Monday, June 12, 2006

Mendel's Garden #1

Lot's of good reading for the first edition of Mendel's Garden, so grab a cool drink and sit a bit and enjoy the harvest.

First up from RPM at Evolgen is an article on the evolution of gene regulation: The Evolution of My Thinking about the Evolution of Gene Regulation. RPM observes that much evolutionary change involves regulatory elements that affect the transcription of protein coding genes, or portions of genes. These elements are classed as being cis or trans regulatory elements. Cis regulatory elements (CRE's) are regions of DNA associated physically with the protein coding sequence they regulate and these cis elements either enhance or prevent transcription when regulatory proteins bind to them. Trans regulatory elements (TRE's) may be in another part of the genome, and code for regulatory protein that diffuses to another part of the genome and may help regulate gene expression of a number of different genes.

RPM's article critically examines the question of which type of element is most important in evolution. Right now, because of the work of Sean Carroll and others the emphasis has been on CRE's but RPM sees evidence for the role of TRE's. So check out his article for some good reading. A useful review of gene regulation is here.

PZ Myers at Pharyngula reviews a new book on the sequencing of the genome of Drosophila in a submission called Won for All from the book's title. For my non genetics readers, if you have left bananas out too long you are probably familiar with these little fruit flies that have played a very important role in understanding genetics. While you are there jump on over to the article on Clausen Keck and Hiesey. He didn't submit this but it is a nice blast from the past and touches on concepts related to many of the other submissions- well at least to my caffeine powered synapses.

Just in case you think that the genetic code is completely understood and that there are only 20 amino acids used for making proteins comes these articles from Sandra Porter's blog on selenocysteine with some choice commentary. Even though I have commented on these elsewhere, these are a great illustration of how science works, along with some interesting cautions about some of our protein data bases, so I offer up for your pleasure Future Shock and Selenocysteine Part I and Part II from her old archive at Blogger.

Dan Rhoads over at Migrations steps back and looks at the evolution of kinases and it's relationship to phylogeny on a grand scale in his post Kinomes: Evolution of an enzyme, from Yeast to Man. Dan notes that analysis of Kinases indicates that different kinases diverged very early in the history of life and that:

"Differences between kinase subfamilies and genes across species strongly reflect changing cellular functions, including the loss of kinases involved in unicellular-specific functions, and acquiring of kinases involved in immunity, neurobiology, cell cycle control, and morphogenesis"

Not too suprising given the importance of these enzymes. By the way here is a nice site dealing with the Human Kinome where you can even download a color poster showing the relationships among human kinases.

Ruth Schaffer provides a couple of short but interesting submissions. The first one from the Biotech Weblog summarizes an article from Reuters on a company planning to use genetically modified chickens to produce human antibodies. The second one from the allergizer blog examines the link between depression and allergies. The article notes that parental depression, more precisely maternal depression is correlated with allergies in children and the authors of the article suggest that there may be common genes related to both depression and allergies. As an aside that may be true, but perhaps the influence is through some sort of maternal affect.

Speaking of chickens, From Coturnix over at A Blog around the Clock we have transgenic chickens only this time a thoughtful gripe about the press releases by which these sorts of technical advances are announced to the public.

Next Hsien-Hsien Lei has a topical article given the sports news lately on Gene Doping in Soccer from her nice blog, Genetics and Health. Apparently a biotech company has engineered a viral vector to deliver the human erythropoetin gene through injections into the muscle to treat certain sorts of anemia. When oxygen levels are low, production of erythropoetin is stimulated resulting in more red blood cells. At least one coach has allegedly inquired about obtaining this product which goes by the trade name Repoxygen. She links to an article in New Scientist called 'Gene Cheats'

A new role for RNA, interference RNA, or RNAi has been in the news recently for its potential to treat various diseases including cancer. Coffee Mug at Gene Expressions provides us with a primer on RNAi, called appropriately RNAi fundamentals. I have read about RNAi but didn't realize that there are two types. The first type called siRNA's start out as pieces of double stranded RNA's from transposons and RNA viruses. The second type called, miRNA's appear to be important in regulation of gene expression. Razib says:

"miRNAs are purposefully endogenously produced to play a regulatory role in several cellular processes. They are conserved across higher eukaryotes, and are estimated to regulate some 30% of human genes."

