Stoddinger, OOA

Against "Out of Africa"

written by Stoddard Bollinger, edited by Littlebook September 9, 2015

/This following is a review of the paper, "Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck", which was published in 2015 in PLoS Genetics./

This is the only time I ever read a 'scientific' study and I actually laughed.

Out of Africa kind of makes no sense on the surface of it for some particular reasons. The main one is that Europe and East Asia have way, way way more unique alleles than Africa. When proponents say Africa is 'diverse' they mean it is diverse in the way that a bus stop is diverse. There have been introgressions to Africa of basal Europeans, San-like south-east Asians, cromagnons, Saami-like hunter gatherers and also Neanderthal all starting at least 70k years ago and continuing to this very day. It's "mixed" and also archaic, not unique as one would expect from a word like "diverse". If you look at PCA charts, African populations are all pulled towards Europe to varying degrees. So this term "diverse" is very disingenuous – it's actually the opposite, they are all much more mixed.

Europe on the other hand is full of uniqueness, and most of that uniqueness is derived alleles. That is, the big difference between black Africans and Europeans are mainly actually very old genes in Africans, many of which are just the same as in chimps and bonobos.

The obvious conclusion here is that Africa is a dead end. They may be more like some very old human ancestors than people outside of Africa, but that is probably due to isolation and very low populations due to malaria and late adoption of farming, not due humanity as a whole originating in this area.

Of course this has to be addressed by Out of Africa proponents, so here comes a hilarious paper on genetic bottlenecks to try to make us disbelieve the proof of our own eyes.

According to the authors of the paper, all these unique European changes were caused by a genetic bottleneck. Once again they throw out the idea of natural selection completely and go to genetic drift. Literally, Out of Africa as described in this manner is impossible if natural selection happens to any significant degree. That is what Marxist truthiscience is saying, and no one seems to care that this flies in the face of science completely. The study even contradicts itself by focusing on some of the many alleles in Europe undergoing weak selection. Yet they say that all of these changes happened during a bottleneck, which led to an extremely reduced population size for a very long period of time which caused extremely high levels of genetic drift, which caused modern Europeans and Eurasians as we know them today to come into being.

Natural selection is merely classic Darwinism. Survival of the fittest, or perhaps more aptly, survival of those best suited for their particular environment. Genetic drift is much different. Genetic drift is basically random, pointless mutations that spread through a small population over time due to inbreeding. The royal family of England is inbred enough that it caused the genes for hemophilia to become very common in their line, for instance. While detrimental mutations genes exist in the general population they are not preserved through selection, so over time random mutations that are not selected on become increasingly rare and ultimately completely disappear, though they can come back as wholly new mutations that take the same form, again through random chance.

Obviously though, inbreeding does not become an issue unless the populations are very small. The only way to effect significant change in this manner is that, by random chance, some new mutation becomes so common in the population that it is guaranteed not to die out. In a population of millions or even tens of thousands, this is virtually impossible. In a small group of say ten or a hundred people it is very easy to propagate mutations through inbreeding, in fact it's too easy and if the group size stays the same for very long the mutations will eventually add up to enough health problems to make the whole population die off. Yet this is the method by which this paper claims the differences between all of Europe and Africa came into being, literally through a time of incredibly tight inbreeding that by random chance produced all of the changes that make up Europeans today.

I think if people really understood the theory in these terms, most of them would find it very difficult to swallow, or even insulting. I can't imagine the reaction someone would get for suggesting that Africans were the result of thousands of years of a small population inbreeding until by random chance they reached some exact form. More than that though, it flies in the face of logic. The changes aren't random, and there IS Darwinian selection on genes. In fact studies have shown there is much, much more Darwinian selection going on even today than anyone would have guessed, and the larger populations become, the faster the selection becomes.

However, if you are determined enough then you can push the case for inbreeding/genetic drift as the basis for the vast differences in populations in Africa and Europe. A bottleneck is very easy to work with in some respects. You can plug in some formulas and get a result that fits your data and while it has no power to prove your case, it shows that it is at least a possibility. You simply estimate how much genetic change there's been, then choose a population size and length of time that the population was limited to that size which fits your data.

There's a couple of problems here, though. First off, you could apply this formula to ANY scenario and come up with results that fit ANY pattern you like. Notice that the numbers they use for genetic drift are usually quite implausible. Such as claiming everyone evolved from an effective population of just 1000 people with a bottleneck of 5000 generations which leads to 838938934398349 mutations. *You could just as easily apply the same logic to account for the evolution of dogs from Africans, though.* All you have to do is say it's 100 people and 50000 generations and bing bang bongo your numbers add up.

