Re: "Anthropology 105, lecture 3: Legs"
I just watched
one of your lectures, 'Legs', which you've put up on your blog - and I
had to let you know that I enjoyed it immensely.Thanks for putting it up and for letting me have a peek into your
classroom. I hope you will continue to put up videos like this.
Thank you so much for letting me know!
I'm still getting the hang of the system, so I expect some of the lectures will be a lot better than this one!
This may sound like a dumb question, but I am trying to understand the difference between “selection on standing variation” and the concept of “exaptation”. They seem to mean the same thing? Am I missing something?Thanks for any help you can provide.
No problem. Exaptation almost always refers to a phenotypic trait, and specifically the case where it used to do one thing, and has changed because of natural selection for some other function.
Selection on standing variation is usually just a contrast with selection on a new mutation. A new mutation that comes under positive selection will rapidly increase in frequency and thereby generate lots of signs we can recognize, for example genetic hitchhiking.
Selection on an old mutation that has already existed in the population for a long time (and is therefore "standing" variation) also can cause the mutation to increase in frequency, but this will not necessarily cause hitchhiking or other easily recognizable patterns, because copies of the mutation that have existed in the population for a long time probably are not all linked to the same set of mutations at other loci.
Practical example: Lactase persistence. We know that lactase persistence in Europeans is selection on a new mutation. If people carrying the key lactase persistence mutation did not all share near-identical region of chromosome 2 around that mutation, we would suspect it was selection on standing variation (when we learned about lactase persistence more than 10 years ago, this was not resolved yet and many geneticists thought it would turn out to be standing variation). Lactase persistence is *arguably* an exaptation, because it uses the mechanism that evolved for one purpose (babies digesting mothers' milk) and changed it under selection for another purpose (adults digesting cow milk).
I have a question about your article "The thrifty brainotype" found
at: http://johnhawks.net/weblog/topics/minds/philosophy/clark-2011-thrifty-b...Instead of having the whole brain evolve as a single type (information
processing efficiency vs energy efficiency) why have only parts of the
brain be one way or the other? Given our brain has evolved from much
earlier brains, why couldn't a distant ancestor evolve a very energy
efficient brain, a later ancestor evolve a visual processing portion
that's extremely information processing efficient and then as we come
into being take these pieces and keep some pieces and discard others?Is there any reason why the issue is being discussed as a single whole
brain archetype, and not as a piecemeal "some of this and some of
that" type?
Thanks so much for this question. I agree entirely, on a functional and evolutionary level of analysis, there is no reason why different cognitive systems should be constrained in the same way. I take Clark's model as a heuristic of how "brain" might be organized along information processing lines, but I think the heuristic fails at the level of a whole organism.
In contrast, the "expensive brain" heuristic really does apply at the organismal level because brain tissue uses energy, and the brain mass is a useful (if imprecise) way of considering energy consumption.
I don't think we can break up the brain into functional modules uncritically, but there are only certain ways in which it is useful to consider it as a whole.
I’m a chemist but I keep a youth love for paleoanthropology and I’m reading with pleasure your blog. Thank you for writing it.
In the page “Neandertals of the North” I’ve read about the hypothesis that, having found ‘mousterian-style’ tools, the site was inhabited by Neandertals.
I have a curiosity: Neandertals and Denisovans were cousins (more closely related than Neandertal and modern humans). What do we know about Denisovans lithic culture? Was it similar to Mousterian or very different?
You wrote that many archaeologists concluded that Neandertals couldn’t cope with the climate change (Heinrich VI event) and explained this way the last findings in southern Europe. Byzovaya seems against this tendency.
Comparing the distribution area of Neandertal and Denisovans, the first ones lived in southern Europe and Middle East while the second ones lived in continental Asia. Denisova is in the very center of Eurasia: continental weather with deep freezing winters even nowadays with this favorable weather (I searched the weather forecast of today of Barnaul (just 150 Km from Denisova Cave) finding this night -25°C/-13°F)
From a climatic point of view the Denisovan were the tough guys of the northern emisphere…and they had no vodka to warm up their nights (!)
About weather, the Heinrich effect causing a shift in the oceanic currents is very effective in Europe but, as far as you go in inner Eurasia (continental weather), the lower is its effect. (or I imagine so, maybe I’m wrong)
Could be that the lithic culture of Denisovan were very similar to Neandertal culture and that the Byzovaya findings are Denisovan versions of Mousterian?
