Science still doesn't get it

The latest issue of Science contains an article by Yudhijit Bhattacharjee about Dan Graur and his critique of the ENCODE publicity disaster of September 2012. The focus of the article is on whether Dan's tone is appropriate when discussing science.

Let me remind you what Science published back on September 7, 2012. Elizabeth Pennisi announced that ENCODE had written the eulogy for junk DNA. She quoted one of the leading researchers ...

What do Intelligent Design Creationists really think about macroevolution?

Intelligent Design Creationism is a huge tent that shelters all sorts of creationists ranging from Young Earth Creationists to those who could be called Theistic Evolution Creationists.¹ Many of them accept common descent so they clearly don't have much of a problem with most of macroevolution.

On the other hand, there are a lot of Intelligent Design Creationists who don't accept macroevolution. It seems to me that this could only be because they are Young Earth Creationists or they believe in some other strange idea where god(s) make every species.

It's hard to figure out what they mean.

Let's look at a recent post by philosopher Vincent Torley. He didn't like my posts about macroevolution [What is "macroevolution"? ] [A chemist who doesn't understand evolution] so he decided to set me straight: Does Professor Larry Moran (or anyone else) understand macroevolution?.

Cosmos presents evolution

The second episode of the new Cosmos series is Some of the Things That Molecules Do.

It's about evolution and it's not bad. I have four comments.

A missed opportunity. Natural selection is important and Neil deGrasse Tyson did a pretty good job of explaining it. It wouldn't have taken a big effort to mention that there's more to evolution than natural selection. He could, for example, have pointed out that some breeds of dogs are prone to certain genetic diseases or health problems because some bad mutations were accidentally fixed alone with the good ones. He could have pointed out that our eyes have a blind spot.

The Theory of Evolution is not a fact. Neil deGrasse Tyson said that the theory of evolution is a fact. This is not correct. Evolution is a fact. Evolutionary theory attempts to explain how evolution occurs. Some of the explanations, like natural selection, are facts but many aspects of modern evolutionary theory are still hotly debated in the scientific community.

We don't understand the origin of life. The episode closed with deGrasse Tyson saying the we don't understand how life began and there's nothing wrong with admitting that we don't know something. Excellent!

There are better ways of drawing DNA. I don't like the way DNA is pictured in the first two episodes, especially in the opening sequence. It looks like the bases grow out of the backbone and fuse to form base pairs. They could have drawn a more accurate representation without losing any visual appeal.

I give the episode a B⁺.

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Monday's Molecule #233

Last week's molecules [Monday's Molecule #232] were all-trans and 13-cis retinal. Retinal is the active protein donor/acceptor in bacteriorhodopsin. The all-trans form is shifted to the 13-cis form when a photon of light is absorbed. The retinal molecules are arranged within the membrane-bound bacteriorhodpsin in a way that binding and release of a proton results in transport from the cytoplasm to the exterior. The creation of a proton gradient drives ATP synthesis.

The winner is Philip Johnson from Switzerland.

This week's molecule (left) is actually a collection of molecules. Name all five molecules and tell me what they have in common from a biochemical perspective. Common names will do.

Email your answer to me at: Monday's Molecule #233. 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.)

Reading Books

Yesterday we watched two episodes of House of Cards and two of our favorite TV shows; Amazing Race and The Good Wife. We also watched a show about working on a Tudor farm and I watched the second episode of Cosmos.

According to Veronica Abbas, I wasted valuable time when I could have been reading [Recommended Reading]. She links to an article by Erin Kelley who says, Reading Books Doesn't Just Make You Literate: It Reduces Stress, Promotes Good Health, and Makes You More Empathetic. I haven't read a book in over four months and I haven't read a novel in years.

I'm doomed to be illiterate, stressed, in poor health, and the opposite of empathetic.¹ It also explains why I don't volunteer to work for a non-profit organization.

