Tag: Evolution

The color of life as a coincidence

By Razib Khan | November 13, 2013 2:35 am

Credit: Eric Hunt

Credit: Eric Hunt

I do love me some sprouts! Greens, bitters, strong flavors of all sorts. I’ve always been like this. Some of this is surely environment. My family comes from a part of South Asia known for its love of bracing and bold sensation. But perhaps I was born this way? There’s a fair amount of evidence that taste has a substantial genetic component. This does not mean genes determine what one tastes, but it certainly opens the door for passive gene-environment correlations. If you do not find a flavor offensive, you are much more likely to explore it depths, and cultivate your palette.

220px-Durio_kutej_F_070203_ime

Dost thou dare?
Credit: W.A. Djatmiko

And of course I’m not the only one with a deep interest in such questions. With the marginal income available to us many Americans have become “foodies,” searching for flavor bursts and novelties which their ancestors might never have been able to comprehend. More deeply in a philosophical sense the question of qualia reemerges if there is a predictable degree of inter-subjectivity in taste perception (OK, qualia is always there, though scientific sorts tend to view it as intractable in a fundamental sense).

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If these bones could talk

By Razib Khan | October 19, 2013 1:34 pm
Credit: Thomas Roche

Credit: Thomas Roche

By now you have probably seen the articles about how a new skull has transformed our understanding of the human family tree. The original paper is at Science, A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo. More colorfully you might say that this publication burns down the “bushy” model of human origins, where you have a complex series of bifurcations and local regional diversity, and then rapid extinction with the rise of H. sapiens sapiens ~50,000 years ago. In general I’m more in agreement with those plant geneticists who are skeptical of excessive fixation on the concept of species, so this is not a shock to me. To me a species concept is not a thing, but an instrument to a thing (i.e., I’m in interested in population and phylogenetics). The reason these sorts of findings overturn the orthodoxy has more to do with human cognitive intuitions about why things are categorized, than the reality of how nature arranges itself.

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CATEGORIZED UNDER: Evolution
MORE ABOUT: Evolution

Man still evolves

By Razib Khan | September 12, 2013 8:02 pm

Still a great book!

Sir David Attenborough is the latest public intellectual who should know better than to opine that evolution has ended for human beings. Here are the quotes from The Telgraph: “Because if natural selection, as proposed by Darwin, is the main mechanism of evolution – there may be other things, but it does look as though that’s the case – then we’ve stopped natural selection. We stopped natural selection as soon as we started being able to rear 95–99 per cent of our babies that are born.

John Hawks does a good job hitting back the balls hanging just over the plate. There are still many parts of the world where 95-99 percent of babies being born do not reach adult. Second, there is still a great deal of variation in fertility. Some people choose not to have any children, while others are quite prolific. For adaptation by natural selection to occur what you need is heritable variation of some sort to correlate with this fertility variation. It seems highly plausible that indeed heritable variation does correlate with fertility variation. As John notes the advancement of genome sequencing over the population will probably answer these questions definitively within the next 10 years (e.g., I am willing to bet that siblings who score higher on impulsiveness and lower on IQ tests will be more reproductively fit than their less impulsive and more intelligent brothers and sisters).

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CATEGORIZED UNDER: Evolution, Genetics

Who needs sex when you have gene conversion?

By Razib Khan | July 22, 2013 4:49 am

Credit: Gross, Liza. “Who Needs Sex (or Males) Anyway?.” PLoS Biology 5.4 (2007): e99.

Bdelloid rotifiers get a fair amount of attention because they seem to be a lineage of obligate asexual metazoans (Richard Dawkins discusses them extensively in The Ancestor’s Tale). The fact that they don’t have sex isn’t that big of a deal. Bacteria do not have sex, and they’re quite successful. Rather, the issue is that they don’t have sex, they are complex, and, they are successful as a lineage. These do not usually go together. One of the posited explanations is that complex organisms are subject to phenomena such as Muller’s Ratchet, where they begin accumulating a load of deleterious alleles. Sex, with genetic recombination, is a way to evade this process, by mixing and matching alleles. By producing offspring with more than the expected payload of deleterious alleles the lineage can slough off unfavorable mutations which might otherwise fix. Without the ability to offload bad mutations over time they build up, and eventually one presumes the lineage would be unviable. This is just one of the myriad reasons biologists give for the long term lack of success of parthenogenetic metazoan lineages. Sex is ubiquitous among metazoans despite its two-fold cost. That is an overwhelming fact against which stands the example of the bdelloids.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics
MORE ABOUT: Evolution

Sexual selection: ignore the blonde?

