Evoluutio on sekä fakta että teoria

I visited Finland for one day in August and now I can publish blog posts in Finnish!

Seriously, Timo Kauppila has translated my Evolution Is a Fact and a Theory into Finnish and put it up on his BioLogiikka web site [Evoluutio on sekä fakta että teoria].

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Science vs religion in the Princeton Guide to Evolution

The Princeton Guide to Evolution is a collection of 107 articles on various aspect of evolution. The editors felt they should address the obvious conflict between evolution/science and religion. There are at least five different approaches they could have taken.

1. An atheist perspective on the incompatibility of evolution/science and religion. Richard Dawkins or Jerry Coyne would be good choices.
2. An atheist perspective on the compatibility of science and religion (the accommodationist view). Michael Ruse or Nick Matzke are obvious choices.
3. A theist view of the incompatibility of evolution and religion. Phillip Johnson could have explained this view but so could a number of other creationists.
4. A theist explanation of the compatibility of evolution/science as long as they stick to their proper magisteria. Francis Collins, Ken Miller, and several other religious scientists could present their case.
5. The editors could have published four articles representing the main viewpoints or commissioned a single article that would have covered all the angles.

The big advantage of an atheist perspective is that it fairly represents the views of a majority of evolutionary biologists. Having a theist write the article would not be as fair. I think we can all agree that option #5 is by far the best choice.

Before reading any further, take a minute to decide what you would do if you were the editors of The Princeton Guide to Evolution.

Elliott Sober illustrates (inadvertently) the problem of definitions

One of the problems in most debates and discussions in the problem of definitions. It's common for two opponents to end up talking past one another because they don't agree on what they are arguing about. That's why an important component of critical thinking is to define your terms so that everyone knows what you are defending (or attacking).

But there's more. If you are going to be a good critical thinker, then you have to be aware of other points of view. If there are other, equally valid, definitions out there then you MUST acknowledge them and incorporate them into your argument. You can't, for example, just make up your own definition of words like "noncoding," "junk," or "function," and declare that you are right. Since you know that there are other definitions out there, you are obliged to show why YOUR definition is the only correct one. That's a crucial part of the debate.

If you don't even know that there are other valid definitions then you are not an expert and you should not be pretending to be an authority on the subject. This is why I object to people who argue against the Central Dogma of Molecular Biology without understanding what Francis Crick actually said.

Let's look at a video of Elliott Sober lecturing on "Some Questions for Atheists to Think About." He begins by asking the members of his audience whether they are atheists or agnostics. Apparently, most members of the audience are atheists and ony a few are agnostics.

Next, he defines his terms ...

Theism = God exists
Atheism = God does not exist
Agnosticism = We don't know whether God exists

The lecture is about something called "evidentialism." Elliott Sober claims that the following proposition is true ...

For any proposition, you should believe it only if you have evidence that it is true and you should disbelieve it only if you have evidence that it is false.

He then goes on to show that we can never have evidence that God does not exist. Therefore, "If 'God exists' is untestable, you ought not to be an atheist. You should be an agnostic."

He suggests that all the atheists in the audience should become agnostics because of evidentialism. If I had been in the audience, I would have pointed out that MY definition of atheist is that an atheist is someone who doesn't believe in god(s). My definition is such a common definition that it's part of the Wikipedia article on Atheism. Since I do not need "evidence" to not believe in something, I'll remain an atheist, thank-you very much. My position is perfectly consistent with the proposition about evidentialism.

Here's the problem. Elliott Sober is a prominent philosopher. Doesn't he realize that his argument relies entirely on his definition of "atheism"? Doesn't he realize that his argument is completely useless if an atheist is simply someone who doesn't buy into the God delusion? This sort of thing makes me livid and it makes me wonder whether there's something seriously wrong with modern philosophy.¹

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1. I am not suggesting that Sober's definition is wrong. He should not be ignoring the fact that many members of his audience don't agree with his definition and that's why they are atheists.

Arlin Stoltzfus explains evolutionary theory

A few days ago, I asked the following questions, Is the "Modern Synthesis" effectively dead?, and What do they mean when they say they want to extend the Modern Synthesis?. The point I was trying to make was that there are many different views on evolutionary theory and it's often difficult to figure out which version of evolutionary theory someone is defending.

For example, which version of evolutionary theory is compatible with the "selfish gene" as a metaphor for evolution? Or for adaptation? Which version of the "Modern Synthesis" is being attacked in the book edited by Massimo Pigliucci and Gerd Müller? Is it the version defended by Ernst Mayr? Does it incorporate Neutral Theory and random genetic drift?

