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Tag: Evolution
Turtles all the way down!
Nature Genetics (2013) doi:10.1038/ng.2615
No time to comment extensively, but check out The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan (open access). The paper and the ScienceDaily press release allude to some phylogenetic confusion as to the relationship of turtles to other reptilian lineages, but my own superficial knowledge of this area left me rather unsurprised by this tree. What am I missing? Though reading the Wikipedia entry it seems that spotty marker coverage has produced a lot of controversy. What’s more striking to me is that so many terrestrial vertebrate lineage seem to have emerged over a relatively short period of time. Though presumably this may simply be an artifact of the reality that most lineages go extinct so we’re only left with relatively deep branching patterns. Someone who knows fossils can chime in.
Reflections on the evolution at ASHG 2012
As most readers know I was at ASHG 2012. I’m going to divide this post in half. First, the generalities of the meeting. And second, specific posters, etc.
Generalities:
- Life Technologies/Ion Torrent apparently hires d-bag bros to represent them at conferences. The poster people were fine, but the guys manning the Ion Torrent Bus were total jackasses if they thought it would be funny/amusing/etc. Human resources acumen is not always a reflection of technological chops, but I sure don’t expect organizational competence if they (HR) thought it was smart to hire guys who thought (the d-bags) it would be amusing to alienate a selection of conference goers at ASHG. Go Affy & Illumina!
- Speaking of sequencing, there were some young companies trying to pitch technologies which will solve the problem of lack of long reads. I’m hopeful, but after the Pacific Biosciences fiasco of the late 2000s, I don’t think there’s a point in putting hopes on any given firm.
- I walked the poster hall, read the titles, and at least skimmed all 3,000+ posters’ abstracts. No surprise that genomics was all over the place. But perhaps a moderate surprise was how big exomes are getting for medically oriented people.
- Speaking of medical/clinical people, I noticed that in their presentations they used the word ‘Caucasian‘ a lot. This was not evident in the pop-gen folks. It shows the influence of bureaucratic nomenclature in modern medicine, as they have taken to using somewhat nonsensical US Census Bureau categories.
- Twitter was a pretty big deal. There were so many interesting sessions that I found myself checking my feed constantly for the #ASHG2012 hashtag. It was also an easy way to figure out who else was at the same session (e.g., in my case, very often Luke Jostins).
- If you could track the patterns of movements of smartphones at the conference it would be interesting to see a network of clustering of individuals. For example, the evolutionary and population genomics posters were bounded by more straight-up informatics (e.g., software to clean your raw sequence data), from which there was bleed over. But right next to the evolution and population genomics sections (and I say genomics rather than genetics, because the latter has been totally subsumed by the former) you had some type of pediatric disease genetics aisles. I wasn’t the only one to have a freak out when I mistakenly kept on moving (i.e., you go from abstruse discussions of the population structure of Ethiopia, to concrete ones about the likely probability of death of a newborn with an autosomal dominant disorder, with photos of said newborn!).
What the substrate tells
One of the weird things about genetics is that it encompasses both the abstract and the concrete. The formal and physical. You can talk to a geneticist who is mostly interested in details of molecular mechanisms, and is steeped in structural biology. For these people genes are specific and material things. In contrast there are other geneticists who focus more on genes as units of analysis. In this case genes are semantic labels for the mediators within an intersection of phenomena. Recall that genetics predates the knowledge of its concrete substrate by 50 years! By the 1920s Mendelian genetics had been fused with evolutionary biology to create a systematic framework in which we could understand the patterns of inheritance across the generations. In the 1950s the DNA revolution was upon us, but as W. D. Hamilton recalls this had only a minimal impact on the evolutionary genetic thinkers of the era. With the Lewontin and Hubby allozyme paper in the mid-1960s this sort of benign disciplinary evasion was no longer possible; the field of molecular evolution came into its own.*
Today with genomics these human-imposed artificialities are fading away. Consider the concept of genetic recombination. Originally an abstraction in a formal Mendelian system, today it is of great interest to molecular biologists who are curious as to its exact mechanism and purpose, and genomicists who are interested in the constraints upon the phenomenon due to its physical parameters (e.g., recombination hotspots). If we were to discover alien beings I assume that there would be some sort of genetics in an abstract sense. But would they package their genes in chromosomes? Would their complex organisms tend toward dioecy? I wouldn’t be surprised if the genetics of alien species have their own particular kinks subject to the contingent nature of the physical scaffolding of the process.
