Why some like it hot: awesomeness

Mr. Jason Goldman has a post up, On Capsaicin: Why Do We Love to Eat Hot Peppers?. We don’t need no stinkin’ science for this. Do some ethnography with an N = 1: me. Those of us who love spicy food are just awesome! Recently I went to a Thai restaurant for the first time in 4 years which I used to frequent weekly in 2006-2007. Every Saturday I’d go and get a beef salad, which the chef would specially prepare for me by rubbing in a habanero paste into the meat ahead of time. That was the “four star” spicy level. When I reappeared after all this time the host exclaimed, “It’s Mr. four star!” Despite the years much of the staff which had been around back then remembered me. Back in the day sometimes they’d even watch me eat the dish to observe if I’d live to tell the tale. I can tell you similar stories from other restaurants. My very high spice tolerance threshold has reached such a level of virtuosity that people are often taken aback, and strangers will often comment upon it.

My point is that consumption of spicy food isn’t just a experience of the palette, it is deeply social. It is a signal of awesomeness, like having big antlers.

Here are some of Jason’s ideas:

Perhaps we seek out the painful experience of snacking on chillies while consciously maintaining awareness that there is no real danger to ourselves. After all, people seem to enjoy – and actively seek out – many other sensations that are otherwise undesirable but are ostensibly safe: the sensation of falling provided by rollercoasters or skydiving, the feelings of fear and anxiety while watching horror movies, the physical pain experienced upon jumping into icy water, or even the feelings of sadness that come while watching a tear-jerker. Perhaps it is this cognitive mismatch itself that provides the thrill: like strapping into a rollercoaster or popping Hostel into your DVD player over and over again, the burn of capsaicin only seems to be threatening.

Image credit: Andrew Bushby

Modern humans in Arabia >100,000 years ago

The genetic model of the “Out of Africa” scenario is getting more complex. There may be two waves, as well as the likelihood of admixture between the Neo-Africans and “archaic” hominins, such the Neandertals and Denisovans. From what I can gather the genetic evidence is now converging upon the sequence of events where African populations diverge >100,000 years ago (e.g., a deep separation between the ancestors of the Bushmen and the ancestors of West Africans), and a radiation of non-Africans at most ~75,000 years ago, and more likely ~50,000 years ago. There are still many holes to be plugged in. While we’re waiting on genetics, here’s an interesting paper using archaeological methods in PLoS ONE, The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia:

Despite the numerous studies proposing early human population expansions from Africa into Arabia during the Late Pleistocene, no archaeological sites have yet been discovered in Arabia that resemble a specific African industry, which would indicate demographic exchange across the Red Sea. Here we report the discovery of a buried site and more than 100 new surface scatters in the Dhofar region of Oman belonging to a regionally-specific African lithic industry – the late Nubian Complex – known previously only from the northeast and Horn of Africa during Marine Isotope Stage 5, ~128,000 to 74,000 years ago. Two optically stimulated luminescence age estimates from the open-air site of Aybut Al Auwal in Oman place the Arabian Nubian Complex at ~106,000 years ago, providing archaeological evidence for the presence of a distinct northeast African Middle Stone Age technocomplex in southern Arabia sometime in the first half of Marine Isotope Stage 5

Dienekes has extensive commentary up.

On structure, variation, and race

I noticed yesterday that Andrew Sullivan, Ta-Nehisi Coates, and a cast of others were having a roiling debate on race and I.Q. My name came up in several comment threads on various issues. I’m aware of this because I have Google Alerts set for my name. I don’t have the time or energy to get immersed in this particular debate at this moment, but I did review some older material in the course of following links placed elsewhere. In particular, I encourage all of my newer readers to check out my friend Armand M. Leroi’s article in The New York Times from 2005, A Family Tree in Every Gene. Though dated in a few particulars (e.g., we know the locus responsible for most variation in blue eyes now, and it seems likely that Andaman Islanders and Malaysian Negritos are not the original settlers of their domains) I think the general outline has held up rather well. Compare it to the numerous vociferous responses over at SSRN. One wonders at the motivation for what seems like massive retaliation! Here are a few critical paragraphs from Armand’s piece:

The identification of racial origins is not a search for purity. The human species is irredeemably promiscuous. We have always seduced or coerced our neighbors even when they have a foreign look about them and we don’t understand a word. If Hispanics, for example, are composed of a recent and evolving blend of European, American Indian and African genes, then the Uighurs of Central Asia can be seen as a 3,000-year-old mix of West European and East Asian genes. Even homogenous groups like native Swedes bear the genetic imprint of successive nameless migrations.

