What would disprove evolution?

July 9, 2012 • 4:27 am

If evolution is a scientific theory worth its salt, then there must be some conceivable observations that could show it to be wrong.  I just wanted to put down, for the record, what some of those observations might be. First, let’s reprise what I see as the major components of the theory of evolution.

  1. Evolution occurs, that is, there is gene frequency change in populations over generations.
  2. Significant evolution takes time—that is, it usually (though not always) requires hundreds to thousands of generations to occur. It is not instantaneous, and it is the population and species rather than the individual that evolves.
  3. Lineages of organisms split, or speciate, so that the single lineage that gave rise to life 3.5 billion years ago has undergone numerous splitting events to produce the millions of species alive today (and also the even more millions that went extinct).
  4. The converse of #3: any pair of living species has a common ancestral species some time in the past.  That is, if you trace any pair of twigs on the tree of life, you will find a node where the line from the trunk bifurcates to produce them.
  5. The process producing the appearance of design in organisms is blind, purposeless natural selection. (There are, of course, evolutionary forces other than selection, including genetic drift, but they don’t produce the marvelous design that was once seen as the prime evidence for the hand of God.)
These parts of the theory don’t all stand together. For example, you could have evolution without branching: that would mean that only one long-evolved species would be alive today. Or you could have evolution, but not occurring by natural selection. (The complete absence of natural selection is hard to imagine, though, given that organisms replicate their genetic material, and some genes will replicate better than others in different environments. Lamarckism and teleologically-driven evolution, however, were once seen as the main drivers of adaptation.)  Finally, you could have evolution but not gradualism: every population could experience great saltational leaps in one generation.

In my general talk on the evidence for evolution, I give a list of seven observations that, if repeated and confirmed, would disprove parts of the theory of evolution described above. This shows that it is a scientific theory in the Popperian sense of being falsifiable.  Here are some of those conceivable observations:

  • Fossils in the wrong place (e.g., mammals in the Devonian). If the fossil record were all out of order like this (a single anomalous fossil might not overturn everything, of course, since it could be in the wrong place for other reasons), we’d have to seriously question the occurrence of evolution.
  • Adaptations in one species good only for a second species.  There are plenty of adaptations in species that are good for other species, but also help members of the first species: these are the basis of mutualisms. (Cleaner fish, for example, remove parasites and dead tissue from other marine fish, but thereby gain a meal.) But we don’t expect to see—and don’t see—adaptations in one species that evolved solely for the benefit of another species.
  • A general lack of genetic variation in species.  Evolution depends on genetic variation. If most species had none, they couldn’t evolve.  However, the universal efficacy of artificial selection (I’m aware of only three lab experiments that failed to show a response to such breeding experiments), shows that genetic variation is ubiquitous in nearly all species.
  • Adaptations that could not have evolved by a step-by-step process of ever-increasing fitness. This is of course the contention of advocates of Intelligent Design like Michael Behe. But adaptations like the flagellum, which Behe and other IDers cite as features that couldn’t have arisen by a step-by-step process of increasing adaptation, have been shown to plausibly arise by just that process.  We don’t need to completely reconstruct the evolution of things like flagella, but simply show that their evolution by a stepwise adaptive process was plausible.
  • The observation that most adaptations of individuals are inimical for individuals or their genes but good for populations/species.  Such adaptations aren’t expected to evolve often because they would require the inefficient process of group or species selection rather than genic, individual, or kin selection.  And indeed, we see very few features of organisms that seem inimical to organisms or their genes but useful for the population or species. One possible exception is sexual reproduction.
  • Evolved “true” altruistic behavior among non-relatives in non-social animals. What I mean by “true” altruistic behavior is the observation of an individual sacrificing its reproductive output for the benefit of individuals to which it is either unrelated or from whom it does not expect to receive return benefits.  In this “true” altruism your genes give benefits to others and get nothing back, and this shouldn’t evolve under natural selection. And, indeed, we don’t see such altruism in nature. There are reports that vampire bats regurgitate blood to other individuals in the colony to whom they’re unrelated, but those need confirmation, and there may also be reciprocal altruism, so that individuals regurgitate blood to those from whom, one day, they expect a return meal. Such cooperation can evolve by normal natural selection.
  • Complete discordance between phylogenies based on morphology/fossils and on DNA. While individual genes can show discordance by lateral transfer—rotifers, for example, have incorporated into their genome from DNA from very unrelated organisms, and this is also common for bacteria. But lateral transfer of genes, as opposed to their direct descent from parent to offspring, is relatively uncommon.  So, for example, if we sequenced the genome of a blue whale and found that on the whole the species was more closely related to fish than to mammals, we’d have a serious problem for the theory of evolution.
We don’t see any of these anomalies, and so the theory of evolution is on solid ground. As I say in my book, “Despite a million chances to be wrong, evolution always comes up right. That’s as close to a scientific truth as we can get.”

That’s my list, and I would be delighted if readers conversant with evolutionary theory and natural history would add others.

203 thoughts on “What would disprove evolution?

  1. Splendidly put; and echoes of JBS Haldane’s “Rabbits in the Devonian”, or some such form of words. So that one’s been around for a while, and the pseudopopperian opponents of evolution are without excuse.

    “the universal efficacy of artificial selection (I’m aware of only three lab experiments that failed to show a response to such breeding experiments)”

    I for one would value a catalogue or leading review references to the numerous artificial selection experiments to date. I’m not sure Behe’s notorious QRB article would fit the bill!

  2. There are, of course, evolutionary forces other than selection, including genetic drift, but they don’t produce the marvelous design that was once seen as the prime evidence for the hand of God.

    I might quibble with this (possibly). Drift is likely to be hugely important in, for example, the evolution of “molecular machinery”. Such “machinery” is seen by creationists as designed.

    1. Drift is always neutral.

      If a mutation increases or decreases fitness, it’s under the rubric of natural selection, by definition.

      1. Sure and it turns out that neutral mutations are pretty important in the evolution of some complex protein related coolness. Much of this is complex and leads imagination and curiosity deficient creationists to conclude that it looks, and indeed was, designed. Hence my minor quibble.

        An example of this kind of research:


        The conclusion provides a helpful general summary:

        Overall, experiments have now demonstrated two clear mechanisms by which neutral genetic drift can aid in the evolution of protein functions. In the first mechanism, neutral genetic drift fixes a mutation that increases a protein’s stability [24,25,55], thereby improving the protein’s tolerance for subsequent mutations [26-28], some of which may confer new or improved functions [28]. In the second mechanism, which was the focus of this work and the recent study by Tawfik and coworkers [44], neutral genetic drift enhances a promiscuous protein function. This enhancement poises the protein to undergo adaptive evolution should a change in selection pressures make the promiscuous function beneficial at some point in the future.

        1. A neutral trait that becomes more common through genetic drift could, at a later date, become beneficial to survival (i.e. through environmental change).

          1. Well exactly. Hence the importance of neutral mutations, including in giving the appearance of design.

          2. It would be phased out, according to the evolutionists. For there to be a beneficial trait, it must have already been built into the organism. Something that is an example of this is the immune system. There are several components to the immune system.
            “When a microscopic invader breaches the outer defenses of the body the immune system swings into action. This happens automatically. The molecular systems of the body, like the Star Wars anti-missile system that the military once planned, are robots designed to run on autopilot. Since the defense is automated, every step has to be accounted for by some mechanism. The first problem that the automated defense system has is how to recognize an invader. Bacterial cells have to be distinguished from blood cells; viruses have to be distinguished from connective tissue. Unlike us, the immune system can’t see, so it has to rely initially on something akin to a sense of touch. Antibodies are the «fingers» of the blind immune system—they allow it to distinguish a foreign invader from the body itself. Antibodies are formed by an aggregation of four chains of amino acids (Figure 6-1):”
            Source: https://reasonandscience.catsboard.com/t2322-the-immune-system-and-irreducible-complexity

            This is just a first step. There must be some way for the body to know when what is part of the system and what isn’t.
            This could not have been something that was slowly evolved into.
            We all know that a compromised immune system means death. If the system does not respond to the invasion, there is nothing to keep the invaders at check. It will not have time to jury rig some kind of defense. The infection ends when the organism is dead.
            This has been seen over and over again when a person has there immune system deliberately chemically compromised to allow their body to accept a transplant. Or is irradiated to kill off cancer cells. This also kills off the immune system.
            If any organism had ever become infected it would have died, before it even had a chance to “evolve” the beginning of an immune system.

            The wonder of the immune system is augmented when you think about how the fetus of the mother is not part of the body of the mother. And the body would actually reject the fetus were it not for the design feature that allows the body to accept the growing fetus.

      2. Are you overlooking preadaptation? It’s quite easy to enivision a mutation that is neutral under present conditions, but later on when conditions have changed turns out to be as useful as all get out.

      3. No, drift is not always neutral, it has nothing to do with neutralism.

        A real good mutation that gives a huge advantage to the first mutant can disappear by drift because the mutant got eaten or caught a cold and died or sprained its ankle while running or maybe it had also a bad mutation that made it sterile in addition to the good one. Random luck.

        A bad mutation can also prevail (or simply don’t disappear) because of random luck. I’m sure you can come up with situations for this.

  3. Curiously creationists sometimes say things like “you never see a cat giving birth to a dog” as if it were a criticism of evolutionary theory whereas such an event would actually disprove the modern theory.

    1. that’s an awesome response: “And if it did, evolution would be wrong.” Would sure throw them for a loop.

    2. Don’t forget we’re not talking about intellectually honest people here. We’re talking about con artists who’ve managed to con themselves as well. It doesn’t have to be a good criticism of evolutionary theory as long as it works as a criticism of the straw man they like to pretend evolutionary theory is. If it succeeds in convincing the uneducated fools they target, and gets them to donate money and/or vote for cdesign proponentsists, it will survive.

      1. “Don’t forget we’re not talking about intellectually honest people here.”

