappointed that Egnor said nothing about me even though he posts quite a few comments on Sandwalk. Guess I don't get much respect.

I wonder why David Klinghoffer didn't mention Casey Luskin's voice?

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Jason Rosenhouse agrees that evolution is a threat to religion

Jason Rosenhouse also read the accommodationist article by Phil Plait [The Creation of Debate] and he also sees the problem.

I argued that, contrary to what Phil Plait believes, evolution is a threat to all superstitious beliefs, including those of theistic evolution creatinists (see my post at: The real war is between rationalism and superstition).

Read Jason Rosenhouse's post at: It’s Not Just Fundamentalist Religion That Has A Problem With Evolution. Here's the important part ....

So, after all, that, let us return to Plait’s argument. He tells us that the problem is too many people perceiving evolution as a threat to their religious beliefs. Indeed, but why do they perceive it that way? Is it a failure of messaging on the part of scientists? Is it because Richard Dawkins or P. Z. Myers make snide remarks about religion? No, those are not the reasons.

It is because these people have noticed all the same problems the scholars of Darwin’s time were writing about. It is because evolution really does conflict with their religious beliefs, but not because of an overly idiosyncratic interpretation of one part of the Bible. It is because the version of evolution that so worried the religious scholars of Darwin’s time, that of a savage, non-teleological process that produced humanity only as an afterthought, is precisely the version that has triumphed among modern scientists. And it is because the objections raised to that version of evolution in the nineteenth century have not lost any of their force today.

So I think the issue is just a tad more complex than Plait suggests. It manifestly is not the case that only the most narrow of fundamentalists has a problem with evolution. Evolution challenges the Bible, refutes the argument from design, exacerbates the problem of evil, and strongly challenges any notion that humanity plays a central role in creation. These are not small points, and Plait needs to acknowledge them.

I hope Phil Plait is listening.

I hope Ken Miller, Francis Collins, and Simon Conway-Morris are listening. They are not on my side in this war.

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Does an understanding of evolution help scientists understand the secrets of biology?

You're probably wondering why I would ask a question like, "Does an understanding of evolution help scientists understand the secrets of biology?" It's not my question. It's a paraphrase of a question asked by someone who goes by the pseudonym "PaV" on Uncommon Descent. Here's the full context from her post: Does Evolutionary Theory Really Help Scientists?

For a number of years, many of us at UD have made the argument that evolutionary theory, in practice, is of almost no help whatsoever in getting at the secrets of biology. I’ve taken the position personally that it actually hurts, and that it is not a matter of indifference to the study of biology whether evolution is employed or not. ID is the way to go.

Now, besides the fact that she is an IDiot, you may be asking why anyone would write such a thing.

Here's the scoop. Someone was looking at unknown RNAs in zebra fish and discovered that one of them encoded a protein that hadn't previously been characterized. This sort of thing happens all the time in various species so why is PaV so excited?

Here's the answer ...

They’ve studied this embryonic stage for 20 years, and couldn’t figure out the decisive signals for initiation of the gastrula. They had to look to “non-coding” RNA, i.e., “junk DNA,” in order to solve their new found secret.

And why didn’t they study “junk DNA” before? Well, evolutionary theory posits that it is “junk” (their word, not ours), so why investigate.

See? Evolutionary theory actually impedes scientific progress. And you wonder why we call them ....

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The real war is between rationalism and superstition

Phil Plait of Bad Astronomy watched the debate between Bill Nye and Ken Ham. He decided that both of them are wrong because the debate was framed as a war between evolution and religion. Like a long list of accommodationists before him, Phil Plait thinks he has the answer in his post: The Creation of Debate.

I can’t stress this enough. The conflict over the teaching of evolution is based on the false assumption that evolution is antagonistic to religion. This is why, I think, evolution is so vehemently opposed by so many in the United States. The attacks on the specifics of evolution—the claims about irreducibility of the eye, for example, or other such incorrect statements—are a symptom, not a cause. I can talk about how we know the Universe is old until the Universe is substantially older and not convince someone whose heels are dug in. But if we can show them that the idea of evolution is not contrary to their faith, then we will make far, far more progress.

That’s not to say I’ll stop talking about the science itself. That still needs to be discussed! But simply saying science is right and faith is wrong will never, ever fix the problem.

