Writing synopses of science articles is hard


Really, it’s harder than you think. Individual science papers typically build on a larger body of knowledge and don’t stand alone; it is assumed that the reader has significant amounts of training in the subject at hand so that the authors don’t bother to fill in all the background. When writing a summary of the article for a general audience, one has to provide a lot of context, without simply reiterating the contents of, for instance, a molecular biology textbook and a year’s worth of upper level biology education. And if someone writing a summary of an article lacks that knowledge altogether, the misinterpretations can be disastrously wrong.

Take this article in TechTimes, Massive Genetic Study Reveals 90 Percent Of Earth’s Animals Appeared At The Same Time. The title alone is creationist clickbait, and the author of the story clearly didn’t understand the article at all. She gets it all wrong.

Landmark new research that involves analyzing millions of DNA barcodes has debunked much about what we know today about the evolution of species.

In a massive genetic study, senior research associate at the Program for the Human Environment at Rockefeller University Mark Stoeckle and University of Basel geneticist David Thaler discovered that virtually 90 percent of all animals on Earth appeared at right around the same time.

More specifically, they found out that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago.

No, it didn’t. The paper says nothing of the kind.

The paper is an analysis of DNA barcodes. DNA barcoding is a process that uses a short stretch of mitochondrial DNA to map an individual organism to a species — it’s a technique that lets you look at a sample of a few cells, amplify and sequence a single gene (COI or COX1 are commonly used in animals), and then unambiguously identify the specific species those cells came from. Being able to do this relies on an interesting property of a species: there is limited variance in the barcode sequence within the species, but there has to be greater variance of that sequence from other, even closely related species. In other words, DNA barcodes form tight little clusters of similarity that correlate well with other criteria for defining a species.

That raises questions. You can read the original article, Why should mitochondria define species?, for yourself and see. The question is about why variations within a species should cluster so tightly. Stoeckle and Thaler propose a couple of hypotheses to explain that phenomenon.

Either 1) COI barcode clusters represent species-specific adaptations, OR 2) extant populations have recently passed through diversity-reducing regimes whose consequences for sequence diversity are indistinguishable from clonal bottlenecks.

It’s a meaty paper that goes through the evidence for both of those hypotheses, and I’m wishing I’d seen this paper last semester, when I was teaching evolutionary biology — there is a lot of useful evolutionary thinking going on here. Maybe I can revoke all of my students’ degrees and tell them they have to come back for one last thing? I think we can go through the paper adequately in about a week, so I’m sure they won’t mind.

Their final conclusion, after analyzing millions of barcodes, is fairly straightforward, I think.

The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.

This is not saying that there was a single instant in the last 200,000 years from which all modern species arose simultaneously. It’s a statement about the process of speciation: species arise from isolation of a limited subset of an existing population, which is why they have limited variation in their DNA barcodes, followed by an expansion of the new species’ population, during which the DNA barcodes accumulate variation slowly.

No, they did not find out “that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago”. New species arise continuously, but they do so by going through a population bottleneck in geologically recent times. Homo sapiens arose as a distinct species between 100,000 and 200,000 years ago, but that notorious London Underground mosquito may have evolved in the 18th century…which is still within the past 200,000 years, you may notice.

It’s a bit like reading a statement that almost all people are less than 100 years old, and then wondering, publicly and in print, about what happened in 1918 to cause every human being on Earth to have been suddenly born in that year. That must have been some orgy to celebrate the end of the Great War.

Comments

  1. says

    “mitochondrial uniformity within the past 200,000 years”

    There’s no need for a population bottleneck to explain mitochondrial uniformity in modern species. As mitochondria are only inherited through one parent, I suspect (I’ve not done the calculations) that for animal populations of a few tens of thousands to a few million, simple random chance will mean that the current population will all have inherited their mitochondria from one distant ancestor in that sort of time scale. Of course, their other genes will be from a large proportion of the ancestors of the time of their mitochondrial common ancestor.

  2. zetopan says

    “The title alone is creationist clickbait”

    It has already happened – a creationist numbskull made that claim on the first of this month. For those who don’t already know, Bryan Fischer is an idiot young earth creationist who will eagerly cite scientific articles that do *not* support his willfully ignorant view as somehow magically supporting his view. Misrepresentations run amuck within that slack jawed obscurantist crowd.
    https://www.afa.net/the-stand/faith/2018/06/science-confirms-genesis-again/

    Note that Hemant Mehta has covered this in detail, and that is also worth reading.
    http://www.patheos.com/blogs/friendlyatheist/2018/06/04/young-earth-creationists-shouldnt-cite-pro-evolution-articles-to-make-a-point/

  3. chrislawson says

    Paul Durrant–

    Mitochondria still evolve and accumulate genetic changes (but I repeat myself), which means population bottlenecks will show up as reductions in mitochondrial variation.

    This should not be confused with the “mitochondrial bottleneck” phenomenon when oocytes arise in developing embryos. This process allows oocytes to counteract the accumulation of adverse mutations in their mitochondria. There are similarities between the two processes (hence the confusing names), but they’re not the same thing.

  4. weylguy says

    I think we’d know a lot more about evolutionary biology if we only knew what Nature’s real purpose is. There is some reason to believe that life is simply an efficient way to convert low-entropy sunlight into high-entropy infrared radiation, but that doesn’t explain the underlying purpose. Christians believe it’s God’s plan, but that not only doesn’t explain anything, it’s just a convenient way to reject scientific thinking while kicking the can down the road.

