You mean leaving your technical inaccuracy aside…
There is no amorphousness in proper usage. If you, or the layman, can’t be arsed to use the word “allele”, that’s your lookout. Don’t expect us to accord lazy usage any respect.
Consider the statement that “every human has exactly the same genes.” Even in formal usage of the word, what we are talking about is a nickname applied to a defined DNA location sequence with a (typically) known association for outcome. We give the polymorphisms within that sequence a “gene X” nickname even if the outcomes are substantially different. That way we all know which part of the genome we’re talking about. To use “exactly the same genes” in that context is a silly statement; a gene in that sense is “exactly the same” because it has exactly the same nickname given to (roughly) the same sequence and location.
The gene is not exactly the same across all humans in any other sense. Even a single amino acid substitution may change “exactly the same gene” (nickname for the group of polymorphisms) from ordinary to advantageous to lethal.
That’s why I complain about the use of the phrase, “we all have exactly the same genes.” It’s taking a word used in a very narrow way without clarifying that what is exactly the same is the group nickname for the general location and not the genetic material itself. And colloquially we use “gene” as a word for genetic material in general. This is true even in scientific discussions, because of the fluidity of language.
Notice the use here:
“Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in…”
This is from a recent article talking about Neanderthal introgression of genetic material into modern non-african lines. (Current estimates are that something like 1-4% of the genome for non-african lineages is from archaic Neanderthal lines, and perhaps 20% of the Neanderthal genome survives overall in non-african lineages.) Here the word “gene” is not used to mean “exactly the same.” The whole point of the article is that this is completely different genetic material, and “gene flow” uses the word “gene” colloquially to mean introgression of quite different genetic material.
As a naturally pedantic 
person, I don’t mind if you stick to a more formal use of “gene” as long as what is being communicated is clear: Humans are very different genetically, and genetic pools are very different among different populations, even though the gene variants we’ve studied have exactly the same nickname that part of the genome. Given how early we are in sorting out what the whole genome does though, it’s a bit of a step of faith to say we all even have exactly the same genes in any sense of the word. Genes tend to get their group nickname after we figure out what that sequence does in that location (and in the milieu of other genes). So until we get the whole thing parsed out and named we won’t have an exact idea of how much we vary at the “gene” level.
Blah blah blah “nickname” blah blah blah “nickname” Oh, stop, your smithing of the words, it is killing me.
Yes, it is.
It’s a technical term, one don’t have to clarify when not using the For Dummies version.
You might. Some of us know better.
No. “gene flow” is a technical term all of very own. It is not an ad hoc conjunction of the technical term “gene” and the noun “flow”, and you don’t get to parse it as though it is, to make your (ever-increasingly pedantic) point.
No, they’re not. Variation of 0.1% is in no way “very different”
No, they’re not. What’s 7% of 0.1% ?
We have exactly the same genes in the proper sense of the word.
We don’t need an exact idea to know the outlines.
You are apparently confusing yourself if you think 7% of 0.1% has anything to do with a number suggesting the amount of genetic information which varies among populations. It is utterly meaningless to maintain that the nickname for gene locations barely varies across populations. Hello.
Perhaps you have conflated “exact same genes” with the idea that the genetic information is exactly the same. Easy to do when you think the phrase is remotely relevant to a discussion about genetic differences. “Exactly the same” is wordsmithing solace. Nothing to do with the degree to which evolution has driven genes.
Here are two places to indulge yourself reading more.
First, an an article from Eric Wang studying how many SNPs and genes seem to exhibit Darwinian selection. These, then, are not silent and incidental SNP differences. These are not founder or bottleneck-driven happenstance. These are genetic changes driven by evolutionary pressure because of the reproductive advantage they bring. Considering that fewer than 30,000 genes are thought to be active (in coding proteins, at least), 1,800 is a bit higher percentage than 7% of 0.1.