And this won’t be easy. As long as this discussion is framed as “science versus religion” there will never be a resolution. A religious person who doesn’t necessarily think the Bible is literal, but who is a very faithful Christian, will more likely be sympathetic to the Ken Hams than the Bill Nyes, as long as science is cast as an atheistic dogma. For example, on the Catholic Online website, the argument is made that both Ham and Nye are wrong, and casts science as an atheistic venture.

That must change for progress to be made.

This is the classic accommodationist position. Problem is, it's been tried and it doesn't work in the United States. And the reason it doesn't work is that Americans aren't that stupid. They realize that these debates really are about science vs. religion. They know that evolution is, in fact, antagonistic to religion.

Jerry Coyne points this out rather forcibly in his response to Phil Plait. Read Coyne's article: Debate postmortem II: Phil Plait goes all accommodationist. I'll get back to Jerry Coyne in a minute but first let me quote Phill Plait's "solution."

And who should do this? The answer to me is clear: Religious people who understand the reality of science. They have a huge advantage over someone who is not a believer. Because atheism is so reviled in America, someone with faith will have a much more sympathetic soapbox from which to speak to those who are more rigid in their beliefs.

It's possible that "religious people who understand the reality of science" is a very small group and it's even more possible that they will be opposed to science and evolution precisely because they DO understand the reality of science. Plait is probably thinking about Ken Miller and Francis Collins but it's not clear to me that they truly understand what science is telling us. Science is telling us that there's no need for god(s) in order to understand the world around us. Evolution tells us that life has no purpose.

What Phil Plait is saying is that the best people to defend evolution are those who think that there really is a creator god but he/she/it mostly used evolution as a method of creation. In other words, we atheists should rely on theistic evolution creationists to convince other creationists to adopt a somewhat different view of creationism! That probably means we should keep quiet unless we are willing to make the case for one version of supernaturalism. Why would we do that?

That may be acceptable to some people but it misses the point of the conflict as far as many atheists are concerned. Jerry Coyne said it best in response to the accommodationist views of Micheal Ruse some years ago. Coyne's letter, which appeared in Playboy after Ruse's article was published, said ...

[Ruse] fails to grasp the real nature of the conflict. It's not just about evolution versus creationism. To scientists like Dawkins and Wilson, the real war is between rationalism and superstition. [my emphasis, LAM] Science is but one form of rationalism, while religion is the most common form of superstition. Creationism is just a symptom of what they see as the greater enemy: religion. While religion can exist without creationism, creationism cannot exist without religion.

This passage has been widely quoted and I wholeheartedly agree with Coyne's view.¹

For many of us the real war is between rationalism and superstition and the battle over evolution is just a minor skirmish in that war. What this means is that New Atheists are not inclined to recruit people who believe in superstition in order to fight a war against superstition.

That may be acceptable to people like Phil Plait because they're not interested in fighting a war against all forms of superstition, including religion. Instead, they seem content to promote some forms of superstition over others. The accommodationists should not expect all atheists to agree with them and they should acknowledge the fact that many of us think science and religion are incompatible.²

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1. There's some doubt about whether Coyne actually said this in his letter. I'm quoting a second-hand source: Dawkins in The God Delusion.

2. I'm not saying we are correct. I'm just saying that after all these years it's disappointing to see so many accommodationists who just don't get it.

Creationist scientists and bottoms of barrels

One of the interesting quirks of creationists is their intense desire to gain credibility by finding religious scientists who agree with them about god(s) and creation. We saw a good example in the Ken Ham vs Bill Nye debate where Ken Ham managed to find several people who are Young Earth Creationists but nevertheless made a contribution to science or technology. Some were physicians and some were engineers but some were actually scientists [see the debate at: Bill Nye Debates Ken Ham].

I'm reminded of a passage in The God Delusion (p. 100) where Richard Dawkins says ...

The efforts of apologists to find genuinely distinguished modern scientists who are religious have an air of desperation, generating the unmistakably hollow sound or bottoms of barrels being scraped.

Dawkins goes on to point out that efforts to find creationist Nobel Prize winners in Physics, Chemistry, or Physiology & Medicine have been largely unsuccessful.

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