        Exactly correct. Watching, reading, and participating in more than a few “debates” on line has left me unceasingly amazed at the willful misrepresentations, ignoring of facts, shifting of goalposts, wholesale torchings of straw men — and most of all, pure, bald-faced, outright lying — on the part of creationists.

    3. On the same vein: the “Crocoduck.” Creationists ask to see a crocoduck (presumably half crocodile half duck) as proof of evolution when it would actually be a disproof.

      1. If they knew anything about evolution, they would pick two genera (families?) that were further apart, like a Crocoguana, or a duck-billed Platyduck.

  4. Here’s a question, on a bit of a tangent, that’s been buzzing around in my head for a while and I don’t have the knowledge to answer it. We know that evolution can happen rapidly by selection acting on standing genetic variation. For instance, the work that Kingsolver has done with sticklebacks recently. But, how much change in possible on standing genetic variation alone? Can speciation occur, or does that require novel mutations?

      1. Thanks for that! Interesting research.

        My question is driven by papers like:

        Pandolfi, Connolly, Marshall & Cohen (2011) Projecting Coral Reef Futures Under Global Warming and Ocean Acidification. Science Vol. 333 no. 6041 pp. 418-422.

        One of their arguments is that adaptation and acclimatisation have not been incorporated into models that predict the effects of climate change on coral reefs.

        Presumably, evolutionary adaptation would be initially selection on standing genetic variation. But, at some point genetic variation in the traits under selection would become depleted. Then continued adaptation would require new mutations. Right?

        Having a high degree of genetic diversity would provide ‘fuel’ for rapid evolution. But, surely high diversity only increases the probability of rapid evolution. It doesn’t guarantee it because there is no certainty that the genetic diversity contains variation in advantageous traits. Right?

        So I guess my question really is: How common is dramatic change like that seen in the cichlid and stickleback research? Is it likely that a large proportion of coral species will be able to adapt? And will they hit an ‘adaptive wall’ when the standing genetic variation runs out?

    1. Also, speciation by allo- or autopolyploidy doesn’t even require genetic variation at all, except for differences BETWEEN species. (This may also hold for diploid hybrid speciation, as in Loren Rieseberg’s sunflowers). Speciation by polyploidy occurs as a result of hybridization alone, and could occur even if there were no genetic variation within each of the two hybridizing parental species.

  5. Might the regurgitation of blood to non-kin in vampire bats be a “byproduct”? I.e., the behavior is primarily for kin – but others get the occasional free meal?

    1. I might also add the possibility that such behavior, if it in fact does occur, could easily be presexual, similar to a male Clark’s Grebe presenting a fish to a female as a prelude to mating with her.

  6. One more:

    Geographical distribution uncorrelated with phylogeny when such a correlation would be expected.

    For example, if the existing species of Birds of Paradise were to be found in Alaska, South Africa and New Guinea, we would have a hard time explaining that through evolution. Similarly, if the fauna of the Galapagos Islands had been related to that of Madagascar instead of South America we would be stumped.

      1. Broken biogeography would dispute both Evolutionary Biology and the Theory of Plate Tectonics. Revising estimates of how fast tectonic plates move around wouldn’t solve the problem presented by andreschuiteman’s Birds of Paradise hypothetical observation, you’d need to come up with a completely different mechanism for explaining both the current distribution of non-biological features on the Earth’s surface (mountains, coastlines, earthquake-prone areas, etc.) *and* the new biology.

      2. Hmm .. what would that bring into question?
        Our understanding of evolution?
        Or our understanding of how (fast) plate tectonics works?

        Or, probably the weakest and most complex link in the chain that makes up our understanding : our understanding of the dispersion history of, in this question, Birds of Paradise.
        Trying to generalise the question, a distribution of taxon X, leaving X present at non-contiguous areas, and with several non-populated areas between the existing “outcrops” … would make me anticipate a former wide range for taxon X, encompassing (more or less) the current geographic extremes and intervening areas. Then, for whatever reason, the main distribution of taxon X on the main continent is wiped out (disease ; ecological niche competitor ; whatever), leaving only the geographical extreme populations.
        (Obviously, “taxon X” consists of multiple interrelated species, evolving in lineages ; if I’d meant “species X”, I would have typed that.)
        To examine this hypothesis, I would of course look for fossils of the “missing” taxa in the geographical areas intervening.
        Now … isn’t that, in a nutshell, part of Gingerich’s (spelling?) published logic for searching for early whales in Eocene-Palaeocene marginal deposits of the Tethys Ocean … and coming up with search areas in Egypt and Pakistan. Then searching. And finding. And slamming a lovely heavy door on the fingers of Creationists.
        (These examples have the further complication that, at the appropriate times, IndoAustralia was barrelling through the middle of Tethys, out of contact with the coastal regions. So … before proto-cetaceans could have arrived in IndoAustralia, they’d probably have had to have committed to an aquatic life before they could get there. So … to study the return of mammals to the sea, IndoAustralia would not be a constructive place to search. Similar thinking about our putative Alaskan Birds of Paradise, Anchored Down in Anchorage.
        In other news … I’ll be fossil-hunting on the Scottish Laurentian Foreland at the weekend, in search of, amongst others, Ollenellus-group trilobites. Their trans-Atlantic, but not trans-British, distribution was a great puzzle before the acceptance of plate tectonics. And playing “hunt the meteorite crater” too. No doubt in driving rain and sleet, this being Scotland in summer.

        1. Assuming that evolution is true, one would, naturally, try to explain disjunctions in the distribution of taxa by various known factors, such as regional extinction, long distance dispersal or plate tectonics. I merely tried to imagine what we would observe if, for example, aliens had created the earth’s life forms and had planted them at various spots on our planet. Unless they had wanted to deceive us by planting them exactly where you would expect them to be if evolution had happened, one should be able to detect anomalies in the distribution patterns.

          There do exist some strange, unexplained distribution patterns, but they are quite rare. An example is a small, leafless flowering plant called Thismia americana, which occurred about a hundred years ago in a prairie near Chicago, where it was last seen in 1916. No species of Thismia has ever been found anywhere else in North America, and the nearest relatives of T. americana are believed to live in Australia and New Zealand.

          If this kind of anomaly would be the rule rather than the exception, there could be reason to doubt evolution, I should say. As it is an exception, I am confident that there is a perfectly good explanation that doesn’t involve overthrowing the Theory of Evolution.

          Enjoy the trilobite hunting. Sounds fun.

    1. While it doesn’t completely disprove your point, the concept of parallel evolution could explain similarities in the traits of species in different locations. Good tricks for one species in one biome may develop completely separately for another species in another biome. In addition, there are many creative ways to show dispersion of phylogeny over time, which weakens the argument. Odds are that if we found two exact species in two completely different and seemingly completely disconnected locales, there would be some reasonable explanation even without evidence.

      1. Phylogenies are nowadays reconstructed using DNA rather than morphology, so we would not be fooled by parallel or convergent evolution.

        ‘In addition, there are many creative ways to show dispersion of phylogeny over time, which weakens the argument.’

        That’s just hand waving.

        1. “Phylogenies are nowadays reconstructed using DNA rather than morphology, so we would not be fooled by parallel or convergent evolution.”

          Ha! You don’t work on squamates, do you?

          There are enormous amounts of phylogenetic information in morphology, which it has become unfashionable to know anything about. (Clue: palaeontologists reconstruct phylogenies)

          Convergent evolution also occurs in molecular sequences, more than you’d expect just by thinking about it.

          1. There is undoubtedly a lot of information in morphology, but you need molecular methods to find out which morphological characters best trace phylogeny in a particular group 🙂

            That said, it’s true that molecular methods have their own problems.

    2. “Geographical distribution uncorrelated with phylogeny when such a correlation would be expected.”

      Perhaps another way to exemplify this would be: all living species from a given environment sharing more genetic similarity with other species from the same environment, independantly from their taxonomic levels, than with species from a corresponding taxon but living in other environments. For example, if jaguars and caimans living in the same jungle forest shared higher genetic similarity than jaguars and lions (or caimans and Nile crocodiles), this would be difficult to reconcile with common ancestry.

      Desnes Diev

  7. …adaptations of individuals are inimical for individuals or their genes but good for populations/species…
    One possible exception is sexual reproduction.

    Sexual reproduction leads to greater diversity than asexual reproduction therefore more residence to pathogens or parasites and therefore more offspring.

      1. I’m not sure that it is rational to anthropomorphise an iPhone by providing it with the attribute of stupid.

        By the way, how do you turn the stupid thing off?

  8. I think the question these days is misguided, and really there are two questions at play.

    1. what would potentially falsify evolution?
    2. what given what we know would potentially falsify evolution?

    Given the theory, it’s easy to come up with plenty of examples of things that would just go against evolutionary theory. But how many of those could really do the falsification notion any good now given that so many predictions of evolution have been overwhelmingly demonstrated in the empirical research?

    For those who look for some a priori means that could do away with evolutionary theory, evolution is going to seem a lot more unfalsifiable than it is because the case has already been made. Evolution really is the closest thing we have to scientific truth!

    1. Perhaps this consideration – a good one – can be worked out by time indexing the relevant claims to approximate periods of time for which they mattered. For example, until the discovery of radioactivity, evolution was vulnerable to the “age of the earth” problem as pointed out by Kelvin.

    2. The problem in this general case is that “falsification” and “truth” are philosophical notions. Theory failure doesn’t work like that, testing doesn’t work like that. And facts don’t work like that.

      Rejection becomes harder and harder as you have competed, expanded and deepened theories over time. And there is no map between “falsification” and the market of ideas process what I know of.

      Granted, testing isn’t enough to predict competition, you would need some market model for that. But at least you would predict that it can be used under all these cases. Some theories will not be rejected by testing alone but by elimination under competition. Wallace’s theory (only natural selection as mechanism as I understand it) were inferior to Darwin’s, but it didn’t fail by failing testing.

      Of course evolution as a process and now as a valid theory are observable facts. I don’t think we should confuse that with how well tested those observations are.

