Category: human evolution

Svante Pääbo on human evolution – a must-watch lecture

November 27, 2017 • 10:00 am

by Matthew Cobb

Last week (20-22 November) there was a paleogenomics jamboree at the Wellcome Genome Campus in Cambridge (the real one, in the UK).  At the meeting, entitled “Human Evolution: Fossils, Ancient and Modern Genomes”, the great and the good of the ancient DNA and human evolution worlds got together to discuss the latest research in a field that, over the last decade, has transformed our understanding of human evolution.

The man who has been the driving force in the field for nearly three decades is called Svante Pääbo (pronounced ‘pair-bo’). He has made some of the most extraordinary discoveries, including the identification of a hitherto unknown human relative, the Denisovans, and above all the realisation that our ancestors mated with both Neanderthals and Denisovans and left traces in the genomes of modern non-African populations. (Jerry, myself and Greg have posted on these discoveries over the lifetime of this site – here is a list of the posts.)

Pääbo was invited to give the opening talk at the meeting, and the lecture is now available on YouTube. It is an hour long, but it is limpid, informative, and brilliant. Please watch it, and think about both the incredible technical tour de force that lies behind these discoveries, and also the brilliant, mild-mannered man who has done so much to take the field forward:

I bumped into Pääbo last year at Cold Spring Harbor Laboratory on Long Island. He was sat quietly in the canteen, and I went up to him and started burbling like a fanboy. I lost all intellectual control and just started chuntering about how brilliant his work was. Nevertheless, I managed to apologise to him, because I remember a ‘journal club’ when the lab I was in discussed his first paper on Neanderthal mitochondrial DNA, and we dismissed the results as being due to contamination from modern DNA. We simply did not believe it was possible to identify a DNA sequence from so far back. And yet, thanks to the brilliance of Pääbo and his colleagues, it was all absolutely true.

A lovely graph that tells our story

October 9, 2017 • 8:00 am

by Matthew Cobb

I came across this beautiful graph in an article in the journal Cell this week. It shows declining levels of genetic variability among 51 populations of humans across the planet, plotted against the distance of each population from East Africa:

The data in the figure are from a 2008 paper in Science by Jun Li and co-workers [JAC: reference at bottom; free access] looking at human genetic variation. They studied 938 unrelated people and  650,000 genetic variants, measuring the levels of heterozygosity in each population – this the frequency with which individuals had different copies of a each genetic variant.

This striking result is additional evidence that we originated in Africa and gradually moved around the planet, losing genetic variability as we went. The last places we reached in this survey – the Americas, show the smallest levels of variability.

This is exactly what you would expect: in species that have spread geographically, the ancestral populations have the highest levels of genetic variability. Populations that have moved into new areas tend to lose variability for two reasons. First, they initially contain just a subset of the variability present in the original population. This is probably the explanation for most of the effect on this figure, as many of the genetic variants they have studied will be in ‘junk’ DNA that has no effect on the phenotype. Where the variants are in genes that have an effect, variability can be lost again as the population is subject to new selection pressures in their new environment, which further reduces heterozygosity. Or, as the authors put it:

This trend is consistent with a serial founder effect, a scenario in which population expansion involves successive migration of a small fraction of individuals out of the previous location, starting from a single origin in sub-Saharan Africa.

The final reason why this figure is so pleasing is that it gives a straight line—that doesn’t happen very often in biology!

However, if we look closely, it’s not totally linear – in particular, African populations can show varying levels of variability that do not appear to be related to geographical distance from East Africa (in fact, from Addis Ababa). If you plotted only the African data, you wouldn’t be very impressed. This African variability may be for a number of reasons: the origin of humans may not have been precisely in East Africa, or humans have lived for far longer in Africa than anywhere else on the planet, and may have been subject to particular selection pressures reducing their variability (for example, in an isolated group). An explanation of those four African points at the top, which show essentially identically high levels of variability, may be that there were consistently high levels of gene flow between these groups, maintaining the variability.

Whatever the case, this figure underlines that we are a global species, spanning out across the planet, adapting and losing genetic variability as we traveled.

____________

Li, J. Z., D. M. Absher, H. Tang, A. M. Southwick, A. M. Casto, S. Ramachandran, H. M. Cann, G. S. Barsh, M. Feldman, L. L. Cavalli-Sforza, and R. M. Myers. 2008. Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. Science 319:1100-1104.