Wow a whole new regulatory pathway! In fact both type of RNAi are collectively small regulatory RNA.

Gene expression is on everyone's mind it seems, and Salva Almagro at Vivalaevolution , discusses a really neat article from PLOS that notes that gene with high G or C content in the third codon base tend to be expressed at higher rates. Interesting since all U--->C (think wobble) and most A ---->G substitutions in that position don't make any difference in the amino acid coded for by the codon.

Veering away from molecular genetics we have a clutch of articles that more of an methodological, historical and philosophical bent. The first one is from Jacob at Salamander Candy with a wonderful synthetic article on the mistakes geneticists make in reasoning about the causal relationships between genes and environment, pointing out some logical and interpretive errors in some published literature. By the way Salamander Candy is put together by a group of grad students at Oregon State who describe themselves as:

"...a hive mind of geeky zoology graduate students in Oregon who have nothing but vast amounts of spare time in which to write silly blog posts."

I suspect the Blog is really a form of stress release for them, but hey that's OK. :-)

In a related vein, but getting a bit more into the societal aspects of genetics is an interesting discussion of the heritability of IQ and other traits related to well, "getting ahead" called Why genetic determinism is inevitable in a meritocracy from Razib also at Gene Expressions.

Razib comments:

"The title says it all, I make an argument that assuming particular
genetic parameters you can make some long term sociological
predictions which might undermine intuitions. In this case, the
heredity principle might win in a meritocracy over the long haul...."

Razib argues that in a meritocracy social mobility may actually decrease over time. This is because in lower class environments heritability of say intelligence is relatively low. This would be expected if, he argues, the poor are "buffeted" by more influences that can adversely affect intelligence, whereas the rich are in a more uniform environment for intellectual development. If you improve education so that everyone is in a rich and uniform environment then the variation in intelligence that is available will be due to genetics, and the result would be a sorting based on genetics and a reduction in social mobility.

Razib says:

"In a perfect meritocracy, where environmental variables are mitigated by equal opportunities the differences due to genetics would be paramount because those are the only major non-stochastic parameters."

Now Razib is not arguing that we should not improve educational opportunities, so this is no Bell Curve type of argument. Also there are lots of other factors he is ignoring and assumptions he makes, but the article is worth reading if only because of the explanations about heredity. It also has an extensive set of comments about social mobility. A nice entry to lead into a more general question about whether or not our species is still answer FYI is yes by the way.

Finally A Blog Around the Clock never stops and I have to include Coturnix's Lysenko Get's a D-Minus On My Genetics Test. Lysenko is the Soviet era biologist usually blamed for the failures of Soviet Agriculture. I can remember being taught way back when something to the affect that he believed that environmental effects on the phenotype could be inherited, a la the inheritance of acquired characteristics. Coturnix places Lysenko in the context of some of the debates that were raging at the time about the role of genes and environment. He notes in contrasting science in the United States with Soviet Science that:

"..1948 U.S. was genocentric and Soviet science was Lamarckist. Who is to say which is "worse"? They are both wrong. They were both consistent with the information available at the time."

That of course does not mean Lysenko's science was correct, but Cortunix argues that there are a number of threads leading to Lysenko's stance. Indeed Cortunix even attempts to relate the sort of competitive view point taken by Darwin and other early evolutionary theorists vs the cooperative view of evolution taken by Lysenko.

Thanks for everyone who submitted and I hope those who stop by at the Garden to visit the blogs and submissions have as much fun as I did. Remember if you are interested in hosting Mendel's Garden on your blog, visit the Garden's home page or feel free to e-mail me. ;-)

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Coalescent said...

Hey, the link to "Kinomes: evolution of an enzyme" appears to have died.

Dan said...

Indeed, for the kinomes post and the rest of my blog, I had to move it to a new blog host - that domain and it's server were too unreliable.

The article has been moved to here:
Kinomes: evolution of an enzyme