Razib Khan One-stop-shopping for all of my content

October 4, 2017

What is molecular biology?

Filed under: Biology,Molecular biology — Razib Khan @ 8:46 pm

In Massive Migrations? The Impact of Recent aDNA Studies on our View of Third Millennium Europe there is a reference to “molecular biological work.” I regularly see scholarship in evolutionary and population genomics and genetics referred to as “molecular biology” outside of the field, because since the 1960s molecular methods have been part and parcel of the discipline.

I get where this is coming from. In the case of ancient DNA there is some serious “bench biology” going on, and the skills of a molecular biologist come in handy. But I don’t consider a lot of evolutionary and population genomics work “molecular biology.” The first authors mentioned in the ancient DNA papers cited in the review are not trained as molecular biologists, but rather come out of computer science, statistics, archaeology or population genetics.

To illustrate the difference between population genomic type work and molecular biology (in this case, genetics), let’s look at the LCT locus, which is implicated in lactase persistence (lactose intolerance).

Here is something out of the population genetic/genomic tradition, Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene:

… To assess the population-genetics evidence for selection, we typed 101 single-nucleotide polymorphisms covering 3.2 Mb around the lactase gene. In northern European–derived populations, two alleles that are tightly associated with lactase persistence (Enattah et al. 2002) uniquely mark a common (∼77%) haplotype that extends largely undisrupted for >1 Mb. We provide two new lines of genetic evidence that this long, common haplotype arose rapidly due to recent selection: (1) by use of the traditional FST measure and a novel test based on pexcess, we demonstrate large frequency differences among populations for the persistence-associated markers and for flanking markers throughout the haplotype, and (2) we show that the haplotype is unusually long, given its high frequency—a hallmark of recent selection. We estimate that strong selection occurred within the past 5,000–10,000 years, consistent with an advantage to lactase persistence in the setting of dairy farming; the signals of selection we observe are among the strongest yet seen for any gene in the genome.

Now, compare to something which I would classify as molecular genetic, T −13910 DNA variant associated with lactase persistence interacts with Oct-1 and stimulates lactase promoter activity in vitro:

Two phenotypes exist in the human population with regard to expression of lactase in adults. Lactase non-persistence (adult-type hypolactasia and lactose intolerance) is characterized by a decline in the expression of lactase-phlorizin hydrolase (LPH) after weaning. In contrast, lactase-persistent individuals have a high LPH throughout their lifespan. Lactase persistence and non-persistence are associated with a T/C polymorphism at position −13 910 upstream the lactase gene. A nuclear factor binds more strongly to the T −13 910 variant associated with lactase persistence than the C −13 910 variant associated with lactase non-persistence. Oct-1 and glyceraldehyde-3-phosphate dehydrogenase were co-purified by DNA affinity purification using the sequence of the T −13 910 variant. Supershift analyses show that Oct-1 binds directly to the T −13 910 variant, and we suggest that GAPDH is co-purified due to interactions with Oct-1. Expression of Oct-1 stimulates reporter gene expression from the T and the C −13 910 variant/LPH promoter constructs only when it is co-expressed with HNF1 α. Binding sites for other intestinal transcription factors (GATA-6, HNF4 α, Fox and Cdx-2) were identified in the region of the −13 910 T/C polymorphism. Three of these sites are required for the enhancer activity of the −13 910 region. The data suggest that the binding of Oct-1 to the T −13 910 variant directs increased lactase promoter activity and this might provide an explanation for the lactase persistence phenotype in the human population.

I bolded the sorts of words which are good “tells” about the field that the paper is coming from. Traditional molecular biological work focuses a lot on mechanistic details. That is, the questions being asked are in relation to mechanisms on the scale of molecular machinery. Usually, there is talk about binding affinities, interactions, activities and references to protein products, macromolecule complexes, and often something to do with a reporter gene. Mentions of methods such as co-purification in the abstract would not be present in population genetics publications.

In contrast in the first paper, you see references to associations, selection, which is an evolutionary genetic parameter, and statistics such as Fst. Basically, the authors are focused on patterns of variation over time and space, and genetic markers are the currency they are using to perform the book-keeping. When scholars focus on phylogenetic questions there is even less attention to genomic functional detail than if they are curious about population genetic parameters (e.g., genic vs. inter-genic). The molecular data are inputs into methods of inference, not the ends in and of themselves.