“By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection”…
The 1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host– pathogen interactions, reproduction, DNA metabolismcell cycle, protein metabolism, and neuronal function…
We outline several predominant biological themes among genes detected with this strategy and suggest that selection for alleles in these categories accompanied the major ‘‘out of Africa’’ population expansion of humankind"…
Second, may I suggest you read or re-read some of the literature around Neanderthal introgression? The average estimate for out of africa lineages is 1-4%. There is some interesting speculation that in-africa lineages may have also had introgression from other archaic lines.
See, for example, here.
“Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1 to 3% of their genomes from Neandertal ancestors.”
This idea we all have exactly the same genes–oops; genetic material–sort of homogenously distributed across all populations is looking more and more like Creationist pap every day. “Exactly the same genes” just contributes to the confusion since all that phrase means is “exactly the same nicknames for coding sequence locations that drive very different results.”
Someone’s confused, alright. I, at least, cited what I meant by variation.
Who said anything about variation in active genes? Only you. So I give a shit whether the numbers match.
And I notice how blithely you use a cite that has the correct usage of allele :rolleyes:
Why should I? Ancestral introgression is relevant to within-human variation, how? It’s not as though there hasn’t been genetic backflow to Africa* as I have already cited in this thread.*
Are you outright claiming that the genetic variation between an average African and an average Out-of-African human is 1 - 3 %? Or more? If so, cite something that says that, and just that, otherwise you’ve done nothing to counter the 0.1% figure (which could be as high as 0.4%. Whoopie!)
Of course it’s at least 1-3%, just based on Neanderthal introgression alone. I just gave you the cite! Sure; there has been some backflow, but not nearly enough to change those rough percentages.
But the overall average variation in those two pools is way, way more than the variation from archaic lineage introgression. I just gave you another cite that showed Darwinian selection for 1.6 % of the 1.6 Million SNPs in the Perlegen Sciences database, involving about 1,800 genes (lets call that 7% of the typical number given for the number of active genes in the human genome). That’s a lot!
Why are the pools different, on average, when those genes are all over the place? Why not just look at any two really diverged groups? Well the answer is that you can. But when we look at the history of human migration, we have one splitting point at out of africa for most eurasian groups, somewhere around 70kya (give or take). And as it turns out, on average self identification with black, white or asian creates average pools that reflect that historic splitting point.
What makes the whole topic so confusing is the wordsmithing around “defining race biologically” and “amount of genetic diversity” and other such things that have nothing to do with whether or not the out of africa migration created two very broad average pools that in turn correlate with self-identification. On average.
All of the out of africa lineages have created a broad pool of genes that have had 70kya to diverge from all the non-out of africa lineages. Some backflow has occurred. Some parallel evolution has occurred. Absolutely. At the same time, these are two average pools of genes. Genes that changed in africa are more common collectively in africa today, and genes that changed out of africa–woops, gene polymorphisms!–are more common collectively out of africa. We’ve even shown pretty wide penetration for some genes–woops again; gene variants!-- which suggest they either brought something to the evolutionary table, or else were part of early founders (MCPH1 haplogroup D, e.g.).
Most of that teeny tiny percentage nonsense you see conflates the nickname “genes” with gene polymorphisms, and to boot ignores the newest data showing 1-4% of non-africa gene pools is 300,000 years removed from the african ancestor of anatomically modern humans. The other nonsense you’ll see is how there is so much more diversity between any two individuals, or within africa or this or that–all missing the more fundamental point that self-identification creates two different average pools of descendant gene polymorphisms because there is a splitting point out of africa.
We don’t have to use that splitting point. We don’t have to use any splitting point. We don’t have to define, or care, about “race” period. But when we self-assign, we drop into average pools that reflect that splitting point.
What severely complicates these sort of “estimates” is the fact that, because humans lived in Africa for so, so long before living outside of Africa (in addition to back-migration and contact between African and non-African groups), some African groups are more closely related to the group(s) that left Africa (and their descendants in Asia, Europe, and elsewhere) than to various other far-flung African groups. Thus there’s no way to have a group based on genetic ancestry that includes all African groups without including all non-African groups as well.
