May 9, 2010

The amount of Neanderthal DNA we have is the equivalent of one totally Neanderthal great-great-great grandparent.

Observes anthropologist John Hawks (who writes "Neandertal," which I presume is the official academic spelling). Hawks also has a lot more detail, written comprehensibly, so check it out, if you want to understand how the news about Neanderthals was discovered and what it means. Excerpt:
Does this mean that Neandertals belong in our species, Homo sapiens?

Yes.

Interbreeding with fertile offspring in nature. That's the biological species concept.

Now, some paleontologists might still disagree -- maintaining that species are units that can be distinguished morphologically, or by one or more derived features, or any number of other definitions. That's fine with me, as long as they're clear. But understand: It does define all non-Africans today as an interspecific hybrid population.

So maybe they want to rethink that one?
That makes me want to go back to the poll we did on Friday and think about what that means. The 4% of you who were disturbed at the idea of not being fully human can take comfort in the notion that Neanderthals were fully human. (If you are 100% African, you don't have to deal with this issue.) The 21% of us who thought it was thrilling to have some Neanderthal are perhaps less thrilled. But 75% percent of us didn't care one way or the other. Now, there's even more reason for there to not be a difference.

89 comments:

edutcher said...

'Neandertal' is the pronunciation, if not the spelling, of the town nearest the place where the first Neanderthal (I also refuse to call the capital of China Beijing (actually pronounced Bay-ching)) was found.

I've got no problem with the whole idea. Evolution is turning out to be so overrated.

Jeff with one 'f' said...

"Now, there's even more reason for there to not be a difference"

Why?

tim maguire said...

If you are 100% African, you don't have to deal with this issue.

Initially I was going to make the observation that we are all 100% African, but then another, more snarky possibility occurred to me--are "100% Africans" fully human?

Fortunately, since I have no intention of applying to Harvard Law School, I can ask that question.

Skyler said...

So then the question would emerge, assuming the announcement of interbreeding to be correct, "Is it better to have Neanderthal genes or worse?"

What do these genes do? Do they even know? It's pretty meaningless except as shock journalism until you know what that 4% might entail.

Or could it simply be that living in a colder climate causes one to retain certain genes that are not so beneficial if you live in Africa?

How do we know that it wasn't the Africans that lost these genes when all the other populations retained them?

I think the conclusions are premature and we will learn in about ten years that there is another theory that is better in explaining what they see. And then another theory will follow that.

Do not be so quick to accept the conclusions of scientists who do not yet fully understand a new science.

Fred4Pres said...

Cave man body hair?

John Hawks said...

Thanks for the link, Ann!

The name comes from a place -- and the Germans changed the spelling of the place from "Neanderthal" to "Neandertal" around forty years after the bones were discovered. It was a spelling reform that had to do with German unification.

Meanwhile, the "-thal" was already formalized as a species name, Homo neanderthalensis. Species names don't change. And the "-thal" is the version that made it into everyday English, where of course, "Neanderthal" means "stupid backward chauvinistic hairy-footed rube" or some such.

In most of Europe today, they're amused by the trouble this causes in English, because they all pronounce a "th" like a "t" anyway.

But in America, a scientific counter-culture got started in the late 1960's, that adopted the "progressive" "Neandertal" as a way of talking about them without invoking the whole hairy-footed rube thing. Meanwhile, the scientists who thought that they really were hairy-footed rubes continued to use "Neanderthal" -- which was what you'd be forced to use if you thought they were a different species from us.

This has gone on for forty years -- some scientific sources using "-thal", others "-tal". It's really one of the rare cases in science where your "politics" about the subject are on display right there in the way you spell a word!

Will the "-tal" supporters carry the day? Have we set aside the fur-backed apeman image once and for all? Or will we be hung up on taxonomic formality as neanderthalensis remains a subspecies of Homo sapiens?

I imagine we'll keep arguing about it for a while.

mc said...

Another question: would it upset you if you learned your daughter were dating one?

Hagar said...

The Neanderthals also came out of Africa, just one or two interglacials sooner. We are all on the same evolutionary branch.

TangoMan said...

The final nail in the coffin of the proposition that race is a social construction.

Synova said...

"but then another, more snarky possibility occurred to me--are "100% Africans" fully human?"

Yes, apparently. And the rest of us are hybrids, slightly.

"Fortunately, since I have no intention of applying to Harvard Law School, I can ask that question."

;-) Ha ha.

Even so. There is probably something profound to be learned from studying the different reactions people have to the idea of being part "cave-man" if anyone will dare to study it.

Will Africans and particularly people of African decent react to the notion of being purely modern human in an aggressively positive way, stick it to the eugenicists of the past century, "up-yours" sort of way?

I would suppose a few Europeans will be appalled but I predict that most will either be entirely uninterested (as shown in the poll) or react with "Hybrid vigor, Hoo-aah!"

And will Asians care at all?

traditionalguy said...

And a Happy Mother's day to all you Homo Sapiens trying to let your Neandertal selves come out out to play.

ricpic said...

Stand tall stand proud all you hairy backed guys
Cause you've just been humanitized.

The Drill SGT said...

mc said...
Another question: would it upset you if you learned your daughter were dating one?


Most likely these genes didn't get into the pool via dating or what we consider marriage today.

Rather, raiding of neighboring groupings with the resultant taking of female/child captives as slaves.

and vice versa of course, but the gene lines that are 95% Neanderthal and 5% cro-magnon didn't make it into the history.

D. B. Light said...

If anyone is interested, there is a neat Bloggingheads diavlog featuring Jphn Hawks and Razib Kahn talking about Ardi here.

http://bloggingheads.tv/diavlogs/23155

Check it out. It's worth the time.

Duscany said...

Ann, Why would the 21% of us who thought it was thrilling to have some Neanderthal now be "perhaps less thrilled?"

Because this means black Americans are genetically different from European Americans?

I think it's only liberal professors and the professional commentariat who are worried sick that there might be genetic difference between the races. Most Americans don't give a hoot one way or the other.

Besides, most black Americans do have Neandertal genes since most black Americans have white ancestors too.

rcocean said...

Paint me skeptical. I have no confidence the "professor" has any idea what really happened 1500 generations ago, or whether there was such things as "neanderthals" or whether they really make up 1-4% of our DNA.Whatever that means.

BTW, 50 percent of our DNA is shared by Corn. Which means of course, my great-grandfather was a corn stalk.

TangoMan said...

Because this means black Americans are genetically different from European Americans?

It's always been clear to most people that there are noticeable and functional genetic differences across races. There was an interregnum in which the fiction that race is a social construction gained currency and smart people claimed to believe this as an all-encompassing notion, but that social fiction has been eroding quite steadily over the last few decades.