Could be that searching in Byzovaya, a so cold place, we’ll be so happy to find even better preserved bones for DNA analysys?
Thanks so much for your message.
Yes, I agree with you that the existence of Mousterian people in the Arctic is pretty strong evidence about their ability to survive a climate extreme. I think they would have eaten a Heinrich event for lunch.
The Denisova stone assemblage is distinguishable from other Mousterian, but I would say it is not qualitatively different. The situation in the Altai is archaeologically very complex, also, so I do not think we have a secure understanding of the relation of the Denisovan biological population and the stone artifactual record. Seems clear there is not a radically different intrusive culture but I would not be very hopeful about finding strong archaeological connections to other parts of East or Southeast Asia.
Cold places are always hopeful for DNA recovery; hope they find some human remains.
Re: "Is humanistic research a waste of time?"
Dear John,
Criticisms of humanities research like Bauerlein's may have merit in some cases, but number of citations of recent work is not the right measure of relevance. Here are several interrelated points.
First, what matters is the network of influences. Within the humanities, as in the sciences, there are scholarly communities, more tightly connected within communities, and more loosely connected between communities. A scholarly work may influence distant nodes of the network in ways that don't lead to citation. To take the extreme case, suppose that only one person, X, reads work A by another author, but X's A-influenced writing is widely read by others. Work A might never merit a citation from anyone but X, even if what is so interesting about X's work depends in essential ways on what X learned from A. Sometimes the network goes through a single individual: X cites A in an early work, but X's subsequent, more influential work, only cites X's own earlier piece in which X's ideas were being developed partly in response to A. (Suppose that only Husserl read Frege, to whom he responded in an early work. How many Continental philosophers these days have read Frege? Some might not even have read Husserl, I suppose, despite his indirect influence on their thought.)
Second, a work can influence thinking in respects which are more subtle than those which merit citation. Reading someone else's work may suggest patterns of thought, styles of research, etc. Or a work might convince you that certain paths are not worth following, leading to research of a different kind. This influence won't necessarily warrant citation. (I've gradually become aware that pervasive aspects of my research were loosely inspired by ideas in works I read years ago. I want to give credit where credit is due, but according to academic standards the connection between my current research and these works is simply not direct enough to warrant citation in some cases, however. I'd describe these connections in print only if I were writing an intellectual autobiography or writing for a Festschrift on the author of the influential works.)
Third, some works might have significant influence decades after their publication. (I recently became aware of a 19th Century engineering professor who has written on ideas related to mine.)
You can quote me by name if you want.
Best wishes,
Marshall
Thanks for writing!
I don't disagree with your point that citations are not a perfect measure of relevance. Possibly we should ignore citations entirely.
And yet…Frege has a whole lot of citations every year. Probably anyone we can name off the top of our heads counts among the most widely cited of scholars.
I have sympathy for your argument that every single interaction has the potential to unexpectedly influence someone down the line. The principle is that any action may be the tipping point. But it seems like a horrible marginal use of time. A semester with the chance to touch and influence 20 students is on balance a better chance of attaining that tipping point than a never-read research article.
I would argue that we should value research, and we can do this by doing research that people find relevant. Easier said than done, though!
Re: "Introgression and microcephalin FAQ"
Hi Dr. Hawks,
I just ran across your introgression and microcephalin FAQ on your blog, and I wanted to ask you one quick question. Now that we have a draft sequence of the Neanderthal genome, has anyone yet looked to confirm that one of the modern human microcephalin alleles was bestowed upon us by admixture with Neanderthals?
Thanks in advance!
Thanks for writing!
Lari and colleagues published on this last year: 10.1371/journal.pone.0010648, [1] they didn't find the derived (presumed introgressed) allele in Monti Lessini 1. We have no sign of it in the Vindija genomes, either. So far, no sign of it. The other encouraging gene region was an inversion including the MAPT gene; this also has not yet been found in a Neandertal.
So now we have tons of evidence of introgression, but none of the genes that we thought were strong cases before the ancient DNA. That doesn't rule out that we'll find these other cases in some ancient specimen, but in the meantime we're working on what we have.
Re: Neandertal introgression, 1000 Genomes style:
Long-time reader of your blog, non-paleo/anthro/genetics person, here. But please read on:
Just a couple of brief questions.
(i) It seems that it would make sense to look at pairwise comparisons (of shared derived Neanderthal SNP alleles) both within a population (e.g., Asians, or CEU) and between them, and build a histogram of how often they overlap.