Actually, for averages, it just depends on how much of a lumper or a splitter you are.
If you are such a splitter that any division has to be perfectly defined, you won’t get suitable groups until you find really isolated populations.
If you just want large lumps, such as self-defined black/white/asian, you’ll get reasonable average pools. At the out of africa split, most of the world would be (mtDNA) M-N descendants, and (sub-saharan) africans would be mostly the L groups and those lineages.
Plenty of exceptions. For any given individual, self-identification might be totally off the genetic mark. But as a broad average pool, there is a split at africa and out of africa lineages. That’s why you’ll see so many papers and articles making a distinction between african and non-african lineages when talking about the genome.
For example, a Nat Geo piece on two of the papers I cited above:
“…because the genomes of people living outside Africa today are composed of some 1 to 4 percent Neanderthal DNA…
Some parts of non-African genomes are totally devoid of Neanderthal DNA, but other regions abound with it…
It seems quite compelling that as modern humans left Africa, met Neanderthals, and exchanged genes…”
(underlining by CP)
This debate seems to be constantly raging here!
Chief Pedant, not sure if you’ve followed Piffer’s work? This is commented on here:
The author of that post ‘Chuck’, who has posted here previously, goes on to look at other ancestry mapping studies and the association with educational outcomes.
No. That’s not what that cite says.
This sort of simplistic estimation (the “lumping”) might be useful to explain some phenomena, but unless your argument is that certain specific African groups (not all African groups, but just some specific ones that are related to each other but not to outside groups) have some greater likelihood of having certain genes/alleles, it’s deceptive and inaccurate for statements about the genes/alleles all African groups.
Which is just one of the many reasons why I “demand” actual genetic evidence. There’s no possible phenomenon based on evolution and genetic ancestry that would affect only all African groups, since any that affected all African groups must have also affected non-African groups. And if you think “it’s not all African groups – just some”, then more information is needed – which groups? Which genes/alleles? What is their prevalence in various populations, and how was their relationship to intelligence determined? Absent such information, the most reasonable explanation is the same explanation for various other test-score gaps (and other outcome gaps) – changes in culture and society, for example, explain why the Irish now score so much higher than the Irish from 100 years ago. With all the reasons to believe that culture and society treat black people differently than white people in many ways today, I’m inclined to believe that it’s culture and society that are still responsible for test-score gaps, when the “pattern” has been around for such a short period (a few decades of testing), with very few “nurture” elements eliminated (SES and very little else), and with such paltry efforts for correction.
I guess I don’t know what to say, then…
On average, 1-4% of genetic material–particularly for eurasians, I guess, since they are the ones who get studied–are thought to be from archaic hominids such as Neandertal or Denisovans. Those archaic lineages are thought to be on the order of 500,000 years removed from the out of africans into whose gene pool the Neandertal genes introgressed.
Now you could come up with some other reason why this is not “genetic variation” in toto. After all, if you find a bunch of variation within sub-saharan lines and figure out some other way to quanitfy “variation,” you’ve got yourself an out. Plus, of course, the gene nicknames are largely the same . After all, we were apparently genetically close enough to produce fertile offspring, at least if Dad was Neanderthal. I think it’s fair to say if this guy’s gene pool is all from ancestor X derivatives and that guy’s gene pool is from 98% X and 2% Y, and Y is an ancestor with another half million years of evolution in his gene (variants), those are qualitatively different pools you got there. (Or not, if evolution forgot to work.)