      But that only brings your initial observation, such as it is, into sharper focus. What is the best test for evolution?

      I would say that Theobald’s “A formal test of the theory of universal common ancestry” is the strongest observation ever made, and that will ever be made, in all of science: the monophyly of life has a likelihood of ~ 10^2000 against polyphyly!

      The complexity of the process that makes such strength possible is also what makes so many test possible, further strengthening this pearl of the science oyster.

  9. One should remember that there is significant “play” — i.e., room for auxiliary hypotheses to absorb anomalous observations — between the predictions of evolution (meaning, common descent) and the data. Jerry didn’t mention the universality of the genetic code in his list of seven predictions, but one can find it in nearly any evolution or biology textbook between 1966 and the mid-1980s. The late Bernard Davis of Harvard expressed the prediction as follows (1985, 256): “If organisms had arisen independently they could perfectly well have used different codes to connect the 64 trinucleotide codons to the 20 amino acids; but if they arose by common descent any alteration of the code would be lethal, because it would change too many proteins at once.” Mark Ridley (1985, 11) completes the point: “Thus we expect the code to be universal if all species have descended from a common ancestor.”

    Think about this for a moment, then check this NCBI page:


    1. Very interesting. It stands out at once that the variations are minor. But rarely (very rarely) creationists ask useful questions, and we should take the opportunity to learn from them. This looks to me, a non-expert, like an example.

      Can one construct a phylogeny from the codes themselves? (Indeed, we do this to some extent, when we use it to relate mitochondria to bacteria) How many of the changes would have tolerated two variants at once? And how do we envisage the consequences of a change in code?

      1. I think Theobald’s work is on top of that, see my longish comment below. Our YEC troll happened to “forget” that the qualitative, and now quantitative, question of monophyly has already been answered. With _the strongest answer ever_ in all of science! =D

        But even if the presence of proteins that depends on, and is necessary for, the genetic machinery shows how they both are monophyletic (whether or not how it is rooted), the phylogeny of the machinery is worked on and pretty well known IIRC.

    2. Universality of DNA code, that’s one more point. There is only one tree of life so far.

      So, if in the future another evolutionary tree with different set of DNA molecules is found (either in this earth or “in heaven”), it must be a totally separate tree from the one we have now, with totally different members.

        1. – Monophyly or polyphyly of genetic machinery isn’t really a test of evolution. Theobald goes through all of the pathways that an evolutionary process could take to an UCA, including bottlenecking from a condition of large horizontal gene transfer between independent or once divergent paths.

          This is in the same way that the process from chemical to biological evolution isn’t a prediction and test of evolutionary theory as such.

          – There are many known evolved differences in the genetic machinery, from coding special amino acids directly instead of making them by later modification (happens in mitochondria a lot, as they can diverge easily without problem(, to modifications of how the code is read (say, bacteria concatenated genes vs archaea/eukaryote exons with introns).

          If it could have happened after the observed monophyly bottleneck, it would almost certainly have happened. The monophyly originated a long time ago.

          To use the context, around 1 000 000 times longer back than our YECs beliefs once originated in its own peculiar (oh, so peculiar!) monophyly. If such a funny phylogeny can evolve, certainly mundane genetic machinery can evolve. “Theology, ergo evolution.” =D

    3. Creationists shouldn’t comment on science, it only shows how ridiculous they are.

      – The first one who made a formal test of monophyly of life was Theobald. [A formal test of the theory of universal common ancestry>/a>”, Theobald, Nature, 2010.] It happens to be the best observation of all of science ever, and ever expected to be seen, with a likelihood of ~ 10^2000 against polyphyly.

      So your creationist criticism happens to be the most ridiculous comment ever, and ever expected to be seen, on all of science.

      – There is no philosophical “play” in making conditions of experiments, which such observation of the process of evolution is, fit what is observed. The conditions are either experiment dependent or theory dependent, so the theory is enriched and constrained. Such strengthening is the converse of inserting gods of the gaps!

      Theobald’s results is actually an excellent example, since he has commented on that in answering some criticisms in a later paper. [“On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence“, Theobald, Biol. Dir., 2011.]

      “But by 1973, in his famous essay on the explanatory power of evolutionary theory, Theodosius Dobzhansky laid out the existing evidence for UCA as if it were beyond dispute [4]. According to Dobzhansky, the primary support for UCA is given by several key molecular similarities shared by all known life: (1) the “universal” genetic
      code, (2) nucleic acid as the genetic material, (3) shared polymers such as proteins, RNAs, lipids, and carbohydrates,
      and (4) core metabolism. These are today still the main arguments for UCA.

      The standard presentation of this evidence is, however, strictly qualitative; it does not quantitatively assess the likelihood that these commonalities could be arrived
      at independently from multiple origins. Each of Dobzhansky’s arguments for UCA has its weaknesses, and Sober and Steel provide several criticisms of these standard
      arguments [11]. While a detailed analysis of these lines of evidence for UCA is beyond the scope of this article, as a case study let us briefly revisit the “universal”
      genetic code, widely considered the most persuasive evidence for UCA [5,6,10,24].”

      Furthermore, we also know now that
      the genetic code is far from “frozen”, and that it continues to evolve [27].

      Of course, reasonable and persuasive verbal arguments can be made on this point [25], and the qualitative evidence compellingly supports universal ancestry. But quantitatively estimating these probabilities is non-trivial. To calculate these probabilities we need formally specified stochastic models for how genetic codes evolve under both hypotheses — namely, we need well-defined likelihood functions, probability distributions for the observed data given each of the competing hypotheses. We currently have no such formal models for genetic code evolution [11,12,25,27]. The calculations are further complicated by the fact that there are other plausible hypotheses for the evolution of the code with empirical support [25,30], not all of which are mutually exclusive. Consequently, it is currently impractical to construct a formal, quantitative test of UCA using evidence from the genetic code.

      Fortunately, however, we do in fact have ready-to-use, well defined, and widely accepted stochastic models for the evolution of protein sequences.

      [My bold.]

      So that was a ridiculous claim too.

        1. Thanks. Theobald Biol. Dir. 2011 addresses exactly the qustions I was raising (even if the answers are, so far, far frm exact). And cited there, [27], Nat Rev Genet. 2001 Jan;2(1):49-58, Rewiring the keyboard: evolvability of the genetic code. Knight RD, Freeland SJ, Landweber LF

          addresses directly the question that Nelson raises.

    1. Yes. I was about to say something similar:

      The evidence for evolution is so firmly established that if a fossil human were to be found in the Cretaceous, I would assume that it was evidence of the future invention of time travel.

      1. Maybe some future guy put the fossils there and dinosaurs are actually the descendants of birds and not their ancestors.

      2. The problem with the time travel interpretation is that General Relativity (which is at least as firmly established as evolution) says that there is no such thing as a time machine that can send you back to a time before the machine existed. It’s like a railroad: you have to lay the track before travelers from the future can use it to visit you.

        1. Well, keep in mind that the time machine may not be man-made, and may have already existed in an alien culture some billions of years ago. Logically to get around the train tracks issue, there’s no reason we couldn’t trek out into space for millions of years, find someone else’s old train tracks, use them to go back in time, then travel back to pre-historic Earth and make changes. All within the confines of Special Relativity. Neil Degrasse Tyson is particularly well-versed in and pursuing such possibilities.

          1. This point, and Buzz’s following, falls flat immediately as not actually dealing with the problem. In exactly the same way that “panspermia” hypotheses for the origin of life on Earth literally just move the problem elsewhere.
            Somewhere, there was an origin of life by chemical means, regardless of whether life is then distributed through the universe by hyper-intelligent pink elephants.
            Likewise, if time travel cannot happen back to before the invention of the first time machine (which by implication could only travel into the future, on it’s first trip), then there must be a species (possibly the same hyper-intelligent pink elephants) who become the first time travellers.
            Cue Fermi : “Where are they?”

          2. A time travel ‘machine’ could be a found natural object coughed out of the Big Bang, not an artifact.

            We can haz evolution and TT plz?

        2. We don’t have to have built the machine ourselves. It could already be out there, operated by an alien species, which will let us use it to revisit our own history, once we make contact with them.

          And anyway, GR does not actually say that. That’s merely a property of the most plausible type of time machine that might be allowed by GR.

          1. In that case you’re confronted with a Fermi Paradox in which you have to wonder why these aliens, with arbitrarily advanced future technology at their disposal, have made no visible mark on the cosmos except for this single anomalous fossil.

            With just that one fossil as evidence, then some sort of hoax seems to me like a more parsimonious explanation than either time travel or the falsification of evolution.

          2. Gregory:

            That’s easy. They developed things in a different order than us. They invented their time travel technology BEFORE they discovered how to put cat videos up onto the internet.

        3. Time machines aren’t allowed when you look at generic gauge theories though, the implode the light cone or in GRs case the cosmology.

          [Um, refs: have to get back on that one if asked. I have them … somewhere. Or had them somewhen. There is a time machine when you need one?]

          Another test that rejects time machines is the Turing-Church theorem. You can’t build time machines by way of physics, not ever, because they would give computational machines practically infinite resources.

          TC must hold or the complexity classes of computer science breaks down. If they do, all of physics becomes trivial, and life couldn’t exist. [See Scott Aaronson on that one.]

          1. Another test that rejects time machines is the Turing-Church theorem. You can’t build time machines by way of physics, not ever, because they would give computational machines practically infinite resources.

            It may be true that if you could construct a time machine then you could calculate a non-general-recursive function, contrary to the Church-Turing thesis, but if this is so it is not obviously so. I would be interested to know what you mean by saying the machine would have practically infinite resources and why you think this matters. Remember a Turing machine is assumed to have an infinite tape.

            OTOH if this is true it gives us very good reasons for supposing a time machine cannot be constructed. But it is not a proof of the impossibility; in essence it would mean that such a machine would be a counter example to the Church-Turing thesis.

