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?


Rare and Superior Gene Variants

It turns out that there’s a rare variant of a gene involved in Alzheimer’s Disease that protects the carriers against age-related cognitive decline.  It even, apparently, protects against other known genetic risk factors for Alzheimer’s.  This is totally the kind of thing I can imagine parents paying big bucks to have inserted into their kids — rare genes that already exist in the broader population, that confer disease resistance or other advantages, but which haven’t had time to become prevalent under natural selection, or which confer an advantage that won’t have obvious reproductive consequences.  We’re going to start accumulating a library of these potential genetic revisions and, I suspect, within a couple of decades, making sure that our descendants carry them disproportionately.

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.

Moms market

Further developments in India’s commercial surrogacy market.  As the government mulls more detailed regulations, existing rules are already being neatly side-stepped.  For instance, sex-selection is not permitted in India, but it is in Panama, so the embryo screening is done on the isthmus, with those selected forwarded to the subcontinent for implantation.  Egg banks in India now stock a wide variety of ethnic backgrounds from international donors.  It’s a baby smorgasbord.  Gattaca, here we come!

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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The holes in my woolens

I discovered a couple of small holes in one of my my merino sweaters this morning.  Moth larvae.  My fault for not using camphor or some other kind of deterrant.  At first, I was bummed because I thought this represented a flaw – I love wool, and especially merino, because it’s warm even when it’s wet, it wicks, it doesn’t smell, it doesn’t burn and melt like plastic, it’s durable and comfortable and not based on petrochemicals.  But moths can eat it, and it can mold.  It requires more care than fleece.  Thinking just a little more, it occurred to me that actually, these holes are in some sense a feature, not a bug.

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The Sequence: a play about the Human Genome Project

It turns out that Pasadena has a wonderful little theater called The Boston Court.  It’s a non-profit organization, producing some classics, but perhaps more interestingly, also some first-run original pieces by SoCal playwrites.  Michelle saw an adaptation of the Mesopotamian Epic of Gilgamesh there last year, and we went and saw 1001, a story weaving the Arabian Nights with commentary on the modern Arab-Israeli coflict and the War on Terror.  The casts are essentially dedicated amateurs – the auditions page lists a $300 rehearsal stipend, plus $25/performance.  The space is so small that there is no need for amplified sound, and the sets are fairly minimalist.  They have student discounts and matinees, and late night salons for discussion after the plays are performed.  I have a hard time imagining a better setting and scale for theater.  Even better, it’s easy biking distance, and they seem to have a bent toward plays that are relevant to the modern world.

On Friday, we went to see The Sequence, by Paul Mullin, who has also written about Louis Slotin’s death during the Manhattan Project due to a criticality accident while “tickling the dragon’s tail’, and The Ten Thousand Things, an exploration of the meaning of deep time in human society, inspired by The Clock of the Long Now.  The Sequence is a play about the Human Genome Project, and the race between Craig Venter‘s Celera, and the publicly funded project headed by Francis Collins, to complete the sequence first, and also about a young journalist, Kellie Silverstein, who is covering the race, who struggles with her own genetic destiny, knowing that her mother died from breast cancer due to the BRCA1 mutation, which she likely also carries.  The Sequence was commissioned by the Alfred P. Sloan Foundation.  Ironically, Mullin cannot afford to be a professional playwrite, and instead works in a clerical position at Amgen to pay the bills.  Like Copenhagen, the play has only three characters.

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What is Human

The utter primacy of H. sapiens in all the theistic religions is one of the things that bothers me most deeply about them. I believe we are unique and unusually important amongst life on earth (as were the first oxygenic photosynthesizers, and the first eukaryotic organisms, and the first macroscopic multicellular life forms), but I don’t think that the earth without humans would be without value. Diminished, certainly, but still a precious place. By the same token, I think that we diminish the value of the earth by causing the extinction of other species.

I think this may actually be somewhat related to the abortion question, and the difficulty of coming to any kind of common ground on it. I don’t consider non-viable fetuses human, but to me that doesn’t mean they are without value, or undeserving of any kind of legal protections. I just don’t think those protections should be as extensive as our protections of humans.  People are resistant to the idea that “humanity” is a continuum.  Some might even say repelled by it, but it seems inescapable to me.  I also believe that severely mentally disabled people are “less” human, and that a brain-dead human is, for all intents and purposes, a cell culture with no more moral value than a side of beef.  This might seem like something we had better not talk about, since it starts off all kinds of slippery slopes to horrible places, but I think eventually, we will have no choice, because some time in the next few decades, or at most the next few centuries, we will be confronted with positive deviations as well as negative.

What will it mean to be human, when there exist super-humans?  When some portion of the population is genetically or cybernetically enhanced, will they have super-human rights, privledges, and responsibilities, or will they simply be more powerful through extra-legal means?

A person, even a politician, can stand up for human rights while condoning abortion if they do not consider the fetus human.  The core of the abortion argument is what does it mean to be human? Is it a discrete, or continuous classification?  Unless we can come to some consensus on these questions, the abortion issue, and many others, will remain vexing indefinitely.

We need more Dionysian Science

Michelle and I just finished reading The Botany of Desire by Michael Pollan. It was good. He can get a little rambling at times, but overall it was entertaining and enjoyable. The book follows the relationships between people and four plants, through history. The four plants are: apples, tulips, cannabis, and potatoes. It pairs with them four desires, respectively: sweetness, beauty, intoxication, and control. The connections are more than a little tenuous, but the histories are certainly worth examining. The apple chapter in particular has inspired me to learn more about hard cider (since it turns out that’s largely what Johnny “Appleseed” Chapman’s apples were used for, all across 19th century America). And who can resist an examination of cannabis’s relationship with humans, written at least partially while stoned?

One theme Pollan has touched on repeatedly, in this book and his others, is the competition between Apollonian and Dionysian impulses in nature and society. Apollo representing order and control, Dionysus wildness and chaos, both being utterly necessary for civilization to be dynamic and persistent, for knowledge to increase and broaden through time. E.g. our Apollonian monocultures of Russet Burbank potatoes are vulnerable because of their uniformity, but are also productive and economically efficient. The Andean potato farmers of antiquity grew dozens of different varieties in different micro climates, all the while allowing the plants to hybridize with the local wild potatoes, maintaining a possibly less productive, but certainly more diverse and robust system of potato cultivation, in which new biological innovation was constantly taking place, and in which the farmers were well protected against catastrophic collapse in any one year… unlike the potato farmers of Ireland in the 1840s. The potato chapter in particular focuses largely on a very recent interaction with the potato: the introduction of a genetically engineered variety called the “New Leaf” by Monsanto, that produces Bt toxin to guard the plant against the Colorado potato beetle and other insect pests. Continue reading We need more Dionysian Science