I have a plan for faster-than-light travel now

Both Phil Plait and Sean Carroll and Mano Singham are tentatively reporting that they may have an explanation for the recent anomalous report of neutrinos traveling faster than light: it may have been a case of a faulty connection in a timing circuit. If that bears out, it may be a bit embarrassing.

But it does suggest an important possibility. When we get around to building the first starship, don’t have those fussy, punctilious physicists wire it up. Gather a gang of sloppy slapdash biologists to stick it together with spit and chewing gum. We’ll have it going a heck of a lot faster than light than those experts can even imagine.

(Also on Sb)

Epistasis and pathways in fly eye pigmentation

I was going to talk about a cool recent paper that described the evolution of novelties by way of modifying modular gene networks, but I started scribbling it up and realized that I was constantly backtracking to explain some fundamental concepts, so I stopped. I was concerned because one of the most common sources of confusion I’ve found in my students in the past was difficulty in distinguishing phenotypes from the complexities of the underlying genotype, and I have to be slow and thorough in setting up those differences early on until it sinks in, a habit I’m continuing here. It’s so easy for students to reify a trait, like eye color, into a single discrete property that must be somewhere on a chromosome. It’s not. It’s so much messier than that.

Let’s talk about eye color in flies. Drosophila eyes have a characteristic brick red color, and the most famous mutation in flies is white, which produces distinctly white-eyed flies. Eye color is too complex to be described as the product of a single locus and only two alleles, though: there’s actually a whole battery of genes that work together to produce eye color.

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The problem with evo devo

Last week, I gave a talk at UNLV titled “A counter-revolutionary history of evo devo”, and I’m afraid I was a little bit heretical. I criticized my favorite discipline. I felt guilty the whole time, but I think it’s a good idea to occasionally step back and think about where we’re going and where we should be going. It’s also part of some rethinking I’ve been doing lately about a more appropriate kind of research I could be doing at my institution, and what I want to be doing in the next ten years. And yes, I want to be doing evo devo, so even though I’m bringing up what I see as shortcomings I still see it as an important field.

I think of myself as primarily a developmental biologist, someone who focuses on processes in embryos and is most interested molecular mechanisms that generate form and physiology. But I’m also into evolution, obviously, and recently have been trying to educate myself on ecology. And this is where the conflicts arise. Historically, there has been a little disaffection between evolution and development, and we can trace it right back to Richard Goldschmidt and the neo-Darwinian synthesis.

There is minimal consideration of development in the synthesis. The big man in the interdisciplinary study of evolution and development at the time of the formulation of the synthesis was Goldschmidt, who actually raised some grand and important issues. He was interested in sex differences; the same genome can give rise to very different forms, male and female. He was interested in metamorphosis; the same genome produces both a caterpillar and an adult moth. And he was interested in phenocopies; the same genome can generate alternative forms under the influence of environmental factors. He had some very speculative ideas about global systemic mutations that haven’t really panned out, and his ideas were tarred with the label “hopeful monsters”, which didn’t help either. It was non-Darwinian! It argued for abrupt transitions! I’ll defer to Gould’s defense of Goldschmidt, though, and would say that those weren’t good reasons to reject some challenging ideas.

The charge that stung, though, was Ernst Mayr’s accusation that Goldschmidt believed that new species could arise by a single fortuitous macromutation in a single individual, that Goldschmidt had abandoned or failed to grasp one of the most essential principles of evolutionary thought: that evolution occurs in populations, not individuals. He did not understand the concept of population thinking. I don’t think he was entirely guilty of that, but I have to concede that there was a disjoint there: as a developmental biologist, Goldschmidt would wonder first and foremost about the kinds of genetic rearrangements that would generate an evolutionary novelty, and just assume that a superior morph would propagate through the population, a process of relatively little interest; while an evolutionary biologist would be less interested in the developmental details of the generation of the phenotype, and much more interested in the mechanics and probabilities of its spread through a population.

Evolutionary biologists and developmental biologists think differently, and that creates a conflict between the evo and the devo. I’m not unique in noting this: Rudy Raff included a table in his book, The Shape of Life, which I’ll reproduce here, with a few modifications of my own.

Quality Evolutionary Biologists Developmental Biologists
Causality Selection Proximate mechanisms
Genes Source of variation Directors of function
Target Trans elements
(coding sequence)		 Cis elements
(regulatory)
Variation Diversity & change Universality & constancy
History Phylogeny Cell lineage
Time Scale 101-109 years 10-1-10-7 years

Modified from Raff, 1996

Those different emphases can lead to biases in where we place the importance of various processes. I’ll focus on just two: causality and variation.

