Another day, another creationist

My conversation with Perry Marshall about “evolution 2.0” is now online on the radio show Unbelievable.

Marshall is sales and marketing guy who has written a book titled Evolution 2.0: Breaking the Deadlock Between Darwin and Design, in which he claims to have worked out a reconciliation between science and religion based on arguments he had with his missionary/theologian brother, that hints at the quality of the science you’ll find in it. He has a superficial view of a few biological processes, like DNA error repair and transposition, and has shoehorned them into his religious belief that these are the tools used by some kind of engineering force that makes them purposeful.

He has a challenge with a $100,000 prize. All you have to do is show an example of Information that doesn’t come from a mind. Basically he’s making the clueless argument that there are no processes in genetics that produce novel information. I think Jeffrey Shallit ought to step up and claim it. Actually, he might have to fight through a mob of information theorists to get his money (if it exists, and if the judging wasn’t rigged).


Over on Twitter, I was startled by the assertion that many scientists convert from evolution to creationism, convinced by the evidence.

What was startling about it was that I’m getting used to mainly hearing from atheists calling me a mangina or such on that medium, so it was a break from the usual. On a lark I took a look at the video.

It’s Jerry Bergman. I’ve debated that loon.

How anyone can be convinced by that babbling incompetent is a mystery — I guess he just tells them what they want to hear.

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Smug and stupid

Orac once again takes down Vox Day. Day read a study and misinterpreted it, which isn’t too surprising — Day is not particularly bright. In this case, the study was looking for correlations with Personal Belief Exemptions (PBEs). That is, they were trying to figure out what kind of traits underlie anti-vaccination attitudes. What wasn’t surprising is that they found a lot of well-off white people who oppose vaccination.

That played right into Vox Day’s biases. He opposes vaccination, so smart people oppose vaccination; he’s white and well-off, which to him is synonymous with being intelligent and right, so it turns into a regular orgy of confirmation bias.

The news that anti-vaxxers are whiter, wealthier, and better-educated than those who place blind faith in vaccines won’t surprise anyone who has actually engaged a vaccine enthusiast on the subject. None of them know anything about history, few of them know anything about science, and all of them are prone to simply repeating the usual vaccine scare rhetoric

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Dinosaur 13


Last night, I watched an excellent documentary, Dinosaur 13, so I’m going to recommend it to you all — it’s available on Amazon streaming video and Netlix. It’s the story of the fossil T. rex, Sue, and it’s enthralling and depressing.

The fun part is the beginning, when some commercial fossil hunters discover tyrannosaur bones eroding out of a hillside in South Dakota. I had some mixed feelings — those bones belong in a museum, not serving for profit! — but it’s clear that this team from the Black Hills Institute were pros, and were also skillful preparators. It’s a difficult balance, because while they are trying to make money selling specimens, it’s the nature of fossils that they really are just weathering out of the rocks, and if someone doesn’t collect them, they’ll just be lost rubble.

And Sue was an amazing find. The skeleton is 80% complete, and she was the largest of her species found to date. Peter Larson and his crew were enraptured.

Then the documentary turns grim. The law stepped in and argued that since it was found on federal land, the Black Hills Institute had no right to the specimen, and seized everything. It got tied up in an ugly legal wrangle for years. They decided that the rancher, Maurice Williams, who had let Larson dig up the skeleton for $5000 had no right to sell it either: he was leasing government land for his livestock, so it wasn’t his (apparently he hadn’t been paying for it, either).

There’s an incredible injustice. Larson is found guilty of not filling out some forms, and is given a punitive sentence of 2 years in federal prison. Sue is auctioned off for about $8 million dollars, and the money goes to…Maurice Williams? That part made no sense. It should have gone to paleontological research, if anything, not another lucky parasitic rancher who contributed nothing to the discovery.

At least Sue went to a good home, the Field Museum. And now I’m thinking that maybe this summer I’ll take a weekend drive out to the western side of South Dakota and visit the Black Hills Institute Museum.

Evo devo in the real world

I disagree with Razib Khan on a lot of things, but he’s exactly right on recent fads in biology.

Periodically I get frankly stupid comments that seem to imply that the incredible swell of results coming out of molecuar genetics and genomics are revolutionizing our understanding of evolutionary and population genetics. Over the past generation it’s been alternative splicing, then gene regulation and evo-devo, and now epigenetics is all the rage. The results are interesting, fascinating, and warrant deeper inquiry (I happen to see graduate school admission applications for genetics, and I can tell you that conservatively one out of three applicants mention an interest in epigenetics; the hype is grounded in reality, as epigenetics may be a pretty big deal in human health that we can effect).

All those phenomena he mentioned are real and often very interesting, but they’re not changing deep concepts in evolutionary biology. You’re most often going to hear that they’re revolutionary from people who don’t understand evolution very well.

He’s got a good assessment of evo devo, too.

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The difference between science and porn…

…seems to be the number and size of the cameras, and their location. “Scientists” (who are not named, nor is any published work cited) placed tiny cameras on a penis and inside a vagina and recorded intercourse between two people. Why, I don’t know. There doesn’t seem to be any question asked or answered. It also seems to perpetuate a lot of invalid myths, like that sex in the missionary position is better for conception, and generalizes stories about the G spot to all women.

