28.2.07

Quote of the Day

Barbara McClintock, 1980, re: Transposable Elements

"Since the types of genome restructuring induced by such elements know few limits, their extensive release, followed by stabilization, would give rise to new species or even genera"

via A. Fontdevila

24.2.07

Genomania! Book-a-rama!

Michael Lynch has a new text book coming out next month. It's called The Origins of Genome Architecture and is published by sinauer and Associates (who also have some other great science titles). Briefly:

Under Lynch’s hypothesis, the genome-wide repatterning of eukaryotic gene structure, which resulted primarily from nonadaptive processes, provided an entirely novel resource from which natural selection could secondarily build new forms of organismal complexity.


By nonadaptive processes I think they are refereing to drift and mutation and how these two random processes interact to provide the material for Natural Selection.

An important point to keep in mind when thinking about Natural Selection is that it is at least a two-step process. The first, random stage (where drift and mutation come into play) is where all the variation is generated that in the second, nonrandom stage are eliminated (i.e. survival of the fittest). I look forward to a treatment of organismal complexity with regards to drift and mutation.

You can get a feel for what is to come with a recent review in Science: Mutation Pressure and the Evolution of Organelle Genomic Architecture.

Another book that I want to try and tackle soon is West-Eberhard's Developmental Plasticity and Evolution. Although I have heard great things about it, it doesn't seem to be a very accessable (i.e. easy to get into) book.

And also, a potentially interesting textbook on Evolution by CSHL comes out this summer, but who know if it offers anything about what is already available (but the webpage sure is nice).

The RNA Intermediate

I came across this great paragraph in Principles of Population Genetics by Hartl (3rd ed):

The central role of RNA in gene expression is one of the oddities of biology taht makes sense in the light of evolution. That gene expression is configured around RNA is a legacy of the earliest forms of life when RNA molecules served both as carriers of genetic information and as catalytic molecules. The role of RNA as carriers of genetic information was gradually replaced by DNA, and the role of RNA as catalytic molecules was gradually replaced by proteins. At every step along the way, as the RNA world evolved into the DNA world, the role of RNA was indispensable in the processes of information transfer and protein synthesis, and so the RNA intermediates became locked in place.

An apt summation of the idea. An interesting aspect is that indeed RNA still does retain it's catalytic capabilities (i.e. regulatory) in many organisms and also it serves as information storage in many viruses, and there is even some evidence of that role in plants. So despite the ancestry of this division of labour, RNA still seems to maintain it's "ancestral" roles, and is not simply an intermediate between DNA and protein. I wonder what the future holds in terms of DNA as catalytic and protein as information storage. Perhaps some findings will change the dogmatic views of the roles of these molecules also.

23.2.07

Danger

Today was the last day for the Annual Spring Meeting here in Cologne. The topic this year was "Evolution on Immunity and Pathogens". The two most exciting talks for me were from Max D. Cooper who presented an exciting model of adaptive immunity in agnatha which is quite distince from that in the gnathostomata. The other exciting talk was an overhead talk (as is typical) by Polly Matzinger discussing her Danger Model of Immunity and her adamant debunkment of traditional views into immunology.

20.2.07

The Gay Allele

There was an interesting News and Views published last month in Nature. This piece discusses a paper by Gravrilets and Rice in PNAS outlining population genetics models of how a genetic basis for homosexuality would be maintained in a population.

The problem:

Homosexuality has a cost to fitness — that is, the ability of an individual to produce offspring that survive and reproduce — and it can only evolve if it otherwise provides indirect benefits to reproduction.

The models:

First, in the case of overdominance, a 'gay allele' would result in homosexual behaviour in an individual who has received this allele from both parents (homozygous), but would provide an advantage to the heterozygote

In the second case, sexually antagonistic selection, a gay allele would result in a cost when expressed in males ('feminization' and loss of fitness), which would be counterbalanced by a fitness advantage when it is expressed in females.