But in simple terms, something like 1-4% of the non-african gene pool is not even from our anatomically modern african ancestor 200 kya. It’s from a completely different gene pool dating back 700kya give or take. You’d have to go down to an SNP level and just treat them all the same if you want to make some “same amount of variation” argument. And that kind of quantitative mumbo jumbo is pap for the masses. We know for sure SNP variations don’t mean a hill of beans until we study the outcome. The way evolution works is to sling around SNP variations in a totally random manner and then let successful reproduction sort out which ones were really good. So if Sam’s group gets really lucky, their one lucky SNP might be worth a thousand of the ones Tom’s got, and only their descendants would luck out for reasons of historic migration patterns. Mother Nature does not seem to take a particular interest in being fair.
Fair enough?
I think I understand that you believe the reason africans have largely come out second best in civilization clashes is a guns/germs/steel type of argument. Let’s leave that alone for now.
But if you are saying that whatever evolution did for groups that left africa it must have done equally for groups which remained in africa, you don’t understand evolution. Evolution does not have a direction in mind. It’s essentially a combination of chemical processes not creating perfect replication, along with pure luck. Luck for which imperfect replication turned out to be reproductively advantageous, and which external circumstance promoted that new variant.
If you split two groups, from that splitting point on, each set of descendant lines will get a shot at post-split variants only back to the point of the split, and those new variants will not be available to the other set of post-split descendant lines. Any reproductively advantageous new variants that appear are not a product of evolutionary pressures working in some sort of direction. They are basically blind luck. This rodent line gets tiny because of a gene variant that lets them occupy one niche; the other descendant line gets big because a different variant lets it occupy a different niche. Luck.
The notion that evolution which affected one group must have affected all groups more or less equally is quite badly mistaken. That’s why the Mbuti probably won’t have their chance on the NBA stage even when their cultural influences catch up and they start preferring basketball over schooling.
This is not what I’m saying. I snipped the rest because it doesn’t dispute anything I’ve said. Whatever population left Africa and split into Asians and Europeans logically and necessarily was more closely genetically related (in terms of shared ancestors) to certain African groups (the sibling groups) than those closely related African groups were to certain other far-flung African groups. This should be obvious – Somalians are quite a bit more closely related, genetically speaking (including sharing more in the gene pool) to Yemenis than they are to Namibian groups. Certain Senegalese populations will be more closely related to certain Malian, Mauritanian, and Moroccan groups than they are to groups in Mozambique.
The cite says nothing about African DNA, the only DNA studied is from European and East Asian individuals. So you can make no inference from it as to the relative differences. Especially given that we know there has been large-scale gene flow back into Africa, something even you have acknowledged while somehow maintaining the cognitively dissonant stance that Out Of Africa is some monolithic population blocker.
I recommend additional reading if you think the sub-saharan and out of africa populations probably have about the same amount of Neanderthal and Denisovan DNA based on things like “large-scale gene flow back into africa” and so on.
To your point of genetic backflow, the above statement is oversimplified. “…no Neanderthal DNA” is an exaggeration. But as a general gene pool, there is a marked disparity. And as you know, most back flow on any scale has been in eastern africa and certain populations in the Sahel. This is not enough to change the average pool differences for the broad split at L3/M-N, including Neanderthal and Denisovan introgression into M-N descendant lineages.
I should note here (and have before) that this is not the only reason those gene pools differ. About 1.6% of SNPs are thought to have been selected for by evolutionary pressures, and evolution generally drives divergence. So out of all the “variation” in SNPs that we see, 98.4% is more or less noise, while 1.6% is significant. And that 1.6% clusters by self-identified “race” because of historic migration point splits isolating descendant lines.
The intra-african diversity is astounding. But “diversity” has nothing to do with an argument that two different gene pools are created at migration splits for descendant lines, and that new variations post-split are available only to one side of the split or the other.
Suppose we have a thousand completely diverse groups inside africa. Group X leaves and splits again ten times.
