Good Math, Bad Math

Today’s bit of basics is inspired by that bastion of shitheaded ignorance, Dr. Michael Egnor. In part of his latest screed (a podcast with Casey Luskin of the Discovery Institute), Egnor discusses antibiotic resistance, and along the way, asserts that the theory of evolution has no relevance to antibiotic resistance, because what evolution says about the subject is just
a tautology. (I’m deliberately not linking to the podcast; I will not help increase the hit-count that DI will use to promote it’s agenda of willful ignorance.)

So what is a tautology?

A tautology is a logical statement which is universally true, by nature of its fundamental structure. That is, even without knowing anything about what the statement means,
you can infer that it must be true.

To make that a bit clearer, let’s look at a couple of the most classic examples of tautologies.

  1. “A⇒A” – A implies A. You don’t need to know what A means. You don’t need to know if A itself is a true or false statement. The statement that A implies A: that is, if A is true, then A must be true – must be true.
  2. “A∨¬A” – A or not A. In classical first order predicate logic, either A is true, or A is false. So A or not A must be true. Again, we don’t need to know what A means, or whether A is true or false; it doesn’t matter. This statement must be true.
  3. “(A⇒B)∧A⇒B” – A implies B and A implies B. This is just a basic statement of one of the fundamental inference rules of logic. Once again, it doesn’t matter what A means, or what B means; and it doesn’t matter whether A or B are true or false. No matter what, by virtue of the structure of the statement, it must be true.

That third tautology is particularly important – because it’s an example of a fundamental principle of logic. If you take any proof – any sequence of statements and valid inferences from those statements – and you combine all of the statements of the proof together, the resulting statement is, by definition, a tautology. The obvious implication of this is that you can take any statement which is provably true, and present it as a tautology.

And this brings us to Egnor’s idiocy. It’s a common tactic among idiots to criticize various scientific theories as tautological. And it’s pretty much always done to mislead. Because all actual scientific theories are based on inferences from observations, and use the result of those inferences predict that future observations will match prior observations. So by taking the statement of the observation and the inference, you can derive a tautological statement from any scientific theory.

The theory of gravity? If you let go of something, it will fall – therefore, if you let go of something, it will fall.

Relativity? Light bends when it passed through a gravitational field – therefore, if I shine a light through a gravitational field, it will bend.

Evolution? The things that survive to reproduce are the things that survive to reproduce.

Tautological statements of theories don’t invalidate the theories; and they don’t mean that the theories are useless and have no explanatory value. The only time that a tautological statement of a theory is a problem is when it’s the only statement of the theory – that is, when the theory itself consists of nothing more than a tautological structure. A theory that consisted of nothing more than the fundamental statement “A=A” isn’t a theory – it’s gibberish dressed up to look like a theory.

For an example of where tautological reasoning is a problem, you can do things like look at
arguments presented by lazy objectivist/liberatian Ayn Rand worshippers. Please note that I’m not saying that all objectivist libertarians use this kind of nonsense – I’m describing arguments by intellectually lazy objectivist libertarians! The fundamental statement of Rand’s philosophy is “A=A”. But a lot of lazy objectivists take that, and use it to make ridiculous arguments. The arguments are ridiculous not because they involve a tautology, but because they use a tautology in place of an actual argument. You can find objectivists arguing that, for example, tax=theft, because tax=”government taking your property away from you without your permission”, and theft=”someone taking your property away from you without your permission”. But the real argument there isn’t in the “A=A” part = it’s in the definitions chosen for “tax” and “theft”. To make the objectivist/libertarian argument about taxes, you need to justify the definitions – not just assert definitions, and then use the tautological equivalence of the unjustified assertions as your argument. If you read some objectivist literature, you can find some pretty good arguments about why that definition of tax is valid. But most of the time, you have people just blindly spewing the definition, and then shouting “A=A” at the top of their lungs when anyone tries to disagree with them. To repeat, the problem isn’t that there’s a tautology – it’s that the truth of the tautological statement is used as the whole of the argument, when in fact, the argument relies on the truth of something other than the tautology. The libertarian argument about taxes is not a simple “A=A” argument. It relies on the inference that there exists an A such that taxes=A, and there exists a B such that theft=B, and that A=B, therefore taxes=theft. The step of showing the validity of defining taxes and theft as equivalent things is crucial – and omitted from the lazy version of this argument.

To return to Egnor: he asserts that the theory of evolution is irrelevant to bacterial resistance to antibiotics, because after all, all that evolution says is “If you have an antibiotic that doesn’t work on a bacterium, then that antibiotic won’t work on that bacterium”.

Well, yeah. It does say that. But it also predicts that if you use antibiotics on some population of bacteria, and you don’t kill all of them, that over time, the population of bacteria will change to become resistant to the antibiotics.