          2. A time machine can infinitely multiply the computational power of any computer. Crunch your problem for a certain amount of time, package up the state of the machine, send that state back in time, and let the machine start not from scratch but that much farther done with the problem. And, as soon as you complete the problem, send that state back in time. The end result is that all computational problems are solved the instant you turn on the time-chip-enhanced computer.

            And a time machine also allows you to construct a perpetual motion machine. Make a recording of the random motions of a gas (etc.) at thermal equilibrium. Analyze the recording to determine the timing of opening gates to pass energetic particles to one side. Send your analysis back in time, follow the program, and you’ve just created Maxwell’s Demon.

            “Time is nature’s way of keeping everything from happening at once.” The instant you have time travel, there’s an unbelievably powerful incentive to be the first to go the farthest back in time possible, be that the Big Bang or the invention of the first time machine. He who controls the past controls the future, after all. Even if your machine only permits communication, the first message to come out of it won’t be “Hello, world!” from yourself ten minutes into the future. It won’t even be yourself from ten years in the future sending you the winning lottery numbers. It’ll be an unimaginably sophisticated hack attack that instantly succeeds even as it fights off an infinite number of other hack attacks of equally-unimaginable sophistication…except it won’t even be that, because the future in your timeline would eventually invent an even more powerful hack that would do better still. Reducto and all that — time travel is clearly division by zero, tan(π/2), etc.



          3. The simple answer is that the Church-~Turing thesis does not involve time. It merely states a relationship between one mathematical abstraction, namely, a Turing machine and another, namely, a general recursive function. As far as this relationship is concerned, all the calculations of the Turing machine could be instantaneous.

            But let’s look a bit more closely at this. Suppose you construct a time machine that moves back from time t1 to t0 and does some calculation between times t0 and t1. Take a very simple calculation such as starting with 0 and adding 1 on each cycle and storing the solution. Now on each cycle more memory is needed and, perhaps more importantly, the calculations become more complex with every cycle.

            Now even to calculate such a simple function it would seem that there would be some number N such that the Nth cycle cannot be performed between times t0 and t1. Now maybe your time machine engineer could overcome this problem but, if not,maybe he/she design the time machine so that there were a monotonically increasing sequence of times t1, t2, t3… such that the nth calculation is done in the interval t0 to tn.

            If this could be done then in some sense the whole of the sequence 0, 1,… would be available, in the sense of being stored somewhere at time t0. Now imagine a more general time machine that we program to calculate something more complicated. The question is:

            “Does the possibility of such a machine contradict the Church-Turing thesis?”

            The answer is:

            “Only if the function so computed is not general recursive.”

            The reason for this is that the Church-Turing thesis does not refer to time.

            Now suppose I could construct a computing time machine T1 that made available a non-general-recursive function in its entirety at some time t0 then surely I could construct another machine T2 that behaves exactly the same as T1 except that it never loops back in time, then T1 and T2 calculate the same function. So either both are counterexamples to the Church-Turing thesis or neither is. But one involves time travel and the other does not. So we may conclude:

            Whether the Church-Turing thesis is true has absolutely nothing to do with the possibility of time travel.

          4. There’s also the fact that any physical time machine must have finite bandwidth. So your ability to perform infinite amounts of computation effectively instantaneously would be hampered by the need to transmit partial results back through a finite channel.

          5. bernardhurley wrote:

            The simple answer is that the Church-~Turing thesis does not involve time. It merely states a relationship between one mathematical abstraction, namely, a Turing machine and another, namely, a general recursive function. As far as this relationship is concerned, all the calculations of the Turing machine could be instantaneous.

            Hmm…you’ve got a good point. There is, however, another side to the coin that Gregory points to:

            There’s also the fact that any physical time machine must have finite bandwidth. So your ability to perform infinite amounts of computation effectively instantaneously would be hampered by the need to transmit partial results back through a finite channel.

            I have, of course, been taking the physicist’s spherical cow approach to the problem, assuming that communication through a time machine somehow comes free. Claude Shannon quite clearly demonstrated that there’s no communication without energy (or matter) transfer.

            Not only would an instantaneous Turing machine require an infinite rate of energy transfer, simply communicating with the past represents a violation of conservation.

            Consider charging a battery in the future, and then sending the charged battery back in time. Lather, rinse, repeat, and you’ve got yourself the perpetual motion machine to end all perpetual motion machines.

            Now, don’t send the battery back, but just send a message. Throw away the message (or don’t) and tap the carrier wave for its energy — no need to even bother constructing a Maxwell Daemon in the first place. Your receiver for the messages from the future is itself a perpetual motion machine.



          6. Ben, I’m afraid you’ve missed my point. I was not arguing that a time machine would be physically possible, I was saying that even if physics were such that time machines (and perpetual motion machines etc.) were possible, you could not use this fact to provide a counter example to the Church-Turing thesis. To do that you would have to demonstrate that such a machine would allow you to compute a function that is not general recursive. The mere fact that all the infinitely many values of such a function would be available at once is irrelevant. If you think that being able to go back in time would make a function that is not general recursive calculable then the onus is on you to specify what that function is and how it is calculated. I guarantee you won’t be able to do that.

          7. Ben, I’m afraid you’ve missed my point.

            Didn’t I concede it with my first sentence?

            One last thing I’ll mention: it is generally possible in practice to trade computing power for memory (and vice-versa). I haven’t thought this all the way through, but my gut tells me that there may well be calculations that require infinite resources that could be computed with a finite machine that included a time machine. If so, that would further imply that such a machine could be used to solve the insolvable, such as the Halting Problem.

            That’s all pure speculation on my part, but I’d bet a good meal that a qualified logician could come up with a formal proof to that effect.



          8. Ben, I’ve been thinking about how one might plausably solve the halting problem with machines that go back in time. I’ve just realised that the idea of a machine going back in time is ambiguous. If I think of me going back in time, it could mean:

            1. someone in the state I am now exists at the same time as my old self so that I, for instance, could meet my old self;


            2. My old self gets changed so that it has some or all of the attributes of my new self; thus I (past) might have access to my present memories so that I (past) can make different decisions.

            I had been subconsciously assuming scenario (1).

            This gets a bit complicated and so I think it is best not to continue the discussion here. I will put a post up about it on my own blog as soon as I have figured out the best way to express the mathematics of the situation. (I will post a comment with a link as soon as I’m done).

            In outline I will be arguing as follows:

            In scenario (1) we get an infinite sequence of partial solutions to the problem all available at once, but this is no use to us because we do not have a general recursive function that will pick out where in the sequence the answer to our problem is found.

            Scenario (2) is problematical because, on the face of it, it seems internally inconsistent. I can see no way around the inconsistency and getting a solution of the halting problem without (a) adding various ad hoc rules about what things the future can and cannot change about the past and (b) assuming that information for the solution is sent back from arbitrarily far in the future and (c) assuming that a completed infinite tape can be made available (via some sort of continuity assumption in the physics.)

            Assuming (a), (b) and (c) you can get a solution to the halting problem, if by that you mean an infinite data structure could exist to which we have immediate access that we could use to solve this problem. However much more than just time travel is going on here and you have to assume some fairly weird physics. The Church-Turing thesis is not about physical realisablity in some fantasy universe but about the idea that the intuitive notion of something that can be calculated by an algorithm is identical with the notion of being formally calculable on a Turing machine. Now what appears to be going on in this situation is that you are building non-recursiveness into the physics, since the limiting process required for (c) has to be formulated in terms of non-recursive functions. If you can have a non-algorithmic physics then obviously you can have mon-algorithmic “machines.” However time travel on its own does not seem to get you into this situation.

  10. What would falsify evolution? A booming voice from the heavens saying, “Fools, I created you all one by one six thousand years ago.”

  11. A beautifully concise, readable summary!

    The following statement is slightly out of date:
    “(Lichens, for instance, are a mutualism between algae and fungi.)”

    The alga/fungus relationship was once viewed as mutualism or as symbiosis. It’s now thought to be more complex and varied than that:

    “Relations between the ‘partners’ in the wide variety of lichens run the gamut between a fairly innocuous, mild parasitism to a rampant, photobiont-destroying disease….although strictly speaking the lichen symbiosis is a kind of controlled parasitism of the photobiont by the fungus, the lichen itself retains many aspects of a mutually beneficial partnership.”
    (Brodo and Sharnoff, 2001: THE LICHENS OF NORTH AMERICA, Yale University Press, p. 6-7).

    The full discussion covers some of the mechanisms of the alga-fungus association.
    I think this part of lichen biology is interesting because it suggests how some of the earliest terrestrial life forms may have evolved.

  12. Crocoducks would falsify evolution.

    That’s another common creationist canard. That evolution means that you get mixing of one species with another.

    Um…no. That would mean DNA is so labile and plastic that there would be no sense in the word “species” at all.

    1. I’m going to insist that ‘Duckodile’ is the correct name; the convention is that the male species precedes the female in the name, viz. liger and tigon.

      Logic dictates that the croc would make a postcoital snack of the duck either way. If the crock was the daddy, he would simply be playing with his food.

      Plus, a female duck would not likely survive such amorous attention.

  13. I think you missed an obvious one that you hinted at in your preamble, and that’s Lamarckism. If parents with amputations gave birth to children with amputations, for example, that would throw all kinds of monkey wrenches into the current theory.

    Also, as somebody mentioned above, organisms of one species with descendants of another species (a dog giving birth to a cat), or unrelated species mating and giving birth to a hybrid (a crocoduck), or a single member of one species transmuting into another species (an adult dog turning into an adult cat.

    Actually, you could probably take any Creationist list of “disproofs” of ToE and show how everything they describe that the ToE says would instead constitute invalidation of the ToE were it true. That might actually be a rhetorically more effective list of ways to invalidate the Theory.