More on biology and race

August 29, 2017 • 9:15 am

by Greg Mayer

Jerry posted yesterday on an article at Quillette by Bo Winegard, Ben Winegard and Brian Boutwell on biology and race, commending it for its sensibleness. I thought I’d chime in with my own thoughts. Jerry’s a population geneticist and I’m a herpetologist, but our views turn out to be quite similar.

So, here, in a nutshell, is what biology has to say about race. To begin with, race is not a technical term in biology—it is used loosely for any differentiated subdivision of a species. For example, there is a fruit fly in Wisconsin that feeds on hawthorn and apple, and the flies that feed on the different trees are somewhat different, and so people refer to the “hawthorn race” and the “apple race”. Often, as in fact is true in this case, the term “race” is used because people aren’t quite sure exactly how different the forms are from one another.

In zoology, the term “geographic race” does have a well-defined meaning. It means that if you look at an individual of a species, you can tell where it is from, or conversely, that if you tell me where the individual is from, I can tell you what it looks like. For example, there’s a species of lizard in Jamaica that if you brought one back and showed it to me, I could tell you whether it’s from the vicinity of Kingston, or Montego Bay, or Negril, etc. Lizards from these various places are members of the same species because they interbreed with one another where they are in geographic proximity; they are geographic races because I can tell where they are from by looking at them. Geographic races, if they are given taxonomic names, are called subspecies.

With regard to humans, most of the genetic variability is within populations, not between local populations or races. This was pointed out by Dick Lewontin in 1972 (Dick, of course, was Jerry’s dissertation adviser, and my de jure adviser). However, just because most of the variation is within populations doesn’t mean you can’t tell where someone is from by looking at him. The geneticist A.W.F. Tony Edwards later called the mistaken notion that a majority of variation being within populations precludes identification of population membership “Lewontin’s Fallacy”. [I’ve no idea where I got the idea he was called “Tony”. I’ve never met him, and people who do know him have assured me he’s called “Anthony”.]

As a former student of Lewontin’s, I’m not especially fond of Edwards’ choice of term, but nonetheless Edwards is entirely correct. It is of crucial importance to note that the scientific questions asked by Lewontin and Edwards were different. Lewontin asked “What proportion of genetic variation (in the analysis of variance sense) in humans is within and among populations?” The answer is that roughly 85% is within populations, the rest among local populations and races. That is the answer Lewontin gave in 1972, and it is entirely correct, confirmed by much more molecular data since that time. Edwards asked “Can individual humans be assigned to races from genetic data?”, or, alternatively, “Can human races be diagnosed (in the taxonomic sense of subspecies)?” The answer is yes, they can. Edwards shows that his answer to his question is entirely compatible with Lewontin’s answer to Lewontin’s question. A paper by Rosenberg et al. (2002) clearly illustrates for a large data set the truth of both Lewontin and Edwards’ answers to their respective questions. Lewontin goes on from his finding (with which Edwards entirely agrees), to argue further that this level of difference between races is not worthy of taxonomic recognition. Edwards doesn’t actually express an opinion about whether human races should be recognized taxonomically, but does show that the 85/15 division of within/among population variation is no bar to doing so.

One thing a bit off in the Quillette piece is their claim that Lewontin’s conclusion “was based on a peculiar way of measuring genetic variation.” It was not; it was based on a perfectly natural and obvious way of measuring genetic variation, and, indeed, Dick was right, as Edwards acknowledged. The distinction between single and multi-locus genotypes mentioned by Winegard et al. does not at all nullify Lewontin’s conclusion as to the apportionment of variation. What Edwards showed very clearly is that multi-locus genotypes allow individuals to be reliably assigned to populations, even when most of the variation is within populations. In understanding patterns of genetic variation in humans, it is very important to see that Lewontin and Edwards asked different questions, and that they are both right in their answers to their respective questions.

Lewontin and Edwards agree on the moral equality of human beings; Edwards just doesn’t want that moral equality to depend on any contingent facts of genetic similarity. Lewontin wouldn’t want it to, either, but sees the high genetic similarity among human races (genetic similarity is much lower among races in some other species) as empirical reinforcement for his moral conclusion. The problem with basing human moral and civil equality on empirical claims about human biological similarity is that such claims may prove to be mistaken. Because it does not depend on some empirical finding which new data may put into question, I think Edwards has the more robust basis for his moral conclusion.