Obviously, this semantical issue is not a big deal. It’s just I have friends who are molecular biologists…and what they do is very different from what I do.

April 10, 2012

DNA Replication

Filed under: Biology,DNA — Razib Khan @ 3:37 am

Most of you have probably seen this stylized graphic somewhere along the away (I think it was on PBS at some point). But it’s still cool….

July 14, 2011

Here be snow leopards!

Filed under: Biology,Conservation — Razib Khan @ 12:32 am

I really love the fact that I live in the early 21st century for a host of reasons. That being said, one aspect that’s certainly true is that when it comes to charismatic natural variety and geography there are very few “blank spots” on the map. You can get a sense of what I’m talking about if you browse National Geographic from the early 20th century. Most of the map had been filled in, but there were still nooks and crannies waiting to be illuminated. So I always find stories like this interesting, because they capture a sliver of the wonder that once was so commonplace, Snow Leopard Population Discovered in Afghanistan:

The Wildlife Conservation Society has discovered a surprisingly healthy population of rare snow leopards living in the mountainous reaches of northeastern Afghanistan’s Wakhan Corridor, according to a new study.

The paper is in the International Journal of Environmental Studies, Saving threatened species in Afghanistan: snow leopards in the Wakhan Corridor:

The Wakhan Corridor in northeast Afghanistan is an area known for relatively abundant wildlife and it appears to represent Afghanistan’s most important snow leopard landscape. The Wildlife Conservation Society (WCS) has been working in Wakhan since 2006. ...

June 28, 2011

Reify my genes!


In the comments below Antonio pointed me to this working paper, What Do DNA Ancestry Tests Reveal About Americans’ Identity? Examining Public Opinion on Race and Genomics. I am perhaps being a bit dull but I can’t figure where its latest version is found online (I stumbled upon what looks like another working paper version on one of the authors’ websites). Here’s the abstract:

Genomics research will soon have a deep impact on many aspects of our lives, but its political implications and associations remain undeveloped. Our broad goal in this research project is to analyze what Americans are learning about genomic science, and how they are responding to this new and potentially fraught technology.

We pursue that goal here by focusing on one arena of the genomics revolution — its relationship to racial and ethnic identity. Genomic ancestry testing may either blur racial boundaries by showing them to be indistinct or mixed, or reify racial boundaries by revealing ancestral homogeneity or pointing toward a particular geographic area or group as likely forebears. Some tests, or some contexts, may permit both outcomes. In parallel fashion, genomic information about race ...

May 25, 2011

The rise of real meat factories

Filed under: Biology,Lab Meat,Meat Things — Razib Khan @ 10:17 am

I’ve been taking about ‘meat things’ for nearly 10 years, so I was really excited by the new Michael Specter piece in The New Yorker about artificially grown meat, Test-tube Burgers. You can’t read most of it online, so I want to copy this small section:

…One study, completed last year by researchers at Oxford and the University of Amsterdam, reported that the production of cultured meat could consume roughly half the energy and occupy just two percent of the land now devoted to the world’s meat industry….

I say real factories because we are all aware I assume by this point of the nature of ‘factory farming’. But mass production of animal stock is an ad hoc kludge. Domesticated animals have been bred for meat production, but they remain organisms with all the range of activities and ends which the term ‘organism’ entails. Raising raw tissue in cultures may seem ‘yucky,’ a point Specter covers in assessing the reaction of some environmentalists and animal-rights activists who don’t seem as excited by the shift from conventional livestock raising to growing tissue as one would expect if they ran the numbers, but it is probably inevitable if it is feasible. ...

Biology to the masses

Filed under: Biology,Biotech,Personal genomics — Razib Khan @ 8:17 am

Josh Roseneau, when he’s taking time off from the evolution-creation wars, is poking around his own genome. Some sage advice:

On DNA Day, 23 and Me had a sale on their personal genomics service. They’d do their standard scan of your genome for free, as long as you paid for a year’s worth of their online subscription service.

