The new African “multi-regionalism” & pan-Neanderthalism

We live in times when our understanding of the origin and diversification of modern humans is undergoing great change. More concretely, our understanding of what it means to be human is transforming. The terms are overused, but perhaps it could be called a “revolution” or “paradigm shift” between the year 2000 and today.

At the end of 2010 ancient DNA made it highly likely that people outside of Sub-Saharan Africa had non-trivial Neanderthal ancestry. That is, enough ancestry that it is detectable genomically. I should also add that I think it is highly probable that the good majority of people within Sub-Saharan Africa have Neanderthal ancestry. Some of this is due to recent attenuated Eurasian back-migration (e.g., many West Africans, Nilotic people, and KhoeSan have Holocene gene-flow signals which derive from the agricultural expansions of the past 10,000 years). But, I think once deep Pleistocene genomes of African humans are sequenced we will see evidence of some Eurasian back-migration at a very ancient date (there is already some suggestive inferential evidence of this).*

Talking with a few friends this week, I realized that the famous “We are all Africans” t-shirts, which have turned into recognizable memes, should be supplemented with “We are all Neanderthals” t-shirts. So yeah, now selling them on DNA Geeks. If the Richard Dawkins Foundation can make quid on it, why not the Razib Khan et al. Foundation?

This has all been on my mind due to a review paper in Trends in Ecology and Evolution, Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? (OA). If you read this blog closely you’ll see there’s not much new in it. But, it is a signpost, a marker, of the times we live in. Here’s the important bit:

Together with recent archaeological and genetic lines of evidence, these data are consistent with the view that our species originated and diversified within strongly subdivided (i.e., structured) populations, probably living across Africa, that were connected by sporadic gene flow…This concept of ‘African multiregionalism’…may also include hybridization between H. sapiens and more divergent hominins (see Glossary) living in different regions…Crucially, such population subdivisions may have been shaped and sustained by shifts in ecological boundaries…challenging the view that our species was endemic to a single region or habitat, and implying an often underacknowledged complexity to our African origins.

The first person who explicitly used the term “African multi-regionalism” that I recall was Alwyn Scally, though the general framework was shaping up years before. Frankly, I was waiting for someone to use that word. If Richard Klein’s The Dawn of Human Culture, published in 2002, was the apogee of the old model, often inchoate and more crisp in popularization than within the scientific community that we are all descended from a single East African tribe, this review paper heralds the emergence of a more complex and pluralistic framework. The emergence of modern humans within Africa then may have been a polycentric gradual and interactive process; not a singular explosion against the firmament of the antique savanna landscape.

By the late 2000s, even before the 2010 Neanderthal draft genome paper, it was starting to be evident due to genome-wide analyses of contemporary populations, that the extreme bottleneck clear in non-African populations was much more modest within Africa. That opened the possibility for the existence of deep structure within the continent that pre-dated the “Out of Africa” event. A deeper look at African hunter-gatherers indicated to many researchers that these groups diverged from other modern humans in the range of ~200,000 years before the well. Recent paleontological work has confirmed this genetic insight.

Where we are today is that some people are now arguing for the overthrow of the “Out-of-Africa” idea, whether by replacing it with an “Into-Africa” model of some sort, or resurrecting a more polycentric classical multi-regionalism (“some people” as evident in the increased frequency of emails and Twitter messages I get in this vein). I don’t think we’re there yet, not by any measure. But, it is now in the realm of very unlikely, not extremely unlikely (at least the “Into-Africa” model; it is clear that strong overwhelming demographic pulses from somewhere singular dominate the genome of most modern humans).

* I don’t think it is all that implausible that some Neanderthal back-migration into Africa occurred at some point in the last ~500,000.

Beyond “Out of Africa” within Africa

It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past). For the vast majority of humans then the last 60,000 years is characterized by a branching process, some reticulation (e.g., South Asians merge West and East Eurasian lineages) between these branches from a common ancestor, as well as introgression from archaic lineages like Neanderthals and Denisovans.

Though I do accept that it seems that modern humans probably migrated out of Africa before 60,000 years ago, mostly due to the results from archaeology, I think the genetic evidence is strong that these groups contributed very little genetically to contemporary populations.

The situation within Africa is very different. Being conservative it seems likely that the Khoisan ancestral lineage diverged from some other Africans ~200,000 years ago. I say conservative because there are researchers who want to push the divergence much further back. Additionally, several different research groups are now converging in a result that West Africans are a mixture between eastern Sub-Saharan Africans (think the population ancestral to Mota in Ethiopia) and a lineage basal to all other humans. That means that the Khoisan are not the most basal, so even assuming the conservative 200,000 year divergence point for Khoisan, modern humans share a common ancestor earlier than 200,000 years ago.

