Dawkins’s answer to the Edge question: the genome as palimpsest

As I posted yesterday, a lot of contributors gave their answers to the 2017 annual Edge Question, “What scientific term or concept ought to be more widely known?” (See all responses here.) In the last 24 hours Richard Dawkins has weighed in with his answer, “The genetic book of the dead,” which involves reverse-engineering our DNA sequences to reconstruct the ancestral environments of living species. While Dawkins has discussed this before, most notably in Unweaving the Rainbow, not everyone’s read that book. It’s worth considering that an organism’s genome may be a palimpsest of its ancestry, which in turn reflects in part the environments to which those ancestors were adapted.

You can read Richard’s piece for yourself; I’ll give one brief excerpt:

Given a key, you can reconstruct the lock that it fits. Given an animal, you should be able to reconstruct the environments in which its ancestors survived. A knowledgeable zoologist, handed a previously unknown animal, can reconstruct some of the locks that its keys are equipped to open. Many of these are obvious. Webbed feet indicate an aquatic way of life. Camouflaged animals literally carry on their backs a picture of the environments in which their ancestors evaded predation.

But most of the keys that an animal brandishes are not obvious on the surface. Many are buried in cellular chemistry. All of them are, in a sense which is harder to decipher, also buried in the genome. If only we could read the genome in the appropriate way, it would be a kind of negative imprint of ancient worlds, a description of the ancestral environments of the species: the Genetic Book of the Dead.

Naturally the book’s contents will be weighted in favour of recent ancestral environments. The book of a camel’s genome describes recent milennia in deserts. But in there too must be descriptions of Devonian seas from before the mammals’ remote ancestors crawled out on the land. The genetic book of a giant tortoise most vividly portrays the Galapagos island habitat of its recent ancestors; before that the South American mainland where its smaller ancestors thrived. But we know that all modern land tortoises descend earlier from marine turtles, so our Galapagos tortoise’s genetic book will describe somewhat older marine scenes. But those marine ancestral turtles were themselves descended from much older, Triassic, land tortoises.  And, like all tetrapods, those Triassic tortoises themselves were descended from fish. So the genetic book of our Galapagos giant is a bewildering palimpsest of water, overlain by land, overlain by water, overlain by land.

We can already reconstruct the features of ancestors by looking at some bits of the genome, especially those “dead genes” that were useful to our ancestors but no longer to their descendants. For example, as I mention in WEIT, the human genome contains three dead genes that are very similar in sequence to active genes that make proteins in the egg yolks of living birds and reptiles. That’s almost irrefutable evidence that we descended from animals with yolked eggs. That says a bit about our ancestral environments, but we can do better. Humans also have a number of dead “olfactory receptor genes” that enabled our ancestors to smell particular molecules (one per gene). Those genes are still active in our relatives like dogs and mice. This tells us that our lineage experienced reduced selection for olfaction, almost certainly because our lineage became more dependent on vision and hearing.

In fact, whales have a huge set of olfactory genes, but every single one of them is inactive. That tells us that the environment of their ancestors was terrestrial.

Can we go further than that? Yes, in principle it’s possible. Richard suggests this solution:

I have a sort of dim inkling of a plan. For simplicity of illustration, I’ll stick to mammals. Gather together a list of mammals who live in water and make them as taxonomically diverse as possible: whales, dugongs, seals, water shrews, otters, yapoks. Now make a similar list of mammals that live in deserts: camels, desert foxes, jerboas etc. Another list of taxonomically diverse mammals who live up trees: monkeys, squirrels, koalas, sugar gliders. Another list of mammals that live underground: moles, marsupial moles, golden moles, mole rats. Now borrow from the statistical techniques of the numerical taxonomists, but use them in a kind of upside-down way. Take specimens of all those lists of mammals and measure as many features as possible, morphological, biochemical and genetic. Now feed all the measurements into the computer and ask it (here’s where I get really vague and ask mathematicians for help) to find features that all the aquatic animals have in common, features that all the desert animals have in common, and so on. Some of these will be obvious, like webbed feet. Others will be non-obvious, and that is why the exercise is worth doing. The most interesting of the non-obvious features will be in the genes. And they will enable us to read the Genetic Book of the Dead.