We now have “a hundred times more diversity in africa than in the rest of the world!” Fabulous. And irrelevant if we self-identify to “africa” or to “the rest of the world.” Any genes–sorry, gene variants!–that arose post split in the out of africa group are vastly higher in frequency for non-african groups than they are for in-africa groups, and vice versa. The earlier those variants arose in the out of africa group post-split, and the more reproductively advantageous they are, the higher penetration we will see in the post-africa group. But because evolution acts so randomly, we can be sure of one thing: all of those gene variants on both sides of the split will drive divergence much more likely than they will drive in parallel. This is why it’s so silly to think evolution has driven divergence only for physical appearances and disease. Evolution has no idea which DNA amino acids to select for in order to maintain overall fairness.
I’ll leave out addressing the evolution straw-man stuff. No one is arguing that evolution only drives physical appearance and disease. You can seriously stop bringing up that nonsense that disputes no one and no arguments.
The real world doesn’t bear out these sorts of divisions you discuss – can you, seriously, name any single group in or around the Middle East (where, presumably, the first groups left Africa) that is not equally closely related to neighboring groups on both the Africa and Asia side of the “split”? This is what we mean by clines – every single group on earth is pretty much the same as their neighboring groups, genetically speaking (barring emigrations of the last few hundred years). There are little changes and little differences here and there, and they add up such that Southern Africans and Japanese (for example) have a lot more differences (small as they are), genetically speaking, than any neighboring groups along the way between them. But every group in the Middle East (and elsewhere) is nearly genetically the same as the groups next to it. So there’s no clean split anywhere – “black people” fade into “brown people” who fade into “white people” and others (and vice versa), with a continuous relationship between neighbors both superficially and genetically. There’s no possible clean cutoff for any trait, superficial or genetic. There are no “breaks”.
So it’s ridiculous to talk about the gene pools in groups as diverse as African Americans (for example) as if they’re separate from other gene pools. Even if we can estimate that, on average, an African American has X% of sub-Saharan African genetic ancestry, this doesn’t tell us anything about those genes because SSA genetic ancestry is so damn diverse! It doesn’t tell us that any two African Americans share more of their DNA than any random two people on earth (including one of those African Americans and a random white American).
I’m sure there is some possible evolutionary scenario in which, just at the exact right moment to benefit non-African people, a “super-smart gene” evolved – and for some reason it was extremely useful to those who spread into Eurasia but not advantageous enough to spread back into Africa. But without knowing anything about this supposed gene – or even whether it exists – it just sounds like the fantasy of white supremacists. Test scores for groups don’t tell us anything about genes – they didn’t about the low Irish test scores from 100 years ago, they don’t now, and they don’t anywhere in between. There’s absolutely nothing special about outcomes now – you’ve presented no reason whatsoever to believe that outcomes NOW represent equality of opportunity to succeed (academically, financially, etc.) while all outcomes of the past did not. There is no possible test score data that could tell us anything about genes – it doesn’t matter (in terms of genes) what the difference is between the test scores of rich black kids and poor white kids… this tells us much about society, but nothing about genes. There’s no logical reason to single out test scores for black people now as being special – why weren’t Irish test scores of the past special? Why weren’t the outcomes for Chinese immigrants in the 19th century special? What is it about now that’s special?
Nothing. So if all you have is test scores, then you have no information whatsoever about genes for various groups. If you want to make assertions about the genes for black people, then find the genes you’re making claims about. Barring that, at least make some effort to do real science – recreate the Scarr study, which refutes the genetic explanation, with modern methods. Find out if, inside of groups like African Americans and independent of social identifiers like skin color, larger percentages of African ancestry actually correlate to lower test scores.
The straw man you are inclined to cling to is “clean cutoff.” Nothing in human populations is “clean” if you define it rigidly enough. That’s why we talk about average gene pool differences. And they are gene pool differences, on average, when we self-define by race, because it puts us in average pools driven by historic migration patterns.
But if you think groups descedaed from the Levant exit are as clinal to sub-saharans as they are to adjacent M-N descendant lines, some additional reading will help clear up your confusion and diminish your frustration, I think.