It's important to point out that these are not the only numbers they could choose. You could just as easily choose different population numbers to get a different separation time. This is the perfect sophistry in a sense, because there are literally an infinite number of combinations of numbers that fit any data set. Do you want to show Out of Africa happened 80,000 years ago? Just decrease the population size a bit. Only 20,00 years? Reduce the separation time a bit. Note that you could also choose numbers that fly against their case completely, such as a larger population that is separated by a million years! Not only is nothing provable with this system, but its malleability shows that it should raise alarm bells to see it used to justify anything at all.

The fact the numbers are implausibly low for total populations, and implausibly long for such limited population sizes, shows it's complete shit. Out of Africa is possible but it would require some already existing ancient differences in population structure to be plausible, that is the people who came out of Africa to Europe and Asia would already have to be largely similar to what they are today. The problem with this scenario is that these variations have completely disappeared in Africa, if they ever did exist there, and the differences are too large to be easily believed; however this is POSSIBLE, even if it seems to be strange. It would simply be a geographical movement – proto Europeans pack up and move to Europe.

Yet the whole point of Out of Africa, as a political polemic, is to show we have a very common recent origin and that all humans are literally the same except for some superficial random mutations. Another term for random mutations is genetic drift. Once you admit that these differences are more ancient or that they are due to natural selection, then any political zing is completely neutered. Some people in fact understand Out of Africa to mean that all three main racial groups of humanity (you could arbitrarily break races down into as many as you like) all existed in Africa at some point and then two of them decided to vacate the premises one day. Yet this is not really the case, Out of Africa depends on the idea of Punctuated Equilibrium which claims that Darwinian selection is very rare and that most changes are completely at random. This is a theorem that has been falsified by the age of gene sequencing which allows us to measure both genetic drift and Darwinian selection – and the results show that there is strong selection on thousands of genes in modern times and that genetic drift is completely negligible outside of very tiny populations.

We can see now that a bottleneck of this kind is a very unlikely way to get the results which we see in modern genetics. We could perhaps discard the idea completely because most of the differences between Europeans and Africans are actually archaic genes that Africans possess which Europeans do not. Many of these genes including some for hair and skin and blood type share common ancestry with chimpanzees and other apes so clearly this seems to be a classic case of Darwinian evolution – some of these genes don't fit in all locations well so they have evolved away over time.

There are also archaic differences in Europeans, as well. Not just neanderthals, either. Many of these differences, such as ABO blood type, go back many millions of years and can't readily be explained by ANY migration theory since virtually all of Africa is O+ while Europe has a mix of all different kinds of blood types. This cannot be explained through selection either as the genes are millions of years old and show a pattern of very ancient population structure within Eurasia that seemingly never existed in Africa.

Aside from the fact a bottleneck (ie completely random chance) made all the different variations in people today seems very unlikely, perhaps a bigger and more obvious problem is THERE WAS NO BOTTLENECK.

It's all well and good to talk about bottlenecks and genetic drift until you are blue in the face, the truth is you simply can't know a detailed population history of the whole planet over a long period of prehistoric time. All we get are tiny glimpses separated by tens of thousands of years and many thousands of miles with which to attempt to reconstruct prehistory. This is not providing evidence for how anything happened, it's merely an attempt to fill out an explanation of how you claim things may possibly have happened.

So what is there to support the idea at all? Where does this bottleneck come from? What caused a huge die-off in Europe followed by an extremely long time where the population was forced into incredibly low levels? They don't even try to explain it, they just assume it did happen in some unknown manner because that's what's required for their theory to be correct.

There's simply no evidence of any kind that this happened at all. Quite the opposite. When a new land is discovered, instead of a long period of near-extinction conditions and severe inbreeding that leads to countless random mutations, we would expect to see a gigantic population explosion that served to keep the original population structure of the settlers well-preserved for thousands of years. In short, a founder effect. The population stays the same because there's so little selection – everyone wins the lottery.

A founder effect is the opposite of a bottleneck. In a bottleneck, the population is slowly (or not so slowly) strangled down into a tiny group and then held there for some time. Famines are a good example. Some people (maybe smaller, maybe richer, maybe with a slower metabolism, maybe those with lactose tolerance) survive in much greater frequency than others. The people who died off in the plague were much different than those who survived it, for example. The ones who died were actually much more Neanderthal-like. A bottleneck is SELECTIVE. Again, something totally ignored by this paper in favor of drift: The selection goes in some specific direction, and it weeds out many genes.