As I mentioned over at Mike’s blog, this is something that’s become quite personal to me, because my father has gone through a horrible medical crisis in the last few months caused by
a highly antibiotic-resistant strain of staphylococcus aureus. A strain of staph that
had never been observed as recently as 10 years ago, and which is dramatically different from its ancestors. A strain which is the result of an evolutionary process, where non-resistant bacteria were wiped out, and resistant bacteria filled the niche left behind. Where that simple tautological statement: “if an antibiotic doesn’t kill a bacteria, then it doesn’t kill the bacteria” is a precise description of how the bacteria that paralyzed my father came into being.

So remember: next time someone tries to convince you that you should ignore something just because it’s a tautology, what they’re really saying is, “This is true, and I can’t make any argument that it isn’t”.

Comments

  1. #1 G Barnett
    March 14, 2007

    And then there’s my favorite (and just a wee bit off-topic) definition of Tautology:

    The study of Audrey Tautou. Rowr. ;)

  2. #2 Blake Stacey
    March 14, 2007

    G Barnett:

    I like that definition. I’ll file it alongside the one I heard for euthanasia: “a student population generally better at math and science than euthanamerica”.

    (-:

    MarkCC:

    I can only offer my sympathies for your father’s medical troubles, and express my sincere hopes that he defeats the staphylococcus.

  3. #3 Roy
    March 14, 2007

    There’s an additional problem with the little critters that most medical people forget — strains are emerging that the tests for the presence of their ancestors no longer detect them.

  4. #4 TomS
    March 14, 2007

    (A⇒B)∧A⇒B

    I assume that you mean

    ((A⇒B)∧A)⇒B

  5. #5 Noodle
    March 14, 2007

    TomS said:

    (A⇒B)∧A⇒B

    I assume that you mean

    ((A⇒B)∧A)⇒B

    I thought he meant something like:

    (A⇒B)∧(B⇒A)

  6. #6 Torbjörn Larsson
    March 14, 2007

    And it’s pretty much always done to mislead.

    Exactly like another common misconception ‘can’t prove a negative’. Though the lazy libertarian variant of tautology is close to what I think is the originally intended critique here, “just so stories”.

    As the post explains, an isolated ad hoc without contact with other theory is in a sense analogous to a tautology, describing precisely what it is designed to describe. Even if it does so well, it is likely to be wrong when a more fundamental theory comes along. Or worse, it is put “just so” without checking the prediction.

    The egnorance (Egnorance. (n) The egotistical combination of ignorance and arrogance.) of being not even wrong or that this is all of evolutionary theory not withstanding. The IDiots base claim here that evolution is tautology is also (not correct).

  7. #7 Torbjörn Larsson
    March 14, 2007

    Uups. That was supposed to be “The IDiots base claim here that evolution is tautology is also not correct.”

  8. #8 Beren
    March 14, 2007

    (A⇒B)∧(B⇒A) is not a tautology, though, so presumably that isn’t what he meant (:

  9. #9 Scott Hill
    March 14, 2007

    Please don’t confuse Libertarians with Objectivists. And please try to avoid saying things like “The fundamental statement of Rand’s philosophy is “A=A”.”, because that’s a horrifyingly simplistic generalization. Objectivism is an entire philosophy, not something that can be summarized in three characters.

    Other than that, I thank you for your extremely helpful explanation of the use and definition of tautology.

  10. #10 Norm Breyfogle
    March 14, 2007

    Excellent demonstration of tautology problematics, Mark CC.

    I like using such demonstrations in showing the biases of various God concepts: if God is omnipresent, omniscient, omnipotent, the absolute ground of all being, etc., then the “proof” for “his” existence is an absolutely true tautology: Existence is = God is. But these assumed traits of “God” thus describe unqualified exitence itself, NOT any particular, personal God.

  11. #11 SteveM
    March 14, 2007

    My favorite tautology is “The Bible says it is the word of God. The Word of God is Truth. Therefore the Bible is Truth”.

  12. #12 tgibbs
    March 14, 2007

    Thank you, Mark, for explaining out why I nearly have a fit every time I hear that moronic “natural selection is a tautology” objection, and then get almost as annoyed when I hear defenders attempt to claim that it is not.

    Of course it is a tautology, which means that it has to be true. Living organisms are required to evolve by the nature of inheritance. The only valid scientific question is therefore whether this compulsory mechanism is sufficient to explain all of the observed variation–a question that must be (and has been) answered by observational data.

  13. #13 Ike
    March 14, 2007

    Yes, that’s on of the most idiotic comments ever – but the mechanisms of the evolution of anti-bacterial resistance are very interesting from an evolutionary point of view, first of all because the basis of normal evolutionary theory, i.e. the reproductive isolation definition of a species, just doesn’t work very well for microbes, who are notorioulsy promiscous with their genetic material.