The upshot here is that around 75 percent of the history of modern humans is within (greater)* Africa. The distinctive “Out of Africa” bottleneck and expansion defines most humans only in the last 25 percent of the history of our species. And, within Africa, the dynamics were very different. The biggest difference is that African populations are not defined by a large number of lineages emerging and diverging around the same period, because there wasn’t a massive and singular expansion within Africa analogous to what occurred outside of Africa (at least until the recent past, with the Bantu expansion). That’s why there’s deep structure within Africa today between groups as divergent as the Bantu, Mbuti, Hadza, and Khoisan.

The term “Basal Eurasian” kind of makes sense in the non-African context because of the singular importance of divergence between lineages in the first 10,000 years or so after the “Out of Africa” event. I’m not sure “Basal human” makes as much sense because there wasn’t a singular event within Africa that allowed for the emergence of modern humans. Rather, it was a process, and probably quite resembles something like multiregionalism.

* Some wiggle room here for the likelihood that modern humans were long present in the liminal Near East.

The Ancient Neanderthal Mariner

More recent stuff on Neanderthals of interest, Neandertals, Stone Age people may have voyaged the Mediterranean:

A decade ago, when excavators claimed to have found stone tools on the Greek island of Crete dating back at least 130,000 years, other archaeologists were stunned—and skeptical. But since then, at that site and others, researchers have quietly built up a convincing case for Stone Age seafarers—and for the even more remarkable possibility that they were Neandertals, the extinct cousins of modern humans.

But a growing inventory of stone tools and the occasional bone scattered across Eurasia tells a radically different story. (Wooden boats and paddles don’t typically survive the ages.) Early members of the human family such as Homo erectus are now known to have crossed several kilometers of deep water more than a million years ago in Indonesia, to islands such as Flores and Sulawesi. Modern humans braved treacherous waters to reach Australia by 65,000 years ago. But in both cases, some archaeologists say early seafarers might have embarked by accident, perhaps swept out to sea by tsunamis.

The effective population size of Australian people is just too large for me to imagine that it was only a few individuals swept out on driftwood. There was some sort of sea-going craft which mediated migration to Sahul from Sundaland. Just because we have only recent evidence of sea-going craft doesn’t mean that they weren’t around for tens of thousands of years before that.

I’ve been hearing about Neanderthal tools on islands like Crete, which were never connected with the European mainland, for a while now. It seems that people are finally convinced that this is the real deal, as the stratigraphy came together to confirm dates. One thing that seems obvious from this, as well as Neanderthal “art”, is that the differences between modern humans and Neanderthals were more quantitative than qualitative. Differences of degree, not of kind.

It is hard to deny that modern human expansion between 60 and 15 thousand years ago is sui generis. Hominins didn’t make it to the New World or Sahul, what later became Oceania, until our own kind. There’s also a fair amount of evidence that our lineage pushed the northern frontier of human habitation beyond what Neanderthals ever did. But in the process of marking off our distinctiveness, it seems to me that we’ve overemphasized the differences between us and Neanderthals, and dismissed or ignored evidence of “human-like” “advanced” behaviors from them.

I’ll still go with the prediction that we’ll never find a singular gene which marks us off from other human lineages.

What did modern humans look like during the “Out of Africa” event?


Recently I was having an email exchange with a friend (a prominent public intellectual who is not a scientist), and we were thinking about what “ancestral Africans” looked like. More precisely, the populations which were resident around ~100,000 to ~200,000 years before the present. These are the people who are depicted in paleoanthropology documentaries. Here were some of my major contentions:

1) We don’t know what they looked like
2) They probably were more likely to look like modern Africans than non-Africans
3) But modern Africans are diverse in their looks and we could expect that ancient Africans were too

The neighbor-joining tree above is generated with a naive model of successive bifurcation.

1) Khoisan split off 200,000 years ago
2) Mbuti split off 150,000 years ago
3) Mende split off 100,000 years ago
4) Japanese about 50,000 years ago
5) While Pathan and Basque only 15,000 years ago

The model is wrong in the details. Pathan and Basque have some ancestry is which recently diverged, and much that is deeply diverged. The 15,000 year value is just an average. Similarly, the Khoisan have some Eurasian ancestry. But in the broad sketch it illustrates that some African populations diverged a very long time ago from other groups.

