biology Archives - Amateur Earthling

Metazoa by Peter Godfrey-Smith

Metazoa is kind of a sequel to “Other Minds”, Godfrey-Smith’s excellent book about the nature of cephalopod intelligence. Metazoa takes a broader view, and explores the nature of minds in general, and how they’re inextricably linked to the animal way-of-being: having a unified, unitary body that can sense and react to the world around it. It was also an interesting book to read in combination with Sean B. Carroll’s “Endless Forms Most Beautiful” about animal body plans, and how they evolved through the use of gene regulatory networks and a meta-genetic toolkit that we share with all bilaterians.

This author kind of feels like a Carl Sagan of Marine Biology — very clearly trying to understand the world within a Materialist / Naturalist framework (which I appreciate) but without losing a sense of the mystical nature of existence. He’s asking “What kind of thing is a mind?” and “How can that kind of thing arise through evolution and be composed of nothing but a particular collection of matter and energy?” Why does this happen at all? How general or common a phenomenon is it?

Hacking the President’s DNA

A fun look at our transition to a Gattaca style future, through the lens of an evildoer, designing a customized pathogen meant to kill only the President, using the same tools that can be used to target a particular cancer with a viral drug delivery mechanism. How quickly will these tools be democratized? Is secrecy or transparency the better route to countermeasures? The Wikileaks cables revealed top-level diplomatic directives to collect the DNA of world leaders. For what purpose? Is it possible for anyone to keep their genome private?

Solving protein structures with social computation

In just 16 days gamers solved a protein structure that had eluded computational methods for a decade. Distributed social computing? What other computationally difficult problems are susceptible to this kind of approach?

George Church’s Evolution Machine

George Church wants to automate evolution, in the same way that we’ve now automated genome sequencing. Any trait that can be easily and automatically screened for should be susceptible to the technique. You give the machine a rough draft, and let it mutate the genome in fast forward, and iterate with screening/selection. They’ve already used the technique to engineer a couple of pigments (indigo and lycopene) much more effectively than straightforward genetic designers. Mmm. Custom evolved babies. And virus-proof replacement livers. Sweet, in a creepy kind of way.

Leveraging digital design in synthetic biology

Automatic Design of Digital Synthetic Gene Circuits from PLoS Computational Biology. They seem to be saying look, real biology isn’t generally digital, and all that continuum behavior means we need a bunch of new and complex tools to do anything with it. However, there are plenty of instances of pseudo-digital biological control systems, and we’ve already got a gigantic toolbox from EE/VLSI world for building very complex digital circuits, so why not limit ourselves to using an artificially digitized subset of biology so we can leverage the existing design tools, and see how far we get? Weird to think of this particular kind of very intimate digitization of life. Talk about historical effects. What would our post-dark-age descendants think, rediscovering a strange class of metabolic networks, in which everything is binary?

Code 46 and the dearth of thoughtful science fiction

I recently watched Code 46 again. When I first saw it a few years ago I didn’t like it very much, but this time it seemed more interesting. The storyline doesn’t hold together very well, and from a scientific point of view there are some painful gaffes, but it’s at least attempting to explore some important present and near-future issues, which is more than I can say for most science fiction films. That makes me sad, since I feel at its best, science fiction helps us understand how we interact with and relate to technology, and how technology changes the way we interact and relate to each other. The fact that there’s so little mainstream science fiction trying to do this today is frightening. We’re just blindly stumbling forward into the darkness. Maybe the best thoughtful sci-fi I can recall from the recent past is Gattaca, which depicts in a very stylized way a future society which is starkly divided between those who are genetically enhanced and those who are not. Gattaca is pretty clearly unconcerned with the details as opposed to the implications of its premise, and that makes it easier to gloss over whatever issues it has. It’s less clear that Code 46 is this self aware, but at least on a second viewing, I was willing to give it the benefit of the doubt. Be warned, there are spoilers below.

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Tag: biology