There are a few problems here, though. One is convergent evolution. A marsupial mole evolved its morphology and behavior independently from those of placental moles, and it’s very likely that the genetic signature of a fossorial life will differ at least somewhat between these two groups. Likewise for arboreal koalas and monkeys, and many desert animals. In such cases, looking at the genes might tell us very little about their ancestral environment of animals whose forebears lived underground, in trees, or in deserts. In other cases,  genes no longer used will degrade, making it more difficult to decide what function they served. (That hasn’t happened for olfactory receptor genes or egg-yolk genes, though, telling us that useful genetic information can be preserved for millions of years.) Richard takes that into account when he says the reverse engineering is more effective for more recent ancestors.

Finally, there’s another genetic way to reconstruct ancestral environments: using DNA to make phylogenies, or “family trees” and combining that with the fossil record or the existence of vestigial features. Doing that, for instance, has told us that whales not only descended from terrestrial mammals, but fossils add that it’s probably descended from a deer-like artiodactyl called Indohyus. We can tell what the environment of Indohyus was from its morphology. And in many cases ancestral environments might be better reconstructed from fossils, which bear signs of their adaptations, than the DNA sequences themselves. Also, using DNA-based phylogenies can give us ideas of when certain characters appeared on the lineage: which are ancestral and which are derived. From that kind of reconstruction, for instance, we know that the one species ancestral to social bees was monogamous–singly mated–giving support to the notion that kin selection was an impetus for the evolution of eusociality (kin from single matings are more closely related to each other than kin from multiple matings). The reference is given below.

Regardless, it’s fascinating to see organisms as palimpsests of the past: a thing that we evolutionists have known for a while but that the layperson may not appreciate. Our many vestigial organs (like the muscles that I can use to move my ears) testify to that, and now, with DNA sequencing, we get more testimony from our genes.

Below are the three ear muscles that we inherited but (with some individual exceptions like me) can no longer use. The big muscle atop the ear, and the thin ones in front and back, are the three vestigial ones. In animals like dogs and horses they’re used to move the ear around for hearing; in humans they have no use—except to amuse my students.

muscles-of-facial-expression-40-638

_________

Hughes, W. O. H., B. P. Oldroyd, M. Beekman, and F. L. W. Ratnieks. 2008. Ancestral monogamy shows kin selection is key to the evolution of eusociality. Science 320:1213-1216.

27 Comments

  1. Carl
    Posted January 2, 2017 at 12:20 pm | Permalink

    This is an utterly fascinating and beautiful topic. Another example putting the lie to atheists having a bleak and ugly world view. If I were to take up a sixth career it would involve unlocking more of the information in the genetic code.

  2. merilee
    Posted January 2, 2017 at 12:39 pm | Permalink

    wonderful!

  3. Posted January 2, 2017 at 12:58 pm | Permalink

    Reblogged this on The Logical Place.

  4. loren russell
    Posted January 2, 2017 at 1:08 pm | Permalink

    I’ve always wondered why primates ditched the mobile outer ear. Even/especially with binocular vision, it should be handy to pinpoint and track a sound source while watching something else.

    It might have been especially useful for a classroom teacher in the pre-A/V era to be able to locate miscreants in the class while their back was turned to write on the chalkboard. Or did you, PCC(e)?

    • Michael Fisher
      Posted January 2, 2017 at 5:32 pm | Permalink

      This is purely speculation from a layperson:

      Humans are social beings & our close-proximity non-vocal communication of our emotional state is via the face to a very large extent. We have the most complex facial musculature of perhaps all mammals & perhaps of all primates too [I’m guessing].

      Everyone can learn to wiggle their ears, but most people can never do so without moving their eyebrows and/or foreheads. I assume the brain areas that erected & rotated the ears now do other facial stuff. I’m not sure about the three vestigial muscles Jerry mentions – are they totally functionless or co-opted into other facial functions? I will have to read up know to find out! 🙂

    • Michael Fisher
      Posted January 2, 2017 at 6:02 pm | Permalink

      A quick google search indicates that these three muscles are activated to a small extent in everyone when we smile [also when we swallow] – resulting in the ears pulling back. Humans can learn to tell when someone is ‘really’ smiling as opposed to faking non-aggression, happiness & positive engagement. It is very difficult to fake an emotion externally exactly & there exist “tells” to show it’s fake such as in the case of a smile micro facial movements of the rest of the face musculature [or lack thereof].