Some critics believe that these ambiguities render the very notion of race worthless. I disagree. The physical topography of our world cannot be accurately described in words. To navigate it, you need a map with elevations, contour lines and reference grids. But it is hard to talk in numbers, and so we give the world’s more prominent features – the mountain ranges and plateaus and plains – names. We do so despite the inherent ambiguity of words. The Pennines of northern England are about one-tenth as high and long as the Himalayas, yet both are intelligibly described as mountain ranges.

So, too, it is with the genetic topography of our species. The billion or so of the world’s people of largely European descent have a set of genetic variants in common that are collectively rare in everyone else; they are a race. At a smaller scale, three million Basques do as well; so they are a race as well. Race is merely a shorthand that enables us to speak sensibly, though with no great precision, about genetic rather than cultural or political differences.

But it is a shorthand that seems to be needed. One of the more painful spectacles of modern science is that of human geneticists piously disavowing the existence of races even as they investigate the genetic relationships between “ethnic groups.” Given the problematic, even vicious, history of the word “race,” the use of euphemisms is understandable. But it hardly aids understanding, for the term “ethnic group” conflates all the possible ways in which people differ from each other.

The problem here is the word “race.” It has a whole lot of baggage. So many biologists prudently shift to “population” or “ethnic group.” I don’t much care either way. Let’s just put the semantic sugar to the side. I contend that:

1) Human populations can be easily separated into plausible clusters using a random set of genetic markers

2) The differences between human populations are not trivial

You can say that both positions apply to human races. Or, you can say that race does not exist as a biological concept, and that both positions apply to human populations. Call it what you will, style is secondary to substance. Just as half-siblings and full-siblings are clearly genetically distinct, and those distinctions matter in terms of their traits, so French and Chinese are genetically distinct, and those distinctions matter in terms of their traits.

In the mid-2000s Armand, and at the time myself as well, put a great deal of weight on the importance of the elucidation of population structure for biomedical purposes. How else is one going to get funded by the N.I.H.? At this point I’m not sure that that’s going to be the low hanging fruit in the near term. Rather, I think an understanding of the phylogeny of the human race is a grand story. Population structure in the present is a shadow of histories past. And with the possibility of admixture with archaic lineages and recent adaptations that story has a lot of novel plot elements to keep your attention.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

Genetic Creationism

Carl Zimmer points me to a piece in a publication called GeneWatch, The Crumbling Pillars of Behavior Genetics. I won’t quote from it because it’s kind of a tired rehash of the confusions and misrepresentations found in The Great DNA Data Deficit: Are Genes for Disease a Mirage?, thoroughly refuted by Luke Jostins and Dan MacArthur (and others at Genomes Unzipped). As I have stated before this sort of attack on genetics is basically similar to Creationism. It’s overloaded with technical and scientific terminology bound to impress the public, but which is just used in a confusing manner, to the point where there’s a big overhead in trying to unpack the logic (as opposed to rhetoric) of the argument. I am broadly convinced that we should be very cautious about results which point to specific genes implicated in a complex trait. But, this is not the “bread & butter” of behavior genetics, which has always been about smoking out the relationship between genetic and phenotypic correlations, and therefore heritabilities. Additionally, as I’ve pointed out there are areas of genomics which are going to be a very important helpmate to quantitative genetic analyses. As noted in the piece behavior geneticists did turn out to be too optimistic about genomics as being relevant to their field. But, the main objections aren’t that novel, and the argument is a repetition of very old conflicts.

Addendum: I also feel that in many ways “genetic determinist” is rather like the Left-wing Blank Slate equivalent of Right-wing Creationist’s usage of terms like “Darwinian materialist” or “secular humanist.” It fills the same aspersion-shaped-hole in the heads of the polemicists. The difference though is often, though not always, the terms “Darwinian materialist” or “secular humanist” have some germ of truth (in that many evolutionary biologists are secular materialists who operate with a Darwinian framework in the background). In contrast, though there are scientists who are genetic determinists when it comes to the number of fingers you are expected to have, there are very few scholars who think that behavioral traits are determined purely by genes.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

More than models

Slate recently had a series up on the use of mice as “model organisms.” In particular, it put the spotlight of some limitations of extrapolating from a mouse to a man (or other species). This is in some ways biology’s “WEIRD” problem. There are always going to be obvious reasons why we’d want to use mice instead of elephants as model organisms, but we might be entering into an era when the fixation on a few species might abate at least somewhat. With that, I point you to a piece in The Scientist (in its final issue I believe), Beyond the Model – How next-generation sequencing technologies will drive a new era of research on non-model organisms:

Central goals of biology have always been to understand the basis for diversity within and among species, and to understand how the environment can influence the expression of different traits. These emerging genetic approaches enable studies in a greatly expanded number of organisms and potentially allow genetic approaches to be applied in natural habitats. The use of model organisms is not dead, however. The utilization of previously generated resources and continued development of model systems will support and facilitate research in non-models. But with the ability to address molecular mechanisms in the natural world, we can truly begin to understand how all of these factors interact to generate the biological diversity that motivated the early scientists and continues to inspire us today.

