Blue Collar Scientist

Some interesting research about the evolutionary development of the human skull is being reported by UC Davis. The researchers have concluded that random change - called genetic drift in the parlance - accounts for most of the differences between human and Neandertal skulls.

In their new study, Weaver and his colleagues crunched their fossil data using sophisticated mathematical models — and calculated that Neanderthals and modern humans split about 370,000 years ago. The estimate is very close to estimates derived by other researchers who have dated the split based on clues from ancient Neanderthal and modern-day human DNA sequences.

This is significant, because it tells us that rigorous study of morphological changes in fossils gives us dates in good agreement with that of DNA methods. The picture here is that two separate disciplines offer mutually reinforcing insights into human evolution over this time period.

But then the press release gets a little strange. The principal investigator, Tim Weaver, says:

A take-home message may be that we should reconsider the idea that all morphological (physical) changes are due to natural selection, and instead consider that some of them may be due to genetic drift. This may have interesting implications for our understanding of human evolution.

As a layperson with a pretty solid understanding of evolution, I’ve been suspicious at times of some scientists’ tendency to see natural selection where I felt¹ some things might more simply be explained as neutral features - not selected against, not selected for, just arising randomly without any particular immediately adaptive traits. On the other hand, I’ve always been aware that I’m not the expert, so I’ve been inclined to trust the authorities and quell my own misgivings.

But despite my being predisposed to have sympathy with this conclusion, I have to admit that this is where the press release falls down into a morass of uselessness.

There is, almost certainly, a reason why Weaver thinks that his research indicates genetic drift, rather than selection, has been a major influence on the evolutionary development of the human skull. I’d bet that reason is a really good one, too. But the UC Davis release, as well as the PhysOrg coverage, are completely silent on what that reason might be. The closest they come to giving a reason for their belief is that they used “sophisticated mathematical models.”

I think it is problematic for a press release to pass up an opportunity to explain not only what we know, but how we know it. As has been often repeated, science is not a collection of purported facts. Science is a process for finding things out. A press release that gives such thin treatment of how a discovery was made, in favor of discussing what the discovery was, fails in its fundamental task of informing the general public.

The model behind this press release may be that laypeople are little people who live outside the University and can’t really understand what is being done, but might have a chance at understanding the conclusions. Or it could be that the public relations writer who wrote the press release² couldn’t understand, or didn’t have time to understand, the reasons why the research led to the conclusions it did.

Whatever the reason, this press release crosses the line between “providing an elegant explanation suitable for laypersons,” and “dumbing down science.” This is an extreme example of dumbing down, because the release appears to make the dual assumption that not only will the public not understand the reasons - however well expressed - but they also will find the principles behind the mathematical model too “sophisticated” to understand.

I call this the Moses model - some bearded guy on a mountain conveying the results of his research on tablets of stone to the masses below. What is demanded of all researchers (and their PR collaborators) in this environment of deplorably poor science education is to provide compelling examples of the scientific method in action, and compelling explanations of their research.

Wondering if I could improve upon the press release, I went searching for the paper. I found it here; and for a measly ten bucks, I can purchase the privilege of being able to read the paper for two days. I’m not going to do that, because (a) the subject is outside my field of expertise, so I’m not likely to get as much out of it as someone more familiar with this field of research; and (b) I’m not actually working on an educational program on human-neandertal skull divergence. But I did read the abstract, and noticed the first line was this:

Recent research has shown that genetic drift may have produced many cranial differences between Neandertals and modern humans.

So, it turns out that this paper does not lead to the conclusion that human skull evolution was driven by genetic drift as opposed to natural selection; it’s the other way around: the conclusion led to the paper. The conclusion was raised as a possibility by previous research, and this paper provides a test of the hypothesis. If only I could be cited back to that previous research, perhaps that abstract would further illuminate me. But I don’t know where to look, because (as is largely customary in abstracts), there is no citation.

The abstract again:

Close correspondence between cranial and DNA-sequence results implies that both datasets largely, although not necessarily exclusively, reflect neutral divergence, causing them to track population history or phylogeny rather than the action of diversifying natural selection.

Now this is fine for an abstract - if you want to learn the reasons why this correspondence is evidence for genetic drift, you are supposed to continue on and read the paper.

But this kind of thing is not fine for a press release, which must provide an accessible explanation of why the scientists believe the things they are asserting. Without doing this, the press release is useless as a tool to increase public awareness or education about the subject. It is far more difficult to write a press release than a research paper abstract, and the system that generated this release has had a major malfunction. However obvious the conclusions are to the research team, they are not going to be obvious - nor necessarily even interesting - to a layperson reading the press release.