For the price (nearly free up front, and a modest cost for the online community provided), my wife and I jumped on the deal. Since I got the results back two weeks ago, I’ve been exploring not only the services and information provided by 23 and Me, but the various other tools that individuals have started producing to help analyze and investigate this insight into my ubiquitous but invisible DNA.

My genome, for instance, revealed a genetic predisposition towards late-onset Alzheimers. The odds of getting Alzheimers are still quite small, but elevated because of this particular mutation to the APOE4 gene. This wasn’t a total surprise, given my family history, and as a healthy, young guy with a background in biology and biostatistics, it wasn’t hard for me to put that information into a context and move on. Down the road, I’ll ...

May 19, 2011

Organismic complexity is just duct tape

Filed under: Biology,Genome Complexity,Genome Size,Genomics,Mike Lynch — Razib Khan @ 11:04 pm

ResearchBlogging.orgThe Pith: Biological complexity may be a particular evolutionary path taken due to to random acts of nature, not because there is a selective advantage to complexity.

The title above basically describes the message of evolutionary biologist Mike Lynch from what I can gather. His basic argument is outlined in long form in The Origins of Genome Architecture, though the outline of the thesis is evident over 10 years back (see Preservation of Duplicate Genes by Complementary, Degenerative Mutations). Verbally I think the easiest way to explain Lynch’s framework is that in species with small effective population sizes the creativity of stochastic forces in generating non-adaptive structure and complexity tends to overwhelm the power of natural selection to prune this tendency toward baroque. I reviewed a paper last year which argued that Lynch’s observation of an inverse relation between effective population and genome size was an artifact, that once you controlled for phylogenetic history it disappeared. Suffice it to say this is an area of dispute and active research, so we shouldn’t take any individual’s word for it. This is science on the broadest canvas. Extraordinary general claims need to backed ...

February 8, 2011

The Price of Altruism: George Price and the Search for the Origins of Kindness

Link to review: The Price of Altruism.

The Imitation Factor: Evolution Beyond The Gene

Link to review: The wisdom of Seinfeld.

The Imitation Factor: Evolution Beyond The Gene

Link to review: The wisdom of Seinfeld.

Species, not arbitrary, but not clear & distinct

Filed under: Biology,philosophy,species,Species concepts — Razib Khan @ 1:48 am

John Hawks and Jerry Coyne are mooting the ‘species concepts’ debate, with particular focus on recent human origins (specifically, the relationship of modern humans to Neandertals and Denisovans). Coyne, who coauthored the book Speciation and remains preoccupied with the issue in his academic work, knows of what he speaks. And of course he wouldn’t think that the discussion of species, how to delineate them, and what they are, is a sterile exercise. He has chosen to allocate a significant portion of his life to the topic. I think very few would disagree with Coyne when he contends that “Species are not arbitrary divisions of an organic continuum.” If there is one taxonomic category which has a concrete basis in reality, that would seem to be species. But, I would observe that I’m not sure that species are necessarily so clear and distinct. After all, we know that there is here and there, but where does here end, and there begin?

I’m of a reminded of the classic Zeno’s paradox:

In the paradox of Achilles and the Tortoise, Achilles is in a footrace with the tortoise. Achilles allows the tortoise a head start of 100 metres. If ...

February 4, 2011

Evolution for Everyone: How Darwin’s Theory Can Change the Way We Think About Our Lives

Link to review:Evolution for Everyone: How Darwin’s Theory Can Change the Way We Think About Our Lives

February 3, 2011

Pandora’s Seed: The Unforeseen Cost of Civilization

Link to review: Pandora’s Seed: The Unforeseen Cost of Civilization

Mother Nature: Maternal Instincts and How They Shape the Human Species

Link to review: Mother Nature: a complicated and morally ambivalent tale

Mother Nature: Maternal Instincts and How They Shape the Human Species

Link to review: Mother Nature: a complicated and morally ambivalent tale

December 13, 2010

To study humankind, AAA responds

This morning I received an email from the communication director of the American Anthropology Association. The contents are on the web:

AAA Responds to Public Controversy Over Science in Anthropology

Some recent media coverage, including an article in the New York Times, has portrayed anthropology as divided between those who practice it as a science and those who do not, and has given the mistaken impression that the American Anthropological Association (AAA) Executive Board believes that science no longer has a place in anthropology. On the contrary, the Executive Board recognizes and endorses the crucial place of the scientific method in much anthropological research. To clarify its position the Executive Board is publicly releasing the document “What Is Anthropology?” that was, together with the new Long-Range Plan, approved at the AAA’s annual meeting last month.