Although extremely explicit (do not watch it at work!), it’s also the most unsexy thing I’ve seen in ages. All it made me wonder about was how they kept fluids from sliming up the camera lens.

By the way, a hint to future “investigators”: dubbing in cheesy porn-style music over the action doesn’t make you look any more serious — it suggests something about the background of the people making the movie, actually. Also, if it’s science, the first thing I want to see is a hypothesis that is being tested, and no, “how close can I get a camera to this woman’s vulva” is not a particularly interesting question.

An honest appraisal of evo devo

In a review of a new book edited by Alan Love, The evolution of “evo-devo”, Adam Wilkins makes a few telling criticisms of the sub-field I enjoy.

Evo-devo has come a long way since 1981 though the Dahlem Conference laid some of the important groundwork for what followed and was, indeed, widely appreciated as having done so. Yet, troublingly, the field remains, for many evolutionary biologists, something of a side-show, a “boutique” subject within evolutionary biology as a whole. Several of us, in the 1990s, warned that this might happen. This is in contrast to some of the early expectations, which involved positing a coming central role for this discipline within evolutionary biology as a whole. A few of the contributors evidently feel that it has achieved such a position but I think that a broad survey within biology would reveal that not to be the case. If it failed to develop its full potential, why? Opinions will vary but my own hunch is that one factor is that the field has largely avoided incorporating much of the rich material that developmental genetics offers for understanding developmental and morphological change. The one general concession to such genetics, noted in passing in one of the chapters, is the insistence that most developmental change in evolution involves alterations in cis-regulatory elements for regulatory genes. There is, of course, good evidence for this but it is not the whole story and ignores both other mechanisms and the possible dynamics of the incorporation of such change in populations. That last thought, however, introduces what is, in my view, the second weakness of the field: evo-devo remains largely a zone devoid of population thinking. The great strength of classical evolutionary biology was that it focused on the nature of transformation of populations over time – both genetically and phenotypically – and provided a crude general mechanism for understanding such transformations. Its corresponding failing was that it largely ignored the details of the source materials for such change. Evo-devo’s main strength and weakness are just the reverse. These reciprocal differences in emphasis amount to perceptual and intellectual differences about what is important in considering evolutionary change. Such differences in attitude continue to create a divide between evo-devo and classical evolutionary biology. This volume does not address this issue at all and I think that is a regrettable omission.

I’ve highlighted the two key points, although I think they’re both rooted in the same problem. 1) I think there is a superficial focus on developmental genetics, but what we’re missing is the experimental perspective. 2) True enough that there is a lack of population studies (I can think of the stickleback work on recent evolution of small populations as a counter-example), but there the problem is that if you’re focusing on the great grand questions of evolution, like where the notochord came from, you’re simply not going to find much variation within extant groups. All fish have notochords. All zebrafish populations have notochords. You’re just not going to have any material to work with if you try to study how the expression of notochords vary in a population that is over half a billion years removed from an ancestral population that did have interesting differences in a nascent structure.

The key problem is that the field has long been interested in morphological and molecular differences at the phylum and class level. What we need to do is ask better questions that are appropriate on a smaller scale, and are more amenable to experiment and genetic analysis. Narrow the scope, more work on differences in fruit fly wings and in the circuitry of tissue specification in closely related species of echinoderms, for instance.

Of course, the appeal of evo-devo is often in those gigantic huge intractable questions that involve comparing fruit flies and echinoderms. Evo-devo without the grandiosity is harder to market.

Wilkins AS (2015) The evolution of “evo-devo”. BioEssays 37(12):1258–1260.

Building a chordate: the notochord


I know this is a horrible photo — I just snapped a picture of the journal hardcopy, which I own, instead of grabbing a PDF from the web, because it’s from 1985 and I’d have to pay to get a copy of my own paper — but this is what I was doing in grad school. I started as somebody who was interested in neurons and the nervous system, so what you’re seeing is a transverse section of the spinal cord of a zebrafish, with a couple of motoneurons labeled black with a tracer enzyme. I spent most of my time teasing apart how those cells grew and made connections.

But all the while there was this one prominent feature of the animal that kept trying to distract me. See that big clear white space below the spinal cord? That’s the notochord. It’s huge, a long transparent cylinder built like a stack of glass coins, running from the neighborhood of the hindbrain all the way back to the tip of the tail. The image from Stemple below is much clearer, since the notochord has been painted pink.


Its superficial function is obvious: it’s a springy rod that the muscles of the fish’s body act upon for swimming and escape behaviors. While I was just doing neural circuitry work, that was sufficient — it’s part of the motor apparatus. Neurons make muscles twitch which flexes the notochord and generates the back and forth motion that propels the animal through the water. Case solved.

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Japan and the awesome Christmas miracle

Toyama Bay got a visit from a mythological being, all dressed in red, on Christmas day. It was beautiful.

It seems to be Architeuthis dux, and is about 4 meters long. It just cruised in, ambled about, and the authorities plan to just let it swim away. If it can — giant squid on the surface tend to be sick and unhappy. But still…! I’m waiting for the day one swims up the Pomme de Terre river to bring me presents.

There’s more discussion about this squid (in English!) on TONMO.