    1. I think your logic is beyond the grasp of most creationists.

      Re: Lamarckism – How many little boys do you know who were born circumcised? L

      1. Honestly, I have never seen why this kind of argument was a very strong one against Lamarckian evolution. Surely the Lamarkians could have argued that only internally produced acquired characteristics would be heritable. So a giraffe stretching its neck to reach higher branches would be inherited; it loosing its ear to an acacia thorn would not.

        All the classic “proofs” of why Lamarckian evolution is wrong therefore seem to be trying to hit the wrong target.

        1. Well, they COULD have argued lists of things. They DID argue for transmission of acquired characteristics. I don’t see how introducing the “internal” modifier changes anything. How many body builders have children born with bulging biceps and six-pack abs?

  14. If it turned out that the earth was only 10 millions years old – that would be a pretty fatal blow to the ToE, too. In fact, this led Darwin to propose an age of the earth much older than some great contemporary physicists (Lord Kelvin) estimated.

  15. “Complete discordance between phylogenies based on…DNA”

    To take an extreme case of that: finding a critter that uses a mechanism significantly different from DNA/RNA would be pretty strong evidence against universal common descent. Though I doubt many scientists would be too upset about it. They’d more likely be ecstatic. Universal common descent isn’t really a necessary part of evolutionary theory.

    1. Yes. It is a key observed feature of the evolution of life on planet earth, but it is in no way necessary for the theory to be valid. It didn’t have to be that way, and the assumption that there is only one lineage is not necessary for a valid theory of evolution.

      If there were two or more different DNA/RNA lineages, that would not invalidate Evolution but it would afford many different avenues for improving our understanding of it. And, as you said, be very exciting.

    2. In fact, there are credible scientists who claim that the idea of a LUCA is unrealistic, given the likelihood of massive amounts of gene swapping in the earliest days.

      Once the three major domains (archaea, prokaryotes, eukaryotes) developed, things calmed down.

      But to find a single organism that is the ancestor of us all? Unlikely.

      1. I think the most enthusiastic horizontal gene transfer-ists have calmed down somewhat. Methods that works on more complete genomes and allow for HGT shows that lineages goes way back.

        In fact, you can nowadays track protein fold families back _through_ the LUCA to the RNA/protein world. [“The evolution and functional repertoire of translation proteins following the origin of life”, Goldman et al, Biol.Dir., 2010. And more like that.] ~ 20 % of the clock proxy stands for the RNA/protein world, another ~ 20 % was the LUCA world (DNA appears), the rest is the modern domain world (translational divergences appears).

        Similarly it appears you can track metabolism to a bottleneck LUCA. [“The Emergence and Early Evolution of Biological Carbon-Fixation”, Braakman & Smith, PLoS Comp.Biol., 2012.] (Interestingly, testing its roots in a RNA/protein or similar non-DNA world by having a double, robust anabolic core of CO2 uptake which doesn’t rely on fine regulation of metabolism or growth.)

        Here they are even more explicit that lineages doesn’t mean you can resolve species but it is a tropic level observation.

        Finally, Theobald’s generic work resulting in a very definite (!) LUCA with ~ 10^2000 against polyphyly. He too discusses, IIRC, that the bottleneck doesn’t mean an undiversified population as much as an assemblage of unknown size.

      2. How is this supposed to contradict existence of a LUCA? If we assume several ‘distinct’ ancestors (themselves with no common ancestor, but fortuitously with compatible genetic mechanisms) capable of rampant gene-swapping, then each of them would be a UCA. Either one of them was also the LUCA, or one of their common descendants was LUCA.

        ‘Finding’ LUCA is a whole nother matter, even more than the idea of finding the bones of Mitochondrial Eve. You want me to dig up the fossil of the cell that divided to give rise to Bacteria and Archaea? You’re out of luck, pal.

  16. Eric, Agreed that universal common descent isn’t really necessary but would an ‘alien’ species be able to survive or would it be competed out of existence?

    1. Three possible choices: 1. Be out-competed. 2. Out-compete (dominate). 3. Co-exist.

      Can’t possibly know the answer to a hypothetical.

      However, alien species tend to dominate environments because of the lack of natural predation and lack of defense mechanisms against the alien species by what that species eats. I’m thinking things like the zebra fish, the emerald ash borer, Dutch elm disease, and the like.

      Even the Florida “love bugs”.

      As long as it finds something tasty to eat…the alien species will be fine.

      1. A fourth possibility (with aliens) would be incompatibility. There’s lots of carbon-based organic stuff that we can’t eat and/or which is immediately toxic to us. There’s no reason to think an alien ecosystem or alien critters – even if they started with liquid water and a CHON backbone – would be compatible with earth life in any way.

        For example, remember that most of the oxygen in our atmosphere is a result of life, not the earth’s starting conditions for life. Oxygen-breathing is contingent result of earth’s evolutionary trail. As Gould said – rewind the tape, and you’d probably get something different.

        1. But there really aren’t any chemically plausible alternatives to oxygen-breathing for high-energy metabolism. Sure, the specific evolutionary pathways that led to photosynthesis and aerobic metabolism are historically contingent. But the benefits of those adaptations make them powerful attractors in the adaptive landscape, with (I’m guessing) lots of evolutionary trajectories leading into them. So on that view we should expect to find similar adaptations on other planets, different in biochemical detail, but with the same basic underlying chemistry.

          1. >>But there really aren’t any chemically plausible alternatives to oxygen-breathing for high-energy metabolism

            Are you sure? It seems to me a failure in imagination to say that statement.

          2. Sure, but there are no sulfur-consuming eukaryotes or metazoans. For that level of metabolism, you need oxygen.

            So if you count a world full of sulfur bacteria (and nothing else) as an “alien ecosystem”, then OK; you have a point. But that’s an evolutionary dead end; you’ll never get a Cambrian explosion on that world. An Earthlike ecosystem, full of complex life and high biodiversity, is necessarily going to be an oxygen-breathing world.

          3. Not an alternative to mitochondria but a possible variant, after oxygenation mind: complex multicellulars living anaerobically on hydrogen (hydrogenosomes being variants of mitochondria). Up to 1 mm large organisms are known, with a lot of neurons (Loricifera).

            Maybe such an endosymbiosis could be possible without the roundabout through high energy oxygen, but I doubt it. Hydrogenosomes are very derived.

          4. That’s the point. The inability to imagine an alternative may be saying more about our failure in imagination than about what’s possible.

            Having said that, the fact that life on earth does in fact have alternatives to oxygen metabolism should raise the question if we just got lucky the explosion of complexity happened on our line of oxygen breathing organisms. It could have happened on the line of anaerobic organisms.

            The Great Oxygenation Event that killed off most hydrogen-breathing organisms, relegating their modern descendants to the intestines of cows and humans, happened around 2 billion years before the Cambrian explosion, and 1 billion years from the beginning of life on this planet. In other words, oxygen-breathers took twice as long to explode compexity than hydrogen-breathers got time to try. Who knows if the hydrogen-breathers were given 2 billion years, if they could not have created their own complexity explosion. Of course once complexity explodes on one line, that shuts down the opportunity for other explosions because the complex organisms that got a head start would quickly fill out all the niches.

          5. “It could have happened on the line of anaerobic organisms.”

            I’m not convinced that it could have, or if it did, that it wouldn’t have been out-competed by a later explosion of aerobic complexity.

            Energetics aside, one big problem with hydrogen is that it’s too light to be retained by Earth’s gravity and escapes easily to space. So even if life had gone down that path, there would have been no Great Hydrogenation Event, because the free hydrogen wouldn’t hang around long enough to build up in the atmosphere.

            For complex hydrogen-based life, you want to look at big gassy planets like Jupiter, not small rocky ones like Earth.

          6. Even if they are biochemically similar I’m reminded of the phrase “Perhaps looking-glass milk isn’t good to drink”

            They might be similar and incompatible.

            There is plenty of living stuff on the planet sharing our DNA which is only marginally better than rock for us as food even ignoring traits evolved for discouraging consumption.

        2. Oxygen is extremely poisonous stuff, and the oxygenation of the atmosphere was probably the worst catastrophe for life ever.

          But it likely did usher in the domain divergences, see the two papers I referred to @ #19. The scientists that looks at energy constraints (Lane, Valentine, Smith) seems to think that the domains are pretty predictable. Cells seems to be mainly constrained by energy needs: ~ 1:10^3:10^6 energy difference between survival of DNA repair, maintenance by cell repair, growth and procreation by fission.

          – Archaea competes by minimizing energy needs: less permeable membranes means less futile ion cycling (and having specialized and low energy metabolisms, small genomes) Predicts 6 out of 6 groups ecology, as well as the environmental growth conditions distinguishing archaea and bacteria. [Valentine, Smith].

          – Bacteria competes by being medium energy generalists. [Valentine].

          – Eukaryotes competes by being high energy users (large genomes, high motility: predators, complex multicellulars, immune systems) from mitochondria symbiosis: ~ 10^5 energy difference yet again. [Lane]

          Maybe the source of oxygenation is an open question? At least when the Smith paper on metabolic divergence came out, someone noted that there are hypotheses on the initial oxygen surge coming from UV on the ices of global glaciation. Effectively reverting cyanobacteria – oxygen – glaciers to glaciers – oxygen – cyanobacteria.

    2. It would mots likely be competed out by more well adapted species, since known cases of intrusion has depended on sufficient similar environments. Even generalists have labored under that problem.

  17. OFF-topic
    I am having a debate with someone about the Out of Africa theory. I have seen some articles on the web arguing about multiple points of origin, but they don’t seem very reliable to me. I would love it if someone more in touch with the science can tell me if there is any good evidence against this theory or does it still stand today. Thank you.

    1. Out of Africa is *mostly* right. Most modern human genes are of African origin. But see Templeton’s “Out of Africa Again and Again”. Some genes (like the recent reports of Neanderthal introgression) come from Eurasia.