This Neandertal news simply makes it that much harder to cling to the fiction that race is just a social construction.

Lem said...

Our ability to Jacky Robinson any old event knows no bounds.

I dont mind.. this is not a put down (or something) I just wish we.. its lame .. first are lame.

maybe i'm misreading this.. nyc does that to you

Jon said...

Contrary to the hype, these results actually do not prove that there was interbreeding with Neandertals- that's the simplest explanation for the common DNA, but not the only explanation.

From the Science article:

"Although gene flow from Neandertals into modern humans when they first left sub-Saharan Africa seems to be the most parsimonious model compatible with the current data, other scenarios are also possible. For example, we cannot currently rule out a scenario in which the ancestral population of present-day non-Africans was more closely related to Neandertals than the ancestral population of present-day Africans due to ancient substructure within Africa (Fig. 6). If after the divergence of Neandertals there was incomplete genetic homogenization between what were to become the ancestors of non-Africans and Africans, present-day non-Africans would be more closely related to Neandertals than are Africans. In fact, old population substructure in Africa has been suggested based on genetic (81) as well as paleontological data (86)."

http://www.sciencemag.org/cgi/content/full/328/5979/710

Michael McNeil said...

Interbreeding with fertile offspring in nature. That's the biological species concept.

No it isn't. There are any number of what are generally considered to be separate species (though typically of the same genus) that biologically are still capable of interbreeding (all the canines, for instance: dogs, wolves, foxes, coyotes, jackals, African wild dogs, etc.; bison and cattle, and so forth).

The reason that groups that can biologically interbreed are nonetheless still regarded as different species isn't because they genetically can't reproduce, but because in nature they usually don't interbreed — for whatever reason, which might be that they're geographically separated and isolated from one another; or that one group is active during the day, while the other is alert at night, and thus their paths don't cross; or they simply don't find each other to be physically attractive: the reasons are legion — as a result the groups are able to evolve basically independently from one another, and that's what makes for different species.

Indeed, one of the first things that typically occurs as such groups diverge (if not geographically isolated from one another) is the evolution of “attractiveness” flags (e.g., different patches of coloring and the like) that turn off the members of the different groups from each other so they no longer even make the attempt to reproduce together.

In the case of neanderthals vis-a-vis anatomically modern humans, it was the first explanation: geographic isolation (the neanderthals lived in Eurasia, humans in southern Africa) that acted to originally result in their divergence from one another.

Much later, after that isolation was undone as anatomically modern humans began their own migration(s) out of Africa, some genetic interchange began once again, but relatively little — perhaps because of cultural reasons, perhaps because they (mostly) didn't find each other sexually attractive — and thus the two now-separate species did not converge once again, but we (non-African) humans nonetheless ended up with a slight admixture of neanderthal genes.

As species diverge further (oftentimes into the separate families of species known as genera), the accumulation of internal biological differences does eventually begin to act to genetically inhibit even the possibility of reproduction. Note that there's nothing magical about this phenomenon of genetic incompatibility, it's rather like the differences between similar model cars — many parts can be transferred between adjacent models, but as they get increasingly different (in model years apart say), it gets more and more difficult, until eventually it's like trying to repair a Ford car using Chevy parts: it just ain't a gonna work, and an incipient embryo oftentimes dies during gestation, or if it is born and survives, ends up sterile like a mule.

Skyler said...

Thanks, Jon. So it seems that even in the scientific literature being touted, there is already acknowledgement that the theory of interbreeding is not proven and there are several other possibilities.

So, I stand by my criticisms from yesterday, despite some people claiming to be experts and insisting that the conclusion of interbreeding is absolutely proven.

There's a whole lot we don't know about this and no one alive was there at the time. We need to get a lot more information than what we have now before we can claim even "out of Africa" as absolutely proven, let alone Neanderthal inter breeding.

Not that I care. What happened before doesn't change what we are now.

Synova said...

Jon, science is almost never completely without wiggle room or doubts. It's always the best theory presently available. Which means some other theory might be best later.

Which is why it's always best to either ignore or publicly scoff at anyone who claims the "science is settled".

If it is, it's not science any more.

garage mahal said...

Humans interbred with Republicans? Shut up!

edutcher said...

TangoMan said...

Because this means black Americans are genetically different from European Americans?

It's always been clear to most people that there are noticeable and functional genetic differences across races.


Good point. As an example, consider the behavior of dogs in a neighborhood where there is only one race. The races each have a basic scent different from the others. This is why the dogs in a white neighborhood will (or used to a couple of generations ago) go crazy if a black person walks through and they have never been exposed to blacks. The same thing will happen to a white person in a black neighborhood.

Michael McNeil said...

I stand by my criticisms from yesterday, despite some people claiming to be experts and insisting that the conclusion of interbreeding is absolutely proven.

Bullshit. Nobody claimed that it's “absolutely proven” — indeed, the concept of “proof” doesn't even exist in science, outside the realm of abstract mathematics, which is a very different animal.

No, the interbreeding between neanderthals and anatomically modern humans is simply the most parochial explanation for the evidence seen — but nonetheless, it's likely to be true, and your own wholesale rejection of it (due to your own biases) is likely not to be true.

former law student said...

It's always been clear to most people that there are noticeable and functional genetic differences across races.

Sure, but it goes much farther than that. White people are much closer to the great apes than are black people: White people like George HW Bush, have thin lips, like chimpanzees -- black people have broad lips. White people tend to have straight hair, as do apes -- black people have kinky hair. White people tend to have abundant body hair, as do apes -- black people have sparse body hair. Therefore one would expect white people to have apelike intelligence as well.

Ann Althouse said...

"Ann, Why would the 21% of us who thought it was thrilling to have some Neanderthal now be "perhaps less thrilled?""

We think we're sophisticated because we're living our lives like good homo sapiens. But we're really not that different from the animals sitting in the cages in the zoo, and compared to the flowers and the birds and the trees, we are Neanderthal. Don't you get it? I don't feel safe in this world anymore. I don't want to die in a nuclear war. I want to sail away to a distant shore, and live like an apeman.

Michael McNeil said...

Stand tall stand proud all you hairy backed guys
Cause you've just been humanitized.


There's no reason to think that neanderthals were any more (or less) hairy than we are. They may have been, or not, but there's no evidence of it one way or tother.

former law student said...

perhaps because they (mostly) didn't find each other sexually attractive

I don't think this would be much of a barrier: I have seen some butt-ugly people reproduce. Further, men do not seem to discriminate much where they stick their members -- how attractive could the legendary slice of liver in Portnoy's Complaint have been?

Michael McNeil said...

and vice versa of course, but the gene lines that are 95% Neanderthal and 5% cro-magnon didn't make it into the history.