The “What Is Anthropology?” statement says, “to understand the full sweep and complexity of cultures across all of human history, anthropology draws and builds upon knowledge from the social and biological sciences as well as the humanities and physical sciences. A central concern of anthropologists is the application of knowledge to the solution of human problems.” Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.

Changes to the AAA’s Long Range Plan have been taken out of context and blown out of proportion in recent media coverage. In approving the changes, it was never the Board’s intention to signal a break with the scientific foundations of anthropology – as the “What is Anthropology?” document approved at the same meeting demonstrates. Further, the long range plan constitutes a planning document which is pending comments from the AAA membership before it is finalized.

Anthropologists have made some of their most powerful contributions to the public understanding of humankind when scientific and humanistic perspectives are fused. A case in point in the AAA’s $4.5 million exhibit, “RACE: Are We So Different?” The exhibit, and its associated website at www.understandingRACE.org, was developed by a team of anthropologists drawing on knowledge from the social and biological sciences and humanities. Science lays bare popular myths that races are distinct biological entities and that sickle cell, for example, is an African-American disease. Knowledge derived from the humanities helps to explain why “race” became such a powerful social concept despite its lack of scientific grounding. The widely acclaimed exhibit “shows the critical power of anthropology when its diverse traditions of knowledge are harnessed together,” said Leith Mullings, AAA’s President-Elect and the Chair of the newly constituted Long-Range Planning Committee.

Up until the last paragraph this is an anodyne statement. Who could disagree with: “Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.” But the explosion of anger from biologically and scientifically oriented anthropologists on the web is drawn from a deeper layer of lived experience. On a raw level many of them feel that some factions in cultural anthropology are obscurantists who are fluent in rhetoric which they utilize in power-plays and politics. There are anthropologists who do deny the deep insights of the scientific method in illuminating reality. In fact, they reject the naive realism at the heart of science as it is practiced. For them science is a swear-word, and connotes an affinity with oppression and all the negative abstractions in fashion at a given time (e.g., patriarchy, heternormativity, capitalism, Eurocentrism, etc.). Of course as I note above scientific anthropologists are not given to tolerating the verbal circumlocutions and incantations of their non-scientific colleagues with much grace themselves. There is a deep cultural chasm, and these sorts of arguments over words in obscure institutional documents are only triggers for a persistent roiling debate.

As for the last paragraph, it illustrates the selectivity of a discipline which attempts to contextualize, and often has a skeptical relationship toward a positive framework. I believe that race is a social construct. The Hispanic identity, which consists of people of indigenous Amerindian, European, and African ancestry, and all their combinations, has been racialized. The Islamic identity has also been racialized. Benjamin Franklin stupidly contended that only the English and Saxons were true whites, with all other Europeans, including Nordics, being swarthy.

But just because a construct has a social element does not mean it has only a social construct. Because of the Left-liberal anti-racist egalitarian bias of anthropology, the academy in general, and the dominant narrative of Western society as a whole, there is a strong tendency to assert flatly that “race does not exist” as a biological concept. There is no interrogation of the concept of race except to refute its utility. This is not a case of agnostic skepticism washing away illusions, but a case of skepticism applied in a fashion to obtain a clear and distinct objective result which corresponds to reality. When it comes to race many become naive realists who accept that biological concepts can be falsified or verified in a simple and straightforward fashion. There is all of a sudden one Way of Knowing which presents us with indubitable truths.