  18. The theory of evolution is a huge structure with many parts varying in general importance. It includes smaller theories about process and history. Small parts of the theory are falsified all the time by biologists, but the key ideas, such as those outlined by JC, seem solid, though even they could perhaps stand some alteration and we’d still want to call the remaining idea set a theory of evolution. If mammals really did evolve much earlier than we think now, would that really be fatal? I think not. Would it require some major rethinking of the “what happened in history?” part of the theory? Yeah, it sure would.

    1. I think we sometimes confuse the specific information gleaned from investigating evolution with the Theory of Evolution.

  19. Expanding on Ben Goren, if someone could show that mutations are goal directed would overthrow evolutionary biology as we now understand it. The existence of processes conforming to classical Lamarckian teleology, orthogenesis, vitalism, organicism, etc. (that was not itself, like the immune system, evolved through natural selection) would make a wreck of contemporary evolutionary science. This is why such a high bar is set for claims such as those made by Shapiro, Behe, Jablonka, Denton and others.

  20. There are examples, here and there, of organisms with a non standard code for a particular amino acid. I read that the most are in yeast, either eight or eleven (aging memory). This supports the idea that living things could have very different codes, but do not. This is, I think, the strongest support for a single origin of living things on earth today. The idea of a “shadow biosphere” of organisms descended from a second origin of life, is interesting, but lacks empirical support.

    As to crockoducks, take a look at synthetic biology, and see how intelligent designers operate.

    The distribution and relationship of the Aplocheiloid killifishes strongly suggests continental drift as the vicariance events at the family level. I haven’t really looked into concordance between estimated time of origin of the Aplochiloids and drift events.

    1. Be cautious: the whole field of how life arose is still very unsettled. In what I’ve read (all books for everyman, admittedly), there are hints that the DNA code is strongly constrained by chemical energetics, with the implication that given a second earth-like planet, the chemistry of heredity would be closely similar to our own.

        1. Over the last few years, I’ve read a number of well-known popular books on evolutionary topics, plus a few that are less well known. But I haven’t kept track of which book had which interesting and memorable discussion so I cannot, to my profound sorrow, point you to the right title.

          The problem is compounded because my books are not very well organized, evolution cheek by jowl with ancient Egypt in some cases. If you asked me to merely list the evolutionary tomes I’ve read, I couldn’t do it without ransacking the house.


          It’s possible that I see the implication of some discussions by virtue of my education as a chemist, not because I’m a Very Special Snowflake, but because I’m attuned such issues. [I keep hoping to open a box of Cracker Jack and finding a certificate attesting to my Very Special Snowflakery in it, but so far, no such luck.]

          I can see next winter’s reading as being devoted to re-reading those very same books, but this time keeping track of who said what. Please stay tuned. I will try at some point in the future to begin giving references instead of waving at a packed bookshelf and saying “in there somewhere.”

    2. What is more striking is that all life uses the same few bases and deoxyribose backbone.

      There are hundreds of purine and pyrimidine bases and a lot of them have the same hydrogen bonding properties as GATC(U).

      Same with the nucleic acid backbone. People have made DNA analogues with peptide backbones, 6 carbon sugars, different 5 carbon sugars, 4 carbon sugars, and even nonsugar rings, morpholinos.

      They all behave about the same as DNA, base pairing, forming double helixes, and so on.

      There is no physical reason why life could not be based on hexose nucleic acids with different bases than earth life uses. But we never see that.

      1. Mind that there has been a promising development. People hypothesizing on the environment of the RNA world realized that it would have plenty of dissolved iron and little oxygen creating harmful hydroxyl radicals. Turns out RNA ribozymes can be at least one order of magnitude more efficient with iron than with modern magnesium.

        “The gradual oxygen onslaught could have caused a shift in RNA folding and catalysis from iron to magnesium as iron became more toxic and less soluble. Other researchers have suggested that a similar shift occurred around the same time from iron to manganese in protein enzymes.

        This suggested scenario is one of most interesting aspects of the new paper, says Steven Benner, an expert in the chemical origins of life and director of the Westheimer Institute at the Foundation for Applied Molecular Evolution in Gainesville, Florida. “It implies that the biology-driven creation of an [oxygen] atmosphere required the RNA catalysis at the core of biology to be replaced by proteins. These are big changes,” says Benner.”

        It suggests that 1) RNA evolved because of the presence of massive amounts of iron and H2/CO2 instead of oxygen, 2) protein takeover was destined latest after oxygen came around.

        Iron is a common and rockloving mineral that should be found in all terrestrial crust. H2/CO2 should be initially present on terrestrials that aggregates inside the ice line, because the hydrogen seems to be supplied by physiosorption of water on the dust (can resist ~ 500 K and predicts the now observed same amount of mantle water in Earth-Moon and Mars).

        RNA (and then the stabler DNA replacement after proteins evolve) seems to be selected at the ribozyme level, something I saw elsewhere these scientists would pursue. Then it may be a generic product of chemical evolution on terrestrials.

    3. It turns out to be the strongest support, see my comments on Theobald’s work.

      Conversely, the idea of “a shadow biosphere” is shady. It originated with the Templeton deist Paul Davies, who is interested in astrobiology and cosmology for the reason that as a physicist he can then blow the deist (and Templeton) horn – he always do in his books.

      In my more conspiracy theory of days (but see the observable Templeton award!) I think Davies is aware of biologists skepticism against the feasibility of SETI, a small likelihood for complex multicellulars and/or radio technology capable ETIs out there. Then he can strengthen the ‘specialness’ of humans by having many simple biospheres out there.

      But similarly to SETI skepticism, a shadow biosphere is unlikely IMO. We don’t see its effects on material circulation, on isotope ratios, on competition, on having observed organisms, if it would be too unrelated to the dominant lifeforms.

      And if it would be more closely related, by RNA world divergence say, we would have bottlenecked together through the UCA by prodigious early horizontal gene transfer. In fact, maybe some RNA viruses may have evolved that way.


    1. The process producing the appearance of design in organisms is blind, purposeless natural selection.

    Use “phenotype” instead of “appearance of design”, then add an aside that the adaptation of the resultant organization and function to the environment leads many to mistake this process for purposeful design.

    2. Your point 3 would be better as the first, as the fundamental observation leading to the theory of evolution is the phenotype, not the genotype. Phenotype is the phenomenon, genotype the underlying mechanism.

    3. Fossils in the wrong place

    That the same sequence of fossil types is observed repeatedly in many different places is another fundamental observation leading to the theory of evolution. Simon Winchester’s biography of William Smith, “The Map That Changed the World” mentions that this was well known, though though within a small compass, to miners.

    4. adaptations in one species that evolved solely for the benefit of another species.

    These certainly exist! Just look at any domesticated animal, including (curiously enough) mankind itself, a species you might now describe as self-selected as we conquer diseases that formerly spelled an early death.

    My points 2 and 3 are probably fundamental, and I urge them on you because, in my opinion, getting the history right is helpful in leading people to scientific knowledge. My own field is chemistry. I’ve gradually come to the belief that a historical perspective is an important part of teaching the field as it makes clear (a) the observational basis of the science and (b) the extraordinary difficulty in arriving at our present understanding, something that took a great many very smart people a very long time to formulate.

    Likewise, in evolutionary biology starting with easily observable phenomena and asking “how do we explain these?” puts the student’s understanding on a firm foundation.

    And the development of evolutionary theory into its present form since Darwin’s day has involved a lot of smart people and a lot of time.

    Yes, I’m converting your posting into a proposal for teaching evolutionary biology but all of us here are really thinking “how can we persuade people of the truth of evolution?”

    1. On review, I see I left out something very important: the links between geology and evolution. Not just the stratification of fossils, but the distributions of many living organisms contemplated along with plate tectonic theory.

      Also, biological taxonomy, starting with the Linnean artificial system, played an important role too. Once you group the beetles together, the natural question arises “gee, how’d that happen?”, to which evolution is the answer.

      More fundamental is the fact that science is all about trying to understand how and why things are as they are, the causes of what we see, and the causes of those causes. This contrasts profoundly with the incurious attitude of fundies “It is as it is and that’s that. God did it.”

    2. Domesticated animals are not examples of adaptations that exist solely for the benefit of another species. The animals themselves benefit by having their genes propagated. A strain of sheep that produces better wool, or of corn with sweeter kernels, prospers at the expense of its less useful brethren. This is just normal Darwinian selection, with us as the agents.

      1. Take mankind out of the picture, expose the populations of domesticated animals to the “natural” environment, come back in surprisingly few generations, and you’d find a much smaller population of considerably different appearance.

        Gee, how’d that happen?

        I stand my case.

        1. Take penguins out of the Antarctic and expose them to the natural environment of ostriches, and they probably wouldn’t do very well either. So what?

          Human civilization is the environment to which domesticated species are adapted. It does not follow that the adaptations are not to their benefit. Your argument seems to be that an adaptation that benefits a domestic animal (by inducing us to breed it) would not be of benefit to its wild cousin. Fine, but again, so what? It’s not the wild cousins we’re talking about.

          1. Take penguins out of the Antarctic and expose them to the natural environment of ostriches, and they probably wouldn’t do very well either.

            Which begs the question to me of how well penguins would do in the Arctic. Or, for that matter, Polar Bears in Antarctica.
            Depressingly, we may need to find out.

        2. A better analogy:

          Take bees out of the picture and many species of plant would suffer. Nevertheless, producing nectar benefits the plant (not just the bees) because that’s how it gets pollinated.

          By the same logic, producing beef benefits the cattle because that’s how they get bred.

          1. I think it is more accurate to say that it benefits the cattle’s genes. Given how livestock is raised these days, I wouldn’t want to that it benefits the individual cattle. But the genes for fast-growing, fat-laden, cattle are surely doing better than those for those for doing well in the wild.

          2. It benefits the cattle’s inclusive fitness, which is the only kind of benefit that matters to evolution.

          3. Which part of what I said are you disagreeing with or correcting? (assuming not the missing verb… it should have been “I wouldn’t want to say…”)

          4. Not particularly disagreeing or correcting. Just clarifying that I’m using “benefit” in the same sense as Jerry used it in his original post, and that other kinds of benefit, while perhaps interesting from an animal-rights perspective, aren’t really relevant to the point I’m making.