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1. I'm pretty sure Veronica would agree with "illiterate."

On teaching creationism in American public universities

I think that universities are places where diversity of opinion should be encouraged and where fringe ideas should be protected. I'm very much opposed to letting outside interests (i.e. politicians and lawyers) decide what should and should not be taught on a university campus.

Clearly there are limits but those should be decided by faculty who understand the concept of academic freedom. It's not a good idea to offer astronomy courses on an Earth-centered solar system or geology courses based on the idea that the Earth is only 6000 years old. Those ideas are just too far out on the fringe. You're unlikely to find any university professors who want to teach such courses.

However, there are lots of other controversies that aren't so easily dismissed. If some of the more enlightened Intelligent Design Creationists want to teach a science course at my university, I would not try to prevent them. Just as I didn't try to prevent Michael Behe and Bill Dembski from speaking on my campus.

A chemist who doesn't understand evolution

James Tour is an organic chemist. He is a Professor of Chemistry and Professor, Professor of Mechanical Engineering & Materials Science, and Professor of Computer Science at Rice University (Houston, United States). James Tour is attracting a lot of attention on the Intelligent Design Creationist websites because he is sympathetic to their main claim; namely, that evolution is wrong [see A world-famous chemist tells the truth: there’s no scientist alive today who understands macroevolution].

Tour is one of the few genuine scientists who signed the Discovery Institute’s "A Scientific Dissent from Darwinism" (2001) that stated, "We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged." (There are very,very, few biologists who signed.)

What exactly, does Jame Tour mean? He wrote an article on his website that explains his position: Layman’s Reflections on Evolution and Creation. An Insider’s View of the Academy. I think it's interesting to discuss what he said.

He begins with ...

Philip Ball writes about molecular mechanisms of evolution

It's been almost a year since I commented on an Nature article by Philip Ball [see DNA: Nature Celebrates Ignorance]. Here's part of what I wrote back then ...

The main premise of the article is revealed in the short blurb under the title: "On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball."

What nonsense! We understand a great deal about how evolution works at the molecular level.

The worst thing about the Nature article was the misuse of the Central Dogma of Molecular Biology. The second worst thing was the "revelation" that genes are regulated by regulatory sequences as if that was a new discovery. (He mentions the ENCODE results.)

How does molecular biology overthrow the Modern Synthesis?

I think the hardened version of the Modern Synthesis is inadequate to describe 21st century evolutionary biology. I think that it didn't adequately recognize Neutral Theory and random genetic drift and it didn't place enough emphasis on macroevolution and the possibility of hierarchical modes of evolution.

There are a whole host of scientists who want to overthrow the Modern Synthesis for a variety of other (stupid) reasons. Most of them have no idea that the Modern Synthesis has (or should have) been replaced 40 years ago.

Here's another example from last week's issue Science (March 7, 2014). Susan M. Rosenberg and Christine Queitsch have an article entitled "Combating Evolution
to Fight Disease" (Rosenberg and Queitsch, 2014). They begin with ....

Michael Egnor is an expert on cluelessness

The war between science and religion is fought on many fronts. One of the most remarkable campaigns is the attempt by religious zealots to discredit evolution (and science). We see this played out on creationist websites ranging from the most absurd Young Earth Creationist sites to the somewhat more subtle websites of the Intelligent Design Creationists.¹

I can understand why believers want to defend their beliefs—we all do that. The part I don't get is the incredible stupidity of the main defenders of Intelligent Design Creationism and Young Earth Creationism. Not all of them, of course, but enough to make me slap my head.

Let's take Michael Egnor as an example. He is perfectly entitled to defend his Roman Catholic beliefs and to try and poke holes in evolution. But why does he have to use such stupid arguments? Why is such a person promoted on the main Intelligent Design Creationist website, Evolution News & Views (sic). Is he really the best they've got?

Let's look at his latest post: Clueless in Toronto. He begins with ....

