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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Have you ever seen the Grand Canyon? Did it make you believe in god?

Last year we took a helicopter ride to the Grand Canyon [The Magic Canyon Ride ]. None of us converted to Christianity or any other religion.

We may be the exception. According to Time magazine, "It’s hard to be an atheist when you’re looking at the Grand Canyon."

See what Friendly Atheist has to say about this: Time Magazine Says ‘There Are No Atheists at the Grand Canyon,’ Claims that ‘Awe Equals Religion’.

My son and daughter-in-law took a mule ride down into the Grand Canyon. I don't think they were converted either.

Are there any former atheists out there who were converted by the Grand Canyon? Which god(s) did you choose?

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Die, selfish gene, die!

"Die, selfish gene, die!" is the provocative title of an article by science writer David Dobbs [Die, selfish gene die!].

Dobbs begins with ....

The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong.

The article attracted the attention of Jerry Coyne who effectively dismantles the strange ideas promoted by Dobbs. Read all about it at: David Dobbs mucks up evolution, part I and David Dobbs mucks up evolution, part II.

As it turns out, this is just another example of a science writer who has been mesmerized by the latest effort to overthrow modern evolutionary theory by some scientist promoting their own work. In this case it's Mary Jane West-Eberhard.

But there's a more serious issue here and I'm not sure that Jerry Coyne recognizes it. The selfish gene metaphor can be interpreted in several different ways. Here's how Richard Dawkins describes it in the preface to the 1989 edition of The Selfish Gene.

The selfish gene theory is Darwin's theory, expressed in a way that Darwin did not choose but whose aptness, I should like to think, he would instantly have recognized and delighted in. It is in fact a logical outgrowth of orthodox neo-Darwinism, but expressed as a novel image. Rather than focus on the individual organism, it takes a gene's-eye view of nature.

Lot's of people misunderstand the selfish gene metaphor. They think it means that organisms behave selfishly but that's not what Dawkins meant at all.

Jerry Coyne explains this in his book Why Evolution Is True (p. 226) ....

As Dawkins shows clearly, the "selfish" gene is a metaphor for how natural selection works. Genes act as if they're selfish molecules: those that produce better adaptations act as if they're elbowing out other genes in the battle for future existence. And, to be sure, selfish genes can produce selfish behaviors. But there is also a huge scientific literature on how evolution can favor genes that lead to cooperation, altruism, and even morality.

There are two main criticisms of the selfish gene metaphor and both of them are quite valid. It's the reason why Dawkin's view hasn't caught on the the evolutionary biology textbooks. It usually merits nothing more than a footnote.

The most damning criticism comes from evolutionary biologists who point out that the primary unit of selection is the individual and not the gene. Stephen Jay Gould and Richard Lewontin are prominent opponents of what they see as an unnecessary reductionism in Dawkins' writing. Clearly, hierarchical theory (Gould) is inconsistent with the selfish gene metaphor because evolution can also operate at the level of groups and species (according to Gould and others). There are plenty of other evolutionary biologists who object to selfish genes for these reasons.

The second objection comes from the focus on natural selection and "Darwinism" (or neo-Darwinism). Many evolutionary biologists have a pluralistic view of modern evolutionary theory. That view includes random genetic drift where the appropriate metaphor might be "lucky gene" or "accidental gene." The problem with the Dawkins' metaphor, according to these critiques, is not that "selfish genes" don't exist, it's that the metaphor is not appropriate for evolution in general.

While I admire Jerry's take-down of Dobbs, I'm not sure that he (Jerry Coyne) fully appreciates these other criticisms of the selfish gene. Here's what Coyne wrote ...

Let me add one thing, though. I’m constantly puzzled these days by how often people argue that the neo-Darwinian synthesis is wrong, and that we need a new paradigm. Genetic assimilation, epigenetics, horizontal gene transfer—all of these buzzwords are evoked as reasons to jettison our “conventional” view of evolution. But always, when you look at the data, the evidence that these phenomena will overturn neo-Darwinism is nonexistent.