Not only did they not make it into (human) history, but such mostly neanderthal but partly cro-magnon lines didn't make it into any of the neanderthals whose genomes have been deciphered to date. So far the evidence is that neanderthals contributed to the heritage of (non-African) humans but that the genetic transfer did not go in the other direction.

Skyler said...

McNeil, already backtracking, wrote: Nobody claimed that it's “absolutely proven”

Actually, I think you did say that because you said that my skepticism was ignorant and baseless. Fess up. You tolerated no skepticism yesterday.

And we still haven't been told what these 4% genes control. I bet once we learn that, we might come up with different theories.

I'll stand by what I said yesterday, bolstered by even your comments now: We should not accept this as proven and we should be skeptical, and there will likely be new theories debunking much or all of this within the next ten years.

ironrailsironweights said...

There's no reason to think that neanderthals were any more (or less) hairy than we are.

I'll bet Neanderthal women had ... oh no, here I go again.

Peter

M said...

"Interbreeding with fertile offspring in nature. That's the biological species concept."

This is patently false. This is the most prevalent and accepted mammalian species concept. Natural hybridization is quite common in certain clades. Take the cichlids of Lake Malawi, for example -- applying this criteria as a species concept would reduce the number of described endemic species by an order of magnitude.

Overly general statements like that above reinforce the false perception that there are hard and fast rules to split or merge taxa. Species description in the Linnean model is as much art as it is science.

Pastafarian said...

For all those of you who claim that the 95% Neanderthal and 5% Cro-magnon didn't survive, I say:

Check out my avatar. Feel foolish now, don't you?

But in all seriousness, Michael McNeil -- a few questions:

1) Why wouldn't the transfer go the other way?

2) How do they know that the set of genes in question didn't result from natural selection -- maybe these genes result in traits that are advantageous in colder climates, and so both the Cro-magnons and the Neanderthals in those climates had a little bit of convergent evolution?

3) Is it possible that some of us have a little more Neanderthal than 4% or 5%? Because that would explain quite a bit with respect to my in-laws.

Ritmo Brasileiro said...

What do these genes do? Do they even know? It's pretty meaningless except as shock journalism until you know what that 4% might entail.

Aww Christ, Skyler! I thought we already went over this with you. Less than 2% of the human genome encodes genes. Most if not all of these fingerprints were probably in non-coding DNA. Don't you ever listen when scientific concepts form the argument in question?

Ritmo Brasileiro said...

Nor is it clear yet whether the presence of this DNA in modern humans represents positive selection – genetic material worth holding on to – or biological antiques whose functions have long been lost, the researchers say. So far, the inherited material does not seem to be concentrated in genes, but spread somewhat randomly in non-gene portions of the modern-human genomes.

Skyler said...

Aw Christ ritmo. When we KNOW whether they are useful genes or random nonfunctioning genes then we might know better.

Until then it's just barely not wild speculation.

Paco Wové said...

"So then the question would emerge, assuming the announcement of interbreeding to be correct, 'Is it better to have Neanderthal genes or worse?'"

What the hell...? This falls into the category of "Not even wrong."

Skyler said...

And I don't recall accepting your authority to "go over" anything with me.

Ritmo Brasileiro said...

The are non-functioning (or at least, non-gene) portions of DNA.

See all that text in blue in my comment? It's quoted from the hyperlink embedded within it. If you click on it you're directed instantly to the Christian Science Monitor article on the study where they you will find the report that I quoted.

Ritmo Brasileiro said...

And I don't recall accepting your authority to "go over" anything with me.

I suppose sticking one's fingers in one's ears and going "Na-na-na-na-na-na-na" might form a superior authority, of sorts, than cogent and informative (and informed) explanations. In baby-land.

Michael McNeil said...

This is patently false. This is the most prevalent and accepted mammalian species concept.

I agree with your comments in general; however with regard to the foregoing, as I pointed out before, what you're objecting to doesn't even apply to the concept of species in mammals.

Michael McNeil said...

But in all seriousness, Michael McNeil — a few questions:

1) Why wouldn't the transfer go the other way?


Good question. More than probably it could go the other way, technically, genetically. As to why it didn't, I would suggest the reasons are likely more historical than technical. Let me suggest some ways in which it might have occurred.

In the first place, since the three different (non African) modern human genomes examined and compared with neanderthals thus far were found to incorporate essentially the exact same degree and genetic details of neanderthal heritage (in human individuals from France, China, and Papua New Guinea), the explanation for that appears to be that the human-neanderthal interbreeding occurred just as the first anatomically modern humans were migrating out of Africa and passing through the Middle East (where neanderthals also resided), and before those humans went on to initially expand into Europe as well as Central, South, Southeast, and East Asia, and thence on to Australia/New Guinea. That's how all those now geographically dispersed humans could and would incorporate the same neanderthal genetic contribution.

Since the evidence of interbreeding appears in the common (non African) human genomes, it would appear that either some male neanderthals had sex with human females, and the latter thereupon returned to their human communities to have their babies, or else a group of neanderthals entered and was accepted into a human community, where they proceeded to mate with humans there; in the latter case those neanderthals therupon became completely absorbed into a much larger human populace. (Afterwards the neanderthal contribution may have been amplified by that initially rather small in population human group spreading over all of Eurasia and Australia-New Guinea in the course of which greatly expanding in numbers.)

Possibly the foregoing scenario simply happened not to occur in the reverse direction — that's one possible explanation for the evidence we see.

Another possibility is that the reverse gene flow — human to neanderthal — did occur, but those Middle Eastern neanderthal populations which now incorporated some human genes never migrated into Europe, where all the neanderthals whose genomes we've so far deciphered lived (Croatia is where we've thus far deciphered neanderthal genomes). In that case, once we begin to decipher some Middle Eastern neanderthal genomes, we may detect some human contributions to them.

Note that since modern Europeans share essentially the same admixture of neanderthal genes as East Asians and New Guineans, while the neanderthals from Europe whose genomes we've deciphered so far show no human contribution, it appears that the humans and neanderthals coexisting in Europe did not interbreed — for whatever reason: cultural, historic, or some other factor.

Michael McNeil said...

Continuing…

2) How do they know that the set of genes in question didn't result from natural selection — maybe these genes result in traits that are advantageous in colder climates, and so both the Cro-magnons and the Neanderthals in those climates had a little bit of convergent evolution?

In the first place, convergent evolution wouldn't produce exactly the same genes, with the same “silent” genetic coding due to their common (neanderthal) ancestors.

Secondly, if those genes had a selection advantage due to colder ice-age weather, after the end of the ice age, and particularly in very warm places like New Guinea, those genes would have been selectively filtered out, which has not occurred.

