Re: Denisova
Dear John Hawks,
I would like really to know what decisive arguments allowed scientists to tell Denisova finger went from a female, after nuclear genome sequencing.
That is quite simple; if the specimen were a male there would be Y-chromosome sequences in the genome.
My name is Corey Hayes. I am in my final year of Anthropology at MacEwan University in Edmonton, Canada. My Minor's English, and I've been told I have a bent for creative writing, specifically, sci-fi.
A few summers ago I wrote an article in response to Stephen Hawking's warning that humans might go extinct if we didn't migrate into space. I argued that even if we did migrate to other worlds, we would eventually still go extinct (by ceasing to be Homo sapiens, which you spoke of in National Geographic). I then began to speculate on the directions evolution might take us if, as you so brilliantly put it, "Some major new isolating mechanism" takes place.
Suppose five arks head out in opposite directions (the Milky Way is about 100,000 light years in diameter), and those five populations (including Terran plants and animals) remain isolated from one another for hundreds of thousands, or millions of years, on a variety of planets (with different gravities, atmospheres, some with moons, some without, under reddish, bluish, or whitish suns) - would they, during a random encounter among the cosmos, and given the ample opportunities over such vast stretches of time for the loss of history to occur, even recognize one another?
I reckon the DNA evidence would point to a common origin, and many phenotypical traits would be maintained. But I wonder whether linguistic commonalities could still exist along with cultural and ethical remnants. Or, if one population comes from a world illumined by a reddish sun, and another was illumined by a bluish, how might that complicate communication about, say, color? How might the absence of a moon, or the presence of two moons, affect menarche (though I understand that there is no scientific evidence the two are linked, the 28-day cycle is still a heck of a coincidence). How long would the populations have to be isolated for them to became separate species (or be unable to even breed hybrids)?
I'm not necessarily asking you to answer these questions (but if you can, that would be great). But I would really appreciate it if you could point me in the direction of any relevant scholarly articles, essays, or even short stories you may have encountered that may help me answer these questions.
And thanks for thinking ahead. I hope we make it there.
Thanks for writing.
One factor to consider is technology. Language change, for example, has really slowed since literacy became widespread; and the scope of nation-states with newspapers, magazines and radio and television have caused the disappearance or decline of many minority languages across the world. If the people who are part of some human diaspora live in habitats that are suffused with technology; computers designed and programmed on Earth, for example, they might continue their language and cultural evolution at a very slow pace -- at least relative to how human societies have changed during prehistory.
I think the optimal population size for a diasporic group would be large enough to make drift negligible, even on the generation-ship timescale. Selection would kick in much more strongly when the groups reach their ultimate destinations. Then, anything goes.
Re: "Taxonomy on tap", where I reminded readers about my lack of a principled reason to continue using "hominid" instead of "hominin".
The only principle have to stand by is communication. Anybody who teaches and talks with their students should know how stupid this change is. Reading Begun or Harrison can't be compared to Smith, or [redacted]. Reading Early Begun can't be compared with late Begun. Students (and others) have no idea which meaning of hominid is in use in any particular publication, and authors rarely address this. All this confusion to conform to current taxonomy: but does it? Probably not, as Chimps and Humans are sooner or later going to be merged under the genus Homo. Then what? A third seismic change in what it means to be human - or a terminal confusion in a profession already widely recognized to be confused.
Good reason to adopt a clade-based taxonomy. On the other hand, that would force us to split up Australopithecus.
I will add on the topic of the chimp-human "Homo" idea that this is a good reason for a big congress on the definition of Homo. The reason for recognizing us at the genus level has to be defended by the events that led to our evolution, because it can't be defended on the basis of phylogeny.
And from another reader:
Hi John
I'm the kind of person who talks about human paleontology with my
friends, although none of us are specialists. When the news came out
about the sequencing of Neanderthals and Denisovians, I started saying
hominins. My wife asked me why and I couldn't give an answer.
That's an excellent perspective, thanks for sharing!
I've been having a conversation with a long-time colleague who doesn't like the change. Many don't. I personally don't invest that much in the words, but it's clearly an interesting case of contested change in terminology.
Re: graphics
I've enjoyed reading your blog for awhile now as I like the anthropological take on genomic data. A post back in February ( http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/1000-geno... ) was accompanied by some of the more attractive bar plots I've seen (nice alpha, great fonts) -- can you divulge what software you used?
Thanks for the kind words!
These and most of my graphs are done with Mathematica. The fonts are in the PT Sans family, which are free from Google Fonts. The color scheme is stock. I composite almost all my graphs in Illustrator and in particular add nearly all the data labels that way, even though I could do them programmatically, I find it easier to just label by hand.