    In physics one learns that things work the way they do because of the principle of least action, which is recognized as a fundamental law in physics. It’s pretty hard to adapt that principle to life itself because of the overall complexity of everything, but even then we don’t know why Nature has to extremalize anything. Back to square one.

  5. paxoll says

    Mix massive science illiteracy with modern information dissemination, sprinkled with ideological agendas and you get a wonderful cake of bullshit fed to everyone.

  6. emergence says

    For fuck’s sake. Please tell me someone contacted TechTimes to tell them they got this wrong.

    @zetopan

    What do you think the odds are that Fischer will retract his claim if someone calls him out? I’m guessing he’ll just double down, and insist that the paper says something it clearly doesn’t.

  7. anchor says

    @#10emergence: It’s not the first time. TechTimes gets it all wrong frequently. That’s about all they’re really good at.

  8. chrislawson says

    Just finished reading the paper — it’s really interesting, and yes the TechTimes report mangled it completely.

    Having said that, I am not entirely convinced of its conclusion that all modern species of animals experienced bottlenecks in the last 200,000 years. (Contra the TechTimes article, there is no claim that all these bottlenecks were simultaneous or causally linked to each other!) It seems unlikely that every species ever tested, across a wide range of phyla and biological niches, all experienced a severe population bottleneck in what is a relatively short geological time period. (This kind of global bottleneck would only be explicable in a mass extinction event, and although I think we are at the start of an anthropogenic global mass extinction, I don’t think we can push its molecular repercussions back 200,000 years.)

    I suspect that there are as yet unknown (or known and under-appreciated) mechanisms of mitochondrial selection in gametogenesis that limit mutational variation. We already know that embryos conduct an internal bottleneck of their own to minimise the chance of mutated mitochondria being passed on in mature ova. Is it possible that this embryological bottleneck mechanism creates the illusion of a population bottleneck?

    It’s also interesting that one of the paper’s target families is the mussel — a bivalve mollusc and therefore one of the animal groups known to have mitochondrial inheritance from both sexual parents. I wonder if the target species has doubly uniparental inheritance and what effect this would have on the mathematical modelling behind the calculation of mtDNA similarity.

  9. chrislawson says

    emergence@10–

    I’d bet on “no retraction” whatever odds you’re offered.

  10. chrislawson says

    Correction to my comment@12 — bottlenecking doesn’t stop mature ova from carrying a mutant mitochondrial load, but it does make many of the affected ova non-viable.

  11. zetopan says

    “What do you think the odds are that Fischer will retract his claim if someone calls him out?”

    Not at all infinitesimal – absolutely *zero*. Intellectual honesty is a bizarre repugnant concept to these willfully ignorant morons. Besides, who among his regular readers would even have sufficient intelligence to doubt anything that Fischer says? He is a “Young Earth Creationist” for Jibbers Crabst sake!

    “I’d bet on “no retraction” whatever odds you’re offered.”

    You have won an internet bingo!

  12. leerudolph says

    weylguy:

    In physics one learns that things work the way they do because of the principle of least action, which is recognized as a fundamental law in physics. It’s pretty hard to adapt that principle to life itself because of the overall complexity of everything, but even then we don’t know why Nature has to extremalize anything.

    Nature doesn’t “have to extremalize anything” (in physics or anywhere)—but to a first approximation, what we preferentially observe are systems that are in stable states (at some level of observation). In at least a lot of cases (certainly the kinds of physical systems that we first got around to modeling successfully with mathematics of differential equations type) “extremal” states are stable (and, still to a first approximation, stable states are “extremal” in the sense that they at least locally in state space take on extreme values of some parameter(s) naturally associated with the model and, maybe, with the physical system being modeled).

    “Purpose” doesn’t have to come into it. What would “purpose” add?

  13. keinsignal says

    Echoing chrislawson @ 12 – the paper notes a 0.1% average difference between members of the same species in the mitochondrial “barcode” across multiple phyla, and reasons that since “the molecular
    clock as a heuristic marks 1% sequence divergence per million years” therefore all these animals’ mitochondria underwent a genetic bottleneck within the past 100k years, give or take another 100k.

    But that kind of consistency across wildly unrelated animals with all kinds of known evolutionary histories seems to me to demand a stronger explanation. The most obvious (to me) being that there is some kind of ceiling on how much mitochondrial divergence a species can absorb and still remain a species, or that there are forces acting on mitochondria that slow or limit divergence beyond what “the molecular clock heuristic” would predict. The embryonic “mitochondrial bottleneck” (which I wasn’t even aware of prior to reading these comments) seems like a good candidate for the latter; it isn’t mentioned in the paper, though it might be alluded to in the bit beginning ” Candidate processes include bottlenecks and lineage sorting on three different levels”.

    Be interesting to see how this develops, but the notion that every extant species underwent a severe population-bottleneck event comparatively recently beggars belief. (And the caveat that it isn’t necessarily the same event happening at the same time doesn’t make it any easier to swallow – just the opposite, in fact). There’s a fuller explanation out there waiting to be discovered.

  14. emergence says

    Keinsignal @18

    What if new species are just typically started by small founding populations that split off from larger ones?

  15. DLC says

    But . . . 5700 years ago, when everything was created, falls within that 200,000 years window of opportunity, ergo creation! QED! Gotcha Evilloutionists! Ha! *Iron-age-death-cult-happy-dance*

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