As Edwards sums up:

“But it is a dangerous mistake to premise the moral equality of human beings on biological similarity because dissimilarity, once revealed, then becomes an argument for moral inequality.”

Edwards, A.W.F. 2003. Human genetic diversity: Lewontin’s fallacy. BioEssays 25:798–801. pdf

Lewontin, R.C. 1972. The apportionment of human diversity. Evolutionary Biology 6:381-398. pdf

Rosenberg, N.A., J.K. Pritchard, J.L. Weber, H.M. Cann, K.K. Kidd, L.A. Zhivotovsky, and M.W. Feldman. 2002. Genetic structure of human populations. Science 298:2381-2385. pdf

A sensible article on human “race”

August 28, 2017 • 8:45 am

As a biologist, it irks me when ideologues distort biology in the service of politics. My view, which I absorbed from Steven Pinker, is that we should be able to accept scientific facts without perforce turning those facts into government policy.  After all, since morality is subjective and not objective, facts can never by themselves dictate what we should do, which in the end comes down to a reasoned matter of preference. Of course facts can inform policy: learning more about when human fetuses can feel pain might inform debates on abortion. But even so, it’s still a matter of preference to decide whether abortions are permissible, and, if so, at what point in pregnancy should we no longer permit them.

There are three areas where ideology has impinged on biology, trying its best to distort data: differences between human ethnic groups (“races”), between human males and females, and the study of evolutionary psychology. I’ve written about these at length on this site, and won’t go into detail, for this post is just to point you to a good article on race.

The ideologues’ problem with all these areas is the same: were biology to show, for example, that there are genetic differences between sexes, ethnic groups, or cultures, that could be used to justify racism, sexism, and exceptionalism. And indeed, this has happened in the past: all of us know the sordid history of assuming biology translates directly into human rights, which led to eugenics, racism, the denigration of and lack of opportunity for women, and so on.

But there are two ways to respond to any genetic differences that we find. The ideologues’ way is simply to deny the existence of any meaningful genetic (and presumably evolved) differences between human groups or sexes, and to denigrate any findings that show them. (This is, of course, confirmation bias, for these people never look critically at studies that support their ideology.) Evolutionary psychology is denigrated as “pseudoscience”, a phony discipline populated by sexist and misogynistic scientists devoted to propping up the status quo. I’ve been a critic—sometimes quite severe—of evolutionary psychology, as there are a fair number of pretty bad studies. But there are good ones, too, and results showing humans favoring those most closely related, or uncovering evolved differences between men and women in sexual behavior, seem pretty solid. It’s just dumb to say that the entire field is intellectually bankrupt, for if our bodies bear the traces of ancient selection in our ancestors, why not our minds? After all, while non-African human groups evolved in geographic isolation for at most 60,000-100,000 years, males and females have been maneuvering to reproduce for the six million years or so since we separated from our closest relatives.

The other way to deal with distasteful scientific findings is to realize that they shouldn’t even inform political policy, for science is an “is” and policy is an “ought”. It’s unlikely that all ethnic groups, or males and females, will be exactly the same in every aspect of behavior, physiology, intelligence, interests, and so on—down to the third decimal point. But so what? The basis for moral equality and equal opportunity does not rest on genetic endowment, but on philosophical considerations: nobody has a right to claim that they, by virtue of their ancestry or sex, have privileges that allow them advantages over anyone else. Further, the substantial overlap in abilities (except, perhaps, for things like upper-body strength in men versus women) is sufficiently large that it would be just dumb and societally injurious to bar someone from opportunities based on sex or ethnicity.

Further, if you base your notion of moral equality on genetic equality, that makes equality vulnerable to future discoveries in biology that could reveal various forms of genetic inequality. But this can’t happen when the argument for equality and equal opportunity is a moral and philosophical one.

On to “race”, a loaded word if ever there was one. Browsing through Quillette, I found a short but very good 2016 article about race by Bo Winegard, Ben Winegard, and Brian Boutwell, “On the reality of race and the abhorrence of racism“. It’s one of the more sensible pieces on race written for a popular audience, and takes the position I mentioned above; as the authors say, “Promoting a tolerant cosmopolitan society doesn’t require denying basic facts about the world.” Or, as they say, using italics to emphasize their view, “Racism isn’t wrong because there aren’t races; it is wrong because it violates basic human decency and modern moral ideals.”

