Wednesday, July 11, 2007

If you value alternative opinions...

Don't let Time-Warner and other big media outlets squash smaller, independent media voices that serve up more than just the bland, conformist news and opinion that has led to disaster in the US:

Stamp Out the Rate Hike: Stop the Post Office

Whether you're liberal or conservative, it affects you. Follow the link, sign the petition, and spread the word.

I promise to get back to science around here soon - personal things have taken priority lately.

Monday, July 09, 2007

Where is the leadership today?

Damn, times have sure changed. In 1944, FDR could get up before Congress and say this:

"We cannot be content, no matter how high that general standard of living may be, if some fraction of our people—whether it be one-third or one-fifth or one-tenth- is ill-fed, ill-clothed, ill housed, and insecure...

"We have come to a clear realization of the fact that true individual freedom cannot exist without economic security and independence..."

"In our day these economic truths have become accepted as self-evident. We have accepted, so to speak, a second Bill of Rights under which a new basis of security and prosperity can be established for all regardless of station, race, or creed.

Among these are:

The right to a useful and remunerative job in the industries or shops or farms or mines of the Nation;

The right to earn enough to provide adequate food and clothing and recreation;

The right of every farmer to raise and sell his products at a return which will give him and his family a decent living;

The right of every businessman, large and small, to trade in an atmosphere of freedom from unfair competition and domination by monopolies at home or abroad;

The right of every family to a decent home;

The right to adequate medical care and the opportunity to achieve and enjoy good health;

The right to adequate protection from the economic fears of old age, sickness, accident, and unemployment;

The right to a good education.

All of these rights spell security..."

"For unless there is security here at home there cannot be lasting peace in the world."

Today I would also add this: a thriving scientific research community can't be sustained in a country that does not make economic security, including inexpensive access to medical care and higher education, a reality for all of it's citizens. No middle class, no scientists.

More Confusion about Junk DNA and Regulatory Sequences

Back in June, John Greally, a biologist at Albert Einstein, wrote a frustrating Nature commentary on the ENCODE project in which he repeatedly and wrongly suggested that before ENOCODE, biologists were only paying attention to regulatory sequences:

"We usually think of the functional sequences in the genome solely in terms of genes, the sequences transcribed to messenger RNA to generate proteins."

"Now... the ENCODE Project Consortium shows... that the humble, unpretentious non-gene sequences have essential regulatory roles."

"...The researchers of the ENCODE consortium found that non-gene sequences have essential regulatory functions, and thus cannot be ignored."

Now, Greally spreads more confusion on NPR's Science Friday (hear it here at Sandwalk, where Larry Moran is as stunned as I am) by continuing to act as if we had no idea before ENCODE that regulatory sequences were so prevalent or important. In the interview, Greally even goes so far as to suggest (and allow the interviewer to suggest, without correction or clarification) that 95% of the genome consists of regulatory sequences. Nor does he correct a caller on the show who claimed that scientists were ridiculous to even suggest the idea of junk DNA.

The ENCODE project showed no such thing, and it wasn't the huge breakthrough in our understanding of non-coding DNA that Greally is hyping it to be. Non-coding regulatory sequences have been intensely studied, including large-scale experimental and computational surveys from yeast to humans. These sequences have not been ignored; many labs have put a lot of effort into identifying and understanding them.

Nor did the ENCODE project bury the idea of junk DNA. For example, 10% of the human genome consists of hundreds of thousands of copies of parasitic stretches of DNA called Alu elements. (A search on Google Scholar will turn up free copies of this paper.) Alu elements can, on occasion, generate beneficial and novel genomic diversity, but most copies of Alu elements are non-functional and unable to replicate - in other words, junk. In fact, Alu insertions can cause disease - as they hop around the genome, they occasionally break something.

There are many, many other examples of this kind of junk; it's not all poorly understood 'dark matter' of the human genome, as Greally suggests in the NPR interview. When we have finally identified all of the regulatory sequences, I predict that the total amount of functional regulatory sequence will still be much less than that the 45% of the genome comprised of the parasitic LINE and SINE transposable elements.

Saturday, July 07, 2007

Mammas, Don't Let Your Babies Grow Up to Be Postdocs

In most careers, when you do a good job, you get rewarded - a promotion, a bonus, a raise, whatever. These things are the incentives that make you strive to do your best.

In science, as a postdoc, you get penalized for your success.

I did something postdocs are supposed to do - get money by writing a research proposal that you submit to a funding agency. The process is competitive and time-consuming; when you are successful, this is a significant achievement, an essential step in your career.

But the actual payoff is really years down the road. In the immediate aftermath of successfully obtaining a funded postdoctoral fellowship, you lose out:

- Your salary very well may decrease. That's right - if you write a successful research proposal, your salary could go down. The going rate for an NIH fellowship was less than what I was earning as a university-paid fellow; it was only thanks to the timely help of my advisor I avoided a pay cut.

- Your health insurance premiums become fully taxable. Before I was funded by the NIH, my health insurance premiums were taken out before taxes - just as it's done for everyone else in the country with employer-sponsored health insurance. Once you are an NIH fellow however, your insurance premiums (including the hefty 'employer contribution') are not deducted before taxes - the entire cost of your health insurance premiums is considered taxable income. Thus my taxable income jumped up by several thousand dollars, but my take-home pay remained unchanged. (You can of course deduct the premiums at the end of the year, but this substantially complicates your tax filing.)