The primary out of africa expansion 70 kya-ish years ago is not thought to be a continuous stream back and forth beginning at that point. There were other hominin groups that left africa long earlier, such as the Neanderthal ancestors a half million years prior, and perhaps some early out of africa groups who traveled along the coastline with dispersion, or who died out, or who interbred w/ newer groups. But the main migration point into the Levant resulted in a reasonably sharp division; one theory is that the geographic gate permitting that group to exit closed for climate or other environmental reasons.
We can see the results of that split when we look at modern human lineages using mitochondrial or Y DNA lines. But we can also look at how two broad groups were formed by looking at gene variants directly, and Neanderthal introgression is a good example.
Contrary to your implication that all groups are reasonably equally clinal, and therefore no split makes sense, it is the case that at L3/M-N (using mtDNA) the bulk of eurasian lineages trace back to that early Levant-based exit group out of africa. New genetic material that was acquired near that point (such as the 1-4% Neanderthal introgression from hominin lines hundreds of thousands of years more archaic than africa lines that are Eve to sub-saharan lines) descended almost entirely to out of africa lines because the migration was largely one-way and largely non-continuous for tens of thousands of years.
Perhaps the top three diagrams here might help bring clarification visually. Notice that in sub-saharan africa, the color wheel looks quite different, and then look at the adjacent color charts to see which lines descended from where.
In the Y chromosome diagram, almost all of the colors you see except for black, light blue and the E purple represent out of africa lineages descended from that Levant exit group, probably.
In the mtDNA diagram, almost all of the colors you see except for black and grey represent out of africa lineages.
In both cases, the out of africa lines would have relatively small amounts of total backflow into africa, and any genetic material introduced early in the post out of africa split would be available only to non-african lines. That’s why we see Neanderthal DNA in non-african lines at a 1-4% amount, and far less so in sub-saharan lines. MCPH1 haplogroup D would be another example of a gene variant far more penetrated into non-african lines than sub-saharan ones.
A migrations map by mtDNA linesmight also help to visualize the L3/M-N split.
I googled “M-N descendant lines” – it wasn’t very helpful (EDIT – I see below you referred to it as mitochondrial lines). I’ll assume this is a mitochondrial or Y-chromosome line… if so, that is a miniscule (but extremely interesting) portion of the human genome. Further, these lines help my argument – they show relationships that are closer between certain African and non-African groups than between various African groups with each other. If you believe that, in overall genetic ancestry (not just mitochondrial or Y chromosome), there are places in North Africa/Middle East in which such a clinal relationship does not exist, then you’ll need to provide more evidence.
So far I haven’t seen any evidence of a “reasonably sharp division” across the entire human genome. Without significant geographic separation (like an ocean, or impassable mountains), it doesn’t seem likely or possible at all.
This doesn’t seem to be any actual evidence that the relationships are not relatively clinal across the entire genome. Sure, non-African populations have a higher percentage of Neanderthal ancestry – but how does this compare between, say, the Levant and lower Nile river? How about lower and upper Nile populations? Saharan and Sub-Saharan populations (and so on)? Or in the other direction, between Levant and Persian populations, or Balkan populations, and so on? Have they really concluded that, other than some line across (perhaps) Sinai and North Africa, there is no relationship between geography and Neanderthal ancestry? From my understanding, it doesn’t go from “1-4%” to “~0%” across some border or river – it goes from “1-4%” to “a little bit less on average” to “a little bit less on average”, such that, to some degree, the closer one gets in Africa to Sinai, the higher (still very small) levels of Neanderthal ancestry. And, to some small degree, this exists on the “other side” as well – those in the Arabian Peninsula have a bit smaller percentage of African ancestry, on average, than populations farther out into Eurasia.
The colors in the wheels certainly are different. I don’t see what this says about relationships across the entire human genome, though (and obviously, the colors could be grouped in ways to imply nearly any sort of conclusion). Mitochondrial and Y-chromosome lineages don’t track the same way – this should give us some indications that the rest of the genome may also track in different ways.