As far as I can see, their biology is accurate.  Winegard et al. reject, as do I—or any sensible biologist—the idea that there are a finite number of easily-demarcated “races” that differ by single diagnostic genes. Rather, we have a genetic spectrum of populations that are fuzzy around the edges, but still reflect some genetic differentiation that occurred in geographic isolation. You can’t diagnose someone’s ancestry or geographic origin from looking at a single gene, but you can do a pretty good job if you look at many genes taken together, as “allelic” differences among different loci are correlated. Using an entire spectrum of genes gives us the ability to discern groupings. Granted, those groupings are not discrete, but are still useful in finding out where someone’s ancestors came from (including Neandertal ancestors). Were this not true, firms like 23 And Me would be of no use whatsoever.

I recommend you read the article. I’ll just reproduce three “objections” that, say Winegard et al., ideologues or those willfully or simply ignorant of genetics raise against the concept of “race”. (Since that word is now irretrievably loaded and pejorative, I prefer to use the term “ethnic groups”.) Their words are indented (mine flush left), and they deal with each objection at length.

(Objection 1): Human variation is clinal or gradual, not discrete. Skin pigmentation, for example, does not come in four, five, or seven distinct colors, but varies gradually from very dark near the equator to very light in Northern Eurasia.

True, but that doesn’t constitute a refutation of genetic clustering.

The most common objection we meet among those denying biological differences between groups is the next one:

. . . . (Objection 2): Human genetic variation is much greater within human populations than among human populations; therefore, variation that exists between groups is of little scientific interest.

This claim is true in a circumscribed sense, but is largely irrelevant to the question of whether population group differences are biologically meaningful. As pointed out by Jeffry B. Mitton and A.W.F. Edwards, the original finding that genetic diversity among human races is insubstantial compared to genetic diversity within races [JAC: this “original finding” came from an analysis by my Ph.D. advisor Dick Lewontin] was based on a peculiar way of measuring genetic variation. Roughly speaking, the original claim about genetic diversity was based on analyses at single genetic loci (spots on the chromosome where genes are located) and not on analyses that considered the correlated structure of multiple genetic loci (many locations). Failure to consider multiple loci assures that broad, distinct patterns of allele (gene) frequencies get lost in the noise of diversity at single loci. This sounds painfully abstruse, but the basic point is this: patterns that are nearly invisible for individual genes become visible if one examines multiple genes at the same time (i.e., looks at gene 1 + gene 2 + gene 3 + gene 4…et cetera).

Empirical studies bear this logic out. The geneticist Hua Tang and her colleagues, for instance, found that self-reported ethnicity corresponded almost perfectly with genetic clusters from 326 microsatellite markers  (a microsatellite marker is a piece of repetitive DNA in which a series of DNA base pairs are repeated). Other studies have demonstrated even more power to identify people’s ancestry accurately. These studies illustrate that, whatever the meaning of the claim that there is much more variation within than among races, researchers can, if they use the appropriate procedures, distinguish human ancestral groups from each other with remarkable accuracy. The significance of these genetic differences among groups is entirely an empirical question.

Here’s a quote from the abstract of the Tang et al. paper, published in The American Journal of Human Genetics, an excellent journal. The article is free online:

Of 3,636 subjects of varying race/ethnicity, only 5 (0.14%) showed genetic cluster membership different from their self-identified race/ethnicity. On the other hand, we detected only modest genetic differentiation between different current geographic locales within each race/ethnicity group. Thus, ancient geographic ancestry, which is highly correlated with self-identified race/ethnicity—as opposed to current residence—is the major determinant of genetic structure in the U.S. population.

Finally, the last objection:

. . . . (Objection 3): Human racial classifications are arbitrary. For some purposes, categorizing by skin color is useful; for other purposes, categorizing by, say, antimalarial genes, is useful. These classifications, although equally valid, lead to radically different racial categories.  Thus, one particular classification scheme is no better than the other and none are particularly illuminating.

This claim is wrong. While a particular “classification” may be somewhat arbitrary, that doesn’t deny that some classification schemes are better than others. It would be ludicrous, for example, to classify groups simply by the frequency of Landsteiner blood type (A, B, AB, or O), while it makes a lot more biological sense (and tells us a lot more about evolution and human history) to do multivariate grouping using as many genes as you can.

This article is PCC(E) Recommended Reading.