- You have to submit your own tax payments. As an NIH fellow, you are nobody's employee - not the university's, not the government's. But the IRS doesn't consider you self-employed either. You technically don't earn wages. You don't receive a W-2. You're not a student.

Thus you have to spend hours navigating the labyrinthine state and U.S. tax codes to figure out how to submit quarterly tax payments. I thought I had it all figured out - until I suddenly discovered that in my state, quarterly doesn't exactly mean quarterly. It turns out that sometimes you have to submit three months worth of taxes after just two months of pay! (April 15 to June 15). Of course, on my shamefully excessive NIH postdoc salary, it's no problem at all to save up extra taxes on income I haven't been paid yet. I suppose I shouldn't be eating anyway - there is lab work to do!

The list could go on... The sheer hours of bureaucratic combat involved in living off of NIH funding makes the whole process almost not worth it. Almost - there is the fact that your future academic career is not too bright if you don't manage to get some sort of fellowship.

Postdocs are in such a nebulous, in-between world - not students, not staff, not faculty, not employees of any kind. This basically means you're everyone's awkward step-child, only partially claimed by the NIH and the university, left to fend for yourself.

Friday, July 06, 2007

A Plug for Scientific Blogging

And I mean sepcifically, the site Scientific Blogging, not jut blogging in general.

Scientific Blogging features science news and blogs by working scientists (including yours truly). The bloggers cover every thing from math and physics to psychology, and range from lowly grad students and postdocs, like myself, to real science professors, as well as some science-trained bloggers working outside of academia.

On the whole, the site aims to be politically non-ideological. It's not a conservative site, as some seem to think; it's simply much less political than other major sites, like Seed's Science Blogs. Given the pervasive scientific illiteracy in our society, there is definitely a need for blogs that feature science writing that will be read by people from a range of political loyalties.

Not that I'm knocking Seed; I'm a regular reader of Pharyngula, and I need my daily dose of political red (uh... make that blue) meat to keep sane in our current political climate.

Scientific Blogging is still in public beta mode, but it already has some nice features, like a peer voting system (you vote for articles you like), and a place for anyone interested to set up their own blog. There is a set of hand-picked featured writers, but if you like writing science, and you want to write where someone will actually read it, you can set up your own space at Scientific Blogging. We're hoping to create an active community of people who love reading and writing about science, so go over and check it out.

Thursday, July 05, 2007

Junk DNA in the Opossum Genome

Vertebrate genomes are full of junk. Despite the occasional confusing magazine article, the spurious claims by creationists, or obfuscatory statements by some scientists, we know that our genomes are stuffed full of DNA sequence that serves no functional role for the organism. The vast bulk of this junk sequence consists of molecular parasites, called transposable elements, whose only 'function' is to replicate themselves. While our genomes obviously contain critical information required to build and maintain ourselves, they are also vast ecosystems of virus-like parasites that have colonized our DNA.

A recent paper in the journal Genome Research describes the DNA ecosystem of the opossum genome. "Ecosystem" is not an exaaggeration; more than 52% of the opossum genome is comprised of transposable elements, which can be classed into nearly 500 different families. Transposable elements are similar to viruses; they are, one way or another, able to replicate themselves within an organism's genome and get passed on to the next generation. These elements have variety of survival strategies; some elements get transcribed into RNA and then 'reverse transcribed' back into DNA and inserted somewhere in the genome, while other elements never go through an RNA stage. Some transposable elements encode proteins that enable them to spread through the genome more efficiently; other elements don't bother to code for any proteins and instead hijack the proteins produced by those elements that can code for them.

Why do transposable elements exist in our genomes? Because they can. If a DNA element in an organism's genome can get itself passed on into the next generation, whether that element is beneficial to the organism or not, then obviously it will remain in the genome of that species. Since these elements don't generally serve any functional role, there is no reason for natural selection to preserve them, and we thus see piles of defective copies of transposable elements scattered around our genomes. These elements no longer have the ability to spread through the genome and they serve no function - they are pure junk. While our cells do have systems that try to stop these elements from spreading, we, and most animals, have not evolved effective ways to get rid of the junk elements once they are there; these elements therefore hang around and bulk up our genomes with non-functional material. About 45% of the human genome consists of these elements; that fraction rises to 52% for the opossum (which has a genome slightly larger than ours).

Transposable elements are not completely useless. For one, biologists love them because they can be helpful for studying evolutionary history - one approach to teasing out relationships among various species is to reconstruct a rough history of transposable element activity in various genomes. We have also known for some time that these elements can occasionally be recruited for a functional role (such as telemoeres in flies, X-chromosome inactivation in mammals, and centromeres in various organisms).

The opossum paper offers even more tantalizing, although not wholly unprecedented, evidence of a larger role for transposable elements. The authors of this paper looked at transposable elements, common to both opossum and human, that were present in known or suspected regulatory regions of the genome. Transposable elements in these regions are obvious candidates for a functional role. And remarkably, the researchers found that a handful of transposable element families were highly abundant in these regulatory regions - in one case, 70% of all the individual elements of one family were found in regulatory regions of the genome. It is possible that this particular family of transposable elements somehow contains a useful 'regulatory module,' some sequence that has been recruited through evolution to control the expression some genes. If this is true, than this would be a case of transposable elements providing the raw genetic material to create new layers of regulation in the genome.

So while most of the self-perpetuating transposable element ecosystem is undoubtedly junk from the perspective of the organism hosting it, our genomes are occasionally able to scoop up some of the detritus and put it to good use.