Who’s right here? Or just professional envy?

This article, Genetic Data and Fossil Evidence Tell Differing Tales of Human Origins, exposes an interesting meta-debate in science. For most of  the history studying evolution, of any sets of organisms, has depended on the fossil record. For human evolution the “family tree” of hominids has been almost entirely constructed from fossil evidence (“established a reasonably clear picture“).

But, after doing substantial amounts of whole genome sequencing (and other techniques for comparing genomes) an alternative method of studying a family tree is directly through the genome, so-called phylogenetic trees. It turns out that much of the history of any organism is preserved in the genome, in various ways: broken (and now inactive) genes, duplicated (and then mutated) genes, combined or broken chromosomes, transpositions in the chromosomes and so forth. Once complete genomes are available there are now very powerful bioinformatic techniques for comparing them.

So, literally, each of us have some of our evolutionary history preserved in our genome. In human population that are highly cross-bred (i.e. in mobile populations) it is confusing to attempt to create trees. But within populations that are reproductively isolated and also appear to have been living in the same isolated geographical region for a long time there is less cross-breeding and so genomic patterns can be more accurately extracted. For instance the native peoples in Australia migrated there a long time ago and then were isolated. So for relatively “pure” (little cross-breeding with other populations) aboriginal groups any genomic differences between them and other groups can be deduced. However, tracing this all the way beyond homo sapiens (“archaic species“) gets more challenging. But in some cases now extinct species on the hominid tree can be deduced to have existed based on the genomes of living people.

But this is a new way of doing this research and some of the early attempts, such as the ancestral Eve (based on mitichondrial DNA which is transferred directly from mothers only to all offspring) may have been premature or even incorrect. So this “new” (but steadily improving) method of measuring relatedness and extrapolating this far into the past history of hominids is not as well established as the more traditional and far older paleoanthropological techniques. So conclusions from the more modern techniques are controversial (a real scientific controversy, not the fake controversy creationist push in their “teach the controversy” denialism). So using the genomic techniques a paper was published that basically said:

Geneticists studying DNA now say that, to the contrary, a previously unknown archaic species of human, a cousin of the Neanderthals, may have lingered in Africa until perhaps 25,000 years ago, coexisting with the modern humans and on occasion interbreeding with them.

But the trouble with this conclusion, according to paleoanthropologist critics is:

the finding is regarded skeptically by some paleoanthropologists because of the absence in the fossil record of anything that would support the geneticists’ statistical calculations.

So the old and new methodologies have collided and sparked a scientific dispute about these conclusions:

“is a further example of the tendency for geneticists to ignore fossil and archaeological evidence, perhaps because they think it can always be molded to fit the genetics after the fact.”

the claims of interbreeding could be “a methodological artifact” in the statistical assumptions on which the geneticists’ calculations are based

Now this is a highly technical debate that I am totally unqualified to take a position, but what struck me, purely as my amateur observations, were two things:

  1. A common criticism of the creationists against evolution is the so-called “gaps in the fossil record” argument. And the standard rebuttal is simple. Very few fossils have been discovered because: a) most dead creatures don’t turn into fossils, b) the geological strata that might contain fossils are rarely exposed (like the famous Olduvai Gorge), c) relatively few scientists are out digging for fossils, and, d) fossil record research is very expensive and time-consuming and thus likely to be incomplete, as evidenced by frequent announcements of new finds. So not finding a fossil is not the same as: a) no fossil exists, or, b) an organism may have existed for which there are no fossils. The presence of “gaps” is only proof of lack of data, not a particular hypothesis, esp. when there is considerable other and overwhelming evidence to support the “missing link” actually did exist.
  2. Classical techniques, for studying any aspects of life, and newer genomics techniques have collided for many reasons. Digging fossils in hot desert sun and carefully cataloging them and reconstructing skeletons and then comparing skeletons takes a particular type of skill and mindset. OTOH, writing (or just adapting) computer software to study massive quantities of data extracted their laboratory experiments with largely automated high-thruput machines (DNA sequences) takes a completely different set of skills and, importantly, mindset. So to my mind this meta-debate has some of the same elements of the “traditionalists” arguing to ban calculators (or now pocket computers) and instead doing math by long-hand; there is simply a distrust of these “new” and suspect technologies.