This post on heritability has some xy plots also from Mathematica:
http://johnhawks.net/explainer/stats/heritability-and-stature
From a reader:
I'm the TA for an Intro to Philosophy course. This week, we're discussing Paley's Design Argument, Darwin's argument(s), and the evidence that favors Darwin's arguments over Paley's.
Here's my question: I had heard that mammals during early stages of development have vestigial gill slits. But I'm having a hard time finding legitimate documentation of this. Do you know either way? If not, do you know of any other good cases of vestigial traits in humans? Unfortunately, as I'm sure you realize, there are people whose brains simply cannot process evidence for common ancestry, so I try to make the examples as anthropocentric as possible, figuring those examples have at least some shot of convincing.
The "gill slits" in a human embryo are the pharyngeal arches and clefts, which ultimately develop into many different tissues of the head and neck. They are homologous to pharyngeal arches at the same embryonic stage in other vertebrates, but they do not have any role in respiration and do not include any true gill-like tissue. P.Z. Myers has written an accessible account of the history and current understanding of the gill slits (http://www.talkorigins.org/faqs/wells/haeckel.html). They are misleading as an example of evolution because they are not vestigial gills, however, the occurrence of the same structures in embryos of all vertebrates does reflect their common descent.
The wiki page on "human vestigiality" is not bad as a summary of traits that humans have in common with other animals but are basically useless in us. (http://en.wikipedia.org/wiki/Human_vestigiality) For me, the clearest and best examples of common descent are pseudogenes (example: GULOP, which makes vitamin C in most mammals, in anthropoid primates and tarsiers the gene still exists but is nonfunctional, broken). Also, LINE insertions -- a kind of retrotransposon that makes up a large fraction of junk DNA, humans share many nonfunctional insertions with chimpanzees, gorillas, etc., even though they have no function.
Also, a better anatomical example is the recurrent laryngeal nerve -- which takes a path that doesn't make any anatomical sense, except when you consider our ancestry in animals with very different configurations of head and neck: (described well by Jerry Coyne http://geophagus.wordpress.com/2009/07/11/why-evolution-is-true/) It originates in the sixth branchial arch of the embryo, which makes this a natural example to follow up the "gill slit" argument -- a real homology that is not a superficial similarity.
Hope that helps you. The classic response to the Paleyan argument in evolutionary biology is the long list of examples of poor design. Of course, a clever person can often argue that something that works badly is nevertheless well-suited for a vestigial purpose. That makes the DNA comparisons often much more persuasive.
Re: Solutrean publicity blitz:
Dear John,
I normally have a soft spot for unconventional models of
American prehistory. Boas's speculations about the Iroquois
representing a northward back migration from South America always
fascinated me as did his idea that Raven myths found there way from
North America to Siberia. In contrast the thinking behind the
Solutreah hypothesis strikes even me as unimpressive.
It helps that Boas had some observations to go on!
Hrdlicka impresses me, how he traveled around to investigate claims of Pleistocene man in the Americas. That's the spirit I like -- take the claims seriously, go there and investigate, and report whether the evidence is good or not. We have too much arm waving today.
Re: Neandertal ancestry
I stumbled across your (excellent) website this morning and enjoyed a couple of your articles concerning Neandertals. I know you're a busy guy so I'll get straight to it:
Your articles discuss varying levels of Neandertal DNA in present-day human populations. I thought the issue of whether Neandertals and modern humans successfully interbred was still very much undecided?
For reasons I've always presumed to be largely sentimental, I hope the Neandertals "survived" via interbreeding, rather than simply disappeared from the face of the Earth. Your articles are very uplifting.
Great to hear from you and thank you so much for the kind words!
There is no doubt anymore; many of us have Neandertal ancestors. Now we are working on determining which parts of the genome this involves in different living people, and how the pattern of interbreeding took place.
Re: Neandertal gene variants in Yoruba:
If you think in terms of ice-age climate, with sea-level about 150 ft lower than at present and the Mediterranean regularly covered by thick arctic-like ice in winter, it is easy to imagine early humans making their way back and forth over an ice-covered strait of Gibraltar or along an ice-free coastal strip connecting western Europe with West Africa. I think the discovery of relatively large number of neanderthal genes in West African tribes like the Yoruba is one of those unexpected and unpredicted facts that on further reflection makes a lot of sense, justifying the statistical analysis used. After all, if a statistical algorithm only shows what's expected, you have to wonder whether all it's done is to give a statistical excuse for what's already believed to be true.
Indeed, I think this is a possible explanation. On the other hand, there is just as much danger of post hoc generalization the other way!
Testing that hypothesis will require some more sophisticated estimates of the ages of particular gene regions that have been inherited from Neandertals in West African populations.
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!
