On BioScience and Life and Such

Archive for July, 2008|Monthly archive page

Once again Hsp90 changes how we think about evolution

In Uncategorized on July 14, 2008 at 1:37 pm

post to news.thinkgene.com

Hsp90 and it’s possible role in evolution (as a capacitor for rapid change), I have covered extensively in the  5 post series for JustScience week 08 (Revolution Evolution, Presenting….Hsp90, How can chaperones act in evolution, Evidence for Hsp90 involvement in rapid evolution of new traits and Hsp90 to end controversies in evolution theory). Recently I found this thorough review on the subject from which I would like to share the essentials (review written by Roberta L Millstein at University of California, Davis):

Recent work on the heat-shock protein Hsp90 by Rutherford and Lindquist …. has been included among the pieces of evidence taken to show the essential role of developmental processes in evolution;

To recap, the theory is that heat shock proteins can hide genetic variation until a stressful environment exposes them to allow rapid change (evolution) of morphology and subsequently, traits.

Hsp90 acts as a buffer against phenotypic variation, allowing genotypic variation to build. When the buffering capacity of Hsp90 is altered (e.g., in nature, by mutation or environmental stress), the genetic variation is “revealed,” manifesting itself as phenotypic variation.

The theory is backed up by genetic experiments on Drosophila and Arabidopsis. Results from this research on Hsp90 lends support to channeling and “hopeful monster” theory and as such, follows the more controversial line of evolution-thinking. The review sums up many of the controversial sides of conclusions from the Hsp90 research:

This phenomenon raises questions about the genetic variation before and after what I will call a “revelation event”: Is it neutral, nearly neutral, or non-neutral (i.e., strongly deleterious or strongly advantageous)? Moreover, what kinds of evolutionary processes do we take to be at work?

My goal with the previous posts on Hsp90 was to show that the data lends sufficient support to alter and revise how we think about evolution. It seems this is the goal of the review as well.

The primary goal of this paper is to illuminate the alternative scenarios and the processes operating in each. At the end, I raise the possibility of a synthesis between evo-devo and nearly neutral evolution.

Evolution I strongly believe, is not entirely and exclusively driven by a random (and slow) constant mutation rate, but rather controlled by a number of additional mechanisms to ensure that an organism can evolve rapidly. To me, this is not controversial at all, – it does not overturn any Darwinian principles, but serves as an extention to explain the speed of evolution that has sometimes baffled us. Nevertheless, conclusions drawn from Hsp90 research remains controversial to many evolutionists, and Millstein sums it up with:

I find it somewhat ironic that people who are otherwise unorthodox in their thinking with respect to evolution are so orthodox when it comes to adaptationism. After all, as the late Gould argued, nonadaptive approaches were left out of the evolutionary synthesis (Gould 1983) just as developmental processes were (Gould 2002).

Which to me, a molecular biologist gone amateur evolutionist, is a good ending note. Reviews like this, one can only hope, will lend credibility to alternative thoughts on mechanisms of Darwinian evolution. Which is surely needed to fully understand the beauty and complexity of the molecular mechanisms that shapes our world.

Note: the review I have linked to is open access, but apparantly only a draft, the final version is available here, but isn’t open access (shame on you Biological Theory and MIT press Journals).


Even the brain’s a mess, but we’re ok

In Uncategorized on July 9, 2008 at 11:04 am

post to news.thinkgene.com

As a perfect follow up on the previous post “How everything is a mess and still ok” where the subject was noise in gene expression, comes the following piece of news from e! Science news (research published in the July 4, 2008 issue of the Public Library of Science – Computational Biology):

“What we discovered is that brain maturation not only leads to more stable and accurate behaviour in the performance of a memory task, but correlates with increased brain signal variability,” said lead author, Dr. Randy McIntosh, a senior scientist with the Rotman Research Institute at Baycrest. “This doesn’t mean the brain is working less efficiently. It’s showing greater functional variability, which is indicative of enhanced neural complexity.”

and when comparing children to young adults

Researchers found that not only did the young adults score better on the face recognition tasks (i.e. they showed more stable and accurate cognitive behaviour) compared to the children, but the young adults’ brain signal variability actually increased – got noisier.

“These findings suggest that the random activity that we think of as noise may actually be a central component of normal brain function,” said Dr. McIntosh.

There’s this emerging understanding that noise is good. Noise is the diversity/plasticity that ensures proper performance and evolution of specific traits. Noise is the stuff from where melodies emerge.

This is a new way of looking at things. Our world-view used to be that melodies were created from nowhere in brilliant musical minds and noise (presumably as found in the minds of the rest of us) was a barrier that functioned only to obscure and hide the tunes. We are discovering that the opposite is true: chaos is the stuff from where good things emerge. And the brilliant minds (or biological processes if you will) are the ones able to pick the melodies from the chaos.

Quote of the month July 08

In Uncategorized on July 7, 2008 at 11:31 am

Professor Lenski, at the very end of the Lenski Dialog:

I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution. It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live. Isn’t that view insulting to God?

Baffling indeed.

P.S. Take care not to confuse Conservapedia (where the link takes you) with Wikipedia or other objective and neutral sites, – Conservapedia is a conservative christian site.

I too want to have the guts to be this honest

In Uncategorized on July 4, 2008 at 8:57 am

From this bayblab post on sleep by Rob:

The article also contains many other interesting aspects of sleep research including some conjecture on why evolution favoured sleep as such a prevalent behavior,

And then he admirably ends with……

but I didn’t understand much of it.

Thank you for leading the way Rob. I hereby promise to admit more often that I don’t understand things.

The universal PEG

In Uncategorized on July 1, 2008 at 12:00 pm

The most popular publication on SciPhu.com is on gel drying of SDS-PAGE using Poly-Ethylene-Glycol (PEG). PEG is used in many industrial applications as well as in research-experiments in the lab. Now Nature news reports that PEG may have a (distant) future in Medical applications as well. The nature News piece quotes Richard Borgens of Purdue University saying PEG acts by:

absorbing water, promoting the healing of cell membranes and preventing “the exchange of things that cause decay and degeneration of the cell”. Once it reaches human trials, PEG could be carried by trauma units and administered as soon as emergency crews reach victims of blunt-force trauma.

Especially the phrase

…..preventing “the exchange of things that cause decay and degeneration…..

,..appeals to me.

Hurray for PEG, – and may I remind you that using monodisperse PEGs (PEGs with a defined mass) increases the accuracy and reproducibility of anything you would want to use it for.