The other part of a bottleneck is that the population is kept at this small rate for some time. If the famine lasts 20 years it's a 20 year bottleneck. That's just one single generation! And the level of population limitation in any famine in historic times does not remotely approach that proposed by this paper. With out of Africa nonsense we are talking about bottlenecks for hundreds or more generations that affect EVERYONE IN EURASIA or even EVERYONE ON EARTH depending on which scenario you look at. I mean what in the fuck is the justification for this? SURE, this is POSSIBLE. I mean, it's TECHNICALLY possible. Being technically possible doesn't mean that there is a shred of evidence for this. There is not even any attempt to explain what caused these long, long incredibly long periods of very very low population levels.

The most important difference is the very specific and very unlikely population size limits involved with these alleged bottlenecks. Much more is required than a severe limitation on the initial genetic input of a migration into Europe to produce such profound changes by genetic drift. For genetic drift to occur there must be some hard limit on population size. You don't need initial genetic diversity to keep a genetically healthy population, just a population level large enough to permit selection and avoid inbreeding.

If everyone else on Earth suddenly died in some massive catastrophe, even a brother and sister would be able to repopulate the planet and genetic drift still would not play much part in the process. That's because the population will be able to grow and grow with each generation and so random mutations won't creep into the population as a whole (except whatever the brother and sister ALREADY shared). The ONLY time drift can come into play is when populations are very small, and somehow capped to keep from growing any larger for very long periods of time. The problem is, there is no evidence of this, no reason to think this is the case. Moreover the magnitude of the bottleneck goes far beyond anything conceived of in the physical world. The Manitoba event would be nothing compared to this.

They try to present the current day genetic structure as proof, but the current population structure can be arrived at in many other ways. If it had been through drift caused by a long period of isolation then a rapid expansion, the European population would actually be much more homogeneous and have much less rigid internal structure. In fact that would probably be the case for the entirety of Eurasia. Things like blonde or red hair would be evenly distributed throughout Eurasia if this were the case.

Once a population expands past tiny levels, genetic drift simply ceases to affect it completely. In Europe many genes are completely fixed in the population, especially many brain, skin and hair genes. This pattern of certain genes being fixed today (but not in ancient populations) yet still retaining complex population structure differences between ethnic groups in Europe, implies the opposite of what the authors try to prove. Europe is a combination of ancient population structure, including even Neanderthal and earlier structure, and recent very strong selection and fixation of genes – classic evolution.

As you can see, a founder effect is much different than a bottleneck, and it much more capably describes the situation of exploration and population of a new land. It occurs when some lucky (or smart, whatever) small group makes it to an area or situation where they can rapidly expand their population. Colonizing the Americas is a good example. There is no die-off involved as with a true genetic bottleneck (which skews the demographics) and there is no long period of tightly limited populations. It's just a period where a small group grows at an enormous rate. No one would try to claim that Americans evolved by coming here. On the contrary, members of these expansions tend to be good keyholes into the past of the originating group. The Spanish who remained unmixed with natives, are genetically much more distinctly Spanish than the Spanish left in Spain, for example.

In general, relatively large populations are required for effective, strong natural selection of genes in a "survival of the fittest" manner as Darwin envisioned. Conversely, genetic drift which is a relatively new concept and could best be described as simply 'truly random mutations' has absolutely no input into the equation unless populations are very, very small and most importantly kept very small for very long periods of time.

Genetic drift is really not a plausible source of large changes in the human population as a whole. There's no reason to even attempt to use it to explain macrogenetics, except for the purpose of misdirection and deception. Now that we have the full background, back to the paper.

As I said way back in the beginning one of the big discrepancies of Out of Africa is the very large number of derived alleles in Eurasia which don't exist in Africa. This is very hard to explain away and takes some serious mind-killing to put aside. Even if you do believe in Out of Africa then hopefully after reading thus far you will realize that this aspect of it is really just thrown out without any attempt to provide real evidence, and see how arbitrary and easy to manipulate this kind of math is.

