Science Caturday: How do you teach your cat about evolution?

Pascal_innerfish_lolFirst, Pascal the cat thought the book was a guide to eating fish. Then, he thought it was a guide to eating Tiktaalik, a fish with leg-like limbs that is closely related to the ancestor of all land-dwelling vertebrates (amphibians, reptiles, mammals, and dinosaurs).

No, Pascal. Your inner fish is the anatomical similarities you have with fish, because you share a common ancestor with them deep in the past. Though you may think you’re a superior being to your pet hooman, you share the same common ancestor with him, from the first life on Earth until sometime in the Jurassic Period, when all mammals were about the size of your cat toys.

Up and Over

Science Careers has compiled an excellent list of articles and stories about scientists overcoming disability, mental health issues, and scores of other problems. With all of the negativity surrounding maintaining a career in science, it’s refreshing to read about how a scientific career is possible even with a few extra hurdles.

Online journals have not made publication dates irrelevant…

So why is it so hard to find the pub date in the HTML view of PLoS papers? The date needs immediately visible to be somewhere in this space:

PLOSGen

BTW, this is not my paper – it’s by the other, much more productive Michael A. White in whose shadow I’ve lived for years. I’ve never met him, but I have received his mail at one point.

Finding function in the genome part 2: All function is local (almost)

Yesterday I wrote about why negative controls are important in a genome-scale search for functional DNA. Today, I’ll discuss the main focus of our recent work: understanding what makes a piece of DNA functional.

The particular DNA I’m interested in is known by not very functional term ‘cis-regulatory’ DNA – a term that requires six syllables, an italicized Latin prefix, and a hyphen. This is DNA that is crucial in gene decisions: cis-regulatory DNA helps to control when, where, and how much genes are expressed. This happens because cis-regulatory DNA serves as a landing pad for ‘transcription factors’, proteins that land on cis-regulatory DNA and control the expression of nearby (or sometimes not so nearby) genes.

The question that haunts me is this: why don’t transcription factors get lost? My worry follows from these three observations: Continue reading “Finding function in the genome part 2: All function is local (almost)”

The Art of Science: Which Bird Do We Want Back?

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Walton Ford, Falling Bough, 2002

The passenger pigeon, a thriving species in the United States at the beginning of the 19th century, was extinct by the end of it. As Carl Zimmer wrote in National Geographic:

“In 1813, while traveling along the Ohio River from Hardensburgh to Louisville, John James Audubon witnessed one of the most miraculous natural phenomena of his time: a flock of passenger pigeons (Ectopistes migratorius) blanketing the sky. “The air was literally filled with Pigeons,” he later wrote. “The light of noon-day was obscured as by an eclipse, the dung fell in spots, not unlike melting flakes of snow; and the continued buzz of wings had a tendency to lull my senses to repose.”

When Audubon reached Louisville before sunset, the pigeons were still passing overhead—and continued to do so for the next three days. “The people were all in arms,” wrote Audubon. “The banks of the Ohio were crowded with men and boys, incessantly shooting at the pilgrims… Multitudes were thus destroyed.” (source)

Done in by a combination of over-hunting and habitat loss, the passenger pigeon is now the subject of study by a group of scientists, led by Stewart Brand, George Church and Ben Novak, who hope to revive the species through genetic engineering and cloning. (This article gives a brief explanation of the science involved)

The idea of reviving any extinct species is fraught with practical and ethical issues. (Here’s an interesting post about a few of them) So where, you ask, does art come into this issue? Well, when it comes to this particular species, what image of the passenger pigeon you look at might just color your opinion of whether we really want this particular bird back.

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John James Audubon, from Birds of America, 1838

If you look at Audubon’s painting of a pair of billing passenger pigeons, one sleek, beautiful bird leaning down and appearing to kiss its mate on the bough below, you might just think, “Yes! Those are nice. We should bring back those birds.” Now look at Walton Ford’s 2002 painting, Falling Bough, (top) and read his description of it:

“The passenger pigeons were the most numerous birds that ever lived in the history of the planet. It’s almost disturbing how numerous- billions upon billions of birds. It was a fecundity that was almost disgusting. I started thinking about a blame-the-victim kind of attitude you could take to that…to make it seem like they had it coming, that there was this disgusting empire of birds and that it was corrupt like Rome…that it was bound to fall. So I invest the passenger pigeons with every kind of sin that I can imagine. And the bough, this gigantic branch, is falling under their tremendous weight. Meanwhile they go about their bickering and their lusts and foibles and all the disgusting things that they are doing.” (source)

Obviously, the artists had different goals: Audubon aimed to provide an accurate visual record of the passenger pigeon’s physical characteristics, while Ford set out to conjure a dramatic, violent fantasy. The reality of giant flocks of passenger pigeons undoubtedly fell somewhere in between these extremes. They were likely to have been somewhat more frightening, noisy and dirty than Audubon’s, but less menacing and dangerous than Ford’s. I recognize this, but I saw Walton Ford’s painting first. The image stuck. So I say no, no, no, don’t bring back these birds. At least not to any trees near me.