3) Is it possible that some of us have a little more Neanderthal than 4% or 5%? Because that would explain quite a bit with respect to my in-laws.

(Grin!) It's certainly possible in theory; however, since the French, Chinese, and New Guineans all appear to incorporate the same degree of neanderthal admixture, it appears not to be true in practice. Comparisons with more modern human genomes will clarify the situation.

David said...

Michael McNeil said...

I KNOW A HELL OF A LOT MORE ABOUT SCIENCE THAN MOST OF THE REST OF YOU.

That's not really what he said, but it seems to be true. Keep it up, Michael. It's always nice to have actual facts on which to base our opinions.

David said...

As I read things, all this proves for 100% sure is that humans and Neanderthals have a common ancestor. Am I wrong, Michael?

Wandering Geologist said...

"Is it better to have Neanderthal genes or worse?"
---
It would mean more genetic diversity and therefore a better ability to adapt to change as a population than if humans had no Neanderthal DNA at all. From the article:
If Neandertals are one percent of the ancestry of non-Africans, we can be very sure that any gene in a Neandertal that had adaptive value in the later population is here now. That means they were important in an evolutionary sense.

ken in sc said...

Changing the definition of what a species is is a form of bait and switch, after the passing of the endangered species laws. In the 1960s, prior the endangered species laws being passed, a species constituted a group of organisms that could interbreed and produce fertile and viable offspring. Now claiming that organisms that don’t normally interbreed, but could, are different species is bogus on several levels. Not only could that logic be used to cause all kinds of expensive mischief with endangered species, it could be used to prove that Jews and Hottentots are different species.

Skyler said...

That's not really what he said, but it seems to be true. Keep it up, Michael. It's always nice to have actual facts on which to base our opinions.

Except notice that what he is pushing for others to blindly accept is not facts, it is opinion.

The facts are that certain genes are seen in Neanderthal and in modern Homo Sapiens, except for Africans. Okay, those are the facts as known at this time.

The opinion is that there was interbreeding. It's certainly a legitimate, and I personally believe it is likely to be true, opinion.

But it is opinion nonetheless. He even admits as much in between his bouts of insisting that no other opinions are allowed and that anyone expressing skepticism about the opinions must be daft.

So, go feel good about McNeil, but a real scientist would not insist that his opinions were incontrovertible.

Revenant said...

Sure, but it goes much farther than that. White people are much closer to the great apes than are black people

All humans are equally closely related to chimpanzees -- the last ancestor we share with chimps died millions of years before humans evolved in the first place.

John Hawks said...

I was reading through the comments on the earlier post, and there seemed to be a lot of confusion about the 1-4% contribution from Neandertals, compared to the 98% similarity of humans and chimpanzees.

Let me explain with another example.

You are approximately 99.9% similar to any other random human today, and a bit closer to your immediate relatives.

Your great grandmother on average gave you 1/8 of her genes, making up on average 12.5% of your genome.

You are more than 99.9% similar to your grandmother, on average, yet she contributed only 12.5% of your genome.

Now, suppose we don't know she's your great grandmother. We can test the hypothesis that she's unrelated to you by examining whether you are equally genetically similar to her as you are to a randomly chosen individual from your population.

This is a statistical test; in fact some of the people in the population share more genetic similarity with you than others. But if your putative great-grandmother shares substantially more with you we may conclude that she is your relative. Possibly we may specifically conclude that she is a third-degree relative, although our confidence in this may not be too great depending on the genetic variation in the population. We will be able to disprove the hypothesis that she is your mother or sister, and probably your grandmother or aunt.

Although corn does in fact share a substantial part of its genome with us, we can easily disprove the hypothesis that humans are direct descendants of corn.

If Neandertals had not donated any genes to later populations, then the most recent common ancestors of human and Neandertal genes would all be earlier than the divergence of those populations, more than 250,000 years ago. It is the observation of large chromosomal segments that are identical or very near living human chromosomes that shows that, for some genes in some living people, the Neandertals are not different enough. We have to have some of their genes.

Michael McNeil said...

As I read things, all this proves for 100% sure is that humans and Neanderthals have a common ancestor. Am I wrong, Michael?

Well, as I noted before there's no such thing as 100% assurance (i.e., “proof”) in science, however the indications are strong that what you say here is correct.

Beyond that, though, there are two levels of common ancestry at work here. In the first place, both humans and neanderthals are descended from a common… — not (singular) ancestor, but rather group of some thousands of ancestors — dating back perhaps around half a million years, before the two species initially diverged from each other when the neanderthals departed Africa in their migration into Eurasia.

A secondary level of common ancestor or ancestors, at least of neanderthals and (non African) humans, is inferred to have occurred much later — perhaps 100,000 years ago — when some neanderthals interbred with anatomically modern humans, perhaps in the Middle East, as humans began their own migration out of Africa and interacted with populations of neanderthals in the area.

Michael McNeil said...

Skyler now sez:
The facts are that certain genes are seen in Neanderthal and in modern Homo Sapiens, except for Africans. Okay, those are the facts as known at this time.

The opinion is that there was interbreeding. It's certainly a legitimate, and I personally believe it is likely to be true, opinion.

But it is opinion nonetheless. He even admits as much in between his bouts of insisting that no other opinions are allowed and that anyone expressing skepticism about the opinions must be daft.

So, go feel good about McNeil, but a real scientist would not insist that his opinions were incontrovertible.


It is not me who is wavering, rather it was you who earlier stated categorically that genomics couldn't know anything about genes and gene frequencies, and that it was all basically a fraud — that's what I'm calling (taking your term) “daft” — not the conclusion (which is much less than certain though still probable) about neanderthal-human interbreeding.

Now you call the basic genomics data “facts,” and declare that you think that the inference of interbreeding to be “likely.” That's a very far cry from what you were loudly proclaiming as true (namely, that it's all horseshit) earlier.

Ritmo Brasileiro said...

Skyler commits another boo-boo:

The facts are that certain genes are seen in Neanderthal and in modern Homo Sapiens, except for Africans. Okay, those are the facts as known at this time.

Skyler has no idea of the difference between a "gene" and DNA.

There is no other way to account for his continued willful(?) ignorance of the *fact* that the report showed Neanderthal DNA in, wait for it, wait for it, non-coding regions.

Skyler, what's going on exactly? Are you waging a personal jihad against Watson and Crick or something? Have you ever heard of an intron?

Ritmo Brasileiro said...

Michael,

Are you familiar with the distinction between coding DNA and non-coding DNA?

It seems that Skyler isn't and that this bit of ignorance is what is furthering his outcry for some reason.

Skyler said...