Ancient Africans date to ~200,000 years before the present for all the modern populations. Khoisan to Japanese. You could probably use phylogenetic character reconstruction methods to attempt to infer what ancient Africans looked like…but I’m not sure that it would be useful since modern humans have spread over so many ecologies over such a short span of time.

Outside of Sub-Saharan Africa perhaps on the order of 95% of the ancestry derives from an expansion from a small founder group between 60 and 80 thousand years ago. Removing the “Basal Eurasian” component, groups as diverse as Native Americans, Oceanians and East Asians probably derive their ancestry from a common group which flourished between 50 and 60 thousand years ago (this pulse is the majority of the ancestry of Europeans and South and West Asians as well).

The point here is to illustrate that 50,000 years is definitely sufficient for a great deal of diversity to have emerged in human physical variation. And yet the Khoisan are ~200,000 years diverged from their ancestors within Africa. We actually know that indigenous southern Africans have been selected for lighter pigmentation. We also know that loci associated with pigmentation in modern humans exhibits a lot of variation in Africans, and this variation is likely an ancestral feature of our species.

In sum, the number of generations between ancestral Africans and all modern descendent populations is great enough that I’m not uncertain that we can predict what they look like in anything except their skeletal features. Additionally, most of the history of anatomically modern humans was likely highly structured within Africa. That’s another way of saying that ancient Africans themselves were probably physically diverse.

With all that being said, all things equal ancient Africans probably are more likely to look like modern Africans than modern non-Africans. The main reason is simply that modern Africans occupy the same broad ecological landscape as ancient Africans, and many of our features, from our build to our complexion seem dependent upon environmental pressures. There’s lot of evidence that very light skin is probably a derived characteristic of our species (there are consistent signatures of sweeps around pigmentation loci). And, there is also evidence that some of the archaic introgression into non-Africans may have consequences in our morphology and external physical characteristics. For example, Eurasians seem to have very high frequencies of Neanderthal variants of the keratin gene. This is implicated in hair, skin and nail development.

Addendum: Note that even if we have ancient genomes, polygenic characteristics are still hard to predict. Even today common SNPs only explain a minority of the variation in hair color in Europeans.

Arabia as Africa-across-the-sea

In antiquity ostriches and lions roamed the Syrian desert. The cheetah even still clings to a tenuous existence in the fastness of the central Iranian desert. The point being that the new finding of African modern human remains on the southeast fringe of Arabia ~85,000 years ago shouldn’t be too surprising. Old modern(ish) looking humans date to 73,000 years before the present in Southeast Asia. Modern-like ancestry can be found in eastern (Altai) Neanderthals dating to ~100,000 years ago. And the earliest humans may have arrived in Australia 65,000 years ago.

These dates are important because the genetic results indicate that much of the population divergence of modern Eurasian, Amerindian, and Oceanian peoples dates to the period between 50 to 60 thousand years ago. This was the classic epoch for the emergence of “behavioral modernity,” and the older models of “Out of Africa” which posited a rapid explosive demographic growth after a punctuated speciation even in East Africa ~60,000 years ago.

Today with remains such as Ust’-Ishim man, we can peg the admixture of Neanderthal into modern Eurasians 52,000 and 58,000 years ago. About the same period that the preponderance of the ancestry of modern Eurasians and peoples of Australia and the Americas expanded across the world, as noted above.

Most peoples in Western and Southern Eurasia also have substantial ancestry from another group which doesn’t seem to have much Neanderthal ancestry at all, the “Basal Eurasians” (BEu). This population obtained its name from the fact that it was hypothesized to have diverged from the common ancestors of northern Eurasians (the Pleistocene peoples of Europe and Siberia), eastern Eurasians, the ancestors of the Amerindians, and Oceanians, before these groups moved on and then separated (i.e., proto-Melanesians are closer to Pleistocene European hunter-gatherers than they are to BEu). These facts suggest proto-BEu was a distinct population >60,000 years ago.

The maximum range of Neanderthals

 

Because of the distribution of Neanderthal admixture across so many groups relatively evenly it probably came from a single major admixture event. Geography tells us that the most likely area of this admixture would be somewhere in the northern area of West Asia.

