Philip Greenspun, an entrepreneur who became successful at software development after completing a PhD in EE, has a popular essay on careers in science. I tend to agree with his pessimistic viewpoint, but I do think that things are a little different in medical research than physics. I think jobs are a little easier to come by, for one. I think it’s also important to keep in mind that his perspective is based on the extremely competitive east coast academic environment, and that he actually has been successful in the non-academic route.

The main point he seems to be making is that there are less women than men in academic science careers, not because women are less capable or more concerned with family life or anything, but rather that there are more men simply because men are the only ones stupid enough to let their ego influence their career choice.

A lot more men than women choose to do seemingly irrational things such as become petty criminals, fly homebuilt helicopters, play video games, and keep tropical fish as pets (98 percent of the attendees at the American Cichlid Association convention that I last attended were male). Should we be surprised that it is mostly men who spend 10 years banging their heads against an equation-filled blackboard in hopes of landing a $35,000/year post-doc job?

I know that my sense of identity and self-worth is tied very closely to my career. When things are going well, I feel like I’m doing the right thing, but when I can’t get anything to happen, I get depressed. I can certainly understand that women, who tend to experience assaults upon their self-worth from all directions from an early age, are a little better at eventually choosing more appropriate things to base their self-esteem upon.

via infoproc, some commentary from the life science POV at Bayblab

Readers, please permit me a short, non-science related rant. I don’t do this sort of thing often, so if you’re looking for more like this, go here.

The Academic Freedom Act is promoted as allowing science teachers to critically discuss evolution. However, science teachers have always been able to critically discuss any kind of theories in their classroom. No one has ever been fired or reprimanded for critically discussing any theory in the proper context. Critical discussion of the Holocaust or racial differences in intelligence are comparatively WAY more taboo, but you don’t see legislation to protect teacher’s freedoms to discuss these things, so don’t be misled – the one and only purpose of this is to teach creationism to public school children. I’m willing to bet there are churches that will happily sponsor tuition for parents that can’t afford to send their kids to a religious school, so this law is entirely unnecessary even for that purpose.

There’s a common misunderstanding that the purpose of teaching the theory of evolution is to replace the religious accounts of creation. That’s not the case. Evolution doesn’t teach that there is no god, just that there doesn’t have to be one. Evolution can’t answer the question of why we are here and where the universe originally came from, and it’s not meant as a replacement for whatever anyone believes regarding mankind’s place in the universe. It’s just a theory that explains what we can see as far back as we can see it, no further. Since it’s the best one that fits with available evidence, it’s the only one that can be taught in a secular context such as a public school. Stated this clearly, it’s hard to see where the misunderstanding came from, which has led many people to conclude that this actually wasn’t a misunderstanding at all, but rather a deliberate attempt to incite people against “godless atheists eroding our moral foundation”. When you consider that the Dominionists actually do want scripture taught as fact in public schools and they do want the Bible to be the highest law of the land and they do organize to elect leaders whose primary qualification is their faith, it’s easy to see how one could come to that conclusion.

In the end, anyone is free to believe whatever they want, but when they start making decisions on behalf of others, their duty to their constituents supercedes their personal duty to their faith, and there’s no way to justify your actions on behalf of your constituents without basing your decisions in consensus reality, not your personal version of it. I’m under no illusions, by the way, that rational, data-driven analysis underlies most legislation. People make decisions based on “gut feeling” all the time. That’s different, because the decisions made by those who place their personal faith above the duty to their constituents are based upon written scripture and doctrine, not divine revelation to them personally. If our elected leaders were having mystical experiences in the stateroom, it would be a different matter. That’s the last I’ll say about this – back to real science.

So the plan is to get a DNA sample from anyone arrested for a federal charge, and anyone picked up on immigration charges. This will add more than a million records to the database every year.

One of the strongest arguments against consumer genetic profiling is to prevent this information from becoming available to law enforcement. With the horrible record they have of keeping our private information secure, I don’t think they can be trusted with this kind of information, but can it be stopped? Is there any way to prevent the dystopian future of not only medical, but marketing and economic and employment decisions made about you based on your genetic profile?

I know many people take the position that they’ve got nothing to hide, so they’re not worried, and anyways, they’d willingly give it up if it could help apprehend rapists. In fact, enough people who are related to you probably think this way that it doesn’t really matter if they don’t get everybody, but I am starting to feel like this is Pandora’s box.

The average citizen and the average lawmaker doesn’t deal with huge databases, doesn’t understand statistical inference, and just isn’t equipped to consider the effects something like this will have on society. I don’t think I’ll feel comfortable with this information even being collected until there’s a framework controlling who gets access to what, monitoring who got access to what and what they did with it, and providing for remedies to the affected people when someone’s information gets accessed without authorization. We can’t have such legislation until lawmakers properly understand the issues. How many of them don’t even understand the difference between correlation and causation? Many tenured faculty don’t even fully appreciate the difference, so how can a layman?