      Perhaps these 3 vestigial muscles react slightly differently under a fake smile compared with a real smile [but I think I’m really pushing the boat out to far with this 🙂 ]

      • rickflick
        Posted January 2, 2017 at 9:23 pm | Permalink

        Sounds reasonable to me.

  5. rickflick
    Posted January 2, 2017 at 1:44 pm | Permalink

    It’s a fascinating idea. I can easily imagine, as our detailed knowledge of the genomes of all species develops, in addition to evidence from other areas, the statistical analysis will be done as described. After all, it must be the case that ancient animals and their environments were intimately tied together.

  6. Bernardo
    Posted January 2, 2017 at 1:45 pm | Permalink

    I really enjoyed this year’s Edge question. So far, I have only read a few responses, but I particularly liked Steven Pinker’s and professor Coyne’s.

    • Ross
      Posted January 4, 2017 at 10:50 pm | Permalink

      Pinker’s contribution has been raked over the coals by several folks, for example: https://www.sunclipse.org/?p=2230

      • Carl
        Posted January 4, 2017 at 11:22 pm | Permalink

        I only read the first sentence from your link. That was enough to know the author is a rude clod and probably not very bright. I knew I wouldn’t profit from reading further.

        • Ross
          Posted January 5, 2017 at 9:27 am | Permalink

          Pinker’s remarks on poverty are very short-sighted, to put it mildly, as this article points out.

  7. Alan
    Posted January 2, 2017 at 2:01 pm | Permalink

    Interesting post, especially following the recent article on neutral evolution.

    https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0338-2

    • Torbjörn Larsson
      Posted January 2, 2017 at 5:57 pm | Permalink

      Thanks, nice find! I have to read it more thoroughly later, but I am amused and a bit heartened to see productive Koonin say the same as I happened to do (coming from my physics background) at a class presentation of a literature project in Biology. I felt bad because it was my prior idea, and my new formed posteriors wasn’t strong enough to suppress it in the effort of the moment.

      The Genome Biology intro course had already covered how purifying selection is most often the dominant mode on nucleotide level within ORFs (“genes”) even if near neutral null is the global genome level null, junk and all.

      And we were shown that eukaryotes and prokaryotes behave differently on the population level, in the latter case depending on environment/population size. (But I have to check the material again.)

      Anyway, if I made a public mistake based on then available information, Koonin may have made the same one. His reference is to his work with closely related species, I assume a subset of what we can work with.

  8. Hempenstein
    Posted January 2, 2017 at 3:13 pm | Permalink

    Long ago – probably when I was in highschool – I discovered that I could move my ear, but only one (can’t remember which, which would be interesting since I’m left-handed). Many yrs later, probably when in grad school, I thought that if I can move one, the nerves ought to be there for the other side, but how does one innervate a circuit that he’s unaware of?

    All I can say is that after a little concentration I found I could move the other one too. Suspect that most of us can with a little effort.

    • BJ
      Posted January 2, 2017 at 11:16 pm | Permalink

      I can raise both eyebrows at the same time and I can raise my left eyebrow alone, but no matter how hard I try, I cannot raise just my right eyebrow. I simply can’t figure it out, and it annoys the hell out of me. I want to do the Colbert, damn it.

  9. Mark Sturtevant
    Posted January 2, 2017 at 4:04 pm | Permalink

    I was interested in learning of the history of tortoises. I did not know that tortoises had this complex history of switching back and forth between aquatic and terrestrial.