When we’re looking at the process of change within our domains, evolutionary biologists have already mastered the art of population thinking: everything is about propagation of patterns of variation within a population. There aren’t explicit mechanisms that generate subtypes to fit the range of roles available. Instead, a cloud of forms is created by chance variation and the unfit are selected out. Developmental biologists, on the other hand, see an organism with a constellation of necessary and dedicated functions — there must be a nervous system to regulate behavior, there must be a gut to process food — and specific molecular mechanisms to programmatically generate them. Embryos do not proliferate a mass of cells with random variants, and then use the ones that secrete digestive enzymes for the gut and the ones that generate electrical impulses for the brain. A lot of development papers really do talk about nothing but proximate sequences of causal interactions that lead to a specific function or fate.

To an evolutionary biologist, variation is the stuff of interest: populations with no variation are not evolving (it’s a good thing such populations don’t exist, or if they do, chance will swiftly change the situation). To your average developmental biologist, variation is noise. It clutters the interpretation of the data. We want to say, “Here is the mechanism that produces this tissue type,” not “Here is the mechanism that sometimes produces this tissue type, in some organisms, sometimes with other mechanisms X, Y, and Z.” We generally love model systems because they allow us to establish an archetype and see a reliable pattern. In the best case, it gives us a solid foundation to work from; in the worst case, we forget altogether that there is more complexity in the natural world than is found in our labs. I would be the first to admit that laboratory zebrafish, for instance, are tremendously weird, inbred, specialized creatures…but they’re still extraordinarily useful for getting clean results.

I will also be quick to admit that the above is a bit of a caricature. Of course many developmental biologists reach out beyond the simplistic reduction of everything to linear, proximate causes. Raff, in that book, goes on to discuss specifically all of the problems of model systems and how they distort our understanding of biology; I could cite researchers like David Kingsley who specifically study variation in natural populations; Ecological Developmental Biology, which describes the interactions between genes and environment; and of course there are all those scientists at marine stations who aren’t staring at tanks full of inbred specimens, but are going out and collecting diverse forms in the wild. I am admitting a bias, but the best of us work hard to overcome it.

And then…we sometimes slip. I highly recommend Sean B. Carroll’s Endless Forms Most Beautiful: The New Science of Evo Devo as an excellent introduction to evo devo, I even use it in my developmental biology course. In reducing the discipline to a popular science book, you can see what had to be jettisoned, though, and unfortunately, it’s that whole business of population thinking and environmental influences (clearly, Carroll knows all that stuff, but in distilling evo devo down to the basics, that developmental bias is what emerges most clearly). Here, for instance, is the admittedly sound-bitey one sentence summary of what evo devo is from the book:

The Evo Devo Revolution

“The comparison of developmental genes between species became a new discipline at the interface of embryology and evolutionary biology—evolutionary developmental biology, or ‘Evo Devo’ for short.”

Sean B. Carroll, 2005

Again, this is not a criticism of the book, which does what it does very well, that is, describe the mechanistic process of development and the regulatory logic behind it, but notice the missing words in that abbreviated description: populations and environments don’t really come into play. All we’ve got there (and this is a bit unfair to Carroll) is comparisons of genes between species, which is enough to show common descent and relationships between the phyla, but it doesn’t say how they got that way — which is an unfortunate deficiency for a discipline that is all about how things get that way!

That’s what I’m concerned about. Right now, evo devo is far more devo than evo; we really need to absorb some more lessons from our colleagues in evolutionary biology. A more balanced evo devo would weight variation far more heavily, would be far more interested in diversity within and between populations, and would prioritize plasticity and environmental influences far more. If we did all that, it wouldn’t be a revolution — because it would embrace everything that is already in evolution — but would be what Pigliucci calls the Extended Evolutionary Synthesis. What we’d have is a better appreciation of this well-known aphorism:

“Evolution is the control of development by ecology…”

Van Valen, 1973

That’s the holy trinity of biology: evolution, ecology, development. Our goal ought to be to bring all three together in one beautiful balance.

(Yeah, I stole the triquetra. We’ll use it far more wisely than the religious.)

(Also on Sb)

No sympathy for the devil

I don’t get it. First there was Climategate, in which hackers illegally broke into a server at the University of East Anglia and stole a pile of emails from climate researchers. The denialists seemed to be fine with that, and quote-mined the heck out of the documents to find damning statements, lying and claiming that they showed that the scientists faked their data (they did no such thing, of course). All the sturm and drang at that time was over the contents of the emails, not the illegal method of their acquisition.

Now the shoe is on the other foot. The Heartland Institute, a right-wing think tank with an agenda of willful dishonesty, leaked, and leaked hard. Someone mailed a collection of internal documents to Peter Gleick, and Gleick responded by sending a request to Heartland under a fake name, and got additional copies that confirmed the accuracy of the documents. Was this wrong? It doesn’t seem to be illegal, and I think it’s an open question whether it was unethical — it would be unethical if Gleick lied and misrepresented the contents of those documents, as the denialists did with the East Anglia emails, as the Heartland Institute did with those emails.