An ontology of genetic diversity
Implicit in the title The Origin Of Species is the question: why the plural? In other words, why isn’t there a singular apex species which dominates this planet? One can imagine an abstract system where natural selection slowly but gradually sifts through variation and designs a best-of-all-replicators. And yet on the contrary it seems that our planet has exhibited an overall tendency of going from lower to higher diversity. The age of stromatolites may be the last epoch when we had the best-of-all-replicators.
Born to conform
There is a new paper in Nature, Social networks and cooperation in hunter-gatherers, which is very interesting. As Joe Henrich observes in his view piece the panel of figure 2 (see left) is probably the most important section.
The study focuses on the Hadza, a hunter-gatherer population of Tanzania. Their language seems to be an isolate, though there have been suggestions of a connection to Khoisan. Additionally the genetic evidences tells us that like the Bushmen and Pygmies the Hadza do descend from populations which are basal to other human lineages, and were likely resident in their homeland before the arrival of farmers. And it is critical to also note that the Hadza are probably uninterrupted hunter-gatherers in terms of the history of their lifestyle, as agriculture likely arrived in Tanzania on the order of two thousand years ago, and their genetic distinctiveness indicates a separation from groups like Bantus far deeper in time. When it comes to Paleolithic model populations the Hadza are relatively “uncontaminated.”
Out of Africa to Out of Arabia
Dienekes and Greg Cochran have been talking about this possibility for a few years. But a combination of archaeological finds and the current unsettled nature of the human evolutionary genomics literature means that “Out of Arabia” is a real possibility (not laugh-out-loud crazy and weird). So I took the liberty of cooking up a new design for the RichardDawkins.net website. Science is about updating our prior assumptions, so it shouldn’t be too much of an issue. What I wonder: how would the population of the Kingdom of Saudi Arabia feel about replacing Ethiopia and Kenya in human evolution documentaries? Addendum: To be clear, this isn’t to say I accept “Out of Arabia” for the origin of most modern humans, including within Africa. Rather, I think it’s not a crazy idea anymore, especially in light of the weird results which imply that West Africans may be genetically closer to non-Africans than to Pygmies and San (and it would make more sense of older uniparental results which imply back-migration from Eurasia into Africa).
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.
Evolution is haram!
Ruchira Paul points me to this peculiar article, Muslim medical students boycotting lectures on evolution… because it ‘clashes with the Koran’:
Muslim students, including trainee doctors on one of Britain’s leading medical courses, are walking out of lectures on evolution claiming it conflicts with creationist ideas established in the Koran.
Professors at University College London have expressed concern over the increasing number of biology students boycotting lectures on Darwinist theory, which form an important part of the syllabus, citing their religion.
Man is the environment of the rat
The above is a figure from a new paper in PLoS ONE, Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats. Here’s the abstract:
The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.
Evolution skeptical: not just fundamentalists
In the comments below Christopher Mims states:
But evolution? It seems as if denial of evolution comes from a place so basic — religious fundamentalism — that I wonder whether something like this could ever have even the slightest impact.
It’s hard to deny the relationship of religious fundamentalism and evolution denial and skepticism. But, I think it’s important to remember that in the United States the large critical mass of evolution-denying religious fundamentalists has resulted in a “bleed over” of the stance to people who aren’t religious fundamentalists. I know this anecdotally from friends who were of Roman Catholic and Mormon backgrounds who presumed that their religious orientation precluded an acceptance of evolution. In fact, my own first awareness that people might actually not believe in evolution came via a conversation with an evolution skeptic friend who was a nominal Roman Catholic. Nominal in that his family actually never went to church.
What Paul Bloom’s research suggests is that humans find the Creationist narrative intuitively plausible. But, the critical issue is that those who aren’t indoctrinated against the idea of evolution can be convinced of its plausibility.