By Razib Khan | June 23, 2013 2:56 pm

Frank analytic clarity?

Sexual selection is a big deal. A few years ago Geoffrey Miller wrote The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature, which seemed to herald a renaissance of the public awareness of this evolutionary phenomenon, triggered in part by debates over Amotz Zahavi’s Handicap Principle in the 1970s. Of course Charles Darwin discussed the process in the 19th century, and it has always been part of the arsenal of the evolutionary biologist (I first encountered it in Jared Diamond’s The Third Chimpanzee, where he lent some credence to Darwin’s supposition that human racial differences may be a consequence of sexual selection). But this bump in recognition for sexual selection seems to be accompanied by its co-option as a deus ex machina for all sorts of unexplained events. And yet as they say, that which explains everything explains nothing.

To get a better sense of the current scientific  literature I consulted A Guide to Sexual Selection Theory in the Annual Review of Ecology, Evolution, and Systematics. The image above is from an actual box in this review! Normally technical boxes illuminate with an air of superior authority (e.g. “it therefore follows from eq. 1…/”), but it seems to me that the admission that a parameter can be represented by the verbal assertion that it’s complicated tells us something about the state of sexual selection theory. In short: its formal basis is baroque because the dynamic itself is not amenable to easy decomposition.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics

What is a population?

By Razib Khan | June 10, 2013 11:12 pm

Anyone who reads the genomic posts with any interest on his weblog must read Daniel Lawson’s fine review of the topic which he has posted on arXiv, Populations in statistical genetic modelling and inference (via Haldane’s Sieve). Even if you don’t have a population genetic and genomic background the gist is entirely accessible. If you do have a population genetic and genomic background and haven’t used various packages such as STRUCTURE or EIGENSOFT yourself, I would recommend reading Lawson’s characterizations, as they are all spot on.

Also, if you have not, I recommend Lawson’s website for ChromoPainter and fineSTRUCTURE. The utility of these methods is outlined in the paper Inference of Population Structure using Dense Haplotype Data.

CATEGORIZED UNDER: Evolution, Genomics
MORE ABOUT: Evolution, Genomics

Turtles all the way down!

By Razib Khan | April 29, 2013 2:46 am

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.

CATEGORIZED UNDER: Evolution
MORE ABOUT: Evolution

Reflections on the evolution at ASHG 2012

By Razib Khan | November 11, 2012 1:54 pm

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!).

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What the substrate tells

By Razib Khan | September 16, 2012 8:26 pm

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.

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An ontology of genetic diversity

By Razib Khan | September 13, 2012 12:23 am

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.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics

Born to conform

By Razib Khan | January 25, 2012 11:52 am

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.”

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CATEGORIZED UNDER: Culture, Evolution

Out of Africa to Out of Arabia

By Razib Khan | December 20, 2011 3:13 pm

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).

CATEGORIZED UNDER: Evolution, Human Evolution

When trees turn into brambles

By Razib Khan | November 29, 2011 1:00 pm

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.

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Evolution is haram!

By Razib Khan | November 27, 2011 8:47 pm

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.

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CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism, Evolution

Man is the environment of the rat

By Razib Khan | November 25, 2011 3:58 pm


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.

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CATEGORIZED UNDER: Evolution, Human Evolution

Evolution skeptical: not just fundamentalists

By Razib Khan | October 30, 2011 11:36 am

 

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.

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CATEGORIZED UNDER: Creationism, Evolution
MORE ABOUT: Creationism, Evolution

Evolutionary imperialism

By Razib Khan | October 30, 2011 3:16 am

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….

CATEGORIZED UNDER: Evolution
MORE ABOUT: Evolution

The modern human coordination miracle

By Razib Khan | October 17, 2011 12:10 am

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.

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CATEGORIZED UNDER: Evolution, Human Evolution

Of beasts and men

By Razib Khan | September 5, 2011 9:23 pm

“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.”

- Genesis 6:4

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?

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Smart people accept evolution

By Razib Khan | August 19, 2011 12:24 pm

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):

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CATEGORIZED UNDER: Data Analysis, GSS
MORE ABOUT: Creationism, Evolution
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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