Where are the seculars?

Over at Island of Doubt James Hrynyshyn says:

As far as I can tell, North Carolina’s no different from the rest of America when it comes to religion. About a tenth of the population is free of religious conviction….

Well, I was pretty sure that there is a statistically significant difference between most Southern states and the rest of the country in regards to these things, so I decided to check out the data in detail. The US Religious Landscape Survey allows me to see what proportion of each state’s population are atheists; that is, they don’t believe in God. Unfortunately the margin of errors are relatively big because of small sample sizes from the unbelievers for most states, so I wanted an outside “check,” and luckily the American Religious Identification Survey has state-by-state breakdowns as well. But, their breakdowns are for those with “No Religion,” a category where the rule of thumb is only 1/3-1/2 are atheists. Out of curiosity I plotted the number of atheists on the X axis vs. the nonreligious on the Y axis.
atheistvsnoreligion.jpg
The geographic patterns are interesting. Note that the West has many nonreligious, or those who are not affiliated. In contrast, parts of the Northeast have a great number of atheists, but lack of affiliation is relatively rare in comparison to someplace like Washington or Wyoming. The American South is a relatively distinctive cluster as well, with low levels of atheism and high rates of affiliation. The Midwest is a bit more diverse, but you can also see a discernible cluster there, with similar rates of affiliation as much of the Northeast but lower rates of atheism. The raw data is below the fold….

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DNA forensics goes genome-wide

During the recent glut of genome-wide association studies, many researchers were compelled (or chose) not to make all their data public after publication due to vague privacy concerns. Instead, they often made available only genotype frequencies in sets of cases and controls, the idea being that individual-level information is lost when pooled together.

A new paper in PLoS Genetics shows that this assumption is wrong. The idea, obvious in retrospect, goes like this: assume some individual has genotype AA at a particular locus, while the frequency of A in the general population is 10% and the frequency in the pooled sample is 11%. This gives you some (very slight) amount of information suggesting that your individual is in the sample. If your individual is TT at another locus where the frequency of that allele is 25% in the general population and 27% in the pooled sample, this gives you another (again, tiny) bit of evidence that the individual is in the sample. Summing over thousands of loci, this actually becomes quite a bit of information. In fact, the authors are able to reliably tell whether an individual contributes DNA to a pooled sample, even if that contribution is around 0.1%.

In theory, then, police with an unknown person’s DNA could match it against all published case/control studies to find out if that person was involved in the study. A more immediate application could be to determine whether a suspect contributed DNA to a crime scene where the mixing of DNA (ie. blood) from a large number of individuals has muddied the forensic evidence.

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Amazon was not always “pristine”

‘Pristine’ Amazonian Region Hosted Large, Urban Civilization:

The paper also argues that the size and scale of the settlements in the southern Amazon in North Central Brazil means that what many scientists have considered virgin tropical forests are in fact heavily influenced by historic human activity. Not only that, but the settlements – consisting of networks of walled towns and smaller villages, each organized around a central plaza – suggest future solutions for supporting the indigenous population in Brazil’s state of Mato Grosso and other regions of the Amazon, the paper says.

Preliminary interpretations of these data were reported several years ago in 1491: New Revelations of the Americas Before Columbus. Mann’s argument is simple: demographic collapse in the face of Eurasian pathogens wiped away 90% of the inhabitants of the New World within about one century of “First Contact.” And thus ensued a process of the “re-wilding” of vast swaths of the New World. So the woodlands of the North Central United States which the white settlers cut down as they moved west of the Appalachians, or the virgin forests of the Willamette Valley which the pioneers encountered, were relatively recent ecosystems which arose in the vacuum of the collapse of local native populations due to epidemics introduced originally by Spaniards and other Europeans. An important point to remember here is that these epidemics preceded the white settlement in many areas by decades or centuries, so the European experience of the native populations was only in the wake of the massive social chaos unleashed by plague. Imagine if the Chinese encountered Europe first during the Black Death; but on orders of magnitude greater scale (the Black Death killed a large minority of Europeans, Eurasian pathogens likely exterminated whole peoples in the New World).
Secondarily, the possibility that many regions of the Amazon were de-humanized recently should remind us that H. sapiens are part of nature. The heuristic whereby humanity is perceived to be above, beyond and distinct from the natural world may be useful in some contexts, but in the broad historical sense we are just another animal. I am one who suspects that H. sapiens were responsible for many megafaunal extinctions as a necessary if not sufficient cause, but after these initial contacts obviously the local ecology entered into a dynamic symbiosis with human populations. It is false to say that Mother Nature is wiser than humanity, because we are subsets of Mother Nature!

War, rape and group selection

Fortune favours the brave; but the brave are motivated by favours of another kind:

If courage makes it significantly more likely that small bands of tribes-men will win military confrontations with their neighbours, its overall advantages can easily outweigh its risks, a mathematical model has shown.
Some men who carry genetic variants that promote bravery might perish because of them, but the ones who survive may win more battles through their greater daring. The resulting opportunities for rape and pillage can create a net evolutionary benefit.