Let’s look at how this distributes across society using the General Social Survey. The variable BIBLE asks if people think that the Bible is the actually word of god, the inspired word of god, or a book of fables, etc. This seems to be a reasonable approximation of whether one is a fundamentalist, a non-fundamentalist who still accepts the revealed nature of the Bible, or someone who denies the supernatural grounding of the Bible in totality. There are two evolution related questions I can cross with BIBLE. EVOLVED, which asks if humans developed from an earlier species of animal with a true/false response, and SCITEST4, which asks the same question but has a more graded set of responses. Please note that EVOLVED was asked in the mid-to-late 2000s, while SCITEST4 was asked in the 1990s.
Evolutionary imperialism
So there’s a slick new webzine coming out, Evolution: this view of life. It’s another one of David Sloan Wilson’s projects. I don’t agree a lot with the specifics of David’s theories, but I admire his ambition. James Winters pointed me to the fact that they’re trying to raise money for this webzine via KickStarter. Their goal is $5,000. Having run much more bare bones websites for years this seems like a really modest amount in relation to their aims. I admire David’s attempts in this area enough that I gave some money. He tries a lot of things, many of which don’t succeed, but that’s science….
The modern human coordination miracle
Thanks to Ed Yong several people on twitter have encountered my post, The point mutation which made humanity. My broader concern which I was attempting to highlight is that too often when we attempt to ascertain the origins of modern human success in relation to our archaic cousins/ancestors we presume that there must be a qualitative species-wide difference. So, for example, it used to be bandied about that a large effect mutation conferred upon the ancestors of modern humans the ability to speak with the fluency which we take for granted. For various reasons that seems less and less plausible.
Of beasts and men
“There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown.”
The Pith: Pygmies and Khoisan have admixture from a distinct population at the level of ~2%. This population diverged from the other ~98% of their ancestry ~700,000 years before the present, and the hybridization occurred ~30-40,000 years before the present. Most other African groups have only traces of this element, with some West Africans lacking it.
I have read the paper in PNAS which I referred to below. There isn’t that much I can add at this point. A lot of the guts were pushed into the supplements, which aren’t on the web yet. I was correct that the Mbuti Pygmies of the eastern Congo likely have a special place in this possible admixture event. In particular, they seem to possess the diverged variants found in the western Pygmies, the Biaka, and the Khoisan populations of southern Africa. As assumed the pattern of admixture seems to be such that the two Pygmy groups and the Khoisan exhibit elevated signatures of archaic contributions, while other African groups manifest admixture in direct proportion to their known admixture to the aforementioned populations. For example, the Bantu group with the highest proportion of admixture are the Xhosa, who also have the most Khoisan ancestry of non-Khoisan populations. The West African Mandenka seem to have trivial admixture from this archaic group. What does this mean?
Smart people accept evolution
At Culture of Science there’s a little discussion about whether acceptance of evolution indicates intelligence. Looking at the GSS data there doesn’t seem to be a strong causal relationship when you control for other variables. But there is a correlation. That correlation can be explained by the fact that, for example, people who are Biblical literalists tend to be duller than those who are not, and Biblical literalists don’t accept evolution (in fact, I’ve seen evidence that very intelligence Biblical literalists are more Creationist than their duller co-religionists, probably because they’re more coherent in their beliefs).
With that, I’ll leave you with a screenshot of the results for WORDSUM, a 10 word vocabulary test, against acceptance or rejection of human evolution from other organisms (note that the numbers below the proportions are weighted sample sizes):
Evolution is a signal for real Republican populism
New York Magazine has a rundown of the attitudes of some of the G.O.P. candidates for the nomination in regards to evolution. Remember, this is an issue which is split down the middle in the American populace, but elites have a strong skew toward accepting evolution. This is probably why despite a majority Creationist primary electorate in 2008 the majority of Republican candidates still agreed with the evolutionary position. In 2012 it looks like the Creationism or semi-Creationist contingent is going to get larger.
In the General Social Survey they asked in the late 2000s whether respondents accepted that “humans developed from animals.” The response was dichotomous. Here are some results for various population groups:
Evolution doesn't fit our generalities
“Is Evolution Predictable?” asks a piece in Science. Here’s the first paragraph:
If one could rewind the history of life, would the same species appear with the same sets of traits? Many biologists have argued that evolution depends on too many chance events to be repeatable. But a new study investigating evolution in three groups of microscopic worms, including the strain that survived the 2003 Columbia space shuttle crash, indicates otherwise. When raised in a lab under crowded conditions, all three underwent the same shift in their development by losing basically the same gene. The work suggests that, to some degree, evolution is predictable.