So now they publish a new paper, which proves itself by using itself to prove that Out of Africa is true. The logic is once again to ASSUME that these massive differences come through genetic drift from an Out of Africa event, in spite of the fact there is no reason to think an actual bottleneck would occur in an Out of Africa scenario. According to the paper, the number of lightly selected additive deleterious alleles should then have been made higher in comparison to the number of dominant alleles by this massive bottleneck.

* Empirical detection of recessive selection

The B/_{/R} statistic provides a qualitative indication of recessive selection (h ≪ 0.5), in that values over one theoretically correspond to recessivity. This corresponds to a reduction in the average number of deleterious alleles per haploid locus in a founder population relative to a non-bottlenecked population. *We compare European Americans (EA), known to have undergone a relatively intense bottleneck during the "Out of Africa" event*, to African Americans (AA), who have substantial African ancestry that did not experience this founder's event.

A bottleneck and a founder effect are very different things which should not be conflated. You also can't use this as a given fact to support your own case. The point of this paper is to provide genetic means to DETECT events such as a completely inexplicable bottleneck that would supposedly occur with Out of Africa. This is like when Baron Munchausen runs out of rope while climbing down from the moon and pauses a moment to cut the rope above him and have the people below him tie it to the end of the line and then calmly keeps climbing down like nothing happened.

It's also quite ironic they take the African American population that recently came out of Africa and had a die-off followed by a bottleneck and then a giant population explosion to represent the ancient African population, claiming they are the ones who never went through a bottleneck. As much as 90% of slaves heading to the new world died en route and in the early days of slavery the odds of surviving long on the plantation after arrival were grim. That is a classic bottleneck that is absolutely bound to skew the population demographics. That sounds like a lot but in those days it was very typical to lose 30-40% of seamen on their first voyage due to poor hygiene and nutrition combined with exposure to foreign diseases that most people had no immunity to yet – and the crew wasn't chained up in cramped quarters on short rations.

They take an African-related population known to have gone through a bottleneck and present it as the opposite, then compare it to Europeans and claim Europeans are actually the ones who went through a bottleneck. Despite the fact that even if Europeans did come out of Africa there is no evidence to suggest there was any bottleneck at all. They didn't go to Europe in boat rides that lasted a thousand years and killed 99.999% of the passengers, as would have to be the case to produce such a bottleneck. Interestingly, neanderthals were apparently quite sedentary, but for most of humanity until the neolithic this was not the case. There were constant seasonal and even day-to-day migrations.

One of the more amusing things about Out of Africa is that you don't need a rocket ship or even boat to travel between Africa and Eurasia. They are attached to each other and you can simply walk. During most of prehistory the entire gulf of Hormuz was dry as a bone and you could walk across any point and walk all the way to Iran from anywhere in Africa. Climates varied but in much of prehistory including early historic times this entire area is one of the most clement and lush. The same goes for the Persian Gulf. During some periods it's possible you could even walk directly all the way from east Africa to southern Asia. It doesn't take thousands of years, either. Maybe a week hugging the coast in the worst case, and much quicker in the best case. In a diffusion model, people would be constantly traveling in all directions searching for new lands, as hunter gatherers typically do. The only thing stopping African and Arabian nomads from filling up the whole world is constant border patrol. This was true even in ancient Egyptian times!

At any rate the idea they are presenting here is that if you were to suddenly shrink the population in a catastrophe, you would lose most of your unique alleles. This makes some sense for a true bottleneck, because a near die-off event (usually 90% of the population or even more) is definitely a SELECTIVE process. Such as on a slave boat – the ones who had good immune systems and tolerated cold and hunger well survived, the rest did not. It's important to note that this die-off is what causes the selective force and not the inbreeding, which leads to random mutations over time. If you took ten thousand people from a population truly at random and split them off from the whole, then whatever deleterious alleles you already had would be almost completely preserved. Most likely, to really achieve this the die-off would have to be truly huge – a very tiny group of survivors would eliminate most rare disease alleles, but they would likely wind up having the remaining ones at rather much high rates.

It's also interesting that they concentrate on deleterious alleles, as well. I mean, this is it, this is the "diversity" in Africa. Recessive disease alleles such as those for deafness are also quite rare and tend to exist only in certain populations, especially those which are somewhat inbred. Aside from some malaria and pigmentation alleles and a few very archaic ones, that's it, that's all that's unique in Africa. We are literally supposed to believe Africa is more "diverse" because it it has a greater variety of maladies and it lacks some recent modern adaptive alleles that are heavily selected on!

