Tag Archives: Biology

Scientists scooped by evolution

It turns out that your classic experimental trick to mimic protein phosphorylation by mutating serines and threonines to aspartate or glutamate at phosphorylation sites was not first discovered by humans. Pearlman, Serber and Ferrell argue that many phosphorylation sites in proteins evolved from negatively charged amino acid residues, which means that phosphorylation evolved to mimic the effects of glutamate and aspartate. This, of course, occurred long before human scientists discovered in 1987 that you could replace phosphorlated serines and threonines with negatively charged amino acids and still get a functional protein.

“A Mechanism for the Evolution of Phosphorylation Sites”, Samuel M. Pearlman, Zach Serber, James E. Ferrell Jr., Cell Volume 147, Issue 4, 11 November 2011, Pages 934–946 Continue reading

Single cell gene expression linkfest

Gene regulation is an old field, but gene regulation at the single cell level is a whole new ball of wax. Some of us in the lab are trying to get up to speed in this field, and I need to pick out five good papers for consideration.

The place to begin is with this great review, and then work through the references:

Central dogma at the single-molecule level in living cells, Gene-Wei Li and X. Sunney Xie, Nature 475, 308–315 (21 July 2011)

Picking selectively, I ended up with the list below, and unfortunately I need to somehow narrow this down to five… and preferably all five won’t be from Sunney Xie’s group. Any suggestions?

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells, Yuichi Taniguchi, Paul J. Choi, Gene-Wei Li, Huiyi Chen, Mohan Babu, Jeremy Hearn, Andrew Emili and X. Sunney Xie, Science 30 July 2010: Vol. 329 no. 5991 pp. 533-538 Continue reading

If I read the words ‘emergent properties’ one more time today…

… in a developmental biology paper, I’m going to have to start breaking things.

This is almost as bad as referring to the collection of genomic data as the “canonical ensemble” approach. (FYI, Wikipedia: “canonical ensemble”)

I would like to know, when is a response to a morphogen gradient not considered an emergent property?

Don’t ask a biologist to explain the behavior of the solar system

After reading a string of disheartening reviews on the supposedly important future directions of biological research, I’m convinced that the older generation of biologists, those who made their careers in heyday of molecular biology during the 60’s, 70’s, 80’s, have turned biology into an innumerate outlier among the natural sciences. Continue reading

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