During the break I was busy with typical holiday/break activities (including the first half of my daughter’s improbably exciting U11 girls’ basketball season) as well as a lot of intense reading/writing/research related activities. I’ll hopefully be blogging more about the latter in the next several months, but in the midst of them and out of the typical classroom teaching routine, blogging kind of fell by the wayside. Hopefully it will resume at a normal pace starting this week.
In the meantime, here are some good/interesting reads to get the week and semester started:
* Genomic analysis results: understanding, or Fairy dust? – Ken Weiss, writing at the Mermaid’s Tale, gives his latest on GWAS, “missing heritability,” and the reality of biological/genetic complexity:
In the face of this apparent complexity–many argue that life can’t really be that complex. One may feel that it’s just not plausible that hundreds or thousands of genes can be the explanation for traits that show orderly value distributions in populations. That orderliness, and the relatively orderly nature of evolution, and the fact that a trait can be knocked out by single genes, all might be seen as indicating that life must have been able to evolve our complex traits in a way that is not so complex after all. We’re just not understanding–yet!
* Our paper: Assemblathon 2 and pizza – Keith Bradnam provides some discussion of his recent paper at Haldane’s Sieve. It includes a fantastic use of pizza-making as a metaphor for genome assembly (the focus of their paper):
What is true for ‘making pizzas’ is also largely true for ‘making genome assemblies’. There are probably as many genome assemblers out there as there are pizza establishments in Davis, and people clearly want to know which one is the best. But how do you measure the ‘best’ genome assembly? Many published genome sequences result from a single assembly of next-generation sequencing (NGS) data using a single piece of assembly software. Could you make a better assembly by using different software? Could you make a better assembly just from tweaking the settings of the same software? It is hard to know, and often costly — at least in terms of time and resources — to find out.
* Starchy diet may have transformed wolves to dogs – The typical caveats of headlines apply, but this Science News piece blurbs a recent interesting (and not surprising!) paper about the co-evolution of domesticated canine diets:
Dogs can digest carbohydrates better than wolves can, and gaining that ability may have been an important step in taming the animals, evolutionary geneticist Erik Axelsson of Uppsala University in Sweden and his colleagues report online January 23 in Nature. As humans settled into farming communities, wolves may have given up their meat-only diets to scavenge carbohydrate-rich food from garbage dumps. Animals that could best make use of the starchy food may gradually have morphed over generations into man’s best friend.
As humans went through the ecological shift associated with intensified agricultural production and sedentism, a number of genetic variants associated with changing dietary practices because established and more widespread in human populations. The same seems to have occurred during the domestication of dogs (not surprisingly!). This is yet another example of evolution in action and a caution to not treat living things as representative of prehistoric realities. Humans, and human diet have evolved from the Paleolithic. There is a lot to learn about human diet through understanding the evolutionary process specific to human populations and regions, but living humans are not paleo-humans and trying to re-create paleo dietary practices as a health goal is a complicated and, I think, often misguided quest. Dogs have evolved…so have humans.
* Thanks for the Mutations, Dad – Peter Gray, in his latest post at The Evolving Father, talks about the importance of high rates of paternally-derived do novo mutations.
Various studies have suggested that fathers in higher primates (such as humans, apes, Asian and African monkeys) provide 4-6 times as many point mutations as do mothers. In other words, a gorilla baby could trace the vast majority of any novel mutations in its genome to its father rather than mother. In a recent study from Iceland, researchers provided the most rigorous study yet quantifying the sex-specific human parental mutation contribution. Employing whole genome scans of some 78 mothers, fathers, and their children, it turned out that fathers, on average, introduced 55 new mutations, mothers providing 14 new mutations. In other words, fathers provided about 4 times as many new mutations as mothers to their progeny.
* Ruth Benedict, Patterns of Culture: From Culture to cultures and…
* Eric Wolf, Europe and the People Without History – Geography, States, Empires – Jason Antrosio does double-duty with excellent posts on Benedict and Wolf.
UPDATE: And for something a little fun, I recently stumbled upon the WTFevolution tumblr…which is pretty great.