A final point. The article doesn’t deal with another question that’s worth debating: is all research on differences between sexes and ethnic groups even worth doing? That question is a hard one. If you think “yes, because any result would be interesting”, consider whether you’d approve of a project that sets out to determine whether Jews are genetically more acquisitive of money than are other groups.

Researcher: Human sense of smell better than everyone thinks; may rival that of dogs!

May 16, 2017 • 8:30 am

John P. McGann of the Department of Psychology at Rutgers University has spent fourteen years looking at the olfactory (smelling) system of mammals, and has published a new paper in Science suggesting that what we think we know about our own sniffing ability, compared to the reputed Super Sniffers of dogs and rodents, is wrong. McGann suggests, to a fanfare of publicity in various venues, that we’re not that bad: in fact, he notes that humans may be just as good as dogs and mice at detecting odors.

His paper is referenced below, and access is free if you have the free and legal Unpaywall extension (get it!).

McGann suggests that the presumed olfactory inferiority of humans is based on observations of the relatively small size of human olfactory lobes in the brain—observations made by Broca and other early neuroanatomists, and promulgated by Freud, who said that the absence of an acute sense of smell in humans led to sexual repression, since sex was partly based on odors.  After reviewing the historical evidence, McGann gives his biological evidence. Here are his main points:

  • Although the relative size of olfactory lobes compared to brain size as a whole is smaller in humans than in rodents, the absolute size if the lobes is much larger.

This shows the relative sizes of human and mouse olfactory lobes; the mouse lobe is much larger relative to its whole brain:

(From paper): Gross anatomy of the olfactory bulbs of human and mouse. (A) Ventral aspect of human brain, with meninges removed from the cortex. Area indicated by dotted rectangle is enlarged in (B). (B) View of left and right olfactory bulbs and olfactory tracts from (A). (C) Ventral aspect of mouse brain, with olfactory bulbs visible at the top. Up is anterior in all three panels. Dashed lines denote the approximate border between bulb and tract.

But the absolute size of the human bulb, which McGann sees as one key to good olfaction, is much larger than that of the mouse:

(From paper): Comparison of the mouse and human olfactory bulb. View is of the ventral aspect of the left olfactory bulb. Both bulbs are at the same scale.
  • Further, the absolute number of neurons in mammalian olfactory bulbs is relatively constant (McGann sees that as an indicator of smelling ability as well).

This graph shows that the number of neurons in the olfactory regions varies among mammal species by less than a factor of ten, regardless of the much larger variation in body size—and humans aren’t particularly low:

(From paper): ig. 3 Comparison of olfactory bulb neuronal numbers across mammalian species. The number of putative neurons per olfactory bulb for each species, as measured by isotropic fractionation. Numbers are drawn from Ribeiro et al. (48) and Oliveira-Pinto et al.
  • Data showing a larger number of inactivated olfactory genes in humans compared to dogs and mice is questionable. 

In Why Evolution is True, I noted that many human “olfactory receptor genes”, each binding to a separate molecule and allowing us to smell it, have been inactivated by mutations: they’re dead “pseudogenes”. As McGann reports, humans have 1000 such genes, but “only” (his quotes) 390 of them code for receptor proteins. In contrast, mice have 1300 such genes, of which 1000 code for proteins. This has been taken as evidence that mice can smell a lot more acutely than can humans. But McGann points out that 60% of the human pseudogenes are transcribed into messenger RNA in the nose.

But that’s weak evidence, as we already know that many pseudogenes are transcribed into RNA but not translated into proteins, so this says nothing about the number of OR proteins made in humans versus mice. Besides, even if every transcribed pseudogene in humans was made into an active, odor-receptive protein, there would still be 1000 active genes in mice versus about 750 in humans.  Further, McGann didn’t do the comparison for pseudogenes in dogs or mice.

Here’s a table from a 2007 PLoS paper by Nimura and Nei showing those three species. If McGann wants to make the pseudiogene argument for human sniffing, he has to take into account the data below, and the possibility that many dog, mouse, and rat pseudogenes may also produce receptor proteins. Thus, I’m not convinced by his pseudogene evidence. (Note that every olfactory gene in cetaceans like whales is a pseudogene, suggesting they really aren’t used to smell, as those genes aren’t functional underwater.)

  • The structure of the olfactory system differs between humans and other mammals. 

These difference include a larger number of glomeruli (cluster of nerve receptors) in the human olfactory bulb compared to rodents, and the observation that the bits of human cortex used for processing olfaction is more “elaborate” (i.e., has more neural connections) than in other species. To me, this says little about the relative abilities of humans vs. other mammals to detect odors.