Here is L. L. Cavalli-Sforza (my question in italics):

7) Question #3 hinted at the powerful social impact your work has had in reshaping how we view the natural history of our species. One of the most contentious issues of the 20th, and no doubt of the unfolding 21st century, is that of race. In 1972 Richard Lewontin offered his famous observation that 85% of the variation across human populations was within populations and 15% was between them. Regardless of whether this level of substructure is of note of not, your own work on migrations, admixtures and waves of advance depicts patterns of demographic and genetic interconnectedness, and so refutes typological conceptions of race. Nevertheless, recently A.W.F. Edwards, a fellow student of R.A. Fisher, has argued that Richard Lewontin’s argument neglects the importance of differences of correlation structure across the genome between populations and focuses on variance only across a single locus. Edwards’ argument about the informativeness of correlation structure, and therefore the statistical salience of between-population differences, was echoed by Richard Dawkins in his most recent book. Considering the social import of the question of interpopulational differences as well as the esoteric nature of the mathematical arguments, what do you believe the “take home” message of this should be for the general public?

Edwards and Lewontin are both right. Lewontin said that the between populations fraction of variance is very small in humans, and this is true, as it should be on the basis of present knowledge from archeology and genetics alike, that the human species is very young. It has in fact been shown later that it is one of the smallest among mammals. Lewontin probably hoped, for political reasons, that it is TRIVIALLY small, and he has never shown to my knowledge any interest for evolutionary trees, at least of humans, so he did not care about their reconstruction. In essence, Edwards has objected that it is NOT trivially small, because it is enough for reconstructing the tree of human evolution, as we did, and he is obviously right.

L. L. Cavalli-Sforza contends that between population genetic variation is not trivially small. This is clear from the fact that one can discern village-to-village genetic distinctions in Europe. Human variation exists, and it is not trivial. It is useful for phylogenetics, significantly impacts salient phenotypes, and, risks for particular diseases. The social construction of race has real biological raw materials. At one end, the transformation of white European converts to Islam through changes in personal appearance into de facto “People of Color” are matters of social construction in totality. In contrast, the blackness of a Dinka from Sudan is a matter of biological categorization. The categorization of Egyptian Arabs with obvious African admixture as “white” in the US Census is a matter of social construction due to bureaucratic contingency, and illustrates the intersection of biological reality and social fluidity. It is well known that when foreign Arabs with obvious black admixture visited the American South there was often a debate as to whether they were subject to segregation, illustrating the tensions between social norms (which would have coded them as black), bureaucratic function (which coded them as non-black usually), and biological reality (where they were an amalgam of a minor black African component with a dominant white Arab component).

Of course it is true that on any given trait variation can span populations. But even in the case given above, of sickle cell, the correlations with ancestry and population are striking. A lower boundary value is that 75% of sickle cell suffers are of mostly African ancestry, despite only 15% of the world’s population being of mostly African ancestry. These statistics refute a platonic model of race, but they do not refute the population-thinking which is at the heart of much of modern biology, pure and applied.

All that said, the word “race” is fraught with a lot of historical baggage. Therefore to study population wide variation you need to focus on “fine-scale population structure” and what not. This trend would be something of interest for cultural anthropologists of science to study. Race is just a word. Even a term as widely accept as species exhibits a fair amount of flexibility on the margins. But the underlying biological patterns, and the instrumental utility of those patterns, can not be denied.

Addendum: I often use “human” or “humankind” where earlier norms would be to use “man” or “mankind.” My main rationale is I don’t want annoying comments objecting to the term. The concept which I’m pointing to is the same no matter the pointer, and so I don’t mind changing it to facilitate my intent to communicate clearly and without undue extraneous baggage.

December 5, 2010

Extraordinary claims about arsenic

Filed under: Arsenic bacteria,Biology — Razib Khan @ 2:02 pm

Rosie Redfield has a “must read” post, Arsenic-associated bacteria (NASA’s claims). I won’t excerpt it, read the whole thing. To me it is very interesting that many pieces of her critique are ones I’ve encountered in emails or Facebook postings. She stitches them together into a coherent whole. She’ll be writing a letter to Science. Hopefully they’ll publish it. Even if you don’t have a deep background in microbiology and biochemistry I think it was clear that the authors had jumped to some inferences too quickly.

(Acknowledgement, John Hawks)

Update: Also, Arsenate-based DNA: a big idea with big holes:

So the Sargasso Sea tells us that some bacteria are capable of making DNA at very low phosphate concentrations. The most plausible explanation is that the bacterium GFAJ-1 can make normal DNA at micromolar phosphate concentrations, and that it also has the ability to tolerate very high arsenate concentrations.