The study is published in The Proceedings of the Royal Society, but it doesn’t look like it’s online yet. So I’ll have to wait on the details, but it what they’re describing seems like group-level selective events which might be vulnerable to “cheaters” who attempt to hold back and allow others to “bite the bullet,” so to speak, and reap the glory that goes to victorious tribes. Multi-level selection theorists such as David Sloan Wilson would make the argument that the way humans work against these “cheats” is through complex cognitive adaptations which allow for the policing of these anti-social traits, as well as the conventional rise and fall of groups who go through a life cycle of vigor, decline and dissipation.
I am still skeptical of higher than individual level selection in general, but, I am becoming less and less skeptical in terms of humans. I think in many ways our complex sociality is atypical enough to warrant the explanations of higher level selection and dynamics. Peter Turchin, Robert Boyd, James F. Crow and L. L. Cavalli-Sforza have also convinced me that we need to take these ideas more seriously for humans.
Related: Cooperation and multilevel selection, W. D. Hamilton & group selection & ideology and Selection on many levels…..

Virtue, sin and normalcy

Update: Overcoming Bias responds.

Reading excerpts of the memoirs of the Mughal warlord Babur, founder of the dynasty in India, I note that his father was an alcoholic. This is not exceptional in the lineage, the Emperor Jahangir’s reign was marred by problems due to his alcoholism. Nevertheless, these individuals were faithful Muslims by all their other actions. In fact, I have noted before that the early Arab Caliphs, who were responsible for the spread and dominance of Islam across what we now term the Islamic world, were by an large appreciators of wine. I was struck by Babur’s mention of his father’s weakness for alcoholism because I recently read about Glorious Revolution. As you know James II lost his throne because of his sincere Roman Catholicism. He rejected apostasy as the price of regaining his position. If his private correspondences did not attest to his sincerity, his public actions surely did. Nevertheless, despite James’ relative religious seriousness and moral qualms for a ruler of his day (in contrast to his brother, Charles II), he retained his mistress as was customary for British kings.

I point out these moral failings because I have always been struck by starkness of human hypocrisy and its incongruity in the face of avowed beliefs. How can a sincere Muslim drink alcohol? Have can a sincere Christian engage in sexual vice? One might infer from their actions that men such as James II were cynics, but as I note above James was willing to greatly reduce his chances of retaking his throne for the sake of his sincere religious commitment. I have been oversimplifying in reducing James’ moral quandary to these two issues, contrasting the manifest evidence of his religious commitment in the face of inducements to convert to Protestantism with his sexual practices which contradicted Christian teaching. There are certainly other complicating factors, but I think the point stands that sin is common, and human weakness in the face of contradiction the norm. Mens’ hearts are easily divided, and simultaneously sincere in their inclinations.

All this leads to the point that I believe far too many of those of us who wish to comprehend human nature scientifically lack a basic grasp of it intuitively. I have never truly believed in an awesome God of history, so my hypothetical behavior in reaction to this transcendent truth is conjecture. I know how I believe I will behave, but I have no true intuitive grasp. Over the years I have come to the conclusion that many atheists simply lack a deep understanding of what drives people to be religious, and that our psychological model of those who believe in gods is extremely suspect. The “irrationality” and “contradiction” of human behavior may be rendered far more systematically coherent simply by adding more parameters into the model. Too many “rationalists” insist on the primacy of their own spare and minimalist axioms, while normal humans may lack both the eloquence and intuition to communicate to their “rationalist” interlocutors that they are missing key structural variables. When I engage with these sorts of issues with readers of Overcoming Bias or Singularitarians my suspicions beocme even stronger because I see in some individuals an even greater lack of fluency in normal cognition than my own. What I am lacking in becomes all the more obvious when I see with my own eyes those who are even more damned in the eyes of God.

From all this one should not conclude that I see the reality of the mystical truths of gods before unveiled before my eyes. I do not. Rather, my point is that understanding human nature is not a matter of fitting humanity to our expectations and wishes, but modeling it as it is, whether one thinks that that nature is irrational or not within one’s normative framework. Readers of this weblog are well aware and conscious of this issue; that is why I believe it is important to broach topics such as IQ because this variable matters, and most of us would wish that retardation was simply not a phenotype which was extant, but we know that that will not be so. Similarly, those of who are psychologically atypical enough to be rather obsessed with modeling human nature into a framework which is analytically tractable need to be more conscious of the alien complexities of the normal human mind, in all its baroque paradox.