And there’s Peter Gleick beating himself up for exposing the Heartland Institute’s mendacity. I really don’t get that. He’s a scientist. Scientists gather data to make informed decisions. Gleick got the data the Heartland Institute tried to hide. You can’t on one hand condemn Gleick for asking for the information and getting it handed to him, while praising hackers for breaking into a server and illegally taking data.

And then Mann, Trenberth, Bradley, Overpeck, Santer, Schmidt, and Karoly write the most naïve letter ever, pointing out the hypocrisy of the denialists while deploring the acquisition of the documents, and saying this:

We hope the Heartland Institute will heed its own advice to “think about what has happened” and recognize how its attacks on science and scientists have helped poison the debate over climate change policy. The Heartland Institute has chosen to undermine public understanding of basic scientific facts and personally attack climate researchers rather than engage in a civil debate about climate change policy options.

Really, people? Seriously? This is what the Heartland Institute wants, the poisoning of the debate and the undermining of public understanding. They probably read that letter and said, “Yay! It’s working!”

How about if we focus on the content of the leaked documents instead? They do reveal a deep truth: that the Heartland Institute is a propaganda organization with great support from right-wing political organizations and individuals, and that their mission is to parcel out money to disinformation agents like Anthony Watts and Fred Singer, who sow unfounded doubt and confusion about real science. And they plan to poison American education.

Principals and teachers are heavily biased toward the alarmist perspective. To counter this we are considering launching an effort to develop alternative materials for K-12 classrooms. We are pursuing a proposal from Dr. David Wojick to produce a global warming curriculum for K-12 schools. Dr. Wojick is a consultant with the Office of Scientific and Technical Information at the U.S. Department of Energy in the area of information and communication science. His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain- two key points that are effective at dissuading teachers from teaching science. We
tentatively plan to pay Dr. Wojick $100,000 for 20 modules in 2012, with funding pledged by the Anonymous Donor.

No matter how it was obtained, the Heartland Institute has confirmed that it stupidly mailed out internal documents. The denialists are trying desperately to claim that one of the documents is fake, which just affirms that all the others are accurate.

That ought to be the central story here.

(via Greg Laden)

(Also on Sb)

Keep that Santorum out of our science

Jeez…Rick Santorum, young earth creationist, climate change denialist, anti-stem cell research crusader, fundamentalist/evangelical Christian, has just accused liberals of being anti-science. He might have been right if he’d been talking about the liberals who are mushy-headed over alternative medicine, but in this case, he’s pinning his accusation on the fact that we don’t want to burn more coal.

Republican presidential candidate Rick Santorum charged on Monday that President Barack Obama and Democrats were “anti-science” because they refused to exploit the Earth’s natural resources to the limits of technology.

Over the weekend the candidate had been criticized for saying that President Barack Obama followed a theology that was not “based on the Bible.” He later insisted that he was talking about the president siding with “radical environmentalists.”

“I accept the fact that the president’s a Christian,” Santorum told CBS host Bob Schieffer on Sunday. “I just said when you have world view that elevates the Earth above man and says that we can’t take those resources because we’re going to harm the Earth — like things that are not scientifically proven like the politicization of the whole global warming debate.”

The scientific view is that global warming is occurring, and that it’s driven by anthropogenic production of greenhouse gases; the politicized, ideologically demented view is a denial of the evidence. Like Santorum’s nonsense.

This is a speech he gave to the crowds in Ohio:

But if we don’t provide those opportunities for those jobs that can sustain a family, for power in this country that is affordable, not just coal but all energy. It drove the economy of Southwestern Pennsylvania, Eastern Ohio for a long time. And through a variety of things — yes, problems with management, problems with negotiations — but actually there were bigger problems. The bigger problems of environmental regulation. In many cases environmental regulation that has gone extreme, particularly in this administration.

What they have done? And I referred to it the other day and I got criticized by some of our, well, less-than-erudite members of the national press corps who have a difficulty understanding when you refer to someone’s ideology to the point where they elevate Earth, and they say that, well, men and humanity is just of a variety of different species on the Earth and should be treated no differently.

Whereas, we all know that man has a responsibility of stewards of the Earth, that we are good stewards and we have a responsibility to be good stewards. Why? Because unlike the Earth, we’re intelligent and we can actually manage things.

Did Santorum just call the press “less-than-erudite” while arguing against the idea that humans are one of a variety of different species on the planet? What a maroon.