It is not me who is wavering, rather it was you who earlier stated categorically that genomics couldn't know anything about genes and gene frequencies, and that it was all basically a fraud

Never said that. I said that it is unproven and there's a pretty good chance that it could be wrong, or even fraudulent. Science has not recently given us much reason to trust their press releases or other published opinions.

You were too caught up in your own hubris and need to squash any questioning or doubting of the opinions to realize that I didn't say it was absolutely wrong. I only said that it is not proven and to claim it is proven is wrong or fraudulent.

Most of the engineers I know, especially the software engineers I know, are much more circumspect about anything that is not absolutely proven a fact. I suppose that's because their results usually come out very clearly and embarrassingly (and sometimes deadly) if they're wrong.

For other sciences, I suppose it's not too embarrassing when several decades later they start saying, oh, now we think a lot of dinosaurs were actually warm blooded like birds. The fact that generations of scientists had proclaimed that all were cold blooded with no caveats on their opinions is not considered an embarrassment.

This is the type of hubris that allows so-called climatologists to assert that they know what is happening to the world's climate while at the same time they are fabricating and cherry picking data to support their claims.

I think it is irresponsible to assert opinion as fact without clear caveats up front and throughout. They may very well be correct in their claims, but they don't know it as fact and it only serves to create myths and hard-to-die old wives' tales in future generations when theories are put forth as fact. I guess the hubris comes from the misplaced idea that those not immersed in the field of study should not be burdened with the fact that what is being purported is no more than intelligent speculation. The unwashed masses need not worry their little heads about such things.

Skyler said...

Skyler has no idea of the difference between a "gene" and DNA

You keep saying this as though it were true and as though it is at all germane if it were.

The details of the science aren't even germane. The conclusions are opinions that are being asserted as facts. That is my issue.

Ritmo Brasileiro said...

The details of the science aren't even germane. The conclusions are opinions that are being asserted as facts. That is my issue.

Interesting "issue" for someone, who doesn't understand the conclusions of others (that he nonetheless indicts), to have.

Skyler claims the distinction between a gene and something that is not a gene is not germane to what he believes is being misconstrued as a fact, when he believes it is only an opinion.

I suppose such an objection might be credible if it didn't come from the same doofus who stated this:

So then the question would emerge, assuming the announcement of interbreeding to be correct, "Is it better to have Neanderthal genes or worse?"

What do these genes do? Do they even know? It's pretty meaningless except as shock journalism until you know what that 4% might entail.

Or could it simply be that living in a colder climate causes one to retain certain genes that are not so beneficial if you live in Africa?

How do we know that it wasn't the Africans that lost these genes when all the other populations retained them?

I think the conclusions are premature and we will learn in about ten years that there is another theory that is better in explaining what they see. And then another theory will follow that.

Do not be so quick to accept the conclusions of scientists who do not yet fully understand a new science.


But that doofus was... you guess it: Skyler.

Skyler - you might want to get a clue about what you take issue with before, uh, taking issue with it.

Or suit yourself and pretend that you have any credibility otherwise.

Ritmo Brasileiro said...

The study said nothing about Neanderthal "genes", let alone based any "conclusions" off of that. The study is about descent based on DNA that didn't encode any genes. So for Skyler to pop off about how scientists are just trying to make a big commotion about what we can conclude from Neanderthal "genes" being found in modern humans is absolute rubbish.

If he had a shred of intellectual honesty and decency he would account for that. He took issue with nothing other than that tangent he invented.

Skyler said...

Ritmo, you silly goose you.

Such a goofus doofus you are.

So tell me doofus goofus, exactly what are those genes for?

Can't say? Ah, then you must have some supernatural ability to understand that they serve no purpose whatsoever -- Despite that there have been several times that scientists have found that genes previously considered of no purpose do in fact have a purpose.

Don't be so quick to claim you know what you're talking about. Clearly, goofus doofus, you don't.

If you don't know what those genes are for, or what they were for at one time, then you don't understand the science and it is nothing but hubris to state conjecture as absolute fact.

Their opinion could very well be correct. They just don't know that it is. If you look at the report they even say so, but the newspapers and the denizens of this blog seem to think that all skepticism is inappropriate.

Synova said...

"White people like George HW Bush, have thin lips, like chimpanzees -- black people have broad lips. White people tend to have straight hair, as do apes -- black people have kinky hair. White people tend to have abundant body hair, as do apes -- black people have sparse body hair. Therefore one would expect white people to have apelike intelligence as well."

LOL.

I actually thought of this when I was a kid reading Edgar Rice Burroughs. Make no mistake, I love his books, John Carter and Tarzan and several that are one-off adventures... but the man was a product of his time, where we'd discovered inheritance and discovered Darwin and who was more evolved than whom was something discussed by those enlightened enough to reject religion.

But I did always wonder if dear Edgar ever caught the detail he included so confidently, that the more refined and evolutionarily advanced were hairless and his Europeans were eternally plagued with beards.

I think he must have done, because they were always shaving the dratted things off.

Skyler said...

The study is about descent based on DNA that didn't encode any genes.

See? This is how Ritmo, the goofus doofus, likes to argue everything.

He'll sit back and throw little darts like "Skyler doesn't know the difference between a gene and DNA" yet never bothers to explain why that might be important. Finally two days later, he tosses in this bomb.

Too late. I may have framed the argument around terms that might not fit the occasion, but the argument is still sound. Goofus doofus.

The conclusions of interbreeding are based on conjecture and opinion and are being presented as fact. It doesn't matter why, or whether genes or non-encoding DNA are involved. Irrelevent. Claims are made that are not factual, but conjectural. Experience has shown far too often that such conjecture is shown to be in error, incomplete, or based on erroneous premises. I don't need to know what the error is. I only call out that conjecture is not fact.

You get so emotional, goofus doofus. I don't understand why this simple point gets you so lathered up. Clearly you are not a scientist or you would recognize that conjecture is not the same as fact.

But I guess since a bridge won't collapse if they're wrong, then no one is harmed. Lots of books will get sold and novels written based on this conjecture, and then the Discovery channel will make a tv show based on it that will be aired for 15 years, long after the scientific consensus has moved on to another contradictory opinion. No matter, all skeptics must be insulted, first.

Ritmo Brasileiro said...

Rather than answer to the likes of poor Skyler, I'll just sit back and laugh until he figures out which objection he wants to go with. Shouldn't be difficult, but his pride apparently gets in the way of accepting that no one said anything about "genes". He made it all up.

Until he understands what the actual claim *is*, it's useless taking any objection he "has" to it seriously.

Ritmo Brasileiro said...

I don't need to know what the error is.

You don't even know what the evidence is, let alone what the claim is!

I only call out that conjecture is not fact.