      2. I tried for a long time to come up with a difference between artifical and natural selection.

        1. They are both evolution in the first place, defined as how and why life changes through time.

        2. There isn’t really any difference. If we spray a field with DDT and corn borers become resistant to DDT, that is natural selection.

        If we take corn borers in the lab and spray them with DDT to select for DDT resistance, that is artificial selection.

        No real difference.

        Humans are natural and an important part of the biosphere by sheer numbers and technology amplifications. We are simply another factor in evolution with huge effects, by human intention or otherwise.

  22. I love this game!

    What would disprove Heliocentrism?

    1. Space probes take pictures of the solar system and find the Sun goes around the Earth after all.

    2. Newton’s laws of gravity and motion turn out to be wrong. Or maybe the Sun is pretty small.

    3. Epicycles. No really, epicycles. I’m not kidding.

    4. Ceiling Cat. ’nuff said.

  23. How about changes to theories in other fields of science that have major implications for Evolutionary Biology? I’m thinking especially of something like a revolution in Physics that suggests the age of the Universe is much less (massively unlikely), or that the Sun is much younger, or the Earth, or that big parts of Geology (Plate Tectonics, Stratigraphy) are shown to be wrong. Again, not bloody likely, but these would be examples of things that would falsify evolution but lie outside the usual area of expertise of biologists.

    1. Creationists that I’ve met have been extremely uncomfortable with (and hostile to) plate tectonics and the idea that the earth’s crust and even its atmosphere have changed drastically over time.

      1. Then they are idiots.

        With modern instruments, we can actually measure continental drift occurring on year or less timescales. We see it happen.

        Not to mention, where plates collide is where the earthquakes and volcanoes happen. I live on the west coast and plate tectonics is a fact of life. We get earthquakes all the time and there is always another one to wait for.

    2. David Brin did a short story about us sending probes out into space and hitting a crystal sphere.

      Another example of a (highly unlikely) discovery in another field that might call evolution into question. 🙂

        1. Ah, sorry, didn’t provide enough information. The protagonists research the sphere and discover that its designed.

          1. But how does THAT call evolution into question. My house is full of things that were designed, some by me. That doesn’t call evolution into question.

          2. I get the gist of the cited Brin story. I think he recently contributed to Larry Niven’s “Known Space” universe, which includes elements of panspermia, alien design of protohuman life, and all sorts of other fun stuff, but also retains a more-or-less naturalistic “hard sf” setting with evolution, human progress by means of science, etc. Larry propounds only asking the reader to believe six impossible things per story, then develop your story on that.

  24. I would add that finding fossil species (or new living species) that have a mix-and-match of features. For example, fossil birds with mammal-like skulls and teeth, or a four-legged amphibian with an additional set of limbs functioning as wings, or a ray-finned fish that lived in ephemeral ponds with fully developed legs and lungs that it could reply in the dry season.

    An intelligent designer can mix and match whatever it wants, but evolution is bound to work with the DNA inherited from the past.

  25. If these were the rule, and not the exception, then it might be weird for evolution:

    – If species in a given environment (say tropical) were more similar to species in similar environments no matter where those environments are located across the planet, rather than sharing greater similarity with species that are in more proximal locations but in different environments.

    – If basic body plans and morphologies exhibited great variation for similar ways of making a living, rather than a relatively small number of body plans and body structures being tweaked for many varied lifestyles.

  26. I disagree with two of the conceivable observations that can falsify evolution. “Adaptations that could not have evolved by a step-by-step process of ever-increasing fitness” Not all adaptive features have to evolve by gradual adaptive steps. Some steps can be neutral, others could be by-products of something else. Finding an adaptive feature and coming up with an adaptive story of its evolution, is – as Lewontin and Gould called it – a just-so story. Secondly, “Evolved “true” altruistic behavior among non-relatives in non-social animals” I think that would disprove adaptionism, not evolution. There is nothing about the process of descent with modification that says we MUST have some selfish interest in every altruistic behaviour. True altruistic behaviour could originate using other mechanisms than Natural selection.

      1. I am not sure if what I said can disprove natural selection. Darwin explained in the origin that natural selection is one crucial mechanism, but not the only one. Prof. coyne knows that neutral processes can over take natural selection, which indicates that adaptationism is wrong, not natural selection.

        1. If you by “adaptationism” means 100 % adaptation behind traits, then it is as rejected as that “lineages” would be if any horizontal gene transfer would be a blow against.

          I think it means that most traits are fixed by selection however that plays out on the gene level (say, drift can kill a fit gene). And in every case the fitness increases in relation, even if environmental change lower it from time to time.

          So it seems like a minor overreach, if any.

  27. What about discovered errors in beneficial/detrimental mutation ratio assumptions or measured genome mutation rates contradicting assumed mutation rates based on phylogenetic trees (chronogram) created from paleoarchaeological records? Something as discussed by Hawkes at http://johnhawks.net/weblog/reviews/genetics/divergence/roach-family-quartet-mutation-rate-2010.html and further here http://johnhawks.net/weblog/reviews/genomics/variation/human-mutation-rate-review-2010.html . Also at Sandwalk here http://sandwalk.blogspot.com/2010/03/direct-measurement-of-human-mutation.html and here http://sandwalk.blogspot.com/2012/03/human-mutation-rates-may-be-lower-than.html

    1. The final estimates are 60 mutations in one of the children and 50 in the other. Both of these values are lower than the calculated rate and when you combine them with earlier results, it’s beginning to look like the actual mutation rate is about half of the calculated value based on biochemistry.

      Looking at Larry Moran’s blog, won’t make much difference.

      1. These are details and interesting but have nothing to do with falsifying evolution.

      2. To point out one simple fact, what is limiting in evolution is usually not mutation rates. It is selection pressure. You see this in adaptive radiations. Where ecospace opens up there is an explosion of diversity and new species by the first ones there. For example, Hawaiaan Drosophila, African cichlids, Galapagos flora and fauna.

      3. The number of mutations per generation vary by a factor of 2 in two studies using different methodologies. The sample sizes for the data are very small. Two children? Really? In my field, for a robust statistics, we like to see 500 to 1,000 data points. Considering the difficulty and expense of doing these studies, it is understandable. I would just report both numbers and say it needs to be sorted out by more experiments. In either case, it has no bearing on whether evolution is true or not.

      I’m not going to bother with the other two cites which seem similar.

      1. I’ll add here that the human mutation rates determined by direct DNA sequencing are similar to human mutation rates determined decades ago by other methods.

        This tells us we have a good idea of what they are and a difference of a factor of two isn’t going to make much difference.

      2. Am J Hum Genet. 1999 December; 65(6): 1580–1587.

        Mutation Rates in Humans. II. Sporadic Mutation-Specific Rates and Rate of Detrimental Human Mutations Inferred from Hemophilia B
        F. Giannelli, T. Anagnostopoulos, and P. M. Green
        Deleted Copyright © 1999 by The American Society of Human Genetics. All rights reserved.
        Summary.We estimated the rates per base per generation of specific types of mutations, using our direct estimate of the overall mutation rate for hemophilia B and information on the mutations present in the United Kingdom’s population as well as those reported year by year in the hemophilia B world database.

        deleted for space reasons

        . Our data suggest an overall mutation rate of 2.14×10-8 per base per generation,

        or 128 mutations per human zygote. Since the effective target for hemophilia B mutations is only 1.05% of the factor IX gene, the rate of detrimental mutations, per human zygote, suggested by the hemophilia data is ~1.3.

        There are many direct and indirect ways to determine human mutation rates. They all yield about the same number.

        When you have independent lines of evidence that converge on the same conclusion, you can have confidence that you are right.

        That is why evolution is such a well tested theory. It is compatible with everything we’ve found since Darwin in physics, chemistry, geology, and astronomy. It could have been falsified by any of the other sciences in the last 150 years. It wasn’t.

  28. I give a list of seven observations that, if repeated and confirmed, would disprove parts of the theory of evolution described above. This shows that it is a scientific theory in the Popperian sense of being falsifiable.

    I should add to that admirable sentiment the not entirely trivial caveat that even repeated and confirmed observation of certain contradicting facts would not be sufficient to consider a theory thus contradicted to be falsified. Here is Popper on the matter:

    We shall take it as falsified only if we discover a reproducible effect which refutes the theory. In other words, we only accept the falsicication if a low-level empirical hypothesis [i.e. a falsifying hypothesis] which describes such an effect is proposed and corroborated. …

    If accepted basic statements contradict a theory, then we take them as providing sufficient grounds for its falsification only if they corroborate a falsifying hypothesis at the same time.(Logic of Scientific Discovery, section 22)

    This is echoed in Stephen Jay Gould’s “Evolution as Fact and Theory”:

    The entire creationist program includes little more than a rhetorical attempt to falsify evolution by presenting supposed contradictions among its supporters. Their brand of creationism, they claim, is “scientific” because it follows the Popperian model in trying to demolish evolution. Yet Popper’s argument must apply in both directions. One does not become a scientist by the simple act of trying to falsify a rival and truly scientific system; one has to present an alternative system that also meets Popper’s criterion—it too must be falsifiable in principle.

    So, a well-tested theory that has proven true with respect to common problems, like Newton’s did for about two centuries, isn’t thrown overboard as soon as the first contradictory fact is discovered. Two things have to happen for actual falsification: our prevalent problems have to evolve into ones that the current theory does not adequately explain; and a new theory has to be developed whose explanatory content is higher than that of the theory it would replace.

    Take Newton again. His theory could not, for example, account for the precession of the perihelion of Mercury. This fact by itself may have been sufficient to drop any pretensions to the theory being the Truth™ about reality, but not for its being dropped entirely. And even although it was eventually superseded as a comprehensive explanation of certain physical phenomena by general relativity (i.e. a falsifying hypothesis of greater epistemic content that became well corroborated itself), Newton’s theory (or at least his formulas, if you want to be strict about it) lives on, in Einstein’s words, as a limiting case of the more comprehensive theory—still good enough, to its enormous credit, to put a man on the moon.

