Like many people I’ve been following the tales of the Hobbits of Flores, H. floresiensis, with some interest since 2004. And, like most people I have no personal expertise or skill which is relevant to evaluating whether this putative hominin species actually is a new species (as opposed to a pathological modern human). So how are we to evaluate a new PLOS ONE article which comes down on the side that it is a new species? First, my very vague impression is that over the past ~10 years the new-species camp has been gaining ground on the pathological-modern-human set. But setting all that aside perhaps the critical issue for me is that the likely reality of archaic human admixture into our own lineage means that the world is far stranger than we had thought in 2004. For various anatomical and paleoanthropological reasons H. floresiensiswas implausible. But as implausible as the idea that the genome of a Siberian hominin would yield admixture in modern Papuans?
In 1866 the French Academy of Sciences banned discussion of the origin of language. The nature of language in an evolutionary context is a big question which just keeps giving. But obviously the French academy thought that it was giving a little too much without resolution. Despite being fascinated with the topic at one point, and reading books such as The Symbolic Species and The Language Instinct, I’ve come away with the opinion that there’s a lot to the evolution of language which is just unknown. A few years ago some researchers were strongly implying that fully fleshed out language is what led to the behavioral revolution of anatomically modern humans ~50,000 years ago (see The Dawn of Human Culture). But now many scholars are arguing that language may be an ancestral character of the descendants of H. erectus.
Of course to gain some clarity on the evolutionary origins of language we need to think deeply about what language is for. The simplest explanation is that language is to communicate. You tell your mother that you are hungry. You communicate with your peers about whatever cooperative task you are engaged in. But a new article in The New York Times highlighting the discovery in the first generation of a new language emphasizes one aspect that I think we often forget:
A humanistOver fifty years ago C. P. Snow wroteThe Two Cultures. The details of the argument, and his more general worry about the state of his society, are less important than the fact that there has been a persistent and widening chasm in perception, and often in reality, between the two antipodes of intellectualism, the humanities and science. This has not always been so. The great evolutionary geneticist J. B. S. Haldane studied mathematics and “the Greats.” From what I can tell the latter is equivalent to classics. This combination is not unheard of, the eminent UCLA neuroscientist Paul Thompson has a similar educational background (he is also British, like Haldane). The string theorist Edward Witten received his first degree in history, only later shifting toward a focus on mathematics and science. But these are exceptions, not the rule.Most people who end in the sciences began in the sciences, and the majority do not have a liberal arts college undergraduate background.*
The converse situation is also true in regards to experience and familiarity. Most who are enmeshed in the humanities have only a cursory knowledge of science, and a general unfamiliarity with the culture of science (though more students switch out of science to non-science degree programs than the reverse). In most cases I find the ignorance of science by non-scientists sad rather than concerning, but in some instances it does lead to the ludicrous solipsism which was highlighted in books such as Higher Superstition: The Academic Left and Its Quarrels with Science. Though there is often a focus on fashionable Leftism in these critiques, it may be notable that the doyen of “Intelligent Design” has admitted a debt to Critical Theory. The scientist-turned-theologian Alister McGrath positively welcomes post-modernism in his The Twilight of Atheism: The Rise and Fall of Disbelief in the Modern World. The problem is not ignorance of science, as much as the dismissal and mischaracterization which that ignorance can give birth to in the right arrogant hands.
The New York Times recently put up a piece, Has ‘Caucasian’ Lost Its Meaning? Much of the analysis in the article has too much of a feeling of ethnographic ‘close reading’, but I still am excited that the middle-brow journal of record has started to weigh in on the ridiculousness of the whole situation. I’ve been arguing that people should stop using “Caucasian” when they mean white or European for years, because the use of the term in this manner has led to farcical but common instances of semantic muddle such as the below exchange:
****Whate race do GEORGIAN people belong to***? – well if you are georgian or armenian and you go to other country, it is very hard for people to believe that you are white, everyone thinks either you are hispanic or mix so i was wondering what is the name of the race georgians.armenian are?
[One of the answers] As more and more people move around and settle in different locations, it’s becoming more and more difficult to ‘racially’ identify people by regions. Now if it were a few hundred years ago, I would have said Caucasian…but then as time has gone by Middle Eastern seems more appropriate…
Obviously, unlike a few hundred years ago, Georgians no longer reside in the Caucasus mountains. Nor are they any longer the archetype of West Eurasian populations. I am not going to have one of those inane discussions about whether Georgians really are white, though any reader who believes such a thing is invited to start referring to Stalin as the Soviet Union’s only head of state of color in the future. My primary issue with the modern American usage of the term is two-fold:
One of the elementary aspects of understanding genetics on a biophysical scale is to characterize the set of processes which span the chasm between the raw sequence information of base pairs (e.g. AGCGGTCGCAAG….) and the assorted macromolecules which are woven together to create the collection of tissues, and enable the physiological processes, which result in the organism. This suite of phenomena are encapsulated most succinctly in the often maligned Central Dogma of Molecular Biology. In short, the information of the DNA sequence is transcribed and translated into proteins. Though for greater accuracy and precision one must always add the caveats of phenomena such as splicing. The baroque character of the range of processes is such an extent that molecular genetics has become a massive enterprise, to a great extent superseding classical Mendelian genetics.