Oh, and what a brave little soul you must be to point out that one other thing in the known universe (like everything else) is not known to an absolute degree of certainty!

Stick with engineering and leave the science alone. There is no way any form of empirical knowledge will satisfy your craving for a form of absolute certainty that is closer to faith than to any system of observed knowledge.

bagoh20 said...

The concept of race, as we use it, is clearly a social construct. When we decide to make nonessential differences paramount in our relationships, it's a social construct in the truest sense of the phrase. The actual physical differences are nowhere near as clear as our social construct of race. We are not off the hook for that.

Ritmo Brasileiro said...

Clearly you are not a scientist or you would recognize that conjecture is not the same as fact.

The fact is that Neanderthal DNA was found in 1 to 4% of the genomes of human populations that would have had contact with Neanderthals, and not in the DNA of human populations that wouldn't have had contact with Neanderthals. Draw your own conclusions. Use of a functioning brain optional. No insults for contrarian conclusions that have intelligible explanations in light of these facts.

Of course, you could draw no conclusion at all - as Skyler might pretend he would. But then you reduce science to the business of NOT finding answers to questions such as these.

Your real problem is with science, Skyler. Apparently your preferred method is ignorance. It is not the job of science to say what we don't know, just what is more plausible or less plausible based on what there is evidence for. If you don't like that, join a fucking seminary.

Michael McNeil said...

The study said nothing about Neanderthal “genes,” let alone based any “conclusions” off of that. The study is about descent based on DNA that didn't encode any genes.

You keep saying that, and I'm not sure where you're getting it, but it's wrong. As the principal Science report says: “We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.” Note the “gene flow.”

One can even go to the UCSC genome browser and peruse the genetic data and identified genes themselves (follow the link “Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans”).

bagoh20 said...

"It is not the job of science to say what we don't know, just what is more plausible or less plausible "

Ritmo, you really work hard to find a reason to be ignorant in nine out of ten threads. Usually it's a real stretch, but you go the extra mile.

Ritmo Brasileiro said...

“We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.” Note the “gene flow.”

This sounds like it was taken from the background, rather than from anything that the paper concluded.

CSM explicitly reports that they didn't look at coding regions.

Ritmo Brasileiro said...
This comment has been removed by the author.
Ritmo Brasileiro said...

Well, it's not science's job to commit us to absolute ignorance in perpetuity. If something isn't known, then one finds a way to design an experiment, as these guys did.

One wonders how Skyler would have designed an experiment to be more conclusive than this one. Or maybe he just wouldn't have done so. I doubt he has the balls to even proclaim what standard of evidence would suit him, short of a time machine that allows him to travel to a point where he could directly observe human-neanderthal matings for himself.

He is just being a silly lawyer-contrarian and narrow engineer for the sake of doing so and refusing to engage a discussion on what constitutes reasonable standards of evidence from the standpoint of science or any other system of knowledge - solely for the sake of making a ridiculous political point.

Skyler said...

Thank you, McNeil. I never claimed to be a geneticist.

It's clear that Ritmo is either lying or more ignorant than he would purport to be. Par for the course.

Frankly, I hope that all these opinions are proven true. I like to believe that scientists are responsible and accurate. I just haven't seen much of that lately and I prefer to see more humility and caution in such broad sweeping claims.

I suppose the scientists themselves are more cautious, but certainly the press reports are not.

Ritmo Brasileiro said...

Frankly, I hope that all these opinions are proven true. I like to believe that scientists are responsible and accurate.

And here you have it. I was going to point out Skyler clearly seems to have a problem with successive empirical and experimental conclusions as better approximations of the truth rather than absolute truth. And with the above statement he doesn't fail to let me down.

Successive conclusions don't have to corroborate each other, without negating the previous conclusion as a better approximation of "the truth TM" (or knowledge) than the one before it.

Skyler said...

One wonders how Skyler would have designed an experiment to be more conclusive than this one.

Ritmo, you're assuming that there must be a conclusion. There need not be. There could be simply an accumulation of evidence. Conclusions can wait. There really is no hurry.

And that points up a good question: Why do you have such a stake in denying the possibility of error? What possible harm could come from it? Do you have stock in Neanderthal theme parks or something? So far as I know, the future of the world is not relying on an absolute answer to the question about interbreeding with Neanderthals.

If we don't know as a fact, we should say so and not imply that we do know something as a fact.

Skyler said...

quoting myself: Conclusions can wait. There really is no hurry.

There's no hurry, that is, unless you are seeking tenure or funding and need a flashy headline in the news.

Ritmo Brasileiro said...

Why do you have such a stake in denying the possibility of error? What possible harm could come from it? Do you have stock in Neanderthal theme parks or something? So far as I know, the future of the world is not relying on an absolute answer to the question about interbreeding with Neanderthals.

If we don't know as a fact, we should say so and not imply that we do know something as a fact.


This is fine. There is always a possibility of error and each conclusion is always an approximation of knowledge that is less provisional than the one before it, but still provisional. As I've said many times, once we know everything the endeavor of science will cease to be necessary or exist. No finding should be seen as the final answer.

That said, Paabo is an impressive researcher who has pioneered the "molecular clock" studies that have shown, for instance, when humans evolved the form of a gene that in all likelihood allowed for language. I take his work seriously and think there is reason to regard his work as something produced not by a hack, but by someone who has developed incredibly powerful techniques for determining when and how human populations diverged over many, many years.

If you look at his work on the molecular evolution of the FOXP2 gene, I'd find it hard to believe you might not find it similarly impressive.

He might be wrong on this - as any scientist can be on anything, but he clearly seems to know what he's doing when it comes to findings that advance our knowledge on these matters in a tangible way.

Ritmo Brasileiro said...

More on FOXP2. Paabo enters the picture when they start talking about publications as of 2002.

Skyler said...

He might be wrong on this - as any scientist can be on anything, but he clearly seems to know what he's doing when it comes to findings that advance our knowledge on these matters in a tangible way.

So where are we disagreeing?

Michael McNeil said...

This sounds like it was taken from the background, rather than from anything that the paper concluded.

CSM explicitly reports that they didn't look at coding regions.


If you're talking about the Christian Science Monitor, it says nothing of the kind: “The researchers looked at DNA samples from humans living today, and found signs of leftover Neanderthal genes introduced from this interbreeding.” Note the “leftover Neanderthal genes.”

And why are you looking at a news report anyway? I pointed at the original source, the Science article, and now do so again. And yes, my quote was from its Abstract, but so what! There's nothing in the Science report proper about their finding dealing only in non-coding regions of the genome, and it too explicitly mentions “gene flow from Neandertals into modern humans.”

You need to learn to read better, Ritmo, and more deeply into the original sources, particularly before spouting off so authoritatively. Now your embarrassment makes folks like Skyler think that somehow supports his position — which it does not.

