Theory, data, it’s all good

So says Sydney Brenner:

We now have unprecedented means of collecting data at the deepest molecular level of living systems and we have relatively cheap and accessible computer power to store and analyse this information. There is, however, a general sense that understanding all this information has lagged far behind its accumulation, and that the sheer quantity of new published material that can be accessed only by specialists in each field has produced a complete fragmentation of the science. No use will be served by regretting the passing of the golden years of molecular genetics when much was accomplished by combining thought with a few well-chosen experiments in simple virus and bacterial systems; nor is it useful to decry the present approach of ‘low input, high throughput, no output’ biology which dominates the pages of our relentlessly competing scientific journals. We should welcome with open arms everything that modern technology has to offer us but we must learn to use it in new ways. Biology urgently needs a theoretical basis to unify it and it is only theory that will allow us to convert data to knowledge.

“Sequences and consequences”, Phil. Trans. R. Soc. B 12 January 2010 vol. 365 no. 1537 207-212

ESP and genetics

…not what you think. Electronic Scholarly Publishing: esp.org. (How nice to see that domain name devoted to real science.)

The ESP site is dedicated to the electronic publishing of scientific and other scholarly materials. Of particular interest are the history of science, genetics, computational biology, and genome research.

Check out their papers on the foundations of classical genetics, from Aristotle to Malthus, Morgan, and Muller.

(Hat tip to UC Berkeley’s Brad DeLong and his history of econ course.)

Oldie but goodie on junk DNA

Posted last October, Larry Moran on Junk DNA, creationism, and Ryan Gregory’s Onion test is worth a read.

A teaser:

Note that the Onion Test is for people who think they have a functional explanation for the vast amount of putative junk in our genome. What Ryan is suggesting is that such proposals should be able to account for the huge genome of onions as well as the huge genome of humans.

Let me give you some examples. Some people suggest that we need a big genome in order to protect our genes from mutation. If that’s true then why do onions need five times more DNA? Some people suggest that we have big genomes because we’re so complex and we need huge amounts of regulatory sequence. If so, why do onions need more?

Missouri legislative session is off to a solid creationist start

It’s creationism season in my back yard again. The National Center for Science Education has the goods as usual:

First, your typical equal time time bill, complete with inept politicians’ definitions of scientific terms – in defective alphabetical order, no less:

House Bill 1227, introduced in the Missouri House of Representatives on January 10, 2012, would, if enacted, require “the equal treatment of science instruction regarding evolution and intelligent design,” according to the legislature’s summary of the bill. The equal treatment provision would apply to both public elementary and secondary schools and to “any introductory science course taught at any public institution of higher education” in Missouri. Continue reading “Missouri legislative session is off to a solid creationist start”

The genome is a huge haystack. How do you find the needle?

The complexity of the machinery by which our cells run is so extreme that one of the key questions in biological research is, why doesn’t the whole thing just collapse like a house of cards in a tornado? Another way of phrasing this question is to ask, where does the information come from to keep everything running smoothly?

Consider this: the crucial task of gene regulation is carried out in large part by transcription factors, regulatory proteins that recognize and bind to very short, degenerate DNA sequences located somewhere in the rough (sometimes very rough) vicinity of genes. Once they bind, transcription factors recruit the machinery that activates their target genes. (You can also have transcription factors that repress target genes.) This is all good, until you consider the fact that a human transcription factor has to find its target sequences from among the 3 billion base pairs in the human genome. Some plant and fish transcription factors have to search through genomes with more than 100 billions base pairs. So the question is, why don’t transcription factors get lost? Where are they asking for directions?

On finding needles in the genomic haystack Continue reading “The genome is a huge haystack. How do you find the needle?”