In the third hypothesis, kin altruism, homosexuals would help their own family members, increasing the fitness of their relatives and therefore the probability that a gay allele is passed on to the next generation.

The paper itself goes on to discuss models for the first two scenarios, however the major assumption stands:

a gay allele will produce variable degrees of homosexual behaviour, which is equivalent to the fitness cost of that behaviour

This gives a very skewed image of the phenotypic penetrance. In an allele whose phenotype can be covered up it is difficult to make such assumptions as to the correlation between a gene and the extent of the phenotype. You could make a case that social acceptance gives a better correlation to sexual behaviour than genetic factors, if they were ever found.

The last model, which is not discussed in the paper, is also interesting. The classic example of kin altruism is among eusocial insects, however, humans are certainly far from the model of eusociality. worker ants are either prevented or unable to concieve (by parthenogenesis) or to mate unless the conditions allow it. Such a strong distinction between reproducing and non-reproducing castes do not exist for humans.

The News and Views makes a good point about the importance of this paper in that "it generates several testable predictions". It would seem more interesting to investigate homosexual behaviour in nonhuman animals, where unbiases perspectives are more likely.

13.2.07

Wandern

"Wandern" is the German word for "hiking", but when I hear it I can't help but think of wandering. Well, depending on who you go with with hiking really is a lot like wandering.

I like the idea of wandering thou. It reminds me of the wonder that surrounds me. I'd prefer to wander through my ideas, books and papers instead of getting directly to the point right away. At least in those cases where I have time my prefered method is to read a paper and stop at some point, even after the first sentence, and begin to daydream about what I just read. Then I'm off! Wandern! It's usually at these times that I come across the most exciting conclusions and connections to other things I have read.

The idea of wandering though life also fascinates me. I remember reading "Memoirs of a Geisha" (on the very trustworthy recommendation from Oprah). In in the protagonist talks about her water sign and how her life is a reflection of a path of water flowing through a river, it's path bending and guided by the many features surrounding it, constantly changing, moving. In a sense the water just flows, it flows because it flows, always travelling, moving, wanderning through the river. In Buddhism the River comes up when talking about emptiness and impermanence. What is the river? can you touch the river? By the time you see the river and think about it, it is gone. There is no river, it is constantly changing. This is a starting point for a reflection of ourselves. We are the river, constantly changing and moving, there is no real thing that is the person. You can't grab it and call it a person, and in that sense we are rivers and we are wandering. Thorugh forests, life and ideas.

It is also an apt description of evolutionary direction. There is no direction to speak of (although there are, of course, constraints). Mutations act at random, drift acts at random. The collective influence of stochiastic events is incredible. And so it is not just the individual that wanders but it is indeed a reflection of all of nature.

12.2.07

Good Morning, Charles. Good Night, God.

What could be a better day to begin a science blog than on Darwin Day.

Yes folks, today marks the 198th birthday of the grand daddy of Natural Selection. The very name Darwin still ignites excitement in the hearts of many, scientists and religious folk alike, but for very different reasons.

To be honest, I am a bit disgusted at the use of religion as a political weapon but by the same token, I can't agree with people using science to argue with religious institutions. You can find any number of blogs praising evolution and Darwin and in the same breath having utmost contempt for religion.

Perhaps the thing I find most ironic of it all is: Dogmatic religious attitudes are condemned by most of the science establishment, yet their convinction of Darwin and their contempt for religion is in itself dogmatic.

This is my favourite quote about relgion from a scientist:
Buddhism has the characteristics of what would be expected in a cosmic religion for the future: It transcends a personal God, avoids dogmas and theology; it covers both the natural and spritual; and it is based on a religious sense aspiring from the experience of all things, natural and spiritual, as a meaningful unity. -Albert Einstein

That, in short, is what it's all about. I hope to develop this blog into a home for my thoughts and observations on the exciting aspects of my scientific life as well as highlighting the inherent compatibility of science, nay life, with Buddhism. Not ever post will deal with both, or even either.