The most crucial question, however, involves not just neurons or pseudogenes but is this: “How many different odors can humans detect compared to, say, dogs and mice, and do we detect them at different thresholds?” It’s classically assumed that dogs and mice are better sniffers than are humans, but McGann said the data are not convincing, are based on anecdotes, and also rely on tests of molecules that humans wouldn’t have been selected during their evolution to smell anyway. Here are a few quotes (my emphasis if you want just the high spots):

Human olfaction is excellent and impactful

Historical and anatomical expectations aside, is the human olfactory sense actually impoverished? No, the human olfactory system is excellent, although it depends on the criteria employed. For instance, dogs may be better than humans at discriminating the urines on a fire hydrant and humans may be better than dogs at discriminating the odors of fine wine, but few such comparisons have actual experimental support. When properly tested, the primate olfactory system is highly sensitive to many odors and can exert strong influences on behavior, physiology, and emotions.

Humans with intact olfactory systems can detect virtually all volatile chemicals larger than an atom or two, to the point that it has been a matter of scientific interest to document the few odorants that some people cannot smell (i.e., specific anosmias). A prominent recent study calculated that we could also tell virtually all odors apart, with an estimated ability to discriminate more than 1 trillion potential compounds . Although this exact number is highly sensitive to the assumptions made, it is clear that the human olfactory system is excellent at odor discrimination, far better even than the putative 10,000 odors claimed by folk wisdom and poorly sourced introductory psychology textbooks.

One key insight in comparing the olfactory system of primates and other animals has been that different species have different sensitivities to different odorants. . . . A recent experiment tested olfactory thresholds for six sulfur-containing odors in mice, spider monkeys, and humans. Relative olfactory sensitivity varied with odorant : Humans were three orders of magnitude more sensitive than mice or monkeys to 3-mercapto-3-methylbuytl-formate, with all 12 human subjects outperforming all of the individual animals, yet all 12 humans were worse than all of the mice (and comparable to the spider monkeys) on 3-mercapto-3-methylbutan-3-ol. Overall, the humans were most sensitive to two of the six odorants, whereas the mice were most sensitive to four of the odorants. This finding complements older literature. . .

Human behavior is strongly influenced by olfaction. Environmental odors can prime specific memories and emotions, influence autonomic nervous system activation, shape perceptions of stress and affect, and prompt approach and avoidance behavior . Humans can follow outdoor scent trails and even exhibit dog-like casting behavior when trails change direction . The human olfactory system also plays a major, sometimes unconscious, role in communication between individuals. Each person produces a distinct odor that reflects not only dietary and environmental factors but also interacts with the immune system’s “self/non-self” histocompatibility markers to incorporate genetic information that permits the discrimination of kin from non-kin . The contents of this “body odor cocktail” are interpreted in parallel with environmental odors in the brain and can drive mate and food choice, as well as communicating information about anxiety and aggression in other people. We even appear to unconsciously smell our hands after shaking hands with strangers [JAC: Not me!], suggesting an unexpected olfactory component to this common social interaction. Although many of these olfactory experiences do not recruit attentional resources, they can be exceptionally salient in traumatic circumstances . When such circumstances result in posttraumatic stress disorder, olfactory hallucinations frequently become part of the symptomology.

Well. it’s clear from this (assuming McGann is right) that we need good comparative tests involving a variety of different molecules—not just molecules that would have been important in species’ evolutionary past—before we can say that the bloodhound is a better tracker by odor than is a human. But statements like “human behavior is strongly influenced by olfaction” says nothing about our relative sniffability compared to other species. This kind of writing is, I think, a bit tendentious.

The Guardian has a summary article about this paper, and shows that our own Matthew Cobb, who studies olfaction in flies for a living, thought the paper was great:

Matthew Cobb, professor of zoology at Manchester University, said the review had altered his own perspective on a study that he has focused on for much of his career. “We have this myth that humans can’t smell very much,” he said. “McGann’s exploring the actual evidence for that, which it turns out is fairly poor. It’s going to change my teaching next year.”

But others disagree:

Alexandra Horowitz, a scientist at Barnard College in New York, whose work focusses on canine olfaction, notes that while dogs track scents, find drugs and detect ovarian cancer in plasma samples, humans merely “notice if there is a bad smell on the train or someone has been cooking when we come home.”