This seems like the “boring,” but most plausible, explanation.

Update II: David Dobbs reviews the journalistic response. I think that people who write about science were in a bind because of the structural problems that David points out. When I first skimmed the paper it seemed to claim too much, but I had to keep in mind that it got through peer review. On the other hand as I stated once scientists in a position to critique on a genuinely technical dimension started complaining really loudly on social networking, that changed my own perception really quickly.

November 24, 2010

The inevitable social brain

ResearchBlogging.orgOne of the most persistent debates about the process of evolution is whether it exhibits directionality or inevitability. This is not limited to a biological context; Marxist thinkers long promoted a model of long-term social determinism whereby human groups progressed through a sequence of modes of production. Such an assumption is not limited to Marxists. William H. McNeill observes the trend toward greater complexity and robusticity of civilization in The Human Web, while Ray Huang documents the same on a smaller scale in China: A Macrohistory. A superficial familiarity with the dynastic cycles which recurred over the history of Imperial China immediately yields the observation that the interregnums between distinct Mandates of Heaven became progressively less chaotic and lengthy. But set against this larger trend are the small cycles of rise and fall and rise. Consider the complexity and economies of scale of the late Roman Empire, whose crash in material terms is copiously documented in The Fall of Rome: And the End of Civilization. It is arguable that it took nearly eight centuries for European civilization to match the vigor and sophistication of the Roman Empire after its collapse as a unitary entity in the 5th century (though some claim that Europeans did not match Roman civilization until the early modern period, after the Renaissance).

It is natural and unsurprising that the same sort of disputes which have plagued the scholarship of human history are also endemic to a historical science like evolutionary biology. Stephen Jay Gould famously asserted that evolutionary outcomes are highly contingent. Richard Dawkins disagrees. Here is a passage from The Ancestor’s Tale:

…I have long wondered whether the hectoring orthodoxy of contingency might have gone too far. My review of Gould’s Full House (reprinted in A Devil’s Chaplain) defended the popular notion of progress in evolution: not progress towards humanity – Darwin forend! – but progress in directions that are at least predictable enough to justify the word. As I shall argue in a moment, the cumulative build-up of compelx adaptations like eyes strongly suggest a version of progress – especially when coupled in imagination with of the wonderful products of convergent evolution.

Credit: Luke Jostins
Credit: Luke Jostins

One of those wonderful products is the large and complex brains of animals. Large brains are found in a disparate range of taxa. Among the vertebrates both mammals and birds have relatively large brains. Among the invertebrates the octopus, squid and cuttlefish are rather brainy. The figure to the right is from Luke Jostins, and illustrates the loess curve of best fit with a scatter plot of brain size by time for a large number of fossils. The data set is constrained to hominins, humans and their ancestors. As you can see there is a general trend toward increase cranial capacities across all the human populations. Neandertals famously were large-brained, but they exhibited the same secular increase in cranial capacity as African Homo. On the scale of Pleistocene Homo and their brains the idea of the supreme importance of contingency seems ludicrous. Some common factor was driving the encephalization of humans and their near relations over the past two million years. This strikes me as very strange, as the brain is metabolically expensive, and there are plenty of species with barely a brain which are highly successful. H. floresiensis may be a human instance of this truism.

But what about the larger macroevolutionary pattern? Is there a trend toward larger brain sizes in general, of which primates, and humans in particular, are just the most extreme manifestation? Some natural historians have argued that there is such a trend. But, there is a question as to whether increased brain size is simply a function of allometry, the pattern where different body parts and organs tend to correlate together in size, but also shift in ratio with scale. The nature of physics means that very large organisms have to be more robust because their mass increases far faster than their surface area. By taking the aggregate relationship between body size and brain size, and examining the species which deviate above or below the trend line, one can generate an encephalization quotient. Humans, for example, have a brain which is inordinately large for our body size.