We don’t even have appropriate remedies when credit information gets breached. Companies voluntarily decide to offer credit monitoring to affected people. That’s the remedy provided consumers, and it’s based on voluntary disclosure of the breach. How would someone even know that they were affected by inappropriate disclosure of their genetic information?

I know everyone is worrying about the economy, the elections, the war, the olympics, the pope, and everything else that’s grabbing the headlines, but it’s a critical failure to let this slip by without appropriate public comment. The Register, a UK IT publication, is covering the story, but there’s little mention in the domestic media. Here’s a article from the Washington Post, which isn’t on the front page, but can be found by searching for “NDIS federal”. There’s actually nothing on Google News about this either unless you search, which only turns up the article above.

You’ll see a banner between in between the title and post(or another location – this is just an experiment) for some items on the page and in the feed. I won’t see them, because Firefox is blocking them, but they looked relatively unobtrusive and highly targeted in IE. If you have any comments, please leave them here.

After a few months, I’ll re-consider whether it has been worth it.

It’s short, and it’s pretty great. Honestly.

Raj, Bohemian

via

One issue is that cognitive enhancement as a research area suffers from the same problems as life extension, unfortunately, in that it kinda attracts a different sort of person. Most researchers feel it’s more noble to fix something that’s broken instead of trying to improve something that’s currently working, however inefficiently. I generally agree with that sentiment, but certainly there is some worth to improving things, too. I’m not suggesting that more brainpower should be spent on inventing “smart drugs” than on curing cancer, but, as many have noted, this isn’t a zero sum game. There’s just so little that’s been done in the past decade on “nootropics” that there must be just bushels of relatively low-hanging fruit, ripe for the picking, and if gains could be made relatively quickly, they’d have a large payoff because they’d be applicable to everyone, instead of just the people with disorder or disease X. There would also be an additive effect of increasing the rate at which progress could be made in all the other fields.

This kind of work will face the same class issues as other types of medical research like genomic profiling, with people worrying that the discoveries will only be available to those who can afford it, thus widening the have-have not gap still further, but that’s not really a good argument for not doing the research, because it has to be available before it can become affordable, doesn’t it?

It’s a difficult thing to argue for, trying to fix something that ain’t broke, but I’m convinced given the utter lack of progress in this area over the past decade, that just one competent researcher in this area could make significant advances relatively quickly. Am I wrong? Has there been significant advancement in the last decade? Am I being too hard on sports performance researchers?

Checking Usenet, they’re still talking about the same stuff they were 10 years ago:
ginkgo
choline
huperzine
DMAE/centrophenoxine
vinpocetine
piracetam
hydergine

Little of this is available OTC in the US. The only thing I’m aware of with US OTC availability that’s not essentially repackaged caffeine is this stuff.¹ Has anyone tried these? Let me know in the comments.

1. I personally like it; I’m not connected to the company in any way.

Helicos Biosciences is reporting the re-sequencing of the M13 viral genome.
What’s really cool about this is that it’s sequencing-by-synthesis, requiring no amplification before sequence reading, so there’s no biasing of the populations of DNA fragments. Here’s a short overview of how their sequencing by synthesis works:

So it’s still a shotgun-style technique, and the problem has been getting long enough read lengths to assemble the pieces into a whole sequence. Think of it like a jigsaw puzzle. The smaller the pieces are, the more you have that look identical, and the harder it is to figure out where to put them. Given 3 x 10⁹ bases in the human genome, you’d need a read length of about 17 base pairs to be certain of ending up with all different pieces. They report average read lengths of 23 bp, with each individual sequence chunk represented about 150 times, and every part of the genome represented. This allows them to keep the error rate low enough that they could sequence different strains of the virus, and reliably pick up the genomic differences between the two. The paper doesn’t say how long this takes, but their marketing material says the process takes only one day.

The technique as practiced by Helicos has one major drawback, however, that will limit how low it can take the cost/base. It requires very expensive optics, since you’re essentially doing FRET on an array of targets. The list price for their instrument is $1.3 Million, with a consumables price of $18,000/sample, placing it out of reach of many institutions.

Illumina, another company with a sequencing-by-synthesis application, gets around the expensive optics issue by doing a clever solid-phase amplification of their target strands, essentially growing little colonies of identical strands in situ. A sales rep told me they’re selling around $500K, but didn’t have details on the consumables cost.

Long-term, I’d expect the Polonator to be the most widely adopted platform, due to their aggressive pursuit of royalty-free technology and low instrument cost. There’s a good thread to follow here, if you’re interested.

23andme and Navigenics take note: They’re not offering a direct to consumer service, yet, but there’s no way a SNP scan can compete with a full sequence, once the cost comes down.

via HotCites, more on this story at in-sequence.