    This works via plasmids (little loops of DNA), largely, and gene transfers. Imagine a little bacteria that happens to have a gene for antibiotic resistance – say a gene for an enzyme that rapidly digests the antibiotic. The gene can hop from the chromosome to the plasmid and then the bacteria can transfer the plasmid to another distantly related bacteria. This process can then repeat – hence, the evolution of multi-drug resistant plasmids due to the poorly thought out use of antibiotics.

    This is why people need to know about evolution – if you fail to complete your antibiotic regimen, that can lead to the evolution of drug-resistant strains.. it’s also why antibiotics should not be used unless they’re really needed. The opposite side of the question is how did antibiotics evolve in the first place? Answer: the ongoing struggle in the soil between fungi and bacteria for food – biochemical warfare in nature.

    As far as tautology goes, I think the use in this context can be explained thus:
    “Me scientist. Me use big word. Hoot! Hoot! Hoot!”

  14. #14 Richard Edwards
    March 14, 2007

    I wish I was a tautologist, because then I would be a tautologist.

  15. #15 Guillermo Alcántara
    March 14, 2007

    Hi, happy PI day!! I thought I would see some balloons here…

    Anyway, sorry for commenting about something not related… now I’ll proceed to look for the infinite continued fraction of pi…

  16. #16 Torbjörn Larsson
    March 15, 2007

    Of course it is a tautology, which means that it has to be true.

    Of course theories and phenomena are both tautologies and not tautologies. If they exist they are true. But the point is that they don’t have to.

    This comes back to the other subversion of the term. By claiming that a theory is a tautology, the anti-scientists try to make it out as a philosophy by axiom instead of a science by observation.

    Btw, there are several levels of possible tautologies (reality, reality + model, model, within model) and non-tautologies (observations, observations + model) here.

  17. #17 Mark
    March 15, 2007

    I notice that only one other person has done so, even though it is vitally important, so does anyone mind if I “third” the views about Audrey Tautou?

    Audrey Tautou ∧ Rowr! = TRUE

  18. #18 Antonios
    March 15, 2007

    It depends though on whether or not a tautology says anything about the real world.

    For instance, a syllogism such as the following:

    1) Men are sexy
    2) I am a man
    3) Therefore, I am sexy

    This is absolutely correct analytically, or in other words, according to the definitions supplied.

    But to prove whether or not men really are sexy or whether or not I really am a man requires empirical observation and cannot be determined simply due to the definitions supplied.

    Once it has been observed and confirmed that men really are sexy and that I am a man, the conclusion “I am sexy” can be predicted and confirmed by observation.

  19. #19 Ergo
    March 16, 2007

    To say that A=A has no explanatory value is to reveal intellectual ignorance. It is only when we understand and accept that A=A, can we proceed to A is not non-A, B is B, A is not B, etc.

  20. #20 Reb Cabin
    March 16, 2007

    I think you’re saying that “tautological statements are not necessarily empty statements.”

    “2=2″ is an empty tautology.

    “2 = 1+1″ is, at one level, a tautology, but to get to that level, one must understand the definition of “+”, and that’s not an empty definition. So, to appreciate the tautological nature of the statement, one must understand something external to the statement itself.

    There’s a bit of semiotics in what I wrote there. Maybe I’m way off.

    My favorite ‘tautology-cum-empty statement’ is the anthropic principle, which I read as “We’re here in the Universe because if we weren’t here we wouldn’t be able to wonder why we’re here” or something along those lines. It’s evidently true, so I guess it’s a tautology. But it sure seems empty to me.

  21. #21 Torbjörn Larsson
    March 16, 2007

    My favorite ‘tautology-cum-empty statement’ is the anthropic principle,

    Yes, there is a tautological AP. It says that the conditions we observe must be compatible with our existence, and it is valid in all cosmologies.

    But there are others. The next stronger (and the most studied today) is the weak AP. It says that the conditions we see were probable, and it is supposedly valid in cosmologies that allows probability distributions for parameters.

  22. #22 snaxalotl
    March 18, 2007

    I love this very clarifying post, but I feel like you missed a step. The complaint consistent with your series would be:

    Evolution? The things that survive to reproduce are the things that survive to reproduce, therefore the things that survive to reproduce are the things that survive to reproduce.

    To me, the basic observation of evolution (rather than observation + consequence) is The things that survive to reproduce are the things that survive to reproduce. Creationists complain that this is circularity (and therefore the bad, lazy objectivist type of tautology), but the point is that this statement is a description of a positive feedback system, not an argument, and so is not dismantled by its circularity. It is not supported by itself, but by evidence external to itself. It is not a fatuous A=A because it really means The things (or attributes) which … reproduce in one generation are the things … that reproduce in later generations.

