It is famously noted that when Charles Darwin published The Origin of Species he had no plausible theory of inheritance to drive his hypothesis. Specifically, one of the major issues of the “blending” model whereby the phenotypes of the parents average out in the subsequent generation is that such mixing eliminates the variation which is a necessary precondition for natural selection. At the same time that Darwin was revolutionizing our conceptualization of how the tree of life came to be, Gregor Mendel was preforming the experiments which solidified his eponymous theory of inheritance. Though ignored in his own day by ~1900 Mendelism reemerged and offered a relatively parsimonious abstraction which could explain why variation was not eliminated through the fusion of sexual reproduction. The discrete genes themselves were simply rearranged every generation in a digital manner, a genotype was translated into a phenotype, rather than the more analog model of phenotypic mixing which underpins a blending theory.* The fusion of genetics and quantitative evolutionary biology resulted in population genetics (see The Origins of Theoretical Population Genetics), while the cross-fertilization with ecology, natural history and paleontology eventually crystallized into what we would term the ‘Neo-Darwinian Synthesis’ by the middle of the 20th century.

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I am consciously aware that the “Idiot’s Guide” series are not parodies. But when Josh Roseneau introduced me to The Complete Idiot’s Guide to Understanding Intelligent Design I simply assumed that this was a parody or gag-gift. This illustrates the lack of unity of cognitive process. On the one hand as I note above I was aware of the reality that this was a well-known brand of introductory books, but my prejudice against Creationists and Intelligent Design folk, and my perception that they’re stupid, led to me infer reflexively that this was an ironic parody. After all, it seemed mean to point out that those looking to understand Intelligent Design may be somewhat duller, on average, than those who would find the enterprise laughable.
 
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A follow up to the post below, see John Hawks, Selection’s genome-wide effect on population differentiation and p-ter’s Natural selection and recombination. As I said, it’s a dense paper, and I didn’t touch on many issues.

Razib has a nice discussion of an interesting observation just published in PLoS Genetics— that there is a negative correlation between recombination rate in the human genome and population differentiation. This observation, along with the complementary observations of correlations between nucleotide diversity and recombination and between nucleotide diversity and density of functional elements, form part of a growing body of literature establishing that the signatures of natural selection–positive and negative–have influenced overall patterns of genetic diversity in humans.

It’s important to emphasize again that these observations are influenced by both positive selection (the removal of genetic diversity at sites linked to advantageous alleles) and background selection (the removal of genetic diversity at sites linked to deleterious alleles). One important question is the relative role of these two forces in generating these overall patterns (the implications for human evolution of extensive positive selection are somewhat different than the implications of extensive negative selection); there are a couple ways forward on addressing this discussed by the authors here.

The authors here also raise the intriguing possibility of leveraging populations which have diverged at different times to examine differences in the efficiency of natural selection over time; they don’t quite have the data to do this yet, but they certainly will in the next couple years. They do make the observation, using admittedly suboptimally ascertained data, that there does appear to be the same qualitative relationship–perhaps even stronger– between recombination rate and differentiation even between very closely related populations like the Chinese and the Japanese; though only suggestive, this raises the possibility that the signatures of selection (again, both positive and negative) are detectable even on a quite short timeframe. Overall, this is an exciting direction for the use of resequencing datasets that will be coming out soon.

Finally, since John Hawks doesn’t have comments, I’ll make a comment on his post on this paper. In particular, based on the observation above (about the relationship between differentiation between closely-related populations and recombination), he writes:

There are a lot more genes that are geographically circumscribed and low in frequency affecting FST at a more localized level, and fewer affecting major allele frequencies between continental regions.

Though this may be true, the correlation between FST and differentiation between closely-related populations observed here is almost certainly not due to any effect of this sort. The data used in the Chinese-Japanese comparison (for example) is from the Affymetrix and Illumina genotyping chips (ie. HapMap 3), which contain mostly common variation and no (or very few) low-frequency SNPs specific to the Japanese (or Chinese). This effect is likely due to small differences in allele frequency between the Chinese and the Japanese at relatively *common, non-geographically circumscribed* SNPs. That is, imagine two SNPs, one at 55% frequency in Japan and 50% frequency in the rest of the world, and one at 50% frequency everywhere. Their observation (I think) is that SNPs of the former type are more common in low recombination rate areas of the genome, not that they find a bunch of new alleles that have arisen in the last few thousand years since those populations split. One could double-check this, but based on the chips they used, I’m pretty confident this is the case.

Last week Nature published a paper which may have found a new ‘branch’ of the hominin evolutionary bush which may have been coexistent which modern humans and Neandertals. I recommend The Atavism, Carl and John Hawks on this story. Interesting times.

The following passage is from the epilogue of The Real Eve: Modern Man’s Journey Out of Africa by Stephen Oppenheimer:

In this book I have offered a synthesis of genetic and other evidence. Everything points to a single southern exodus from Eritrea to the Yemen, and to all the non-African male and female gene lines having arisen from their respective single out-of-Africa founder lines in South Asian (or at least near the southern exit). I regard the genetic logic for this synthesis as a solid foundation, and I have based the rest of my reconstruction of the human diaspora upon it. Obviously, the ‘choice’ of starting point (mine or theirs) determined all the subsequent routes our ancestors and cousins took. Tracing the onward trails is only possible as a result of marked specificity in regional distribution of the genetic branches The geographic clarity of both male and female gene trees is a big departure from the fuzzy inter-regional picture shown by older genetic studies. The degree of segregation of lines into different countries and continents is in itself good evidence that once they got to their chosen new homes, the pioneers generally stayed put, at least until the Last Glacial maximum forced some of them to move. This conservative aspect of our genetic prehistory also provides a partial explanation for the fact that when we look at a person, we can usually tell, to the continent, where their immediate ancestors came from, and underlies differences that some of us still call ‘race.’