Exam questions for 2nd year students in a critical thinking course

Here are the questions on yesterday's exam for students in my course. Students will be graded on their explanations and not so much on the actual answer they give. The idea is to reward critical thinking and that includes the ability to see both sides of an issue and recognize problems with whatever side you choose to defend.

1. Assuming that the technology is safe and effective, should we, or should we not, have laws forbidding the cloning of humans?
   
   
2. What is the best definition of a "gene"? Explain why you choose that definition and give examples of possible "genes" that don’t fit your definition.
   
   
3. Elliott Sober is a highly respected philosopher. He explains that theistic evolution is a reasonable hypothesis because God could easily cause mutations to occur in a way that scientists would not be able to detect. In other words, a specific, directed, mutation would be indistinguishable from a random mutation. Thus, it would appear that evolution was an entirely naturalistic process while, in fact, its direction was being guided by God. Do you think this is a reasonable argument in support of theistic evolution? Why or why not?
   
   
4. In his book, The Myth of Junk DNA, Jonathan Wells writes.
   

   According to intelligent design (ID), it is possible to infer from evidence in nature that some features of the world, and of living things, are better explained by an intelligent cause than by unguided natural processes.

   What sorts of positive arguments do ID proponents use to support this inference from evidence in nature? Are they effective?

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Today is exam day and "You shall not pass"

Today is the day of the final exam in my course on critical thinking and scientific misconceptions.

I thought my students would get a kick out of this photo.

I'm certain that all regular Sandwalk readers know what I'm talking about but just in case there's any new readers who don't get it, here's a short clip from the movie.¹

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1. Note to IDiots and other creationists ... Gandalf is a fictional character, he doesn't exist. There are many fictional characters who appear to be powerful and menacing but that's only in stories and myths.

Monday's Molecule #227

Last week's molecule was the drug pantoprazole, a proton pump inhibitor used to treat excess stomach acid or acid reflux [Monday's Molecule #226 ]. The winner is Bill Gunn.

This week's molecule (left) is related to one from last April. That molecule, is one of the essential molecules in the human diet and today's molecule is the reason why. This is one of those molecules that everyone should recognize because it's a key metabolic precursor in a large number of species. This is one of those times when all you have to do is supply the common name (Merry Christmas!) and NOT the IUPAC systematic name that correctly identifies the exact molecule shown in the image. However, if anyone wants to supply the systemiac name, feel free to do so.

Email your answer to me at: Monday's Molecule #227. 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.)

What do they mean when they say they want to extend the Modern Synthesis?

As far as I'm concerned, the "Modern Synthesis" has been replaced by modern evolutionary theory that incorporates Nearly-Neutral Theory and random genetic drift as an important mechanism of evolution [see Is the "Modern Synthesis" effectively dead? ]. This extension, and replacement, of the 1940s version of evolutionary theory took place in mainly in the 1970s.

If I'm correct, then why all the fuss in the 21st century about extending the Modern Synthesis?

I think there are two things going on here. First, there are a bunch of biologists who want to incorporate their favorite fad into modern evolutionary theory. They think that their ideas are so revolutionary that this requires an extensive revision of evolutionary theory. Second, those biologists seem to have been asleep during the 1970s when the Modern Synthesis died so they are fighting a strawman.

Is the "Modern Synthesis" effectively dead?

The "Modern Synthesis," or modern evolutionary synthesis, refers to a framework of evolutionary theory developed and promoted by prominent biologists in the 1940s. The term comes from the subtitle of a 1942 book by Julian Huxley. The central theme was the integration of "classic" evolution with population genetics.

Although the original version was fairly broad, the later versions of the "Modern Synthesis" were much less so. The so-called "hardening" of the Modern Synthesis has been documented by many historians; notably, Stephen Jay Gould. By the time of the Darwin Centennial (1959) most biologists thought of the "Modern Synthesis" as a form of Darwinism + population genetics where natural selection was pretty much the only game in town.

Hemant Mehta buys what Chris Mooney is selling

Chris Mooney thinks that humans have certain innate tendencies that predispose them to believe in god(s) and reject evolution. That's why there's such a strong correlation between a fundamentalist religious belief and rejection of science, according to Mooney.