“That there are olfactory specialists, such as perfumers or animal trackers indicates that with attention, we can get much better,” she added. “But not dog-level.”

While I’m not an expert like Matthew or Alexandra, my own take is that this paper is provocative and convinces me that more experiments need to be done, especially involving the ability of different species to detect different odors. Perhaps we’ve been too cavalier in our claims that humans are an auditory and visual species while dogs and mice depend more on olfaction. Old assumptions may be wrong, and McGann’s paper is useful for re-examining a famous set of such assumptions. He may be right, but I’m not convinced that his data show that. At best they show that we need to provisionally withdraw the common claim that we can’t smell as well as mice and dogs. (One thing I can say, though, is that humans smell better than dogs, especially wet dogs! I’ll be here all week, folks.)

__________

McGann, J. P. 2017. Poor human olfaction is a 19th-century myth. Science Vol. 356, Issue 6338,DOI: 10.1126/science.aam7263

Readers’ wildlife photos

May 8, 2017 • 7:30 am

I have a comfortable backlog of photos, but please keep them coming in—I can never have too many. Today we have an unusual contribution documenting ancient human activity in Africa. The photos come from Richard Bond, and his notes are indented:

I have wavered for a couple of years over whether these photographs would interest you, but in view of the recent stir about possible humans beings in North America 130K years ago, I thought that I might as well submit them. The photographs are of an excavation site at Olorgesailie in the eastern Rift Valley in Kenya that has yielded a huge number of stone tools. The site was occupied for possibly as long as a million years until about 200K years ago, almost certainly by Homo erectus.

Entrance to the site is through a tiny but excellent museum. This has examples of stone tools that one may actually handle: photos #1 & #1b. The hand axe in #1 is dated at 780K years old.

Photo #2 shows the first humanoid fossil found at the site. The source of the rock for most of the tools was Mount Olorgesailie, a now-extinct volcano shown in photo #3.

The shallow depression in the foreground used to be a lake. (Sorry about the haze; this appears to be a feature of the Rift Valley during the burst of very hot weather just before the end of the dry season.) The area used to be very volcanically active. Photo #4 was taken a little south of Olorgesailie while flying on an earlier visit to the Masai Mara, and, despite the haze, shows clearly several extinct volcanos.

Photo #5 shows an igneous dyke: note the erosion of the softer sedimentary rock that covered and preserved the site.The tools were first discovered spewing from erosion channels.

Photos #6 & #7 show some of these tools, laid out more or less to represent them as they were discovered.

Photo #8 shows a current excavation; the darker bands across the middle are ash from two of the many eruptions that allow accurate dating of the finds.

Photo #9 gives an idea of the depth of the erosion that exposed the tools, and photo #9b is one example of the many animal fossils found on the site.

One curious aspect is that obsidian tools (now in the Nairobi National Museum) have been found, despite the nearest source of obsidian being 50 km away. This might imply some sort of trading structure based around Olorgesailie.

I have visited many historical sites from the mundane to the spectacular, but this is my favourite. I actually became quite emotional in a couple of places, most unlike me. When I visited in 2013, I was shown round by the curator, a charming, softly spoken man who would dearly like more visitors. Unfortunately, it is not easy to get there. For a start, few Kenyans know about it, and it took a most helpful porter at the Panafric (my favourite Nairobi hotel) about half an hour to find a taxi driver who would take me. Although it is just off the direct Nairobi-Magadi road, the bus takes an alternative route that passes through more villages. (I would not risk the dreaded matatus even though they are better than they used to be.) Taxi (not cheap for one person!) or hire car are the only real options. I did not begrudge the expense, because the drive itself is fascinating, not least for the spectacular views of the Rift Valley. My driver had never known about the place previously, and from his comments on our return drive he was considering the possibilities for lucrative future business, so perhaps by now the Panafric might lay on much cheaper trips by minvan. Incidentally, like most Kenyan taxi drivers, mine was excellent company, very informative, and spoke fluent English.

Nature paper suggests humans inhabited North America 130,000 years ago

April 27, 2017 • 5:43 pm

by Greg Mayer

As Jerry noted yesterday, in a new paper in Nature, Steven R. Holen and colleagues report finding the remains of a butchered 130,000 year old mastodon in San Diego. (If you haven’t already done so, do go take a look at Jerry’s post, which includes a video press release, and illustrations from the paper.)