The "selfish gene" is not a good metaphor to describe evolution

Last December David Dobbs wrote an article entitled "Die, selfish gene die!" in which he promoted some really stupid ideas about evolution. Jerry Coyne wasted little time in showing why Dobbs was way off the mark.

Unfortunately, Dobbs didn't make the best case against the concept of the selfish gene and Jerry Coyne didn't recognize that there was a real problem.

Now the issue has resurfaced because Aeon has announced another dead horse that needs beating [Dead or Alive? Is it time to kill off the idea of the ‘Selfish Gene’? We asked four experts to respond to our most controversial essay].

Once again Jerry Coyne is up to the challenge, taking on four "experts" without breaking a sweat [The “selfish gene” redux: Aeon magazine collects opinion on the metaphor].

And, once again, everyone misses the real point.

Here's what Jerry says in his latest post.

I won’t reprise my criticisms, except to say that the metaphor of genes acting as if they are "selfish" when subject to natural selection remains perfectly good, whether or not those genes (or any bit of DNA) are part of the genome that makes proteins, regulates other genes, or comprises any bit of DNA that has the ability to get itself replicated more often than its competitors.

This is correct as far as it goes. The "selfish gene" is a reasonable metaphor if you want to think about natural selection and adaptation. It's quite reasonable to metaphorically describe genes as "selfish" in such cases.

However, I think that "selfish gene" is often used as a metaphor for all of evolution and not just for natural selection. I think that most people who read Dawkins' book take it to be about EVOLUTION and not just natural selection. They understand that Dawkins is promoting a gene-centric view of evolution—and that's okay—but they come away from reading the book by thinking that all genes are selfish.

As most of you know, I prefer to emphasize Evolution by Accident. That's not to say that natural selection (selfish genes) isn't important, it is. What I believe is that there is a lot more to evolution than just selfish genes and we should not use the selfish genes metaphor as a stand-in for all of evolution.

Once you grasp that idea, it becomes much less useful to use the term "selfish gene" as a metaphor for anything, even natural selection and adaptation. That's why I think we should stop using the term "selfish gene."

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What is "macroevolution"?

Denyse O'Leary on Uncommon Descent wonders Is “macroevolution” even a meaningful term? It’s time to ask.

Here's the problem as creationists see it ...

The evolution that Darwin’s theory accounts for (natural selection acting on random mutation) is, in the real world, small changes that don’t add up to much over the long term.

That is why the term "macroevolution" had to be invented. It was a leap of faith to assume that Darwinian "microevolution" would become "macroevolution" instead of just being washed out by other types of change (what usually really happens).

But gradually scientists are becoming less afraid to talk about this: Macroevolution apparently happens, but not by Darwinian means.

G’bye, Darwin. We packed the crumpets for ya.

Will it soon be: So long, Darwin-in-the-schools pressure groups? Gee, how they’ll be missed in the legislatures and courts.

No, wait, we’ll all be too busy figuring out what really happens in the history of life. It’s a fascinating story and now – for once – we might get to read it without all the interruptions.

I can't tell you how frustrating it is to see this kind of crap over, and over, and over. We have been trying to teach evolutionary biology to the IDiots for decades but they seem to be totally incapable of listening.

True, there was a time when biologists thought that Darwinian natural selection was all there is in evolution. They even thought that all of evolution, from changes within populations to the evolution of new phyla, could be explained solely by natural selection acting on allele frequencies within populations (Darwinism).

Most evolutionary biologists have moved on in the past half century and they now realize that macroevolution is a separate field that combines genetics, population genetics, geology, ecology and a host of other fields in order to explain the history of life. So, Denyse, it's true that macroevolution happens by means other than Darwinism even though natural selection is an important component of macroevolutionary explanations.

The only news here is that it takes IDiots so long to catch up with evolutionary biologists.