(ii) Then one could remove from the data set all such African shared SNPs - assuming that most of them are incomplete lineage sorting but that Africa had the initial superset of alleles before ooA (I know some are likely West Asian or European admixture, reducing the data set slightly more than necessary), and repeat (i) and similar diagnostics. Is the typical unmodified genome chunk length around such sites much longer than in (i) - can one date this? Can one now better quantify the actual admixture percentage outside of Africa?
Wouldn't such a procedure give more insight about how Neanderthal introgression is distributed, when it occurred, and perhaps where it occurred?
I am sure you are already working on similar ideas - just wanted to know if you agree that these may be low-hanging fruit to pursue.
Thanks!
Hi -- thanks for writing!
I started with exactly the approach you describe, when we were working exclusively with SNP data in the spring. For example:
http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/europe-ch...
We were using linked haplotypes rather than single SNPs but the filtering process was the same.
Now I am hopeful that we will have decent age estimates for the introgressing SNPs from a different technique. I would rather find these ages independently of filtering by geographic location, because having this information will greatly simplify testing models of ancient population dynamics. If we succeed at this, we will also have a test of selection based on the same allele ages.
I am continuing to update and you'll see these results not long after we get them!
Re: Jury science
I have followed your blog with inerest for a while now, and I was looking through your
twitter stream and saw this, attributed to Kahneman:"if a court case hinges on regression to the mean, the side that has to explain this to the jury
will lose."I was immediately intrigued by the idea of coming up with a good explantion for a
jury, and here is what I came up with:Its like poker hands - even if daddy has 4 kings and mommy has 4 queens, the kids
aren't going to average much better than two pair, kings over queens.This simplifies and glosses over a lot, but its memorable and avoids the dreaded
'eyes glaze over' effect so common with math explanations for laymen. Perhaps it might be
useful in teaching.
Thanks! That does seem appealing. I do regression to the mean over the course of a whole lecture, using data that my students measure on themselves to replicate Galton's work on stature. I wouldn't envy anyone who had to do it under a time constraint!
Re: Neandertal-human comparisons
Your website states, "of those positions where the human genome differs from chimpanzees, Neandertals have the chimpanzee version around 12.7 percent of the time."
Since the subject is the comparison with supposed MRCA of humans/chimps, shouldn't the correct statement be, "of those positions where the human genome differs from chimpanzees, Neandertals have the MRCA version around 12.7 percent of the time." ?
Or therefore, "of those positions where the human genome differs from chimpanzees, Neandertals have the chimpanzee version around 6.35 percent of the time."
If Neanderthals were something like 2 million base pairs closer to chimpanzee, shouldn't a few thousand of those base pairs be in at least a few modern Eurasians ?
Hi, thanks for your question!
Your point is correct that Neandertals do not have chimpanzee ancestors. If we were considering a comparison of all sites in the Neandertal sequence, you would be correct about the proportions. Neandertals would lack some proportion of the mutations that occurred on the modern human's lineage but they would lack every one of the mutations that happened on the chimpanzee lineage -- except for a very small fraction of parallelisms.
However, the comparison carried out by Green and colleagues was not of the entire genome, but specifically those sites in the genome that underwent mutations on the human lineage. The mutations on the chimpanzee lineage from the MRCA are completely ignored by this comparison.
The chimpanzee genome therefore stands in for the MRCA in this comparison. Sites at which both chimpanzees and humans have undergone parallel mutations have the potential to confound this comparison, because they are not counted (they are not places where the human and chimpanzee genomes differ). But the proportion of human substitutions that are also chimpanzee substitutions from the MRCA is very small, only around 1 percent of the human sites.
The fraction of Neandertal ancestry of Eurasians is around 3 percent, this is calculated differently, by examining polymorphisms within human populations today and considering the fraction shared by different humans' genomes with Neandertals. Eurasian people have around 3 percent more similarity with Neandertals than present-day Africans.
While looking for something else on youtube I stumbled on a video by a New Age wacko named [name redacted]. Part of his schtick is the claim that human DNA is changing rapidly and building up to some kind of big transformation in Dec 2012. I suppose it is inevitable that one's work can be used by anyone, but I thought you might like to know that yours is being invoked by this charlatan.
Thank you so much, I appreciate it. You're right, many, many people are out there finding ways to misappropriate our work -- used to be mainly creationists but lately I have more and more New Age-types.