And yet there are immediate problems looking at relationships between body and brain size, and inferring expectations. Different species and taxa are not interchangeable in very fundamental ways, and so a summary statistic or trend may obscure many fine-grained details. A new paper in PNAS focuses specifically on various mammalian taxa, corrects for phylogenetics, and also relates encephalization quotient by taxa to the proportion of social animals within each taxon. Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality:

Evolutionary encephalization, or increasing brain size relative to body size, is assumed to be a general phenomenon in mammals. However, despite extensive evidence for variation in both absolute and relative brain size in extant species, there have been no explicit tests of patterns of brain size change over evolutionary time. Instead, allometric relationships between brain size and body size have been used as a proxy for evolutionary change, despite the validity of this approach being widely questioned. Here we relate brain size to appearance time for 511 fossil and extant mammalian species to test for temporal changes in relative brain size over time. We show that there is wide variation across groups in encephalization slopes across groups and that encephalization is not universal in mammals. We also find that temporal changes in brain size are not associated with allometric relationships between brain and body size. Furthermore, encephalization trends are associated with sociality in extant species. These findings test a major underlying assumption about the pattern and process of mammalian brain evolution and highlight the role sociality may play in driving the evolution of large brains.

A key point is that the authors introduce time as an independent variable, so they are assessing encephalization over the history of the taxon. This is clearly relevant for humans, but may be so for other mammalian lineages. The table and figures below show the encephalization slope generated by using time and body size as the predictors and brain size as the dependent variable. A positive slope means that brain size is increasing over time.

Two major points:

- Note that the slope is sensitive to the level of taxon one is examining. A closer focus tends to show more variance between taxa. So, for example, humans distort the value for primates in general. Bracketing out anthropoids paints a more extreme picture of encephalization, a higher slope. In contrast, the lemurs and their relatives exhibit less encephalization over time.

- The correlation between proportion of species which exhibit sociality and encephalization of the taxon is strong. From the text:

Encephalization slopes were correlated with both the proportion of species with stable groups (order R = 0.92, P = 0.005, n = 6; suborder R = 0.767, P = 0.008, n = 9; Fig. 2 A and B) and the proportion in either facultative or stable social groups (order R = 0.804, P = 0.027, n = 6; suborder R = 0.63, P = 0.04, n = 9).

The last figure makes it is clear that the correlations are high, so the specific values should not be surprising. Don’t believe these specific figures too much, how one arranges the data set or categorizes may have a large effect on the p-value. But the overall relationship seems robust.

A highly encephalized “alien”

What to think of all of this? If you don’t know, one of the authors of the paper, Robin Dunbar, has been arguing for the prime importance of social structure in driving brain evolution among humans for nearly twenty years. The relationship is laid out in his book Grooming, Gossip, and the Evolution of Language. Robin Dunbar is also the originator of the eponymous Dunbar’s number, which argues that real human social groups bound together by interpersonal familiarity have an upper limit of 150-200. He argues that this number arises because of the computational limits of our “wetware,” our neocortex. Those limits presumably being a function of biophysical constraints.

One interesting fact though is that the median cranial capacity of our species seems to have peaked around one hundred thousand years ago. The average human today has a smaller brain than the average human alive during the Last Glacial Maximum! (see this old post from Panda’s Thumb, it’s evident in the charts) This may be simply due to smaller body sizes in general after the Ice Age. Or, it may be due to the possibility that social changes with the rise of agriculture required less brain power.

Ultimately if Dunbar and his colleagues are correct, if social structure is the most powerful variate in explaining differences in brain size when controlling for phylogenetics and body size, then in some ways it is surprising to me. After all, it does not seem that ants have particularly large brains, despite being extremely social and highly successful. Clearly the hymenoptera and other social insects operate on different principles from mammals. Instead of
developing “hive minds,” it seems as if in mammals greater social structure entails greater cognitive structure.

Citation: Susanne Shultz, & Robin Dunbar (2010). Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality PNAS : 10.1073/pnas.1005246107

October 31, 2010

Leigh Van Valen Obit in The New York Times

Filed under: Biology,Leigh Van Valen — Razib Khan @ 3:22 pm

If you haven’t, check out the Leigh Van Valen obituary in The New York Times. I hadn’t been aware of the breadth of his work, and the disciplinary range he showed over his career.