These innate tendencies are part of our evolutionary history thus providing an evolutionary excuse explanation of religion. It's interesting that these behaviors seem to tilt in favor of the Judeo-Christian gods and not Buddhist or Taoist philosophy. It's also quite interesting that million and millions of non-believers don't seem to have had any great difficulty "overcoming" their genetic predispositions.

You don't suppose that it could be religious brain-washing education that makes people think teleologically or adopt essentialist perspectives rather than the other way around? And what about dualism? Is that an innate belief or does religion teach you to think you have a soul? Nah, that would be too simple [Why don't people accept evolution?].

Here's Hemant Mehta explaining why people Americans have a natural inclination to believe in god(s) and not in evolution [7 Reasons Why People Believe in God and Don’t Accept Evolution].

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Time magazine's person of the year is Pope what's-his-name! WTF?

It's hard to think of anyone who's more irrelevant to my life or the life of my friends and neighbors. Time has also become irrelevant. PZ Myers asks: Seriously, Time magazine?. Hemant Mehta says, Pope Francis Named Time’s Person of the Year, Despite Not Changing the Direction of the Church. What were the editors of Time thinking? You have to wonder whether this isn't some kind of sick joke.

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Razib Khan doesn't like Gould and doesn't like new-fangled ideas like "neutralism" and "random genetic drift"

The article by David Dobbs [Die, selfish gene, die] has stirred up a lot of biologists. Some of them (Coyne, Dawkins) pointed out why David Dobbs is wrong about this particular attack on Darwinian ordodoxy while others (PZ Myers) have defended Dobbs.

Razib Khan has weighed in [Evolutionary orthodoxy may be boring, but it is probably true]. I strongly disagree with his post but it's important to be clear about the disagreement. If "evolution orthodoxy" means evolution by natural selection then, yes, it is definitely true. That's not being disputed. The question isn't whether evolution orthodoxy is correct, it's whether it is sufficient.

I'm also not defending the specifics of Dobbs' article. Many of the most recent attempts to extend evolutionary theory are misguided and Dobbs happens to focus on one of these misguided attempts. However, the main point of Dobbs' article was that the "selfish gene" metaphor is an inappropriate metaphor for evolution and I agree strongly with this conclusion even though Dobbs' argument was faulty.

Monday's Molecule #226

Last week's molecule was sucrose 6-phosphate or α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside 6-phosphate [Monday's Molecule #225 ]. The winner is Jean-Marc Neuhaus (again). He appears to be the only Sandwalk reader who has a copy of my book!

Today's molecule (below) looks a bit strange. It should be obvious that this is not a "natural" molecule. What is it and what does it do? You don't need to give me a long systematic name. The common name will do quite nicely.

Email your answer to me at: Monday's Molecule #226. 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.)

Steven Pinker defends "neo-Darwinism," whatever that is

Jerry Coyne posted a couple of tweets (see below) from Steven Pinker (photo) at Dawkins responds to Dobbs.

We shouldn't be surprised at the first one since Pinker is an evolutionary psychologist with a strong tendency to adaptationism. I don't know exactly what he means by "neo-Darwinism" (does he?) but I strongly suspect that it's very much like Darwinism. I'd love to know whether he thinks Neutral Theory and random genetic drift have been successful challenges to neo-Darwinism. If not, then it must mean that neo-Darwinism has incorporated those views. In that case, neo-Darwinism must have begun in the 1970s and somebody picked a very bad name for this view of evolutionary theory.

I think it's more likely that Pinker is just not thinking about Neutral Theory and random genetic drift when he says that challenges to neo-Darwinism have all failed to hold water.

The second tweet means that molecular biologists never knew about tRNA genes or ribosomal RNA genes or the genes for other RNAs that have won Nobel Prizes. I find this very surprising. It's true that some biochemists and molecular biologists are a bit behind in their field but I don't think it's fair to say that "molecular biologists" (i.e. the knowledgeable experts in the field) re-defined the word "gene" in that way.

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Valley girl talk

Last summer we took a short drive through the San Fernando Valley on our way from Thousand Oaks to Griffith Park. I happened to mention "valley talk" ("uptalk") but none of us could do a good job of talking like a teenage girl from the valley.

That's a shame because now it looks like Valley girl speak is, like, on the rise! I believe it. Not only have I heard girls speak like this on the university campus here in Toronto but I've even heard this language in Ottawa and that's about as far away from California as you can get.

I hope my granddaughter and grandson don't grow up speaking like this. They live in Los Angeles.


Moon Unit Zappa Valley Girl by mrjyn

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