I have a psychic³ prediction to make: this paper is going to have virtually no penetration into the public awareness. But it could have had widespread penetration, and it could have been an important event in educating the general public about human evolution, if only some kind of explanation of the conclusions had been offered that the average person could not only understand, but embrace as interesting and logical. As it stands, UC Davis gives us only a dry set of assertions.

Fail.

1. For no good reason, admittedly. [↩]
2. Most press releases are not written by anyone on the research team; the research people provide information to the PR department of their university, and then it is largely out of their hands. [↩]
3. Not! [↩]

I owe a small debt of gratitude to Martha Knox for pointing something out that I had not realized: that “irreducible complexity” would be found in organisms was a prediction of evolutionary biology made by a Nobel prizewinning geneticist in 1918 - and not the “discovery” of intelligent design creationists in 1996.

If you already know what irreducible complexity is, feel free to skip ahead to the triple-asterisks. Otherwise, settle in and I’ll explain.

“Irreducible complexity” is the pseudoscientific claim that some biological systems are too complex to have evolved from more primitive, less complete predecessors. It was originated as an argument against evolution, or at least popularized for this purpose, by Michael Behe in 1996. He defined an irreducibly complex system as one “composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning”¹. In other words, the creationist claim is that any biological part which cannot be broken down into smaller parts and still remain useful (a) cannot have evolved, and (b) therefore must have been created by an intelligent designer - presumably god, or space aliens².

Behe gives several examples of biological “parts” that he claims are too complex to have evolved but his work in this field is deeply ignorant, and every example he has put forth has been blown apart by a massive amount of research by real scientists. This was demonstrated, perhaps most dramatically, at the Dover trial, which at one point turned into a massive review of the research in the fields Behe has made his claims. His work did not stand up to scrutiny well - in fact, Behe couldn’t even convince a conservative judge appointed by George W. Bush that he wasn’t full of baloney. Wikipedia has a decent summary of Behe’s humiliations at that trial, so there’s no real reason to go over his failures here.

***

Anyway, it turns out that all this is in some ways a moot issue. Behe and his minions consider the appearance of “irreducible complexity” in organisms to be really good evidence against evolution. But it isn’t.

It is actually evidence supporting evolution, as was explained in a research paper ninety years ago.

In 1918, Hermann Muller published a paper about his pioneering work with fruit flies. It was called by the appealing title “Genetic Variability, Twin Hybrids, and Constant Hybrids, in a Case of Balanced Lethal Factors.” Muller’s paper is available online [pdf], and it contains a description of irreducible complexity, along with an explanation of how it comes about through the simplest of evolutionary means. It amounts to a prediction that “irreducible complexity” will actually be found in organisms, and it begins on page 42 of the pdf file (which is the same as page 463 of the original journal):

Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect which it produced upon the “reaction system” that had been brought into being by the many previously formed factors in cooperation; thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former.

Now, what exactly is he saying here? It is a lot simpler than it sounds. Genes mutate, and when they do, they can change in such a way that they become absolutely dependent upon their interaction with some other gene to fulfill their function. If those genes interact to make a particular piece of anatomy, and you take one of those interacting genes away, you will have a non-functioning, pointless biological structure as a result of this dependence.

That looks to me to be what Behe defines as irreducible complexity, all laid out in a very accessible way in a well known paper, by a very famous Nobel prizewinning researcher, who did this fundamental work in evolution seventy-eight years before Behe published his book.

It is simply bizarre to consider that, convinced he had found irreducible complexity in real organisms, Behe somehow thought that finding it soundly refuted the prediction of evolutionary theory that it would be found!

1. Darwin’s Black Box, page 9 [↩]
2. Space aliens are seriously entertained as creators of life by some intelligent design creationists. Other intelligent design creationists will not admit to believing that the intelligent designer is a god, but also won’t admit they believe in space aliens. So I’m just going to stick with the two candidates that I know of - god and space aliens. <shrug> [↩]

Andrew Kitchen, Michael M. Miyamoto, and Connie J. Mulligan report in PLoS-ONE on their development of a three-stage model for the colonization of the Americas by Homo sapiens. This issue is of deep interest to anthropology outreach in Alaska, and I’m accordingly very interested in the paper. The attention that these ideas will likely receive in Alaska suggests several major avenues for effective public outreach:

• It provides an opportunity for “what is the nature of science and knowledge” education. The concepts of falsifiability and refinement of knowledge over time are particularly rich opportunities with these new results.
• It provides an opportunity to provide some “cutting edge” science to students. As noted below, many of the interpretive materials in greater Anchorage on these subjects reflect what was “cutting edge” twenty years ago, but which is now largely rejected in paleoanthropology.
• This paper is largely about analysis of genetic populations, and statistics. Therefore, it is an open door to talk about mutation rates and evolution, and some simple statistical exercises could easily be devised to give students an idea of what the authors are doing in their analysis.
• It provides an example of multidisciplinary work in science. The authors present a genetics analysis but subject it to controls imposed from other fields.
• Because some broadly similar studies of the past have not been subject to those controls, it provides an example of why there might be apparent disagreement about knowledge amongst scientists. For example, I’ve heard about genetic data that supports migration into the Americas both much earlier, and significantly later, than well-dated archaeological sites. By not imposing constraints from other fields of study, such findings result in apparent disagreement, without necessarily being valid disagreement. The distinction is worth teaching since organized antiscience uses such cases as a wedge.