Back in the days of talk.origins, this topic (macroevolution) came up so frequently that I wrote a little essay to explain it in a way that even the most profound IDiot could understand. The latest version is from 2006: Macroevolution.

Wouldn't it be nice if the creationists could make an attempt to understand modern evolutionary theory instead of just repeating the same old tired arguments that they used 50 years ago?

The suggestion that macroevolution should be divorced from microevolution provides Creationists only with a debating point. It allows Creationists to say that there are some evolutonary theorists who distinguish the mechanisms studied in classical population genetics from those they take to be involved in large-scale evolutionary change ... But this is not to suppose that the distinction drawn by heterodox evolutionists is that favored by the Creationists.
                                                               Philip Kitcher (1982) p.150

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Everything you thought you knew about sex is probably wrong

The evolution of sexual reproduction is one of the great mysteries of biology. I've been teaching this to undergraduates for several decades but it seems that most undergraduates don't get the message. Most of them think that sex has been explained and the answer is that sexual reproduction generates diversity.

I usually give them some reviews to read and, invariably, the experts who write the reviews will say that sex is a great unsolved mystery. If the experts think that this is a mystery then why do so many people think they have the answer?

Here's what Douglas Futuyma says in the 2nd edition of Evolution (p. 340).

Prayer at Mississauga City Council

I am reliably informed that meetings of the Mississauga City Council¹ still begin with a prayer. I'm not sure why city councilors feel the need for extra divine guidance since Mayor Hazel McCallion² is already present in the room.

Like most places in Canada, Mississauga is a diverse community with a substantial number of nonbelievers and a substantial number of non-Christians. Prayer has no place in a secular society and beginning a City Council meeting with prayer sends out all the wrong messages. Imagine that you are a nonbeliever waiting to petition City Council over some grievance and you have to watch your council member praying before you can speak.

What did Joe Felsenstein say about sex?

Today we talked about the evolution of sex. The take-home message is that sex is one of the most difficult problems in biology. We really don't know why sex evolved and why it's so important in eukaryotes.

The evolution of recombination is part of the discussion. It's not necessarily the same as the evolution of sex but many of the explanations for the evolutionary origin of sex invoke homologous recombination.

When I asked my students to explain the evolution of sex they mostly came up with arguments about why it is advantageous to generate genetic diversity in a population. Some of this diversity requires recombination to create new combinations of alleles on the same chromosome. The problem with this argument is that for every new combination produced, an old one will be restored. As John Maynard-Smith pointed out in 1968, when genes/alleles are in linkage equilibrium then recombination does not result in a change in allele frequencies (i.e. evolution).

This led Joe Felsenstein to write the following in 1988.

It is worth noting that Maynard Smith's argument invalidates the earliest genetic argument for the evolution of recombination, that advanced by East (1918). That argument is also the one commonly found in textbooks, which tend to be a bit out of date (in this case, by over 50 years). East argued that recombination creates new genotypes. So it does. An AB/ab parent will have among its gametes not only the two types that formed it, AB and ab, but also Ab and aB if there is recombination between the two loci. But if the population is in linkage equilibrium, then somewhere else an Ab/aB parent will be undergoing recombination, which will remove Ab and aB gametes and replace them by AB and ab. These two processes will exactly cancel each other if the two types of double heterozygote, coupling (AB/ab) and repulsion (Ab/aB) are equally frequent. This will happen precisely when the population is in linkage equilibrium. In that case no new genotypes arise by recombination.

...

We have that anomalous situation that a detailed population genetic analysis analysis reveals not only that the standard explanation for the evolution of recombination will not work, but also that there is a good evolutionary reason for believing that modifiers will be selected to eliminate recombination.

Is it true that what students are being taught is wrong? What did Joe Felsenstein really mean?

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Felsenstein, J. (1988) "Sex and the evolution of recombination." in The Evolution of Sex: An Examination of Current Ideas. R.E. Michod and B.R. Levin eds. 74-86. [PDF]