    1. Newton’s equations living on is relevant in another way, in that it shows how scientists keep around useful models even if they aren’t philosophical truth.

      Newtonian mechanics is a correct enough estimate in many cases to get the job done. Its simpler to use than relativistic equations but yields basically the same answer in lost of cases. So we use it for those cases.

      Likewise, its doubtful evolution would disappear from textbooks now even if we discover some modified/replacement theory. Like newtonian mechanics, we could expect that it would continue to be used for that subset of cases for which it (1) works well enough but (2) is simpler to apply than the ‘real answer.’

      1. Interestingly Newton theory is good for placing humans on the moon but not in low earth orbit. Orbital change, docking, landing – all relies on GPS so on GR nowadays.

        Note that GR isn’t the ‘real answer’ either, it is known to be an effective theory too. Effective theories predicts facts as much as more fundamental theories (say, QM), just not as many.

        It is a curious phenomena that philosophy can’t get to grip with facts. Newton theory is a valid part of the everyday physics which is completely understood today. It isn’t rejected, it is accepted as correct within its domain of validity and sufficiently useful in comparison with GR there.

    1. A Darwinian pillar falls hey? Just cos A.J. Bateman did his experiment badly it hardly falsifies sexual selection.

      1. I think this is a point worth making again: an experiment, observation, series of observations, or formulation of a theory done poorly does not count as evidence against the larger theory it was conducted under.

        Science does not rely on argument from authority, which seems to be a major sticking point for many creationists, accustomed as they are to accepting and repeating the speeches of their local authority figures – if Darwin didn’t know about something (his view of heredity was seriously flawed, for example), then all of Evolutionary Biology must be wrong. Similarly, if one famous scientist lied or badly misinterpretted their data, then everything related to their work (not just their own work) must be similarly suspect. These kinds of arguments appear often on this website and similar discussions.
        Was it here or somewhere else that I saw one IDiot claim that because Pluto had been declared not-a-planet, then all of modern physics (and by extension, the rest of science including evolution) must be wrong?

        Science isn’t anywhere near so fragile.

  29. Adding to your list, the following would disprove evolution:

    Biogeographic anomalies. For example, on isolated oceanic islands, we originally find only the organisms that could have dispersed there by natural means. Thus, isolated oceanic islands are devoid of terrestrial vertebrates except for birds and bats. If we found salamanders, frogs, snakes, lizards, rodents, shrews, ungulates, and elephants naturally occurring on Hawaii (the most isolated geographic region on earth), it would cast doubt on evolution.

    Freshwater fish are sometimes found on isolated oceanic islands but they always turn out to be more closely related to nearby ocean fish than to freshwater fish elsewhere in the world. Again, if this were not the case, it would be a biogeographic anomaly that would disconfirm evolution.

  30. Please don’t falsify evolution, mmmmm-k? I haven’t been to church in 45 years and I really don’t want to go back!

  31. I’d put a caveat on these observations that they only work over the long term with stable environments. For instance, altruism could be high-jacked in the short term, repeatedly. Imagine we discover an alien planet and there are many instances where humans give their lives to save aliens with no predictable benefit to the humans. This repeatable pattern, even if every human was willing to do it, wouldn’t be evidence that we didn’t evolve, but rather our altruism evolved in a different environment and this was something new.

    These observations need to be made in long-term stable environments.

  32. Any new evidence that disproved evolution would quite likely simultaneously disprove many other fields such as genetics, plate tectonics, radiometric dating and so on.

    There is so much over lapping and consistent data from diverse fields of science supporting evolution that it’s highly unlikely that only evolution would be affected by such a discovery.

    1. Any evidence against evolution might be completely out of left field.

      Say we discovered that a species of dinosaur had mastered genetic engineering – might not “disprove” evolution – but it might radically alter our conception of it, with little impact on other scientific fields (except paleontology). Unlikely, but the dinosaurs were around for a long time, and we’ve only just found evidence for them eating grass in the Cretaceous, there is plenty of room for whole civilisations to have risen and fallen in the gaps of our knowledge. Indeed our view of Greek engineering has taken a boost with the Antikythera mechanism and that is basically within recorded history (although not recorded in as much detail as we would like).

  33. Great post Jerry. I’ll add a few of my own that hopefully make sense:

    1. No weaknesses or imperfect adaptations in species. For humans, no blind spot, or appendix, or urethra trapped within a prostate gland (for males). Even better, for all mammals, no left recurrent laryngeal nerve. (I’ve recently seen the documentary where the Giraffe’s neck was opened and the nerve traced. Incredible.)

    2. No vestigial organs. No hind legs buried in the tissue of whales.

    3. No convergent evolution. A continent like Madagascar would have a fossa living like a normal mongoose, not evolving to fill the niche normally occupied by cats. Same goes with lemurs and monkeys.

    4. No sexual selection. No dimorphism between males and females in species. If they were created perfect in the first place why should the sizes alter?

    Keen to get my test results now!

    1. No atavisms which are different from vestigal features.

      No whales born with legs which sometimes happens.

      No humans born with tails which also sometimes happens. No humans born covered with fur, rare but known.

  34. I don’t think the theory of evolution can be disproved anymore. It’s so big, regular observations won’t affect it. They will remain there, uncomfortable and ugly until someone explains them in terms of the theory.

    I take issue with your idea of altruism. “In this “true” altruism your genes give benefits to others and get nothing back, and this shouldn’t evolve under natural selection. And, indeed, we don’t see such altruism in nature.”

    We do see it, more than occasionally. Adults will adopt babies from other families or even species as a byproduct of a general maternal instinct – time, energy and resources for which the adoptive parents get no evolutionary gain. Not every trait built by natural selection is as finely-tuned as you imply. Many times “good enough” really means “good enough” and further improvements have no effect on fitness.

  35. http://en.wikipedia.org/wiki/Transfusion_(short_story)
    This is a precis of a story about humans being planted one earth by aliens (human aliens}. Chad Oliver, the author, was an anthropology professor at University of Texas. There is a Chad Oliver teaching award named in his honor. To name drop, I took introductory physical anthropology from him. He wrote fiction illustrating anthropological themes. This story illustrated the constraints of culture in attempting to solve problems.

  36. This is a really great post and thread (say, reminding us about the biogeography that was so important for Darwin and Wallace both, unless I am mistaken)! Thanks all for the comprehensive list.

    I don’t really have much to add but rather what I believe expands and strengthens of #3 & 4.

    – My preferred stronger observation (i.e. demanding less) is that tree structures, whether resolved to bi-, tri-, … n-furcations maps to nested sets. Some observation on the math of trees in computer science that I picked up on the web.

    – The generalization is that a structure of nested sets appears to be a fact for genes, so traits, so populations (and so species).

    So any observations that break the nesting in general would be a test: too many fossils in the wrong place (order), too many populations in the wrong place (biogeography), too many traits in the wrong place (literary, on the organism), too many genes in the wrong place (too much horizontal gene transfer and you would have something else than evolution I presume – an amorphous “population melt”).

    Relatedly, since we are on the topic of what would test evolution, it could be interesting to look for the dual question what would predict evolution. (In a sense of dual somewhat analogous to the physical sense.)

    My own idea is that nested sets in biology can only be predicted by a process of populations descending through inheritance to populations. I don’t know how to make that formal however. Conversely, it makes the test above as a true dual should.

    So unless my handwaving is too weak it should be a core concept (but you knew that).

  37. Your penultimate point remains unfalsifiable because the notion of recipricol expectation is an unfalsifiable response to every claim of “true” altruistic behavior. Does a bat really regurgiate because of an expectation? Who knows and who can know?

    Otherwise, I have been convinced. Thank you for the post.

  38. I see what you did there. You went to one of those university things and got a high-level science education. You researched peer reviewed studies and, probably, did some repeatable experiments yourself, furthering the truth of the theory of evolution. I bet you even got to understand the scientific definition of “theory” along the way, as well.

    Well Jerry, that’s just cheating. How do you expect to counter the arguments of those who have only read one book, the Bible, using only scientifically proven facts?

    My advice would be to create the First Church of Evolution and find some random bit of the Bible, or some other text “written” by one of the other 3,500 to 4,000 gods, to “prove” evolution, go on the TV and evangelise about it, and rake in millions of dollars.

    Oops! I’ve just thought of a problem with that. Rational, thinking, educated people wouldn’t waste their money joining or giving to a cause based on superstition, supernaturalism and myths. I guess you’ll just have to stick with science and hope that better education will lead to a better understanding of our universe. The US could start with banning home-schooling, especially by creationists and religious fundamentalists.

    Excellent article, by the way.

  39. Jerry has it generally right about ways the theory of evolution could be falsified, but a major weakness in his blog here and in his book is the conflation of “the theory of evolution” with natural selection as the primary mechanism by which evolution occurs. Evidence of descent with modification is overwhelming and can’t seriously be challenged. But natural selection as the primary mechanism of change can seriously be challenged and I’ve raised a number of issues, including the too-often-swept-under-the-rug issue of tautology/circularity, as well as possible solutions, in this paper:


    I’d appreciate any feedback from those in this forum or from Jerry.

  40. Hi. I have a question, I am a religious person in the sense that I go to church and believe creationism. However I wish to give the entire argument a fair hearing and thus decide what I will hold to…

    Can you please give a suggestion on a place to start? I just find the the reading I do gets so convoluted, as a lay man with regards to much of science I read an evolutionary article, then a creationist article on the same subject and then Im just lost- everyone claiming the other redefines terms and so much… what do you suggest for someone like me?

    Or is the only answer to become a professional in the subject?

    1. Read, Justin. One place to start is the fine book written by our host: Why a Evolution Is True. There are countless others. And you don’t need to be a professional.

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