The authors propose that the population of Amerind ancestors expanded out of east central Asia between 43,000 and 36,000 years ago, and occupied Beringia, the easternmost portion of Asia and the western part of Alaska, including the sea floor which was exposed at the time. A stable population of 8,000 to 10,000 people remained there from that time until around 16,000 years ago, at which time 1,000 to 5,400 of them rapidly expanded into the Americas. The study conforms to prior hypotheses that this expansion occurred either through an ice-free corridor in eastern Alaska and western Canada, or along the coast.

Consistent with other recent work, this paper proposes a single migration, as opposed to studies of the past that considered Amerinds, Na-Dene, and Eskimo-Aleuts to be the result of different migrations. This hypothesis gained popularity in the mid-1980’s, and is the model adopted by a number of interpretive materials in and around Anchorage. The model has been in disfavor for some time in the professional literature, and it seems likely that this new study would help to change these interpretive aids (assuming that scientific evidence trumps political expediency).

The authors point out that the genetic studies to date have strongly supported a single-migration model, but that they have varied significantly concerning the proposed date of the migration, with dates anywhere from about 13,000 years ago, to 40,000 years ago. As a result, that data has been interpreted by a variety of scenarios involving additional migrations, migrations of various ages, and so on. At least from the layman’s perspective, many of these seemed like clever possibilities that had the unfortunate air of being ad-hoc about them.

The new study accommodates some of the more puzzling aspects of the prior genetic studies, particularly ones that come up with very old dates of 30,000 years or more for the migration. A stable population in Beringia for some thousands of years would explain those results, and also explain why there are no American archaeological sites older than around 15,500 years old, while accommodating nicely the archaeological evidence that Homo sapiens was in northwest Beringia by about 30,000 years ago.

The study incorporates data from both nuclear and mitochondrial DNA of both Native Americans and Asians. Mitochondrial DNA evidence was cited in 2005 (with quite a bit of publicity, at least in Alaska) to support the idea that the population colonizing North America was extremely small, so it appears to me that the re-analysis of the mitochondrial data is of particular interest. Also of interest is that this study, unlike some in the discipline, uses archaeology, geology, and paleoecology as opportunities for imposing controls on the analysis of the genetic data. Some of the genetics studies of the past have given the appearance of being statistical analyses that avoided giving very much consideration to what is known from other disciplines. The study constrains divergence time to 15,000 years ago, and by trying out different migration rates between Asia and Beringia (and back), it is shown that the lower (and “more biologically realistic,” as the authors put it) the migration rate the larger the population of Amerind ancestors:

Our results demonstrate that smaller estimates of Ne depend upon a substantial level of migration from Asia to account for present-day levels of Amerind genetic diversity, e.g. Hey’s estimate of ≈70 founders is associated with a mAsia→NW > 9.0, which is twice the migration rate for contemporary Europe (m = 4.3).

Emphasis mine. I agree with the authors that the high migration rates assumed by other studies are implausible. Intuitively, I have a hard time accepting that the rate of migration on a modern industrial continent serviced by jets and trains is substantially lower than that found in east Asia in the Pleistocene, but I’m not an expert.

The authors also build into the paper a very nice opportunity for those doing outreach to talk about “what is science:”

Our goal is to provide a comprehensive model for the initial settlement of the Americas that generates new testable hypotheses and has high predictive power for the inclusion of new datasets. In light of our results, we propose a three-stage model in which a recent, rapid expansion into the Americas was preceded by a long period of population stability in greater Beringia by the Paleoindian population after divergence and expansion from their ancestral Asian population.

In other words, science produces conclusions that are testable. When you come to a conclusion, you are sticking your neck out a bit - because by definition a scientific finding is subject to being disproved at some point by someone who has better data, or is better at interpreting your data than you are.

One of the most interesting aspects of this paper, from an outreach perspective, is the opportunity to discuss how we know the dates. Here in a single paper are incorporated various methods for dating prehistoric events and materials (carbon dating, stratigraphy, genetic statistics, and surely a few others), and all of the methods agree that this recent event in world geological history still took place thousands of years before some believe the world was even created. The contrivances that are required to refute these vastly different, yet mutually-supporting dating techniques are awesome in their implausibility, and that’s where the teaching opportunity comes from.