This implies that BEu was probably resident in the southern area of West Asia, and possibly into North Africa. We do not have any samples which are “pure BEu.” Ancient agriculturalist samples from the western Near East and the eastern Near East are high in BEu ~10,000+ years ago, but these populations are still substantially mixed with a population with affinities to Mesolithic Western European hunter-gatherers (WHG). Fu et al. 2016 use a Pleistocene transect to infer that this affinity between Near Easterners and Europeans dates to the period after ~15,000 years before the present. I presume that this late Pleistocene period was when BEu was admixed away as a pure population by an expanding hunter-gatherer culture with a nexus in Southeast Europe and into Anatolia and the trans-Caucasian region.

The recent Arabian find makes sense I think in the context of BEu and other such populations, which had diverged from the Africa metapopulation ~100,000 years ago, but had not pushed further north and east, and so mixed with Neanderthals.

But what about the older modern human remains which are showing up in eastern Eurasia? I think it is entirely likely that these populations left only a little bit of an imprint in modern groups. A paper from a few years back reported having detected such an admixture in Oceanians. The first ancient genome we have from eastern Eurasia >60,000 years ago that is from a modern human will probably yield much more satisfying results.

The big dynamic looming over the likely existence of anatomically modern human range on the edge of Africa in Arabia is that for several hundred thousand years modern humans existed within Africa as a metapopulation. The proto-Out-of-Africa population can only be understood as part of this broader metapopulation. ~100,000 years before the present humans, inclusive of Neanderthals, Denisovans, and modern humans, our species was probably defined by a set of distinct metapopulations. We know that there was gene flow between these metapopulations, but the strong evidence of purifying selection of Neanderthal and Denisovan ancestry in modern human genomes tells us that this gene flow was minimal enough that biological incompatibilities were beginning to build up and the groups were on their way to speciation as defined by the biological species concept.

There is no evidence of this between any modern populations, even the most diverged (e.g., the Khoisan, who carry Eurasian and African agriculturalist genetic material). This means that within the modern human metapopulation gene flow was sufficient to prevent incompatibilities from developing due to isolation. That being said, with the oldest (proto-)modern human skull dating to ~300,000 years, and likely discernible population structure between various African lineages going beyond 200,000 years ago, there are lots of distinct modern human groups with very long histories within Africa and on its periphery.

The earliest point that you could probably say non-African humans diverged from any African (Sub-Saharan) populations is ~100,000 years ago (and this is probably a bit too generous). A conservative estimate would suggest that modern human lineages were emerging within Africa 200,000 to 300,000 years ago. So most of modern humanity’s existence has been within Africa.

The non-African populations descend from a group which underwent a period of reduced population size vis-a-vis all the African groups. But one thing I think is important to remember is that this was probably not exceptional. We know now that over the past 5,000 years African population genetic structure has been reshaped by events such as the Bantu expansion. But there were surely small and marginal groups with low effective population sizes within Africa that either went extinct or were absorbed by other populations.

The difference in the non-African population is that it was on the edge of the modern human range, and likely occupied territory that was relatively isolated from other modern humans due to the dry nature of the Sahara during most of the Pleistocene. This prevented its absorption into more numerous groups of modern humans further south and to the west. And the strong cultural and genetic barriers with the Neanderthals probably limited gene flow as well.

But even in the inclement conditions of North Africa and West Asia for most of the past 100,000 years, modern humans may have had a larger effective population size than archaic Eurasian hominins. And with this larger effective population size, one can imagine that greater cultural creativity and genetic robustness to dynamics such as population declines gave the modern humans a long-term advantage. In this context, the existence of modern human remains in a diverse array of places across warmer areas of Eurasia before 60,000 isn’t that surprising. And, the demographic wave that swallowed Neanderthals and Denisovans probably swallowed the earlier modern humans who ventured into eastern Eurasia before 60,000 years ago!

Who We Are and How We Got Here, a book worth reading

Yesterday I talked to a friend who has a review copy of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. They gave me a preview (their overall assessment was positive).

I haven’t personally asked to get a copy because, to be honest, I thought there wouldn’t be anything new in it. If you “read the supplements” what more could there be in 368 pages? So I was waiting until the end of the month to buy the book and read it in my own sweet time as due diligence.

Well, this morning I asked a publicist to send me a copy. I will be getting it next week. The reason is that I’m told the latter portions of the book are quite challenging and candid as to what genetics may tell us in the 21st century. Who We Are and How We Got Here is a 21st-century revision and update of The History and Geography of Human Genes. But it’s apparently a lot more.