  10. Mark Sturtevant
    Posted January 2, 2017 at 4:19 pm | Permalink

    I suspect that the main proposal behind Dawkins’ interesting essay may not be possible, unfortunately, since the genetic basis of present and past adaptations is not so much about making new genes but is more often about using old genes in new ways. So the record of adaptation to new ways of life will not often be writ in the coding regions of genes — the regions that make proteins — but is instead in the regions that regulate where and when and how much a gene is expressed. Gene regulatory regions will be overwritten pretty rapidly as a lineage evolves into new ways of life, and I suspect we would be hard pressed to detect their ancestral signatures.

    • Gregory Kusnick
      Posted January 3, 2017 at 12:56 am | Permalink

      I was going to say something similar. A given phenotypic feature may be the product of many genes interacting (including, as you say, regulatory as well as structural genes). Conversely, a given gene may contribute to the development of many phenotypic features. So in general there’s no straightforward mapping from phenotype back onto genotype; the information tends to be distributed holographically.

      This is one reason why Lamarckism is a non-starter: because the transformation from genotype to phenotype is essentially a one-way function whose inverse is computationally intractable.

  11. zoolady
    Posted January 2, 2017 at 5:09 pm | Permalink

    Our (more or less “dead”) vomeronasal organs still get our attention in a few events. For example, anyone who’s heard of/experienced the ”dormitory effect” knows women who live/work together will eventually become congruent in their menstrual cycles. That’s because the pheromones of menstruating women ”trigger” menstruation in others. At one time, it may have been beneficial to have many babies born at once, in order to have a good supply of lactating women/child care.

    • rickflick
      Posted January 2, 2017 at 9:14 pm | Permalink

      Really?
      “After the initial studies, several papers were published reporting methodological flaws in studies reporting menstrual synchrony including McClintock’s study. In addition, other studies were published that failed to find synchrony. The proposed mechanisms have also received scientific criticism. A 2013 review concluded that menstrual synchrony likely does not exist.”

      • zoolady
        Posted January 2, 2017 at 9:42 pm | Permalink

        Perhaps they weren’t really interested in something involving women’s dormitories, offices and other situations where we spend time together. I’ve seen it myself, too often to consider it an ”urban myth” or anything other than fact.

        • rickflick
          Posted January 2, 2017 at 9:48 pm | Permalink

          The next time you read a scientific paper, look for something in the method section describing how the authors used data from their own experience and weighted it over objective data gathered from the field.

        • Posted January 3, 2017 at 7:19 am | Permalink

          I’ve seen homeopathy work myself, and I’ve seen vaccines cause autism – too often to consider it anything other than fact.

          See how that sounds when someone else says it about something else?

  12. Kevin
    Posted January 2, 2017 at 5:55 pm | Permalink

    Adaptations to physical laws. Very interesting idea (think I’ve heard Dawkin’s mention it before).

    There’s an awful lot of research that could be done in this area. Just to summarize two approached: top-down and bottom-up. e.g., DNA -> physical capability; physical requirements -> DNA.

    Technologies that humans make can also fall into these categories. Show an alien an iPhone and ask what kind of species and environment was needed in order to make the iPhone. What’s interesting is that it could have been an Android phone and the results would be very similar, yet the phone are quire different but also different.

  13. Ridahoan
    Posted January 3, 2017 at 10:52 pm | Permalink

    I am trying to remember where I saw this idea of a genome containing a record of ancestral ecology poo-pooed at least a good twenty years ago as vacuous. It may have been SJ Gould, or an article contained in one of the volumes of Conceptual Issues in Evolutionary Biology edited by Elliot Sober. I believe the criticism was essentially that the once popular idea was far too vague and had no predictive power

    Nonetheless I always liked it, not the least for its poetic view of our genetic inheritance. Maybe we will see some hypotheses tested now that we have an abundance of genome sequences, at least.

  14. Andrea
    Posted January 6, 2017 at 2:45 am | Permalink

    I feel like the mathematicians might have bad news, “some differential equations are intrinsically unsolvable. In this event, even though the difference equations of the associated mapping must exist as relationships, we cannot find out what they look like. For some real world systems we even lack the knowledge needed to formulate the differential equations; can we honestly expect to write any equations that realistically describe surging waves, with all their bubbles and spray, being driven by a gusty wind against a rocky shore?” – Edward Lorenz, the Essence of Chaos


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