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Evolution in the Lab

February 21, 2012

It is often claimed that evolution is not a science because it cannot be reproduced in the laboratory. In fact, however, as we discussed at Boskone, evolution is now a laboratory science–and a growing tool of industry.

The most famous example of experimental evolution is the domesticated silver fox bred from wild foxes by Russian scientists starting in 1959. Dmitri Belyaev began this amazing experiment, continuing through adverse political conditions up till the present day, now directed by Lyudmila Trut. In the experiment, wild foxes were selected for “low flight distance” — that is, how close you can get to the animal before it runs away. Animals selected on this basis over generations resulted in descendents with many of the traits and behaviors found in tamed dogs, such as low adrenaline production, raised tail, and floppy ears, as well as foreshortening of limbs typical of “neoteny,” the retaining of juvenile appearance. DNA chip experiments now show that certain brain genes have changed between the wild and domesticated foxes.

In another interesting experiment, mice were selectively bred for “high voluntary wheel running.” These High-Runner mice turned out to differ in their response to dopamine, resembling aspects of ADHD. One wonders, though, whether selection of this particular trait says more about the culture of today’s researchers.

The most advanced form of laboratory evolution involves breeding of bacteria–Richard Lenski’s famous experiment tracking 50,000 generations of E. coli. For this experiment, E. coli  bacteria were put in fresh glucose medium every day, growing up for several generations, then diluted again. Every 75 days, cultures were frozen away–something you cannot do with dogs or mice. And all the sample genomes could be sequenced, thanks to today’s mammoth DNA sequencers. So, in addition to the descendents, you can track the history of every diverging line of cells.

The E. coli experiment produced all kinds of fascinating observations. For example, cells fed on this rather limited diet gradually increased in size (over the generations). Size increase is interesting because it happens so often in animals, such as the evolution of horses. Alternatively “mini” animals evolve, too. So by studying E. coli we may gain clues as to general principles of evolution of size.  Another cute result–one line of descent evolved to eat the citrate buffer instead of the glucose. Tracking back the history reveals other lines that independently evolved this “new” trait. The experiment was impressive enough to earn condemnation by Conservapedia.

Today, what we call adaptive laboratory evolution has become the tool of choice for industrial development of new producer strains of cloned products. Where do you think evolution will go next?

  1. Alex Tolley permalink
    February 22, 2012 10:12 am

    You missed mentioning the industrial development of enzymes that uses “selective breeding” to improve catalysis – rates, specificity, etc.

    Then there is the whole arena of design by genetic algorithms for products. There have been demonstrated successes with this approach. John Koza (still at Stanford?) even patents interesting circuit designs using this approach.

    In extremis when computing power is extremely fast and parallel, evolutionary processes could substitute for thinking, resulting in machines that could evolve complex adaptive behaviors faster than meat brains could think.

    As an aside, we need to bear in mind that evolution encompasses a host of different processes that results in changing population phenotypes. Natural selection, which seems to be the underlying basis of the experiments in the OP, is just one of those processes.

  2. paws4thot permalink
    February 22, 2012 10:37 am

    It is often claimed that evolution is not a science because it cannot be reproduced in the laboratory.
    So geology, palaeontology and archaeology aren’t sciences either? 😉

    • busy bee permalink
      February 23, 2012 1:04 am

      Maybe someone more fluent in ancient Greek than I am can correct me on this, but I was under the impression that “-logy” means “talking about it” and “-nomy” means “knowing about it”. I don’t want to take that argument too far: ecology isn’t related to economy as astrology to astronomy, and I’ve met Jesuits whose work in theology qualifies as proper scientific research, in my opinion. New methods turning aspects of formerly soft sciences into hard sciences are sprouting up like mushrooms (i.e., they’re suddenly noticed when the fruiting body emerges). Nevertheless, it does seem to me that a lot of the sciences whose name ends in “-logy” —including geology, palaeontology and archaeology— are inherently less falsifiable than the exact sciences. It’s the difference between looking for answers to the question how, and looking for answers to the question why, and still being able to falsify your hypotheses.

      The main problem with public discourse about evolution is that too many people with strong opinions about it think the theory of evolution is a far stronger statement than it really is, because they don’t appreciate “the miracle of compound interest”.

      • February 23, 2012 2:22 am

        You mean like genetics vs. genomics vs. geneology is the same as physics vs. physiology, vs. physiognomy? Or cosmology vs. cosmetics vs. cosmetology?

        Perhaps the linguistic differences don’t matter so much?

        Personally, I do like the idea of experimental and evolutionary theology, but I think you have to be a Discordian to do it properly.

  3. paws4thot permalink
    February 22, 2012 10:39 am

    Actually, seriously, now we know what I think of the claim, isn’t evolution a mechanism that changes biology rather than a science in itself?

    • February 22, 2012 11:34 am

      There are a couple of answers to this, but I was taught they were “historical sciences.” Evolution was fairly subjective prior to cladistics, and the nice thing about cladistics is that it provides a quantitative way to objectively test hypotheses about evolutionary relationships based on data. Paleontology has also adopted cladistics, and the biggest problem in the field is lack of data, not shaky theoretical underpinnings.

      In geology, the issue is basically about repeated patterns, which is the basis of science. While we can’t reconstruct the Earth to test our hypotheses, granites tend to form the same way the world over, so you can take them for granite. After all, if you think about it, all chemical elements formed in the Big Bang and supernovas, so ultimately, chemistry is a historical science too, geology on a cosmic level.