So is this debate mostly just a clash of both methodologies and mindsets. Not entirely, I suspect, but I also believe there is an element of this.

 I actually encountered of bit of this meta-debate early in my life and I actually regret I didn’t pay more attention to it. I had had only a single and very traditional (lots of memorizing) biology course so I never considered biology as a possible career for myself. What I didn’t know (as most people, at the time, didn’t know) was in the late 50s and 60s a new discipline, molecular biology was emerging. Molecular biology evolved into many current specialties but in particular also evolved more to: a) using computing and software as the research tool, and, b) actually viewing biological processes as analogous to computing processes. And based on these research techniques then finding genomic evidence to present an alternative view, of a particular evolutionary path, to the traditional techniques (or, for that matter, most any subject of study in biology)

The point of this is that traditional biology doesn’t suit me, but the current biology does and so by knowing knowing biology was changing, at the time I was in college and might have gone down that path, I missed an opportunity.

So to the stories.

I was taking the Grad Records exams up in a large hall at Harvard. During the break between exams some MIT students and some Harvard students were having a heated debate about the biology test they’d just taken. The test was apparently very traditional and thus the Harvard students (at the time almost totally in the classical biology mindset) thought it was a fine test and they’d done well and the MIT students (who mostly were in the new discipline of molecular biology) thought it was a bad test and they’d done poorly. Here, in the early days of the changing world of biology, where the “new”( now almost completely dominates biology today) was the seed of that debate: traditionalist scholars vs computer-savvy technology-driven scientists. I didn’t really understand the substance of the debate, since, well, duh, I’d never heard of molecular biology, but knowing MIT types I understood that their unconventional views were very non-traditional and were likely to become the dominant views in time.

Second, one day at the MIT crew boathouse a very tall woman (women’s crew was just beginning, purely as a “club” sport) came up to me and said, “I know you.” Now I had no clue who she was, but it turned out she’d been a couple of years behind me in my high school and since that high school publicized students who went to “name” colleges there had been some articles about me and it turns out I had, very indirectly, actually influenced her a tiny bit. So I asked her what she planned to study and she said she was really interested in molecular biology and how fascinating it was and how it was the future of biology. Too bad I was in a rush and didn’t talk to her longer. But I mentioned the chance meeting to my parents, who followed the hometown scholastic superstars, and it turns out she’d had been in the first group to receive recognition as a “presidential” scholar that Lyndon Johnson had just established (IIRC, one person from each state was chosen). Now then I was a lot more impressed (and horribly jealous such an award didn’t exist when I was in high school, naturally believing I would have won it (realistically, probably only in top 10 candidates in my senior year)). But the point was again I missed the opportunity to follow up on the chance to consider biology as a major.

Third, a decade or so later I got interested in molecular biology (now much more well known) and acquired David Baltimore’s huge volume on it. For me this was now just a hobby not something I could seriously consider as a career. But this is one of those life events where you remember exactly where and when a Eureka moment came to you. I was riding down I-5 (wife was driving) and reading about Monad’s models of gene regulation in E. coli and it just hit me – this is computing, not all those memorized names of flower parts. Now I have a knack for computing and no knack for traditional biology scholarship, but I realized in that instance I could have done this new kind of biology, enjoyed it, and probably accomplished something in the field. But I’d missed those two chance encounters that might have changed my life (of course who can say whether the infamous road-not-taken would lead to good or bad things).

So it’s interesting to me today that this traditionalist vs “new” (although now completely mainstream) argument goes on today. I believe it is more than purely a science debate but also a debate between people with different ways of thinking. And, of course, since this is science, someday the debate will be resolved by the evidence, not just opinions or personal scholarly preferences, which, of course, so completely contrasts with how religion vs science debates are conducted.

But the life message I’d pass on to young people – when you encounter something and you’re not quite sure what it is investigate it because it might just be opportunity knocking.

About dmill96

old fat (but now getting trim and fit) guy, who used to create software in Silicon Valley (almost before it was called that), who used to go backpacking and bicycling and cross-country skiing and now geodashes, drives AWD in Wyoming, takes pictures, and writes long blog posts and does xizquvjyk.
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