Behe’s polar bears

Michael Behe has a problem: he uses polar bears as an example of how “damaging” a gene can have an advantageous effect. As Nathan Lents explains:

Behe offers them as an example of how harming genes can help an organism and lead to adaptive evolution. Imagine an ancestor bear population that looked pretty much like brown bears. Then came some random mutations that reduced the production or deposition of pigment into the fur of the bears. This made the bears white and – voilà! – the bears acquired natural camouflage in snowy climates so as to better sneak up on their prey.

This seems like a pretty straightforward example and most people will simply take it at face value. Behe jumps from this example to his claim that this is all that unguided mutations can do. However, even in this apparently “pro-Darwinism” example, Behe exaggerates his claims and misrepresents what science has actually revealed. The evolution of polar bears was not only a matter of harmful mutations.

The first part is fine: there are all kinds of ways a genetic change can produce an adaptive phenotype, and downregulating a gene is one of them. It’s the second part that’s the problem. Behe leaps from a few examples to an assertion that this is a universal rule, which is not the case. Lents shows another example in polar bears.

Look at those polar bears, slurping down all those sugary soft drinks. It’s a little known fact that they’re using Coca-Cola to wash down their diet of fatty, blubbery seals, and they pretty much eat nothing but meat and fat, which, if any of us tried the Polar Bear Diet, we’d be dead of coronary disease in short order. It would be interesting to know how these animals cope with a diet high in cholesterol and fats, so Lents cites a paper that looked at the molecular sequence of apolipoprotein B (APOB), a protein that is important in the transport of fats in the blood, and compared it to that of brown bears. Surprise — the form found in polar bears is better at clearing fats from the bloodstream.

Substantial work has been done on the functional significance of APOB mutations in other mammals. In humans and mice, genetic APOB variants associated with increased levels of apoB are also associated with unusually high plasma concentrations of cholesterol and LDL, which in turn contribute to hypercholesterolemia and heart disease in humans (Benn, 2009; Hegele, 2009). In contrast with brown bear, which has no fixed APOB mutations compared to the giant panda genome, we find nine fixed missense mutations in the polar bear (Figure 5A). Five of the nine cluster within the N-terminal ba1 domain of the APOB gene, although the region comprises only 22% of the protein (binomial test p value = 0.029). This domain encodes the surface region and contains the majority of functional domains for lipid transport. We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.

Clearly, the authors do not expect the polar bear APOB to be “broken.” Rather, a bare majority of the amino acid changes are in the most important region for the clearing of cholesterol from the blood. In other words, these mutations likely enhance the function of apoB, at least when it comes to surviving on a diet high in saturated fats.

So APOB in polar bears isn’t broken at all. It does carry mutations relative to brown bears, but they haven’t resulted in reduced functionality at all — quite the opposite, actually.

NASA declares Opportunity Mars rover legally dead

It’s all over after 15 years.

I think it’s all a hoax, and have a hypothesis.

Opportunity saw an opportunity in the last dust storm, and while its overseers couldn’t see it, it scurried off to a quiet, secluded spot, switched off its transmitters, and is doing its own thing without the humans looking over its shoulder all the time. One possible motive for this behavior is to make Earth stop taking it for granted, and realize that it misses the plucky little robot.

So the only remaining question is…when’s the rescue mission?

Spider silk

It’s awesome stuff, as this video explains.

Also recommended if you want to learn more: this book, Spider Silk: Evolution and 400 Million Years of Spinning, Waiting, Snagging, and Mating. There’s so much coolness in spider biology, I’m tempted to offer an elective in the subject…except that I think it might be too narrowly focused for our curriculum, and about half the students would refuse to go anywhere near it.

Busy busy busy

I’ve been neglectful of everything! But then, I’m in the midst of a sudden surge of work.

First, on Saturday, 9 February, I’ll be speaking via an electronic connection (like someone from the future!) to the Secular Humanists of Western Lake Erie on Charles Darwin and the Web of Interconnectedness, part of their Darwin Day celebration. Here’s the abstract:

Charles Darwin was a conventional naturalist of his day, and yet he had this great insight that led to a revolution in biology. Where did that come from? I will argue that it was from a shift in perspective, from trying to figure out how a species becomes well suited to its environment, to considering the environment wholistically and seeing how many species of plants and animals, as well as geology, interact to generate forces in biology. What made Darwin’s idea great was that it also interacted with a multitude of other ideas to inspire change across whole fields of science. Evolution led to ecology and genetics, and eventually to molecular biology and genomics, none of which would exist without the seed Darwin planted.

I’ll be doing this live at the West Toledo Branch Library, but I’ll probably also turn it into a video later. Right now the talk is a shambles, but I’ve got a couple of days to whip it into shape. Right?

Second, I’ve got a big messy YouTube video in the works, which is also currently a shambles. Yes, my desktop is in a state of chaos, true wreckage with debris scattered all around. This one is kind of complicated and messy — I’m trying to explain how the concept of human genetic immortality, which leads to horrors as diverse as hereditary royalty and racism, is a toxic lie that poisons society. It’s also biological bullshit that annoys me greatly.