Genetics ∩ Sociology ∩ Evolution = Genomic Imprinting

praderwillikid.jpgAs I have said before biology is quite often the science of exceptions, of variation. Evolutionary biologists spend a great deal of time wondering about the origin of sex, but across vast swaths of the tree of life sex is simply not a consideration. W. D. Hamilton made his name with models of inclusive fitness, but complex social structures are constrained and fully elaborated to only a few branches of the tree of life. Like economics then what interests us in biology often has normative priors; we are a homocentric species. On a fundamental level we understand that we do not exist at the apex of a great chain of being, but most of us can not help but wonder as to the human relevance of a particular biological phenomenon.
I believe genomic imprinting is one of those biological phenomena that has an interest for humans because of its theoretical peculiarities and pragmatic relevance. Diseases such as Praer-Willi syndrome are the byproducts of the peculiar nature of genomic imprinting, or at least the malfunctioning of the phenomenon. Simultaneously the dynamic which gives rise to these diseases in our species confounds general Mendelian expectations. In the case of imprinted genes the specific parental origin of the allele has direct bearing on the phenotypic outcome. It may be that the copy of the gene inherited from the father expresses while that from the mother is silent, or, it may be the inverse. Why and how genomic imprinting is a question of evolutionary and molecular genetics. A new paper in PLoS Biology, Evolution of Genomic Imprinting with Biparental Care: Implications for Prader-Willi and Angelman Syndromes, extends David Haig’s kinship theory of genomic imprinting which I’ve reviewed before. The paper is very homocentric, as evidenced by the author summary:

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Earthquakes → progress?

Tectonic environments of ancient civilizations in the eastern hemisphere:

The map distribution of ancient civilizations shows a remarkable correspondence with tectonic boundaries related to the southern margin of the Eurasian plate. Quantification of this observation shows that the association is indeed significant, and both historical records and archaeoseismological work show that these civilizations commonly suffered earthquake damage. Close association of ancient civilizations with tectonic activity seems to be a pattern of some kind. In the hope that dividing the civilizations into subsets might clarify the meaning of this relation, primary and derivative civilizations were compared. Derivative civilizations prove to be far more closely related to the tectonic boundaries. Similarly, the civilizations that endured the longest (and that have been described as most static) are systematically the farthest from plate boundaries. It is still unclear how the relation actually worked in ancient cultures, i.e., what aspects of tectonism promoted complexity. Linkages to water and other resources, trade (broadly construed), and societal response seem likely. Volcanism appears not to be involved.

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Why are Finns anxious?

An Association Analysis of Murine Anxiety Genes in Humans Implicates Novel Candidate Genes for Anxiety Disorders:

Specific alleles and haplotypes of six of the examined genes revealed some evidence for association (p ≤ .01). The most significant evidence for association with different anxiety disorder subtypes were: p = .0009 with ALAD (δ-aminolevulinate dehydratase) in social phobia, p = .009 with DYNLL2 (dynein light chain 2) in generalized anxiety disorder, and p = .004 with PSAP (prosaposin) in panic disorder.

ScienceDaily:

Furthermore, the team’s international collaborators in Spain and the United States are trying to replicate these findings in their anxiety disorder datasets to see whether the genes identified by Finnish scientists predispose to anxiety disorders in other populations as well. Only by replicating the results firm conclusions can be drawn about the role of these genes in the predisposition to anxiety in more general.

Haplotter shows selection around ALAD for Africans. PSAP is interesting:

This gene encodes a highly conserved glycoprotein which is a precursor for 4 cleavage products: saposins A, B, C, and D. Each domain of the precursor protein is approximately 80 amino acid residues long with nearly identical placement of cysteine residues and glycosylation sites. Saposins A-D localize primarily to the lysosomal compartment where they facilitate the catabolism of glycosphingolipids with short oligosaccharide groups. The precursor protein exists both as a secretory protein and as an integral membrane protein and has neurotrophic activities. Mutations in this gene have been associated with Gaucher disease, Tay-Sachs disease, and metachromatic leukodystrophy….

Earthquakes → progress?

Tectonic environments of ancient civilizations in the eastern hemisphere:

The map distribution of ancient civilizations shows a remarkable correspondence with tectonic boundaries related to the southern margin of the Eurasian plate. Quantification of this observation shows that the association is indeed significant, and both historical records and archaeoseismological work show that these civilizations commonly suffered earthquake damage. Close association of ancient civilizations with tectonic activity seems to be a pattern of some kind. In the hope that dividing the civilizations into subsets might clarify the meaning of this relation, primary and derivative civilizations were compared. Derivative civilizations prove to be far more closely related to the tectonic boundaries. Similarly, the civilizations that endured the longest (and that have been described as most static) are systematically the farthest from plate boundaries. It is still unclear how the relation actually worked in ancient cultures, i.e., what aspects of tectonism promoted complexity. Linkages to water and other resources, trade (broadly construed), and societal response seem likely. Volcanism appears not to be involved.

ScienceNow, Did Rumbling Give Rise to Rome? has a nice map. Exogenous shocks playing a critical role in cultural creativity? Remember that earthquakes were often interpreted as negative divine omens and elicited a drive toward soul searching….

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