There is a reason for the hype that the 21st century will be to biology what the 20th was to physics.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

When trees turn into brambles

Genetics is powerful. The origins of the field predate Gregor Mendel, and go further back to plain human common sense. Crude theories of inheritance in the 19th century gave way in the early 20th to Mendelism, which happens to be a very powerful formal system for predicting the patterns of transmission of information from generation to generation. But I suspect that the popular accolades showered upon genetics would be more muted if it were not for the concrete discovery of the biophysical medium of that pattern of inheritance, DNA. By visualizing strands of DNA packaged into chromosomes one can gain a substantive understanding of Mendelian processes previously somewhat abstracted (e.g., recombination). In concert with the centrality of genetics at the heart of evolutionary science has been the ascendance of its methods in the older field of systematics. The phylogenetic tree is not only intuitive, but it has concrete reality in the sequences of base pairs or structural elements within the genome.

Whatever skepticism there might be about the dynamic phenomenon of evolution, the material aspect of modern genetics rooted in molecular biology is one of he primary wedges by which one can introduce an element of doubt into minds of a skeptic. The correlation between phylogeny and sequence identity of organisms which were previously adduced to exhibit some sort of biological relationship on the tree of life can not be dismissed out of hand. But this mode of thinking has limits, albeit due to the quirks of human psychology.

I began to think about this when reading Brian Switek’s post, Inside the Columbian Mammoth, Signs of a Woolly Cousin. It’s long and wide-ranging, so let me spotlight the section of particular interest to me:

On an anatomical basis, woolly and Columbian mammoths would be expected to be cousins which diverged from a common ancestor sometime between one and two million years ago. This is not what the genetic investigation found. “[T]he Huntington mammoth mitogenome is largely indiscernible from those of endemic North American WMs [woolly mammoths]”, Enk and co-authors wrote. The genetic readout of the Utah mammoth fell deep within the genetic diversity of woolly mammoths previously sampled from Alaska. This did not appear to be a case of contamination or mistaken identity – at a genetic level, researchers could barely distinguish a Columbian mammoth found in Utah from Alaskan woolly mammoths. What could this mean?

As I said, there’s a lot more detail in Brian’s post, so do read it. But one thing I want to emphasize: I think the results from the mammoth are far less surprising in light of what we’re finding from other widespread large mammals. Consider the polar bears:

The bear family, Ursidae, is believed to have split off from other carnivorans about 38 million years ago. The Ursinae subfamily originated approximately 4.2 million years ago. According to both fossil and DNA evidence, the polar bear diverged from the brown bear, Ursus arctos, roughly 150,000 years ago. The oldest known polar bear fossil is a 130,000 to 110,000-year-old jaw bone, found on Prince Charles Foreland in 2004. Fossils show that between ten to twenty thousand years ago, the polar bear’s molar teeth changed significantly from those of the brown bear. Polar bears are thought to have diverged from a population of brown bears that became isolated during a period of glaciation in the Pleistocene.

More recent genetic studies have shown that some clades of brown bear are more closely related to polar bears than to other brown bears, meaning that the polar bear is not a true species according to some species concepts. Irish brown bears are particularly close to polar bears. In addition, polar bears can breed with brown bears to produce fertile grizzly–polar bear hybrids, indicating that they have only recently diverged and are genetically similar. However, because neither species can survive long in the other’s ecological niche, and because they have different morphology, metabolism, social and feeding behaviors, and other phenotypic characteristics, the two bears are generally classified as separate species.

Long story short: the polar bear as a cluster of phenotypic characteristics may predate the polar bear as a distinctive cluster of genes! Now from John Hawks’ weblog, When anthropological and geological facts collide:

I am concerned with this passage today because of a re-emerging mismatch of evidence from the morphology of Middle Pleistocene humans and the genetics of Neandertals. Some paleoanthropologists have asserted that Europeans of the Middle Pleistocene were the exclusive ancestors of Neandertals. I have in the past written that Middle Pleistocene Europeans were among the ancestors of Neandertals, with sustained gene flow from other populations including Africa. The Sima de los Huesos people, maybe 600,000 years old, resembled the (much) later Neandertals in several aspects of their anatomy, as did other Middle Pleistocene Europeans. The genetic differences between living people and the ancient Neandertal genomes appear consistent with the emergence of distinct African and Neandertal populations only within the last 400,000 years or less.