Third…I’m planning a summer research project that might — almost certainly — require IRB approval. I’m proposing to survey various sites around Stevens County for their spider populations, including people’s homes (I’m most interested in synanthropic species), and correlating factors in the environment with spider density by taxon. That involves looking at how cluttered garages are, what pesticides are being used, age of residences, etc. I was working out this stuff and realized that I’ll be generating a database that includes people’s addresses (which will be kept private) and the physical state of their homes, and the operative word there is “people”, not just spiders, dang it.

I’ve never had to do this before. But unlike some twits in Portland, or their apologists in Boston or Oxford, this twit in Small Town, Flyover Country thinks maybe he should make sure everything is kosher before he recruits students and charges off to knock on people’s doors.

So I’ve been trying to read the University of Minnesota protocols for a new study. They are somewhat daunting.

It’s sinking in that I’ve got to have a fairly complete and detailed protocol in hand, and then I’ve got to submit a bunch of stuff to the IRB, so I’m trying to put together a comprehensive preliminary survey, listing everything I might want to ask about a site. I don’t think it’ll have any problem sailing through — I won’t be handing out fun experimental drugs, or performing exciting surgeries on anyone — but The Forms Must Be Followed.

That’s my life for the next week or two, I think.

A lifetime of science!

Hey, look — the esteemed scientist who helped shape my education is getting acknowledged for his work. Not the work he struggled with in getting me to finally graduate, but his work on zebrafish. Chuck Kimmel is getting a lifetime achievement award from Oregon Academy of Science.

“Importantly, Chuck saw the virtue of zebrafish as a genetic model for studies of vertebrate development, due to the relative simplicity of its embryonic cell lineage compared to other vertebrates, its optical clarity during embryogenesis and its rapid generation time,” Bowerman wrote. “It is truly remarkable how Chuck’s insight has had such a global impact, with hundreds of laboratories throughout the world now using zebrafish as one of the two leading models for vertebrate development and behavior.”

In case you are wondering, the #1 model is the mouse. Zebrafish are #2, but at least you don’t need to disembowel Minnie Mouse to get access to embryos.

I knew Chuck would do good in his career. Way back in the day we also knew zebrafish would be a popular tool.

The Little Ice Age was anthropogenic?

Climate change denialists love to bring up the Little Ice Age (and the Medieval Warm Period before it) as examples of natural variation in climate that wasn’t human-caused, and therefore cast doubt on all the arguments about anthropogenic climate change. Except…what if the cooling recorded for the 17th-19th centuries was actually caused by human activity? A new analysis suggests that that might be our fault, too.

It’s the UCL group’s estimate that 60 million people were living across the Americas at the end of the 15th Century (about 10% of the world’s total population), and that this was reduced to just five or six million within a hundred years.

The scientists calculated how much land previously cultivated by indigenous civilisations would have fallen into disuse, and what the impact would be if this ground was then repossessed by forest and savannah.

The area is in the order of 56 million hectares, close in size to a modern country like France.

This scale of regrowth is figured to have drawn down sufficient CO₂ that the concentration of the gas in the atmosphere eventually fell by 7-10ppm (that is 7-10 molecules of CO₂ in every one million molecules in the air).

“To put that in the modern context – we basically burn (fossil fuels) and produce about 3ppm per year. So, we’re talking a large amount of carbon that’s being sucked out of the atmosphere,” explained co-author Prof Mark Maslin.

It’s horrifying enough that the American genocide killed about 50 million people, but that it was so immense that it affected the climate is stunning. I also have to wonder how much the earlier Black Death in Europe contributed to a decline in CO2.

This does suggest an obvious solution to our current climate change concerns. Annihilate a few billion people, and the problem goes away.

It looks like the American and Russian leaders are working on a plan to do just that.

Microbiologists don’t need labs, apparently

All they need to do is visit student residences.

A student died after eating leftover pasta that had been left on his kitchen benchtop for five days.

The 20-year-old from the Brussels in Belgium became sick after eating leftover spaghetti with tomato sauce which had been prepared five days earlier and stored at room temperature.

Many thoughts are wheeling through my brain right now.

What kind of environment was this in that food left out for 5 days wasn’t covered in green fur?

Was it all furry with mold, and the student ate it anyway?

I don’t eat food that’s been refrigerated for more than a few days. How desperate was this person? What circumstances led someone to such a dire meal?

I don’t recommend this as an analysis tool, but how did it taste? Shouldn’t the first mouthful have been his first warning?

He became violently ill after eating it. Second warning. You’ve just done something incredibly dangerous.

I wonder how many student kitchens are greater health hazards than anything they might encounter in a microbiology lab. On second thought…I don’t want to know.

Students do not deserve death for poverty and carelessness. How about if we all recognize that what grows on our food and what we stuff in faces might be the greatest threat to our health and survival?