One critical structural detail from an evolutionary perspective is that the amino acids which are the building blocks of proteins are generally encoded by multiple nucleotide triplets, or codons. For example the amino acid Glyceine is “four-fold degenerate,” GGA, GGG, GGC, GGU (for RNA Uracil, U, substitutes for Thymine in DNA, T), all encode it. Notice that the change is fixed upon the third position in the codon. Altering the first or second position would transform the amino acid end product, and possibly perturb the function of the final protein (or perhaps disrupt transcription altogether in some case). These are synonymous substitutions because they don’t change the functional import of the sequence, as opposed to the nonsynonymous positions (which may abolish or change function). In an evolutionary context one may presume that these synonymous substitutions are “silent.” Because natural selection operates upon heritable variation of a phenotype, and synonymous substitutions presumably do not change phenotype, it is often assumed that evolutionary change on these bases is selectively neutral. In contrast, nonsynonymous changes may be deleterious or beneficial (far more likely the former than the latter because breaking contingent complexity is easier than creating new contingent complexity). Therefore the ratio of gentic change on nonsynonymous and synonymous bases across lineages has been a common measure of possible selection on a gene.
Last year a paper came out in AJHG which reported that Ethiopian populations seem to be a compound of West Eurasians and Sub-Saharan Africans. This is result itself is not too surprising for a host of reasons. First, Ethiopians and other populations of the Horn of Africa are physically equidistant between West Eurasians and Sub-Saharan Africans. 20th century physical anthropologists sometimes placed them in the “Caucasoid” racial classification for this reason. Second, the languages of the Horn of Africa have Afro-Asiatic affinities. The Cushitic languages (e.g. Somali) have deep connections with more familiar tongues such as Arabic, but Semitic Ethiopian languages (e.g. Amharic) are much closer in historical distance. Third, there has been a fair amount of previous genetic analysis of these populations, and their synthetic character was obvious from those (e.g. mtDNA and Y results suggest a diverse array of haplogroups). What the AJHG paper reported was that the Eurasian ancestors of the Ethiopians admixed with the presumably Sub-Saharan indigenes ~3,000 years ago in a single pulse event, and, their closest modern relations in West Asia today are Levantines. To put a mild gloss on it the dating is controversial (using patterns of decayed genetic correlations of markers across the length of the genome). This is not just clinal variation.
Credit: Sci Transl Med 3 July 2013: Vol. 5, Issue 192, p. 192ra86, Sci. Transl. Med. DOI: 10.1126/scitranslmed.3006338
Right before I was to sleep a reader sent me an email which pointed to a Nick Wade piece in The New York Times, Gene Sleuths Find How Some Naturally Resist Cholera. It’s about new research in ScienceTranslational Medicine, Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta. The authors use the “composite of multiple signals” (CMS) test to ascertain regions of the genome subject to natural selection (look for long haplotypes, high frequency derived alleles, and alleles with high cross population frequency differences). The results aren’t too surprising, I was born in Bangladesh, and I can attest to the fact that it’s a germaphobe’s nightmare. Rather, it is a secondary and very minor aspect of the paper which frankly draws my ire. First let’s quote Wade’s treatment:
As a necessary preliminary to testing for natural selection, the researchers looked at the racial composition of the Bengali population and found that they are an Indian population with a 9 percent admixture of East Asian genes, probably Chinese. The admixture occurred almost exactly 52 generations ago, according to statistical calculation, or around A.D. 500, assuming 29 years per generation. The Gupta empire in India was in decline at this time, but it is unclear whether the intermarriage with East Asians took place through trade or conquest. “We can now go back to the historians and see what happened then,” Dr. Karlsson said.
But sometimes science gets garbled in transmission. What do they say in the paper? Again, the relevant section:
It is generally understood that inbreeding has some negative biological consequences for complex animals. Recessive diseases are the most straightforward. The rarer a recessive disease is the higher and higher fraction of sufferers of that disease will be products of pairings between relatives (the reason for this is straightforward, as extremely rare alleles which express in a deleterious fashion in homozygotes will be unlikely to come together in unrelated individuals). But when it comes to traits associated with inbred individuals recessive diseases are not what comes to mind for most, the boy from the film Deliveranceis usually the more gripping image (contrary to what some of the actors claimed the young boy did not have any condition).
Some are curious about the consequences of inbreeding for a trait such as intelligence. The scientific literature here is somewhat muddled. But it seems likely that all things equal if two people of average intelligence pair up and are first cousins the I.Q. of their offspring will be expected to be 0-5 points lower than would otherwise be the case. By this, I mean that the studies you can find in the literature suggest when correcting for other variables that the inbreeding depression on the phenotypic level is greater than 0 (there is an effect) but less than 5 (it is not that large, less than 1/3 of a standard deviation of the trait value). Presumably for higher levels of inbreeding the consequences are going to be more dire.