Skyler said...

No, Ritmo's errors have nothing to do with my position, I've already said that.

What I've said before and will say again is that there is a difference between the facts discovered and the conclusions and opinions being projected from those facts. In my lifetime I have seen time and again that scientific claims in the newspapers are often exaggerated and given an aura of unassailability that is neither deserved nor appropriate.

Dinosaur extinction was absolutely positively caused by a meteor. Or not. Or by a different meteor. Or not. Or by any other of dozens of theories floated about and later denounced by the proponent of the latest theory.

I find it very doubtful that we really understand yet where homo sapiens emerged. I doubt we've found all the places where Neanderthal lived. There's a lot yet to be learned yet and I think that stating that we know these claims for fact instead of a theory or speculation is irresponsible.

Nothing is radical in what I'm saying. Unless you want scientists to be considered infallible, and that has hardly been the case.

Michael McNeil said...

In my lifetime I have seen time and again that scientific claims in the newspapers are often exaggerated and given an aura of unassailability that is neither deserved nor appropriate.

So if you're really interested and not just complaining, don't read (or don't just read) the newspapers — read the scientific journals such as Science and Nature instead.

Dinosaur extinction was absolutely positively caused by a meteor. Or not. Or by a different meteor. Or not. Or by any other of dozens of theories floated about and later denounced by the proponent of the latest theory.

While there inevitably is controversy among scientists until a particular matter (whatever it is) is far more settled than it yet is, in the case of the demise of the dinosaurs you seem to think that the “meteor” theory was a mere fad that has since been displaced. Not so.

The huge, 180 km (110 mile) in diameter crater known as Chicxulub has been located for a number of years now (it's down in the Yucatan of Mexico) — while the overlaying approximately kilometer of sediments has been drilled through and the crater's chemistry related like an identifying fingerprint with the debris layer left at the Cretaceous-Paleogene boundary in sediments all round the globe — and its age has been measured as dating essentially to the exact moment when the dinosaurs (along with three-quarters of all species on Earth, land and sea) disappeared, some 65.5 million years ago.

Perhaps you think that might be some kind of enormous coincidence, but few scientists do.

Here one can see an image (produced via gravitational measurements) of what that ancient crater looks like today with its overlaying sediments stripped away; and just two month's ago a major study published in Science concluded once again “that the Chicxulub impact triggered the mass extinction.”

I find it very doubtful that we really understand yet where homo sapiens emerged. I doubt we've found all the places where Neanderthal lived. There's a lot yet to be learned yet and I think that stating that we know these claims for fact instead of a theory or speculation is irresponsible.

Nobody claimed that those details are known for certain. Indeed they're not — but the remaining uncertainty does not change in essence the findings that we've been discussing.

Ritmo Brasileiro said...

"Gene flow" is a very broad, general term.

As far as the phrase "leftover Neanderthal genes" goes, I note the term "leftover". If genes are found, they could have been silenced. There are many pseudogenes or silenced relics of genes in the human genome. Perhaps if you knew more about molecular biology this wouldn't be new to you.

Second, don't be disingenuous or worse, a liar. I linked right here to CSM dated MAY 6th, jerkoff, not this April 29th piece you link. And it says, and I quote (again):

"Nor is it clear yet whether the presence of this DNA in modern humans represents positive selection – genetic material worth holding on to – or biological antiques whose functions have long been lost, the researchers say. So far, the inherited material does not seem to be concentrated in genes, but spread somewhat randomly in non-gene portions of the modern-human genomes."

I think you're the one who needs to learn how to read. And an apology wouldn't be of order, either.

Learn molecular biology and then the first sentence in the quote that I supplied (and NOT one from a DIFFERENT article that you misattributed to me) might help you make sense of the disparity between (functional) genes inherited thousands of years ago and their (likely) NON-FUNCTIONAL remnants today.

You need to learn what you're talking about before spouting off, Michael. You tried to make me look bad in front of Skyler and it's not even clear that you understand molecular biology well enough to have made any sense with this utterly fatuous (if slightly unhinged) objection of yours.

Get a grip, dude, and read a book. Obviously not all science is a foreign concept to you. If you lack understanding of molecular biology then just ask or find a Wikipedia page. And, oh yeah, don't misattribute the wrong links to me.

Not that it matters, but I clearly know more than you in this regard. I am not vying for authority, but I find the absurd lengths you are willing to go to in order to declare me in error (especially given the circumstances and length of the discussion) contemptible.

Ritmo Brasileiro said...

The majority of any actual "gene" analysis in the paper (let alone references to actual genes) has to do with the general differences between human genes and Neanderthal genes. It describes no Neanderthal-specific alleles, so far as I can determine, in the human samples. So, in other words, you're wrong, Michael:

Features that occur in all present-day humans (i.e., have been fixed), although they were absent or variable in Neandertals, are of special interest. We found 78 nucleotide substitutions that change the protein-coding capacity of genes where modern humans are fixed for a derived state and where Neandertals carry the ancestral (chimpanzee-like) state (Table 2 and table S28). Thus, relatively few amino acid changes have become fixed in the last few hundred thousand years of human evolution; an observation consistent with a complementary study (57). We found only five genes with more than one fixed substitution changing the primary structure of the encoded proteins. One of these is SPAG17, which encodes a protein important for the axoneme, a structure responsible for the beating of the sperm flagellum (58). The second is PCD16, which encodes fibroblast cadherin-1, a calcium-dependent cell-cell adhesion molecule that may be involved in wound healing (59). The third is TTF1, a transcription termination factor that regulates ribosomal gene transcription (60). The fourth is CAN15, which encodes a protein of unknown function. The fifth is RPTN, which encodes repetin, an extracellular epidermal matrix protein (61) that is expressed in the epidermis and at high levels in eccrine sweat glands, the inner sheaths of hair roots, and the filiform papilli of the tongue.

Ritmo Brasileiro said...

BTW, if it isn't clear, the whole paragraph above is background information.

Michael might want to distinguish what the paper describes for the purpose of providing background information, and what the experiments actually, you know, demonstrated in support of their hypotheses.

The hypothesis in this case is that genetic information specific to Neanderthals seems to have made it into modern humans. But this is all garden variety, non-coding DNA.

No single Neanderthal allele is described as having been found in humans.

That's probably why the authors state:

Features that occur in all present-day humans

Emphasis on the word "all". The paper's contention is that transfer occurred into only some human populations.

It's you who might want to read up, Michael. And learn to put some basic facts together. You know, the way scientists do.

Context, Michael. Context. Read for accuracy, not just precision.

Michael McNeil said...