And yes, we’re intelligent, and we should try to manage things. So what does that make a head-in-the-sand denialist like Santorum who wants to allow unrestricted, unmanaged exploitation of natural resources? Not a good steward, I would say.

That didn’t work: Samsung sucks

Remember that I complained about an obnoxious bug in the Mac OS, which was traced to the Samsung printer driver? I was gratified to see that the Mac update mechanism announced an upgrade to that printer driver (is it possible they actually pay attention to complaints on the web?), so I installed it tonight.

In case you were anxiously awaiting a bug fix yourself, I’ll tell you…it didn’t work. I’m watching printtool eat up all my memory right now, and am about to shut it down and go to bed.

(And you know what? If any idiots start pointless, stupid OS flame wars in this thread, I’ll delete you in the morning, and close thread comments.)

Aaaaand…of course I had to delete a half-dozen comments this morning, although it wasn’t as bad as I feared.

I also had some helpful email: at the suggestion of a correspondent, I also killed this stupid little startup item called SPanel that was installed when I got the printer. It’s behaving so far this morning.

Lots of people suggested that I simply drop-kick the printer into the nearest landfill, which may happen. I don’t trust it anymore; I’m reluctant to use the goddamned thing, because I feel like everytime I fire it up I have to monitor CPU activity to see if it is bleeding memory again, and I have to restart my computer afterwards…whereas I typically go months without a shutdown or restart.

Bottom line: treat Samsung devices as equivalent to vectors for viruses that will corrupt your system and degrade performance significantly. I’ll never buy anything from Samsung ever again — they’ve got plenty of competitors so there’s no reason to risk struggling with their incompetence.

Family matters and cheesy insinuations

What do you know? Richard Dawkins and I have something in common.

In a particularly slimy move, the Telegraph has posted an article that tries to tar Dawkins with the sin of slavery. Not that Richard Dawkins himself has slaves or endorses slavery, but that he had an 18th century ancestor who had a Jamaican estate with over a thousand slaves. The reporter also made the ludicrous suggestion that slave-holding was genetic.

I’d scarcely had time to re-open my lecture notes when he rang back: “Darwinian natural selection has a lot to do with genes, do you agree?” Of course I agreed. “Well, some people might suggest that you could have inherited a gene for supporting slavery from Henry Dawkins.”

So now there’s a slavery gene? That is quite possibly the dumbest assertion I’ve heard in a whole week…and I read creationist websites. As Dawkins points out, he had 512 direct ancestors in that same generation, and that he has a number of ministers in his lineage. Not only is it ridiculous to invent a slavery gene, but it’s a selective absurdity to cherry-pick members of a large population of remote relatives and claim that an individual is responsible for everything every ancestor did. That’s a rather biblical position to take, I think.

So what do we have in common? I poked around a bit in the genealogical records and found this: a piece of the 1820 US census.

It’s not easy to read, but that’s a bit of the records for St Stevens Parish, King William, Virginia. I’ve mentioned before that I’m Scandinavian on my mother’s side, but on my father’s side, I’m English/Irish/Scots and an undefined mingling of who-knows-what, including a bit of Dutch, and they’ve been skulking around North America since somewhere in the 17th or 18th century, and some of them were even Southerners. My great-great-great-great-grandfather, Garland Hurt (1764-1839) was a Virginian married to Martisha Thurston (1768-1818), who had 3 sons and 3 daughters…and also 1 female slave under 14, and 1 female slave between 14 and 25.

Oh no! Do I carry the slave-master gene?

I suppose if I were interested and extremely ambitious (sorry, I’m not), I could trace all of Garland Hurt’s descendants forward, and then we’d find not only that some of you readers might be related to me. I suspect that some of the people who utterly despise me (if they even know of me) are distant cousins. We’re different from each other and from our ancestors.

My family is a bit down-class compared to those fancy-pants Dawkinses, but as you can see, it’s easy to find slave-owners for any of us among the swarms of ancestors we all have, just by going back far enough. I also have at least one ancestor who fought on the Union side (an Iowan who fought with Grant in the Mississippi campaign) in the Civil War. I deplore the slave-owner, but I don’t own his guilt, nor do I get to take credit for the great-great-grandfather who was mustered out in New Orleans. We’re all a great gemisch of subsets of genes from a bounded population. It’s simply silly to start parsing out characteristics from individuals in a complex cloud from the ancestral gene pool and arbitrarily assigning them to single contemporaries. The writer of that article, Adam Lusher, is an idiot…and the Telegraph ought to be embarrassed at publishing such tripe.

A different view of Las Vegas

I’ve been to Las Vegas several times, but every time I’ve spent all my time inside a building, usually a noisy casino. Not this time! I made a hike out to Red Rocks, a very lovely place.

That’s a blurry Vegas off in the distance on the top left, if you were wondering.