Such a recent date seems a poor match for the morphological evidence of Neandertal ancestry in Europe. I can think of several ways to make these morphological and genetic comparisons concordant with each other, all of which balance some shift in one body of inference against the other. As long as we can’t pin down the human mutation rate within a factor of two (“What is the human mutation rate?”), there’s a lot of room to make different population models consistent with the genetic data.

I have been told that the most recent genomic data indicating the red wolf is a wolf-coyote hybrid of post-Colubmian vintage is perplexing to some who have accepted the fossil evidence of a far older derivation from the gray wolf stock. But remember that fossils rely on visible phenotypes, which may diverge from what genes tells us. The modern red wolf may simply be the latest instantiation of a constellation of characteristics which have bubbled out of the froth of the morphological background repeatedly for nearly a million years!

With the expansion of genomics from humans to a wide range of species I suspect that we’ll see a lot more blurring of distinctions between species on the margins. This will be particularly true of those lineages with wide and continuous distributions. It will also be most salient and surprising for mammalian populations, where our prejudices about the primacy of a biological species concept are most strongly developed.

In a phylogenetic sense when you shift the grain of analysis to a finer scale the tree of life becomes much more of a bramble in many cases. We understand this intuitively when it comes to pedigrees which we constrain to within our demarcated species. Many of us have the same ancestor over and over in our lineage as we go back into the past. Similarly, why should we presume that closely related lineages have parted for all of eternity when they speciate? If you pull back far enough monophyly is obviously a pervasive phenomenon, but in many scenarios we’re talking on the scale of ten million years, not one million. In hindsight it seems strange that people thought Neanderthals and African hominins could not interbreed despite a maximal separation on the order of ~500,000 years (in reality it seems plausible there was some gene flow between the two lineages in any case prior to the Neanderthal’s absorption into the Neo-African modern populations).

The second issue is that we must sometimes dethrone genetics from its determinative role in our understanding of how life is properly cataloged and evaluated. It may be that some phenotypes are recapitulated repeatedly from the ancestral genetic variation pool. This may have happened with the polar bear morph. Perhaps it happened with the mammoth lineages, as the Ice Ages waxed and waned. And perhaps it happened with the hominins of northern Eurasia! In the United States genetic criteria have become critical in application of the Endangered Species Act. Genes are concrete and often clear and distinct. Their physical reality and precision though may deceive us in the end. Does it matter if the red wolf of today is a recent hybrid of the gray wolf and coyote, while the red wolf of 10,000 years before the present was a 10,000 year old hybrid between the gray wolf and coyote?

Image credit: Zephyris, PIRN.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

Has twitter peaked?

I hadn’t given the issue much thought, but that’ what Randall Parker asserted in the comments below.

First, let’s look at Google Trends search traffic with Facebook as well:

Facebook dwarfs twitter, so you can’t tell. So with only twitter:

Interesting. Now let’s look with Alexa:

It’s a little more ambiguous using Google Trends estimate of unique visitors:

Finally, Site Analytics:

The New York Times on violence and Pinker

The New York Times has a short piece on Steven Pinker up. Nothing too new to long time followers of the man and his work. I would like to point readers to the fact that Steven Pinker has a F.A.Q. up for The Better Angels of Our Nature: Why Violence Has Declined. He links to my post, Relative angels and absolute demons, as supporting his dismissal of Elizabeth Kolbert’s review in The New Yorker. I have to admit that I find much, though not all, of the coverage of science in The New Yorker to exhibit some of the more annoying stereotypical caricatures of humanists when confronting the specter of natural philosophy.

I should also mention I started reading The Better Angels of Our Nature over Thanksgiving. I’m only ~20% through it, and probably won’t finish until Christmas season gets into high gear, but so far it’s a huge mess. In both a good way, and a bad way. The good way is that it’s incredibly rich in its bibliography, with fascinating facts strewn about the path of the narrative. The bad way is that so far it lacks the tightness of  The Blank Slate or The Language Instinct in terms of argument. This may change. Finally, I think I should mention that Pinker has already addressed some of the criticisms of his methodologies brought up in the comments sections of my posts. Those who have specific critiques probably should read the book, because he seems to try sincerely to address those. Or at least they should address those critiques to people who have bothered to read the book.