October 12, 2010

The naked geneticists

Filed under: Biology,Genomes Unzipped,Genomics,Personal genomics — Razib Khan @ 1:44 am

Girl_hands_out_flyer_at_Loveparade_03John Hawks, Genomes unzipped, unzipped:

What I wonder is, how much will personal genomics be like nude beaches? I mean, it’s been a long time since the first nude beaches, but most people don’t take advantage of the opportunity. Clearly, there’s variation in different countries! But most people neither feel compelled to see others’ data nor feel comfortable sharing their own.

Well, they used the word unzipped, not me!

Obviously John had his tongue-firmly-planted-in-cheek, but I have wondered about this. How deep is the impact of personal genomics going to be for individuals? If a person gets their genome sequenced and has a list of odds ratios in front of them are they going to bone up on the statistical genetic subtleties of the face value?

That is where genetic counselors come in. The necessity of interpretative experts highlights the difference between nude beaches and personal genomics: personal genomics has more potential societal impact. I know of the nudist/naturist phenomenon only tangentially, but it strikes me as similar to the broader New Age health movement. The focus is on individual health returns.  A colon cleanse simply does not have much of broader social effect. Yes, lest my nudist readers strike me down I do understand that there are purported positive social externalities, but set next to personal genomics nudism still strikes me as a fundamentally more individual activity whose benefits redound to the naked individuals, and not the broader clothed society. It does not pick my pocket nor break my leg if my neighbor is a weekend nudist. It is of no concern of mine (in contrast, my experience with public nudity is that it is generally disruptive when unexpected).

pgenI conceive of the social returns to personal genomics as a function of the proportion utilizing it will be defined by an s-curve. When only a few people have been genotyped your understanding of population-wide variation is still spotty. But as you increase your coverage you get a better sense of the variance within the population…but soon enough you enter the phase of diminishing returns.

Here’s a concrete example. In Reconstructing Indian History Reich et al. indicated that it is likely that South Asian castes are endogamous groups which will carry their own recessive risk alleles. In other words, Kayasthas from Bengal may have their own suite of recessive diseases, while Nadars from Tamil Nadu may have a totally different set of risk alleles. In a world with infinite NIH funding there would studies of Kayasthas and Nadars, and doctors and genetic counselors would be aware of what to look for in each group. We don’t live in a world with infinite NIH funding. Let’s assume that 1% of Indian Americans are Kayasthas from Bengal. That’s 30,000 people. If 5% of them make extensive use of personal genomics, then you have 1,500 people with a deep individual knowledge of their personal genomic profile, as well as a set of possible diagnoses or suites of symptons.

We’re still at the individual level. How does this matter on a social scale? Because with modern technology people can form communities online and get a sense of the nature of things from the “bottom-up.” Granted, the information gleaned isn’t going to go through peer review, and “irrational herds” can no doubt emerge. The bigger point is that sum can become more than the parts as motivated individuals pool information in a coordinated fashion. Once there’s some general insight extracted then that will flow to the rest of the group because of interpersonal networks.

This already happens with genealogy. A few highly motivated individuals dig deep into the archives to learn about their own personal history, and once they’ve retrieved the information they freely distribute what they’ve found to their relatives. From one perspective you could say that others are “free riding” on the passion and labor of a few, but you could also characterize this as a spillover effect or positive externality. The consequences of personal genomics are arguably much more substantive than traditional genealogy because of their potential health import.

Note that I’m emphasizing the social good here. Your sample size only needs to be so large to get a good sense of population-wide dynamics. More prosaically, as I noted before the Genomes Unzipped bloggers have opened a window into the genetics of their extended families. If Dienekes analysis is correct Joseph Pickrell and Vincent Plagnol likely have half-Jewish parents. Not that there’s anything wrong with that, though some people are still somewhat reluctant to acknowledge their Jewish heritage even today.

I assume that there will be individual utility as whole populations are sequenced over time. There’s more you can potentially learn by getting yourself sequenced even after ethnic-group or family level risks are ascertained (e.g., what are your distinctive alleles which are de novo mutations?). But this would simply be a classic increase of well being through summing of the parts. And here the analogy to the nude beach would be valid.

Image Credit: Pradeur

Older Posts »

Powered by WordPress