Last month we mentioned the challenges of studying blue whales in a laboratory setting. If we want to know what a particular gene or protein does in an animal that large, we often have to rely on inference based on what a comparable gene or protein does in an animal we can study more readily like a mouse. And how do we know which protein is comparable–or homologous, to use the more technical term? Typically the search for homologous proteins starts with a sequence similarity scan, a check of an entire library of proteins from various species to see which have a large fraction of the same amino acids at the same locations. That’s straightforward enough when the match is at the level of 80%, but at just 20% similarity, it’s a bigger challenge–until now.
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Science Corner: Don’t It Make My Blue Whale Big
I was fortunate to grow up within visiting distance of the American Museum of Natural History in New York City. One item stands out in my memories from periodic visits: the blue whale. Not a live one, of course; it’s a museum, not an aquarium. Even as an inert model, the blue whale was striking to little-boy-me–which is saying something since it shares a home with numerous dinosaur skeletons. Of course, that cohabitation only helps to underline just how much bigger blue whales are than even the biggest dinosaurs or their aquatic contemporaries. Setting aside the highly exaggerated depiction in Jurassic World, even the Mosasaurus that previously occupied the blue whale’s ecological niche was only about 2/3s the size. So of course I was curious about a news story on the genes of how whales, blue and otherwise, get so big.
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Science Corner: Methods Maketh Metaphor
I am generally bullish on the use of metaphors for understanding the world around us. I find Douglas Hofstadter and Emmanuel Sander’s idea that metaphors are central to language and thought to be fairly compelling. I recognize the potential for a metaphor to lead one down a primrose path. At the same time, how else are we to think and communicate about something like the interior of a biological cell, an environment none of us could ever actually visit or experience? If we cannot avoid metaphors, we can at least be transparent about how we use them and think critically to identify when they have reached the limits of usefulness. In that spirit, I greatly appreciated this paper about the role of machine metaphors in understanding cell biology.
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