Also, I make a small cameo in the book, as does Eurogenes and Dienekes. I have always appreciated how the David Reich and Nick Patterson and their whole lab has taken people outside of the halls of the academy seriously. They didn’t need to as a matter of professional necessity but often engage as a matter of decency and seriousness.

Out of Africa to Out of Eden (well, perhaps not yet)

The recent African origins hypothesis for modern humans had several things going for it. First, most of the old fossils that look like modern humans were in Africa. Chris Stringer and others were pushing the African origins of our modern lineage before genetics came to the fore. But of course, you also have DNA. The mtDNA, Y, and autosomal DNA, which tends to show a pattern where Africans are more diverse, and non-Africans are nested within phylogenies of Africans.

In the 2000s the “Out of Africa” model got a little out of control. The stylized narrative was that a small tribe of East Africans developed some genetic mutation that allowed them to exterminate all other human lineages (e.g., language). This is best encapsulated in Richard Klein’s The Dawn of Human Culture. The British science fiction author Stephen Baxter used this idea as a frame in his novel Evolution (the innovation in this novel was religion though). In this view modern humanity was an African saltation, a great leap forward.

We’re at a different point now. The idea of admixture and/or introgression from non-African lineages into African modern humans is widely accepted. Additionally, both genomic inference and paleontology are pushing the roots of modern humanity much further than ~50,000-60,000 years before the present.

So it’s not as surprising to see a paper like this, The earliest modern humans outside Africa:

To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.

Now, the reality is that Israel is arguably part of “Greater Africa” biogeographically. So it isn’t that surprising. Or it shouldn’t be.

But, this reinforces the reality that anatomically modern humans were geographically already widespread ~200,000 years ago. I would say that this informs and updates our estimation of the plausibility of the Jebel Irhoud modern humans in Morocco, who flourished ~300,000 years ago. It also makes more sense of the reality that most of the ancestors of the Khoisan likely diverged from other modern lineages ~200,000 years ago (or more, depending on who you talk to). Finally, it makes recent archaeological finds of modern humans or their artifacts in East Asia tens of thousands of years before the great expansion of neo-African humanity50,000-60,000 years before the present much more plausible.

There has been some genetic evidence for modern(ish) human expansion before the 50,000 year date. So this isn’t resting only on paleontological evidence.

Where does this leave us? In The Guardian David Reich observes that ‘It’s important to distinguish between the migration out of Africa that’s being discussed here and the “out-of-Africa” migration that is most commonly discussed when referring to genetic data. This [Misliya] lineage contributed little if anything to present-day people.’

Obviously, this is an important point. But we know that the first modern humans to settle Europe did not leave any descendants either.  The modern human settlement of Europe was still nevertheless important. Second, these early wave humans may have given modern populations adaptive variants that are present at high frequencies in modern lineages.

Finally, there’s the issue that this may reorient our understanding about the demographic origins of human populations. Ever so slightly our priors as to an African genesis for our modern lineage are getting weaker. You have two very old modern fossils on the northwest and northeast fringe of the continent. Ten years back the arguments was between those who argued for an East African origin (most), or a minority who favored a Southern Africa one. Now the whole continent, and perhaps even Arabia, are game.

Ultimately, as always, ancient DNA is going to be the final arbiter.

Neanderthal vs us: for wont of a SNP?

Recently at a human evolution conference in England Svante Paabo (or someone in his group) was alluding to discovering how modern humans and Neanderthals differed by looking at the ~30,000 genetic positions (bases) where modern humans and Neanderthals exhibit fixed differences. That is, Neanderthals and modern humans exhibit totally disjoint frequencies.

I’ve been saying this for years, but I’ll say it again: this is probably a fool’s errand. I do think there are major differences at loci which we know about, such as at FOXP2. But, it isn’t clear that even at FOX2 Neanderthals and modern humans exhibited complete lineage sorting. That is, there’s evidence that the Altai Neanderthal had introgression from modern (or modern-related) human populations, and that those variants were sweeping. And there is still variation in modern human populations at FOXP2.

All Homo exhibit encephalization, credit Luke Jostins

It looks like Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome (also see Detecting polygenic adaptation in admixture graphs). But it may be that soft selections and recurring gene flow are common features of the broader Homo lineage for several million years.

In other words, looking for silver bullet variants which can explain why we are so special may always fail, because there are no silver bullets (for several years at ASHG I note that there were presentations which attempted to determine the locus of humanity by looking at the loci of functional interest where Neanderthals and modern humans differed). Rather, human exceptionalism is no exceptionalism, and human populations explore a wide space of phenotypes defined by a huge range of allelic variance which spans many of our extant lineages.