If you followed things this far and managed to stay awake I bet your eyes are popping out of your head about now. On the one hand this magic bottleneck knocks out deleterious genes like crazy, but on the other hand, it's also responsible for all the 'random unimportant variation' between Africans and Europeans (skin , hair, eye color, sexual dimorphism, immune system changes). And it does all this while keeping the mutation load almost exactly the same in both groups, even though supposedly Europeans have gone through INCREDIBLE levels of random mutation due to inbreeding and Africans have not. That is, supposedly European underwent truly epic levels of inbreeding for hundreds of generations and yet at the end of it, they were just as healthy as when they started. Maybe more so than ever. That is truly a magic bottleneck.

Likely this scenario sounds quite far fetched at this point but luckily there's another explanation that doesn't require oblique justification laid on oblique justification and special case laid on special case and assumption after assumption to even be possible. An easy, simple one that requires no mind-killing to ignore the giant elephant in the room – an elephant named Selection. Anything drift can do, natural selection can do, but much better and faster. As an added bonus it does not have the side effects such as likely extinction that extreme, prolonged inbreeding would present.

Keep in mind that genetic drift is random, it is more or less the opposite of darwinian selection. That is, it could have gone in any direction on earth but according to Out of Africa proponents it went in a direction that didn't have any negative effects on health, didn't give us extra toes, and so on. Selection is more like the much vaunted invisible hand of the market – genes that work, propagate. Those that don't, or which become irrelevant, eventually disappear. It's not coincidence that Marxists only acknowledge drift as a source of differences in people and populations today – the same people who claim to believe genes are wholly random also claim to believe that success is wholly random as well.

Darwinian selection is the main force that removes deleterious alleles and it's also the main force that creates new derived alleles over time. It is the "default" as it were, classic natural selection and is 100% what Darwin himself believed in. Genetic Drift is random mutations caused by inbreeding in very small populations. It is a special case and to Marxist 'scientists' like Stephen Jay Gould it is the only acceptable case. These guys don't believe in natural selection at all! And in fact you cannot logically believe in it if you are going to choose to believe in a very recent Out of Africa scenario. Europeans are more derived than Africans, that is a fact. Yet the question is where did this come from. To Darwin there was no real question. He believed that Africans were archaic and they were doomed to eventual extinction.

That is harsh and we now know that is not strictly true – genes tend to move almost independently of ethnicity and locale if they have the chance to do so. One person gets a gene from another country that's heavily selected on and eventually everyone in the country will have it, and in a much shorter time than you would think possible. The obvious answer is that groups outside of this isolated area south of the Sahara have simply experienced more natural selection and in some cases simply different, localized natural selection than Africans. Of course Darwin also believed humans originally evolved in Africa, but the key factor of Out of Africa is the recent origin and complete replacement of previous inhabitants of Eurasia. For Marxist political reasons no matter how often data falsifies Out of Africa, it continues on. Neanderthal and Denisovan DNA in people today did not even give the Out of Africa machine a pause for example.

Yet if we dismiss this crazy assumption that Out of Africa "had to" have happened and it "had to" be very recent and it "had to" have an inexplicable bottleneck instead of a classic founder effect, then we no longer need to explain any of these "problems" in the first place! Lots of expanded local variations developing and lots of deleterious alleles being knocked out is what we expect to see in the first place. The difference between black Africans and Eurasians is no doubt a combination of very ancient differences and very new differences heavily selected on in modern times like lactose intolerance.

In fact, how can it POSSIBLY be anything else? Some of these ancient differences like blood type and NUMBER OF TEETH definitely go back millions of years because we can see that some of these genes come from the common ancestor of chimps, apes and men. Chimps have one set, Gorillas another, and men have all of them!

Not only that but in Europe it is a significant portion of the population that has the obviously non-African blood types. Not just rh- but B and also A clearly have little to no influence in Africa! It boggles the mind to think of a scenario where this can happen if Europeans are literally Africans who moved recently to Europe, had a bottleneck to form 'random, superficial' differences (including brain genes shown to increase IQ…) and interbred very slightly with Neanderthals and Denisovans. If it came from breeding to neanderthals (a hilarious "special case" for Out of Africa) then the non-African percentage of ancestry would have to be over 50% to get this result! Of course then maybe there was Neanderthal plus X other mystery hominids. But any way you slice it then what you are really talking about would not be Out of Africa but Multi-regionalism, which could best be described as simply classical Darwinism.

You can believe in magic, or you can believe in science. The choice is up to you.