Oppenheimer wrote the above in the early aughts, as his book was published in 2003. Much of this is generally in line with the ‘orthodoxy’ of the day. I believe that Oppenheimer’s assertion that there was one southern migration out of Africa by anatomically modern humans has gained some advantage over the alternative model of two routes, northern and southern, over the past ten years (Spencer Wells’ The Journey of Man sketches out the two wave model). Other assertions and assumptions have not stood the test of time. In particular, I would contend that generally the ‘conservative aspect of our genetic prehistory’ can no longer be taken for granted. Specifically, it seems likely now that much occurred after the Ice Age and during the Neolithic.

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Bryan Caplan points to a quote from Will Durant’s The Lessons of History:

In the United States the lower birth rate of the Anglo-Saxons has lessened their economic and political power; and the higher birth rate of Roman Catholic families suggest that by the year 2000 the Roman Catholic Church will be the dominant force in national as well as in municipal or state governments. A similar process is helping restore Catholicism in France, Switzerland, and Germany; the lands of Voltaire, Calvin, and Luther may soon return to the papal fold.

Caplan observes that I would not be surprised. Well as I was reading the first sentence I did think, “yes, this is what I talk about all the time….” I remember in 1994 telling a Roman Catholic friend that his church was projected to surpass Protestantism sometime around 2020-2030. Fifteen years later that seems to have been another false prophecy, and data show that Roman Catholicism has had a very hard time hanging onto those raised Catholic in the United States over he past generation. As for France, well:

A poll published in Le Monde des Religions yesterday showed the number of self-declared French Catholics had dropped from 80 per cent in the early 1990s and 67 per cent in 2000 and to 51 per cent today.

The data for Switzerland and Germany are easy to get because church-state separation is not an issue as it is in France (or the USA). Here are some trends (keep in mind Durant wrote in the the late 1960s):

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Daniel Gross has a piece out on the rise of the cash economy, Cash Is King I found this section interesting, though not surprising:

…During the go-go years, it was common to hear theorists talk about the “discipline of debt.” On paper, high debt loads force managers (and homeowners) to make tough, swift decisions to stay solvent. Default, and you lose the company (or the house). But in reality, rather than scrimp, overextended borrowers are more likely to walk away from mortgages, or push companies into Chapter 11 bankruptcy protection. Americans are now discovering that cash exerts a superior discipline. The real discipline of cash may be that it causes executives, consumers, and investors to think twice—and to think about the long-term consequences—before spending. The need for instant gratification is part of what created the current mess.

There’s theory, and then there’s reality. I really don’t know if cash is so much better at enforcing discipline, but I’m sure theorists can invent a new rationale for why it is superior to debt financing in maximizing economic utility. Economic behavior is the most amenable in the social domain to theorizing, but too often it seems to fall prey to false certainty and after the fact rationalization of the status quote as the timeless equilibrium. This of course does not mean that we should not think logically, or deduce inferences from what we know a priori. Rather, in the social domain we should be extremely self-aware of our uncertainty as to the validity of our inferences based on the lessons of history. For example, there’s an obvious straightforward possible social consequence in regards to the spread of cash envelope usage, more break-ins. The greater utilization of relatively concrete paper currency* and its consequent drawbacks will probably make us more cognizant of the benefits of more abstract financial tools such as revolving credit card accounts (e.g., you lose cash, you’re screwed, you lose your credit card, you’re insured).

* Paper currency is itself a relatively new invention over the scope of human history

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Many of you already know this, but I’ve moved from ScienceBlogs to Discover Blogs. There isn’t much to say about this, I had a good run at ScienceBlogs, but Discover Blogs offers some new opportunities. All that matters for you is this, please update your bookmarks and/or RSS feeds:

Bookmarks: http://blogs.discovermagazine.com/gnxp

RSS feed: http://feeds.feedburner.com/GeneExpressionBlog

Also, remember my “total feed,” which covers all the blogs. I also added my occasional Comment is Free pieces to the feed: http://www.razib.com/wordpress/?feed=rss2. I also publish this to my twitter account, but there’s other stupid stuff there that you might want to avoid.

If you have a weblog that links to ScienceBlogs GNXP, I would appreciate you update the link for the same of PageRank.

Finally, I probably will be posting here far less for the indefinite future. While I was at ScienceBlogs there was a tacit understanding that I’d put the less science-oriented stuff here, the historical essays and what not. I don’t really have time to juggle too many blogs anymore, so I’m going to focus on Discover Blogs. In the future I have some ideas about making this domain more of a “user generated” website or an aggregator, but it is formative at this point. Since there are others who contribute to GNXP as a group weblog that feature will continue for the foreseeable future. But in two years I will have had this domain for a whole decade, and all endeavours go through life cycles.

P.S. Edmund Yong of Not Exactly Rocket Science is also moving; kind of like Diasporic Chindia I guess….