Khoisan may not have diverged ~300,000 years ago


A few years ago I contributed to an op-ed which defended the utility of the race concept in biology in USA Today (which by the way prompted a quite patronizing email from a famous doyen of population genetics who wished to correct my ignorance; here’s a clue: “Out of Africa again & again”).

In my initial draft, I had stated that the Khoisan diverged from other human populations ~200,000 years ago. The fact-checker came back and said that this didn’t seem to be a supportable claim. The reason I gave the ~200,000 figure is that I’d button-holed people who looked at these genomes, and they were coming to the conclusion that the divergence between Khoisan and non-Khoisan was further back than we’d presupposed. And that was the number given to me.

Ultimately I compromised and allowed them to change the divergence value to 150,000 years before the present.

Today we’re in a different landscape. The above figure is from the Science paper, Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago, which was earlier a biorxiv preprint (which I mentioned last spring). In concert with the North African find, the media is running with the idea that the origin of modern humans goes back very far indeed. This piece in ScienceNews is actually pretty good in my opinion at staying under control, though not all write-ups have been so measured.

So in a span of two years we’ve gone from me pushing and compromising on a value of ~150,000 years, to researchers suggesting that the Khoisan/non-Khoisan divergence is about two-fold older than that!

Well, I’m here to tell you that a prominent geneticist who is very conversant with these issues is simply incredulous about the likelihood of this particular value. I brought up this preprint to them over lunch and they just didn’t buy it. That is, they are skeptical that the amount of admixture would have skewed the earlier inferences to the magnitude that they seem to have in these results.

The authors in the paper used G-PhoCS and their own ingenious method to come to these inferences of split dates. The problem with these methods is that the inferences generated aren’t nearly as straightforward as an admixture estimate (which can be checked by something as simple as a PCA). I don’t want to get into the details, but I remember seeing models in the 2000s which inferred that East Asians and Europeans diverged ~25,000 years ago, or that there was no Neanderthal admixture in Europeans (to a high degree of confidence). Models can come out with a lot of values.

More importantly, look at the dates of divergence of non-Africans (Sardinians here) from their closest African relatives.

  • 115,000 years before the present (Dinka-Sardinian) for G-PhoCS
  • 76,000 years before the present for their TT-method

In light of the likelihood that the closest population to non-Africans may have been an East African population represented by Ethiopia Mota individual (along with modern Hadza), we can probably drop that estimate down a bit. But G-PhoCS in particular just gives too old an estimate. There are ways it makes sense (lots of old structure within Africa) of course. I’m just speaking in terms of possibilities.

The diversification of extant modern populations seems to have occurred around ~50,000-60,000 years before the present. This aligns with the archaeology, and the ancient genomes which we have on hand.

Of course the methods in this paper might be right. And the fossil from North Africa does add some plausibility to that. But really the whole field is somewhat unsettled now, and we should be cautious of reporting of definitive truths in the media.

The culture of reasoning: the Ummah shall not agree upon error


Because I watch Screen Junkies‘ “Honest Trailers” I get recommendations like the above from Looper, The Real Reason Why Valerian Flopped At The Box Office. Of course no one knows the ‘real reason’ Valerian flopped, aside from “it didn’t seem like a good movie.” The reality is that Valerian and the City of a Thousand Planets based on a French comic book and cast a 31 year old actor who looks like a haunted 15 year old. That’s all there is to say definitively. All the various failure points are overdetermined. But the video above gives you a lot of “reasons” if you want them in a list format in a British accent. All in the service of infotainment.

Hugo Mercier and Dan Sperber’s The Enigma of Reason offers up an explanation for you have things like “top 10 reasons” for pop culture artifacts of an ephemeral nature (for a preview, The Function of Reason at Edge).

I’ve mentioned this book a few times. I finished while in the Persian Gulf (I’ll blog that at some point soon), and have been ruminating on its implications, and whether to mention it further. The issue I’m having is that I am very familiar with Sperber’s work, and those who he has influenced, and research domains complementary to his. Even if I didn’t know all the details of the argument in The Enigma of Reason, in the broad sketches I knew where they were going, and frankly I could anticipate it. I suppose somewhat ironically I managed to infer and reason ahead of the narrative since I had so many axioms from earlier publications.