The key words in the first sentence are ‘butchered’* and ‘San Diego’. The first word indicates that people had taken the bones of the 130,000 year old mastodon apart– which in itself would be a “neat, but what’s the fuss” result. It’s ‘San Diego’ that’s the cause of the fuss. The peopling of the Americas has been a contentious topic for some time, but virtually all the debate has concerned a relatively slim time interval– 12-30 kya (see here for a previous discussion at WEIT, and this news piece in Science about two recent papers with contrasting conclusions). The San Diego find is thus 100,000 + years earlier!

So what evidence do they have for this early arrival? First, they have the mastodon, whose bones were fractured in ways which they find inconsistent with damage by carnivores or the environment, but which appear consistent only with being struck with implements. They did a lot of breaking of elephant bones in order to try to simulate the damage to the mastodon, and concluded that tools alone could do the trick. The mastodon’s remains were radiometrically dated at 130.7 ± 9.4 kya. In addition to the mastodon, they also found stone tools, which they interpret as hammerstones and anvils.

These results would have many important implications for human evolutionary history; but first we must ask, are the results correct?

I must admit I’m dubious. The anvil and hammerstones are not the sorts of objects which are unquestionably manufactured– they are not like finely fluted spear points, whose human origin cannot be doubted. The breakage patterns in the bones do indicate that the breaks occurred perimortem, but I’m not sure the breaks could not be due to non-human causes. The dating is directly on the mastodon, which is good– they’ve not dated some possibly extraneous item which could have been redeposited from earlier strata. But, nonetheless, dating is subject to various artifacts.

As Carl Sagan used to say, “Extraordinary claims require extraordinary evidence.” What makes the current claim extraordinary is that there’s no other evidence of human presence in the Americas for ca. 100+ K years after this find. And it’s not like the late Quaternary of America is an unstudied or poorly known stretch of time! I don’t regard fracture patterns and crude tools to be sufficiently extraordinary evidence to overcome, in a single go, the weight of that 100,000 year absence. It is much more reasonable to think that the new data can be reconciled with all the past data in a way that does not require us to discount the past data. And, thinking, “they must have made a mistake somewhere with the new data”, is a perfectly plausible way of reconciling the two. This conservatism in the face of anomalies is a key part of the method of science– it properly proportions belief to the evidence.

On the other hand, the new data do not threaten to overturn any fundamental principles, merely a seemingly well-attested fact of evolutionary history, and such facts have been overturned before. So, we must ask, but what if they’re right?

The most interesting implication, to me, is that if there were people here 130 kya, they went completely extinct.  It means that human habitation of an entire hemisphere is an iffy thing. The real first Americans got wiped out by something– disease, predators, climate, competitors, whatever. Who would these now extinct people have been? Well, if they got to America not too long before the radiometric date, they would probably be Neanderthaloid (by which I mean the varied archaic Eurasian subspecies of Homo sapiens with which anatomically modern humans interbred after their spread from Africa). If they came much earlier, they might have been Homo erectus (which would make Harry Turtledove’s A Different Flesh, in which the first European settlers of America encounter not Indians, but “sims“, prophetic!).

There would also be a possibility that these first Neanderthaloid Americans survived, and that the anatomically modern human colonizers of ca. 20 kya, interbred with them in the course of replacing them, just as their forebears did in Asia. However, because American Indians are not, as far as I know, enriched for Neanderthaloid alleles relative to other Eurasians (who are 1-4% Neanderthaloid; a bit higher in Melanesia), this seems unlikely. (There are claims out there that Indians are enriched for Neanderthaloid genes, but I don’t know how that got started; East Asians, from which, at least generally, American Indians descend, are Neanderthaloid enriched relative to Western Europeans, which seems to indicate more than one episode of interbreeding on the course of their migration from Africa.)

* I use “butchered” here in the sense of “processed for eating”, as the bones were presumed broken apart to get at the marrow. The paper uses “butcher” in the narrower sense of “cut with a knife or similar implement”. The paper does not say the mastodon was cut with a knife or other sharp tool.

Holen, S. R., T. A. Deméré, D. C. Fisher, R. Fullagar, J. B. Paces, G. T. Jefferson, J. M. Beeton, R. A. Cerutti, A. N. Rountrey, L. Vescera, and K. A. Holen. 2017. A 130,000-year-old archaeological site in southern California, USA. Nature 544:479-483.