The “some degree” part is the catch. I’m a big fan of general ideas, but the more I learn about evolution the more suspicious I become of broad truths. A given dynamic often has some degree of validity, but extending it too far leads to error or confusion in innumerable specific cases. Evolution may be the most robust and powerful theory for deductive inference in biology, but even here rationalism has its limits. For example, before the rise of molecular methods in exploring polymorphism the debates as to the nature of genetic variation in natural populations tended to focus on outcomes based on adaptive pressures. One school followed R. A. Fisher and argued that polymorphism was strongly constrained by negative selection, with periodic bouts of genetic diversity at a given locus as a positively selected allele was in transience between ~0% and ~100%. Sewall Wright on the other hand suggested that balancing selection (e.g., frequency dependence, heterozygote advantage, environmental heterogeneity) would maintain polymorphism within a population. The logic in both cases was clear, crisp, and plausible. But it turned out that in a deep way the argument was in the “not even wrong category.” Neutral theory and its heirs pointed out, correctly it seems, that at the molecular level most variation was driven by non-adaptive forces such as random genetic drift. Though some thinkers had conceptualized the model in its broad outlines prior to the empirical results, it was the latter which crystallized the need for a robust model and marginalized the older debate centered around adaptation and natural selection. But even here neutrality is not a model to explain it all. There are cases where adaptation and natural selection are relevant. In some instances you see classical dynamics with transients generated by positive selection sweeping through populations, and in other cases balancing dynamics may be operative. The overall point is that we must always be careful about bald assertions of the form “the latest research overturns….” in this area. Evolution is such a sprawling and cosmopolitan intellectual empire. Nature is subtle and richly textured, and our conceptual frameworks map onto the shape of reality only coarsely.
As for the paper itself, it’s nice and elegant. Patrick Phillips, who knows a thing or two about evolution and elegans is quoted in Science as saying that “”It’s an amazing study….” The letter to Nature is Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes. Here’s the abstract:
How did modern humans settle the world?
In lieu of lots of text, above is a stylized representation of the routes which Neo-Africans took ~50 thousand years ago from their point of departure to parts unknown. The two colors represent two models. The red lines show two major streams issuing out of Africa, a northern route which pushed into the heart of Central Asia, and a southern oceanic one, which pushed all the way into Australia. The second differs, with eastern and western branches of non-African humanity. The models really start to break down within the last ~10,000 years. For example, by either model India has seen an admixture even between the two branches in the Holocene. Additionally, there may have been “false dawns” and admixtures.
In the early 2000s I accept the probable likelihood of the first model. But today I am more leaning toward the second. What’s your stance, and why? I’ll give my rationale below….
Everything I didn't know about sex
The Pith: The primary reason for the pervasiveness of sex among complex organisms is to maintain genomic integrity, not to increase genetic variation..
I just read a very strange article in the journal Evolution, Sex reduces genetic variation. In it the authors argue that contrary to conventional wisdom and evolutionary orthodoxy the rationale for the prevalence of sex amongst eukaryotic organisms is not maintenance of genetic variation, but rather a constraint upon genetic variation! This is a very peculiar view, and as someone not immersed in the literature on sex totally surprising to me.
The standard model is simple: sex allows organisms to swap genetic material and generate new combinations. This is at a particular premium for large, complex, and slow-breeding lineages, as is the norm amongst eukaryotes. In contrast, bacteria and their ilk have huge population sizes to draw from, and are quite literally protean in their ability to shift strategies to climb whatever adaptive landscape nature throws at them. Carl has a nice review of a paper in Science which reported just this finding in keeping with expectation. Increase the pathogen pressure, and eukaryotes which exchange genes marginalize those which do not because they can dodge the punches that their evolutionary adversaries throw in their direction.
Tightening the interval of the expected
The Pith: The rarer the genetic variant, the more likely that variant is to be specific to a distinct population. Including information about the distribution of these genetic variants missed in current techniques can increase greatly the precision of statistical inferences.