I’ve already written a lot on the epigenetics hype, and have shown that there’s no evidence that a single adaptation in nature involves the fixation in the DNA of an epigenetic alteration of the genome that isn’t initially inherited. Yet people keep banging on about epigenetics.

I’m not sure why the hype continues, but perhaps it has to do with the fact that the main paradigm of evolution—the neo-Darwinian synthesis—is largely consolidated, and is correct. Sure, there are surprises to come, and interesting new phenomena, but there’s no “quantum mechanics” of evolution on the horizon. Some theories don’t need to be overthrown because they’re generally right. Perhaps people don’t like working in a field where there’s no new “paradigm” to forge, and Kuhn has ruined us all!

The "neo-Darwinism is dead" trend may have to do with ambition, or perhaps with boredom. I don’t know. What I do know is that the many recent challenges to neo-Darwinism have all failed to hold water, but people keep pouring liquid into that sieve.

The problem here is that Jerry doesn't really say what he means by "neo-Darwinism." Most of his writing suggests that he's talking about natural selection, albeit updated by a knowledge of genetics. He does mention, from time to time, random genetic drift and other aspects of modern evolutionary theory but I'm not sure if he appreciates the fact that some legitimate evolutionary biologists really do think that neo-Darwinism is dead.

Here's the Wikipedia description of neo-Darwinism. It illustrates the problem.

Neo-Darwinism is the 'modern synthesis' of Darwinian evolution through natural selection with Mendelian genetics, the latter being a set of primary tenets specifying that evolution involves the transmission of characteristics from parent to child through the mechanism of genetic transfer, rather than the 'blending process' of pre-Mendelian evolutionary science. Neo-Darwinism can also designate Darwin's ideas of natural selection separated from his hypothesis of Pangenesis as a Lamarckian source of variation involving blending inheritance.

I think we should refer to modern evolutionary theory as "modern evolutionary theory" in order to make sure we're not talking about "Darwinism," "neo-Darwinism," or the hardened version of the "Modern Synthesis." Modern evolutionary theory includes an important role for random genetic drift, Neutral Theory, and population genetics.

We could clarify a lot of discussion if we stopped talking about extending "Darwinism" or extending the Modern Synthesis or proclaiming once again that the selfish gene has died. In fact, the selfish gene has died, it died almost thirty years ago but most people don't know that. RIP.

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Do you understand this Nature paper on transcription factor binding in different mouse strains?

I've published a few papers on the regulation of transcription of a mouse gene and students in my lab have done the standard promoter-bashing experiment to define transcription factor binding sites. I did ny Ph.D. in a lab that specialized in DNA binding proteins. I've kept up with the basic ideas in eukaryotic gene expression in order to teach undergraduate courses on that topic and in order to write appropriate information in my textbook.

I've been interested in genome organization for several decades and I've been following the literature on pervasive transcription and transcription factor binding in whole genome studies. I'm reasonably familiar with the techniques although I've never done them myself.

I'm not bragging; I'm just saying that I know a little bit about this stuff so when I saw this paper in one of the latest issues of Nature I decided to look more carefully.

Heinz, S., Romanoski, C., Benner, C., Allison, K., Kaikkonen, M., Orozco, L. and Glass, C. (2013) Effect of natural genetic variation on enhancer selection and function. Nature 503:487-492. [doi: 10.1038/nature12615]

Jason Rosenhouse defends Chris Mooney

Jason Rosenhouse read Chris Mooney's article on 7 Reasons Why It's Easier for Humans to Believe in God Than Evolution and liked it. Mooney was arguing that it's easier to believe in god(s) than in evolution because our evolutionary history selected for traits that predisposed us to think more like IDiots than like scientists.

I disagreed [Why don't people accept evolution? ]. Here's what I wrote last week ....