The Enigma of Reason comes out of a particular tradition in cognitive anthropology. What Dan Sperber terms the “naturalistic paradigm” in anthropology. This is in contrast to the more interpretative framework that you are probably familiar with in the United States. No one would deny that the naturalistic paradigm has scientific aspirations. That is, it draws from natural science (in particular cognitive anthropology as well as the field of cultural evolution), and conceives of itself as the study of natural phenomenon.

Scott Atran’s In Gods We Trust: The Evolutionary Landscape of Religion comes out of this tradition, and some of the experimental literature in The Enigma of Reason seem very familiar from the earlier book (as well as Pascal Boyer’s Religion Explained). This is due to the fact that Atran goes to great lengths to show the ultimate nature of religion does not have to do with rational inferences as we understand them. That is, theological is a superstructure overlain atop a complex phenomenon which is not about philosophical reflection at all.

Of course the flip side can be true as well. When I was a teenager and younger adult I explored the literature on the existence of God a bit, from old classics like Thomas Aquinas’ arguments in Summa Theologica, to more recent and contrasting proofs of Norman Malcolm and Richard Swinburne (Michael Martin’s Atheism: A Philosophical Justification was actually a good sourcebook for high level arguments to theism).

When I read In Gods We Trust I realized that my earlier explorations were primarily intellectual justifications, and had little relationship why most people around me believed in God. And yet how did I become an atheist? For me this is a flashbulb memory. I was eight years old, in the public library. I was thumbing through the science books in the children’s section (particular, books on biology and medicine). The third row from the front of the stacks. And all of a sudden I had the insight that there wasn’t a necessary reason for the existence of God.

It all happened over the course of a minute or so. Mind you, I was never really religious in any deep sense. Something I’ve confirmed when talking to religious friends about their beliefs and how it impacts them. Though I nominally adhered to my parents’ religion when I was a small child, I was fascinated much more by science, and that really engaged most of my thoughts and guided my actions (contrastingly, going to the mosque was one of the most horribly boring things I recall doing as a small child).

My point here is that many of our beliefs are arrived at in an intuitive manner, and we find reasons to justify those beliefs. One of the core insights you’ll get from The Enigma of Reason is that rationalization isn’t that big of a misfire or abuse of our capacities. It’s probably just a natural outcome for what and how we use reason in our natural ecology.

Mercier and Sperber contrast their “interactionist” model of what reason is for with an “intellectualist: model. The intellecutalist model is rather straightforward. It is one where individual reasoning capacities exist so that one may make correct inferences about the world around us, often using methods that mimic those in abstract elucidated systems such as formal logic or Bayesian reasoning. When reasoning doesn’t work right, it’s because people aren’t using it for it’s right reasons. It can be entirely solitary because the tools don’t rely on social input or opinion.

The interactionist model holds that reasoning exists because it is a method of persuasion within social contexts. It is important here to note that the authors do not believe that reasoning is simply a tool for winning debates. That is, increasing your status in a social game. Rather, their overall thesis seems to be in alignment with the idea that cognition of reasoning properly understood is a social process. In this vein they offer evidence of how juries may be superior to judges, and the general examples you find in the “wisdom of the crowds” literature. Overall the authors make a strong case for the importance of diversity of good-faith viewpoints, because they believe that the truth on the whole tends to win out in dialogic formats (that is, if there is a truth; they are rather unclear and muddy about normative disagreements and how those can be resolved).

The major issues tend to crop up when reasoning is used outside of its proper context. One of the literature examples, which you are surely familiar with, in The Enigma of Reason is a psychological experiment where there are two conditions, and the researchers vary the conditions and note wide differences in behavior. In particular, the experiment where psychologists put subjects into a room where someone out of view is screaming for help. When they are alone, they quite often go to see what is wrong immediately. In contrast, when there is a confederate of the psychologists in the room who ignores the screaming, people also tend to ignore the screaming.

The researchers know the cause of the change in behavior. It’s the introduction of the confederate and that person’s behavior. But the subjects when interviewed give a wide range of plausible and possible answers. In other words, they are rationalizing their behavior when called to justify it in some way. This is entirely unexpected, we all know that people are very good at coming up with answers to explain their behavior (often in the best light possible). But that doesn’t mean they truly understanding their internal reasons, which seem to be more about intuition.

But much of The Enigma of Reason also recounts how bad people are at coming up with coherent and well thought out rationalizations. That is, their “reasons” tend to be ad hoc and weak. We’re not very good at formal logic or even simple syllogistic reasoning. The explanation for this seems to be two-fold.

First, reason is itself an intuitive process.