      Archeology and anthropology are getting increasingly scientific. One example is from a talk I just heard from an archeologist, about how they now only excavate half a site, so that future archeologists can, if they want, reinvestigate and test their results. The problem with archeology is that it suffers from its Indiana Jones/pot hunting origins, and also from many of the ideological battles dating from the Cold War and before (e.g. with Nazis trying to prove Aryan origins, or Brits imposing ideas of Celtic identity out of Arthurian novels on Stonehenge). They are getting better about it.

      • paws4thot permalink
        February 22, 2012 11:45 am

        Cheers; as you probably guessed I was setting out to ridicule the claim that “science only happens in laboratories”.

  4. February 22, 2012 11:51 am

    As for the original question of where evolution will go next, I’d like to see a study of personal evolution. I don’t mean this in the personal sense, but in the sense that our bodies are microbiomes, and it would be interesting to study things like rates of bacterial evolution on and in people. What are the major drivers of evolution? The host’s genome? The part of the body (do bacteria mutate faster in moist armpits than, say, on dry hair or cheeks?) The host’s hygiene and the skin cleansers used? The number of skin-to-skin interactions (e.g. potential invasions from other microbiomes)? This has enormous public health implications, since these microbiomes are where all our multiply drug resistant pathogens are coming from. I’d love to see whether people’s microbiomes force evolution of similar bacteria, whether there’s a lot of randomness among people, and/or whether we link our microbiomes together through interpersonal interactions.

    One thing students could test is whether their microbiomes change when they start dating someone. Do a couple’s mouth flora become more similar, the longer they are together? Do partners initially make each other sick when they first get together, until they are both immune to each other’s resident pathogens? Undergrads can test that by seeing if they get a cold (or similar) within a few weeks of hooking up with someone new, as well as by doing genetic tests of the bacteria on their skin and mouths.

    One of the fundamental questions is how evolution works. The basic assumption is that evolution is based on random variation, followed by natural selection. However, it’s apparent that in some cases, the same mutation happens multiple times, and it’s also apparent that nature selects the same way multiple times. It would be great to find out if there are patterns to where mutations happen, and if there are islands of predictability in the selective environment.

  5. February 22, 2012 8:43 pm

    Alex is right that there are a lot of processes other than DNA where evolution happens. Genetic “breeding” of software is one area. Another is linguistic evolution; the evolution of language and usage.

    Science “outside the laboratory” is done all the time. Or, to put it another way, one has to establish laboratory criteria outdoors. The biggest challenge is replication and testing of hypotheses. To be scientific, a hypothesis must be falsifiable, whether indoors or out.

  6. SFreader permalink
    February 26, 2012 3:04 pm

    “One thing students could test is whether their microbiomes change when they start dating someone. Do a couple’s mouth flora become more similar, the longer they are together? Do partners initially make each other sick when they first get together, until they are both immune to each other’s resident pathogens? Undergrads can test that by seeing if they get a cold (or similar) within a few weeks of hooking up with someone new, as well as by doing genetic tests of the bacteria on their skin and mouths.” —

    So, you’re suggesting students find out via swabs and lab tests whether that ‘butterflies in the stomach’ feeling is love or a pathogen getting lively? Good topic (excuse) for a mid-term research paper. 🙂 Haven’t twin studies already shown that identical twins separated for several years end up with very different antibody profiles? (I’m assuming that for the purpose of this discussion antibodies can be substituted for microbiomes.) I’ve also read that sexually active people are normally most attracted to those with foreign/unfamiliar antibodies usually detected by smell and the evolutionary reason for this attraction is not to protect themselves (i.e., change their microbiomes) but to pass on as much (as broad an) immunity to their offspring as possible. Perhaps the ‘7-year itch’ might also be partially explained by microbiomical similarlity. (Another undergrad research project: collect/analyze samples from divorced vs. married couples.)

    • February 26, 2012 3:40 pm

      Yes, you would think someone had tested whether microbiomes affect dating. That was actually a plot element in Brain Plague. I’ll look and see whether the real world’s caught up yet.

  7. March 5, 2012 12:27 am

    Lets be honest, the real issue is where did life come from, not how does a escpies adapt over time.From a science perspective, it’s easy to demonstrate that escpies do evolve over time. I well remember the example given in my high school biology class regarding the colours of moths in England as the country burned more soot producing coal, which favored dark coloured moths.As for the origins of life, and the possibility that life evolved from primitive amino acids this is science trying to extend its powers of explanation back in time to a possible scenario for how life began on earth. What’s wrong with considering or experimenting with that?Science is a set of tools, a methodology used to explain the universe. There are limits to these tools, limits to the knowledge spaces where they work. Science is not a panacea for every question a human can pose. Science will never be able to answer the question Why? for example.OTOH, Religion likewise has its domains where it operative, and other domains where it doesn’t really apply. In deep meditation, for example, I know or understand things I could never learn through the scientific method.That is why proponents of “intelligent design” are fighting so hard to get their side represented in the classroom.The point is, what they’re proposing isn’t science. It’s theology. It doesn’t belong in a science classroom.Just as you accuse science of overreaching its domain, the ID proponents are overreaching their domain by trying to inject theology into the realm of science, and calling it science . It isn’t.

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