Second, don't be disingenuous or worse, a liar. I linked right here to CSM dated MAY 6th, jerkoff, not this April 29th piece you link.

Ritmo, of course, cannot help being an asshole. In fact, he did not link to the Christian Science Monitor piece in the posting where he mentioned it, that I was replying to. Nor did he link to it for a large number of postings before that, that I looked through — and I'm simply not going to search through dozens of postings hoping that somewhere he did link to it. If he wants folks to see articles that he refers to, then link to them where they're mentioned!

After looking fruitlessly for a while for a link in Ritmo's postings, instead I went to the Christian Science Monitor site itself, searched for “Neanderthal” and “Neandertal” — and at the time, the earlier piece was the only one that popped up. (I see that the later article turns up in a search there now.)

However, even given a link and the relevant phrase in the CSM article, who cares? It's a single sentence, not in a scientific journal or even a science magazine, but a newspaper, unquoted and unattributed to boot. There's no reason why anyone should favor it over the original sources, which I had already gone to, while Ritmo clearly had not.

As I've already noted, the principal Science article does refer to “gene flow,” and does not state that only “uncoding regions” of DNA are included in the segments that they detected were of neanderthal ancestry in modern humans.

Now Ritmo has finally gone to the Science source, where he claims that the fact that they don't include a list of neanderthal genes in their published text overview somehow proves him right and me wrong. Incorrect.

In the first place, I've already linked to the raw data at the UCSC genome browser, where he or anyone can go examine the DNA segments themselves. As I noted before, simply go to the subsection titled “Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans” (note once again the “gene flow” appellation), zoom in on the DNA and see how it's identified, gene-wise.

Beyond that, the published Science article is a mere overview, while linked within it is the Supporting Online Material which goes into much greater detail (which Ritmo obviously has not examined). Simply follow that link, then go to (pdf) page 142 to see the “Haplotypes of Neandertal ancestry in present-day non-Africans.” Know what a “haplotype” is, Ritmo? It's genes.

The text in that section further confirms that they're dealing with neanderthal haplotypes (i.e., genes) and alleles (i.e., genes) that are now in the genome of modern humans.

Ritmo Brasileiro said...

Ritmo, of course, cannot help being an asshole.

Well, I'd like to think I can and that my decision to be an asshole depends on whether or not the person I'm replying to is acting like an asshole.

In fact, he did not link to the Christian Science Monitor piece in the posting where he mentioned it, that I was replying to.

That's funny. On 5/10/10 at 6:11 PM, in the third paragraph, I did just that.

Nor did he link to it for a large number of postings before that, that I looked through

Actually, I did just that on 5/9/10 at 6:06 PM.

— and I'm simply not going to search through dozens of postings hoping that somewhere he did link to it.

Here Michael declares that where his inability to see something doesn't form a sufficient excuse, his laziness does.

If he wants folks to see articles that he refers to, then link to them where they're mentioned!

I did. Twice. And now I've located where I did so for you. Twice. And here's the same fucking link for the fifth time.

What a douchebag!

After looking fruitlessly for a while for a link in Ritmo's postings, instead I went to the Christian Science Monitor site itself, searched for “Neanderthal” and “Neandertal” — and at the time, the earlier piece was the only one that popped up. (I see that the later article turns up in a search there now.)

Do you have a point?

However, even given a link and the relevant phrase in the CSM article, who cares? It's a single sentence, not in a scientific journal or even a science magazine, but a newspaper, unquoted and unattributed to boot.

The quote corroborates what anyone can see from the findings in the paper.

There's no reason why anyone should favor it over the original sources, which I had already gone to, while Ritmo clearly had not.

Check the posts immediately following the post you're obsessing over.

As I've already noted, the principal Science article does refer to “gene flow,”

So what? We've gone over this. The phrasing is used for explanatory purposes and not to state that any functioning Neanderthal "genes" (although a less egregious ignoramus than Michael would use the term "alleles") were found in humans.

and does not state that only “uncoding regions” of DNA are included in the segments that they detected were of neanderthal ancestry in modern humans.

Michael reveals his ignorance of Paabo's work right here.

Non-coding regions are much richer in the SNPs that allow us to identify the ancestral source of one group or another. They form a much more readily available "fingerprint" of DNA.

Ritmo Brasileiro said...

Now Ritmo has finally gone to the Science source, where he claims that the fact that they don't include a list of neanderthal genes in their published text overview somehow proves him right and me wrong. Incorrect.

In the first place, I've already linked to the raw data at the UCSC genome browser,


Raw data wasn't included in the paper. The researchers findings were.

where he or anyone can go examine the DNA segments themselves. As I noted before, simply go to the subsection titled “Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans” (note once again the “gene flow” appellation), zoom in on the DNA and see how it's identified, gene-wise.

Did the reader notice the word "regions"? I did. Remember hominid DNA is 98% non-gene.

As with the word "gene flow" Michael is obsessing over terminology that the authors use in a suggestive sense, not a conclusive sense. They even use the word "suggesting" when talking of "gene flow".

Beyond that, the published Science article is a mere overview,

No. It's the culmination of the authors work on the matter at this point. People don't publish things unless they consider the finding substantial.

while linked within it is the Supporting Online Material which goes into much greater detail (which Ritmo obviously has not examined). Simply follow that link, then go to (pdf) page 142 to see the “Haplotypes of Neandertal ancestry in present-day non-Africans.” Know what a “haplotype” is, Ritmo? It's genes.

"In a second meaning, haplotype is a set of single-nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated."

The text in that section further confirms that they're dealing with neanderthal haplotypes (i.e., genes) and alleles (i.e., genes) that are now in the genome of modern humans.

If it was worth publishing (i.e. if it was a significant finding) that would have been published.

But such a finding is irrelevant to tracing (partial) ancestry back to Neanderthal lineages, which was the entire purpose of the paper.

Michael McNeil said...

But such a finding is irrelevant to tracing (partial) ancestry back to Neanderthal lineages, which was the entire purpose of the paper.

It is irrelevant to the purpose of the paper, but it is not irrelevant to refuting your loud assertions (based on no evidence in the paper at all, and contradicted by the paper's supplemental material) that only noncoding DNA was passed on to modern humans from neanderthals — which is clearly false, and which you continue attempting to obfuscate.

Ritmo Brasileiro said...

that only noncoding DNA was passed on to modern humans from neanderthals

I never said any such thing. I quoted CSM, which said:

So far, the inherited material does not seem to be concentrated in genes, but spread somewhat randomly in non-gene portions of the modern-human genomes...

And accepted this statement without question due to the fact that hominid DNA is only 2% gene and the utility of using non-coding regions to trace lineage, given how much more rapidly polymorphisms accumulate there than in gene-coding regions.