For the past few weeks we’ve had an intern at the office. I’ve given them a project using Python…a language they barely know. One of the things that is immediately obvious when going through pitfalls is that a lot of the debugging process relies on intuition one accrues over time, through trial and error. When someone is learning a programming language they don’t have this intuition, so bugs can be extremely difficult to overcome since they don’t have a good sense of the likely distribution of probabilities of the errors they’d introduce into the system (or, to be concrete, a novice programmer might not even recognize that there’s an unclosed loop, when that is one of the most obvious errors to anyone).

Second, reason is an iterative process which operates optimally in a social context. While  The Enigma of Reason reviews all the data which suggests that humans are poor at formal logic and lazy in relation to production of reasons, the authors also assert that we are skeptical of alternative models. This rings true. I recall an evangelical Protestant friend who once told me how ridiculous the idea of Hindu divine incarnations were. He was less than pleased with I simply switched his logic to a Christian context. But Mercier and Sperber suggest that these two features of loose positive production of reasons and tighter negative skepticism of those reasons come together in a social context to converge upon important truths which might increase our reproductive fitness.

The framework above is fundamentally predicated on methodological individualism, focusing in natural selection at that level. The encephalization of humans over the past two million years was driven by increased social complexity, and this social complexity was enabled by the powerful ability to reason and relate by individual humans. In some ways  The Enigma of Reason co-opts some of the same arguments presented by Robin Dunbar over ten years ago in Grooming, Gossip, and the Evolution of Language, except putting the emphasis on persuasion and reasoning.

At this point we need to address the elephant in the room: some humans seem extremely good at reasoning in a classical sense. I’m talking about individuals such as Blaise Pascal, Carl Friedrich Gauss, and John von Neumann. Early on in The Enigma of Reason the authors point out the power of reason by alluding to Eratosthenes’s calculation of the circumference of the earth, which was only off by one percent. Myself, I would have mentioned Archimedes, who I suspect was a genius on the same level as the ones mentioned above.

Mercier and Sperber state near the end of the book that math in particular is special and a powerful way to reason. We all know this. In math the axioms are clear, and agreed upon. And one can inspect the chain of propositions in a very transparent manner. Mathematics has guard-rails for any human who attempts to engage in reasoning. By reducing the ability of humans to enter into unforced errors math is the ideal avenue for solitary individual reasoning. But it is exceptional.

Second, though it is not discussed in The Enigma of Reason there does seem to be variation in general and domain specific intelligence within the human population. People who flourish in mathematics usually have high general intelligences, but they also often exhibit a tendency to be able to engage in high levels of visual-spatial conceptualization.

One the whole the more intelligent you are the better you are able to reason. But that does not mean that those with high intelligence are immune from the traps of motivated reasoning or faulty logic. Mercier and Sperber give many examples. There are two. Linus Pauling was indisputably brilliant, but by the end of his life he was consistently pushing Vitamin C quackery (in part through a very selective interpretation of the scientific literature).* They also point out that much of Isaac Newton’s prodigious intellectual output turns out to have been focused on alchemy and esoteric exegesis which is totally impenetrable. Newton undoubtedly had a first class mind, but if the domain it was applied to was garbage, then the output was also garbage.

A final issue, which is implicit in the emergence of genius is that it exists in can only manifest in a particular social context. Complex societies with some economic surplus and specialization are necessary for cognitive or creative genius to truly shine. In a hunter-gatherer egalitarian society having general skills to subsist on the Malthusian margin is more critical than being an exceptional mind.**

Overall, the take-homes are:

  • Reasoning exists to persuade in a group context through dialogue, not individual ratiocination.
  • Reasoning can give rise to storytelling when prompted, even if the reasons have no relationship to the underlying causality.
  • Motivated reasoning emerges because we are not skeptical of the reasons we proffer, but highly skeptical of reasons which refute our own.
  • The “wisdom of the crowds” is not just a curious phenomenon, but one of the primary reasons that humans have become more socially complex and our brains have larger.

Ultimately, if you want to argue someone out of their beliefs…well, good luck with that. But you should read The Enigma of Reason to understand the best strategies (many of them are common sense, and I’ve come to them independently simply through 15 years of having to engage with people of diverse viewpoints).

* R. A. Fisher, who was one of the pioneers of both evolutionary genetics and statistics, famously did not believe there was a connection between smoking and cancer. He himself smoked a pipe regularly.

** From what we know about Blaise Pascal and Isaac Newton, their personalities were such that they’d probably be killed or expelled from a hunter-gatherer band.