–

This blog article is about:

Kitchen, A., Miyamoto, M.M., Mulligan, C.J., Harpending, H. (2008). A Three-Stage Colonization Model for the Peopling of the Americas. PLoS ONE, 3(2), e1596. DOI: 10.1371/journal.pone.0001596

I guess it is stale story day. Having just discussed a three week old astronomy story, now we’re going to look at a week-old news story that apparently just hit the US. By way of the Tracker, I’ve learned that every single blue-eyed person on the planet shares a common ancestor who lived just 6,000 to 10,000 years ago.

The press release has some of the details, but it boils down to this. Blue eyes may have appeared in humans a number of times, but the first time that someone with blue eyes stuck around and had enough children to perpetuate the gene across the globe was 6 kya to 10 kya. The blue eyes were the result of a mutation in a gene called OCA2. As the principal investigator puts it, all blue-eyed people

“have all inherited the same switch at exactly the same spot in their DNA.”

What is the meaning of the mutation?

The mutation of brown eyes to blue represents neither a positive nor a negative mutation. It is one of several mutations such as hair colour, baldness, freckles and beauty spots, which neither increases nor reduces a human’s chance of survival. As Professor Eiberg says, “it simply shows that nature is constantly shuffling the human genome, creating a genetic cocktail of human chromosomes and trying out different changes as it does so.”

This is evolution in action. Evolution isn’t trying to make a better creature, it is just making the next generation different from the previous one. In the original blue-eyed person’s case, they were different in that they had a unique eye color. But their descendants inherited their version of the gene and this variation spread through a fairly significant proportion of the population.

As the PI notes, the change was neither bad nor good, on average. Anecdotally, I’ve observed that my blue-eyed friends tend to have a tougher time with eye fatigue on glaciers, snowshoeing, or cross country skiing, than I do (the BCS is brown eyed). This may or may not be significant, but if it is significant, there is certainly plenty of evidence that blue eyes are subject to sexual selection in the culture in which I live - so that would be a benefit to the blue-eyed crowd. If there’s any downside, it’s offset by an upside, but the PI is probably right - this mutation is neither good nor bad.

There’s a more fundamental issue here, though. The change in gene OCA2 is referred to pretty universally as a mutation. That means blue-eyed people are mutants.

Expect the playground taunts to commence forthwith. :-)

Of course this is true - blue-eyed people are mutants. But so is everyone else. We are all a collection of mutations, some of them good, some of them bad, some of them neutral when it comes to engaging with the world around us. Every gene that we don’t share in common with chimpanzees, and every gene they don’t share in common with us, is proof of the bundle of mutations we’re made with. And you can take that right down the line to each of our ancestors back to the beginning of life - the degree to which we differ from a starfish is the degree to which both we, and starfish, are mutants.

I know some creationists who would strenuously object to being called a mutant. They believe they were made by god, and that god made them perfectly, and that god on purpose introduced any perceived flaws in their construction. Calling someone a mutant radically undermines this perception, and if you bandy this idea about, you’ll get push back from them. Mutants are, in their perception, abominations - things that represent an active fight against god and his supposed desires.

It is yet another illustration that the language we¹ use is completely different from that of creationists. I suppose it goes beyond language, and in fact indicates a completely different reality that we live in. But our reality is, I think, better. A world in which “mutant” is understood to refer to someone who has some sort of small chemical difference in some molecules in their body works for me. A world in which a mutant refers to someone debased, whose very existence flaunts an inner hostility to some supposed king of the universe - that world sucks. And that world is with us today - some of our religions require that we kill those who oppose god - and as I’m sure many of us have noticed, plenty of the religious are willing to do just that. Just my opinion, here, but a world in which I have the freedom to look at a blond, leggy, blue-eyed mutant and see a person of beauty is a much better world than one in which “deformed” babies are abandoned by their parents in the outdoors to die of exposure. To put it into modern terms, if a red-eyed baby were born today, I’d much rather the collective reaction of society be along the lines of “cool!” and “radical!” instead of killing the baby as demon-spawn.

And to be a blue-eyed person, and to know that your blue eyes came to you from an ancestor who lived possibly as recently as 6,000 years ago - what a great sense of connection to humanity, and our collective historical experience, that must give someone.

Blue eyed people are mutants. And looking at this from a scientific perspective allows us to see this as something beautiful, something interesting, something worthy of passion, and something that makes our lives rich and worth living.

It must really suck to be a creationist.

1. i.e., science types [↩]