A few days ago I mentioned in passing an article in The New York Times which reported on results from a paper which illustrated how starkly differentiated populations might be on rare alleles. By this, I mean that some genetic variants are present at very low frequencies. It turns out that many of these are low frequency variants private to particular populations, in contrast to higher frequency variants which span varied human populations. The explanation presented by one of the authors of the referenced paper was that higher frequency variants presumably date back to a time before human populations had become geographically diversified across the world. Shared variants at higher frequencies then are shadows of shared past history. In contrast, rare variants are a reflection of more recent events, narrowing the circle of those effected.
I have now read the paper in question, Demographic history and rare allele sharing among human populations. From what I can gather The New York Times article was really an elaboration upon some of the issues which were highlighted in the discussion. The “meat” of the paper in terms of methods and results is actually rather technical and deeply embedded in the language of mathematical statistics. For example:
After further consideration, I have decided that I shall spare you my own clumsy exposition in plain English as to the details of site frequency spectrum calculations. There are after all enough points of interest in the paper at which I can throw my verbal talents more effectively. First, the abstract:
Disease and human demographic history
There’s a write-up in The New York Times on a new paper to come out in PNAS soon on the relationship of disease variants to human demographic history over the past few hundred thousand years. I’ll probably review the paper when it comes out, but since it is the holidays & all here in the states it might be delayed a bit more than typical. Roots of Disease Found to Vary by Continent is the article. Here’s the most important bit:
The Stanford study also sheds light on major aspects of human population history, like the time at which the first modern humans emigrated from Africa. Archaeologists believe it was about 50,000 years ago, since no modern human remains older than this have yet been found outside of Africa, but geneticists have long favored much earlier dates. Dr. Gravel and Dr. Bustamante now calculate that 51,000 years ago, give or take several thousand years, is the date best supported by genetic data, bringing the geneticists’ date into alignment with the archaeologists’ favored time for the exit from Africa.
The common variations in the human genome were mostly present in the ancestral human population in Africa and have been inherited by all the descendant populations around the world. The rare variants occurred more recently.
“Most of the common variants hark back to pre-Out of Africa,” Dr. Bustamante said. “Most of the rare variants come after the Neolithic revolution.” This is the event that marked the beginning of agriculture about 10,000 years ago and led to significant increases in the size of human populations.
On the first part, I’ll have to wait on the paper. I’ve kind of become more and more skeptical at taking these estimates at face value. Though the point about the lack of archaeological finds is a major alternative confirmation of the result though which should make us amenable to its plausibility. When it comes to rare variants being different across populations, the logic of this should be pretty obvious. Imagine for example if natural selection results in the rise to higher frequency of a range of rare variants from novel mutations which happen to be favored in the Neolithic environment. This is going to differentiate groups as far as the Neolithic events occurred to different populations, since they’ll draw from a different random set of mutations. One can make the same sort of case for demographic events such as population bottlenecks, which could reshape the pattern of population substructure in a historically contingent manner and groups are subject to fission over time.
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Razib’s Pinboard
- Alice E. Kober, 43 - Lost to History No More - NYTimes.com
- Genome Biology | Abstract | Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance
- Why 3D Printing Is Overhyped (I Should Know, I Do It For a Living)
- Whose genome is it anyway? | Inspiring Science
- Paternity testing: Personal genomics companies will reveal DNA secrets. - Slate Magazine
- Egg freezing: Why the procedure is worse than PMS but better than the dentist.
- Apotheosis of cynicism and deceit from scholarly publishers
- Life as One of the Most-Persecuted Ethnic Groups on the Planet - Jeffrey Stern - The Atlantic
- Medieval Europe: Why was water the most popular drink?
- Census finds Islam on the rise, Christianity declining in Britain - UPI.com
- High Plains Aquifer Dwindles, Hurting Farmers - NYTimes.com
- Roots of future tropical rainfall: Sea level influenced tropical climate during the last ice age
- About That Dissertation | National Review Online
- Study: Kids Are Prejudiced Against Fat People by Age 4 - Lindsay Abrams - The Atlantic
- Portland fluoride vote: Will medical science trump fear and doubt? - Slate Magazine
- Investigative Genetics | Abstract | Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history
- Archaeological genetics: It's not all as old as it at first seems
- Trends in Genetics - Properties and rates of germline mutations in humans
- www.culturalcognition.net - Cultural Cognition Blog - Annual "new study" finds 97% of climate scientists believe in man-made climate change; public consensus sure to follow once news gets out
- Will Google Glass finally make doing this gauche? - Quartz