    Creationists certainly make cretinous attacks on the “problem” that predictions are effectively restatements of theories (most of paleontology springs to mind), but their problem with survival of the fittest is a different straw man

  23. #23 Leni
    March 18, 2007

    I’m really glad you posted this.

    I encountered someone a few years ago with this argument, and I hadn’t seen it before but it really threw me for a loop. I mean, it is technically true!

    Ultimately I dismissed it because it failed to explain predictability, but that was my only reason and I could barely articulate that. F=ma is true by definition. But also because it works. I can use it to predict specific outcomes, not just to describe things that have already happened. But I think the way you put it was really good.

    Also, I’m so sorry for your dad and I wish the best for you and your family. My father died from a nasty infection a few years ago. He spent nearly 3 very painful comatose weeks in the hospital before we let him go. I know just how you feel about Egnor’s remarks. They are not just idiotic, but insulting- especially given the harsh reality, and especially coming from a doctor. And ultimately, if everyone believed them, they’d probably also be harmful.

  24. #24 Torbjörn Larsson
    March 18, 2007

    The things that survive to reproduce are the things that survive to reproduce. Creationists complain that this is circularity

    And if one is nitpicky, it is actually not a circular part of the model itself. Fitness means the characteristics to survive to reproduce, but not a guarantee. (Shit happens.)

    It is not supported by itself, but by evidence external to itself.

    I think this is true, which is a bit hidden in the post’s description. Future observations shouldn’t be included in the current support to imply circularity, even if they are predicted to be. (Unless one has a static, philosophical view of complete knowledge.) After all, the theory could possibly be wrong.

  25. #25 truth machine
    March 18, 2007

    Because all actual scientific theories are based on inferences from observations, and use the result of those inferences predict that future observations will match prior observations. So by taking the statement of the observation and the inference, you can derive a tautological statement from any scientific theory.

    You’re rather confused; you can’t “take” the statement of the observation:

    The theory of gravity? If you let go of something, it will fall – therefore, if you let go of something, it will fall.

    There’s no tautology there, since it isn’t necessarily true that, if you let go of something, it will fall. “If it’s true that, if you let go of something, it will fall, then, if you let go of something, it will fall” is a tautology, because it’s a specific case of P implies P.

    Relativity? Light bends when it passed through a gravitational field – therefore, if I shine a light through a gravitational field, it will bend.

    There’s no tautology there, because it’s not necessarily true that light bends when passed through a gravitational field. “If light bends when it passed through a gravitational field, then if I shine a light through a gravitational field, it will bend” is a tautology, because it’s a specific case of P implies P.

    Evolution? The things that survive to reproduce are the things that survive to reproduce.

    That is a tautology, because it’s a specific case of P=>P (if something is in the set of things that survive to reproduce, then it is in the set of things that survive to reproduce), but it isn’t at all in the same form as the previous examples.

    It would seem that, as was the case with Godel, you really don’t know what you’re talking about here.

  26. #26 truth machine
    March 18, 2007

    TomS said:

    (A⇒B)∧A⇒B

    I assume that you mean

    ((A⇒B)∧A)⇒B

    I thought he meant something like:

    (A⇒B)∧(B⇒A)

    Why would you think that? What TomS wrote is a tautology, corresponds to what MarkCC wrote about it, and simply adds some missing parentheses to MarkCC’s formula, whereas what you thought he wrote isn’t a tautology, doesn’t correspond to what MarkCC wrote about it, and has no relationship to MarkCC’s formula. I could see it if you wrote “I thought he meant … but I now see I was wrong (duh), thanks” or “I thought he meant … but I obviously don’t understand this stuff at all, so you’re probably right; thanks”, but instead you wrote something that amounts to “I’m an ignorant dolt who is so arrogant as to think that my baseless opinion is more valid than that of people who actually know something”.

  27. #27 Mark C. Chu-Carroll
    March 18, 2007

    tm:

    Please tone down the personal insults. There is absolutely no reason to do things like other commenters “ignorant dolts” and such. I don’t mind strong opinions, and I don’t mind commenters insulting me, but I really object to commenters insulting each other.

  28. #28 truth machine
    March 18, 2007

    My favorite tautology is “The Bible says it is the word of God. The Word of God is Truth. Therefore the Bible is Truth”.

    That’s not a tautology or anything like one, it’s a circular argument (and a flawed one at that; proper circular arguments are valid).

  29. #29 truth machine
    March 18, 2007

    I hear that moronic “natural selection is a tautology” objection, and then get almost as annoyed when I hear defenders attempt to claim that it is not.

    Of course it is a tautology

    “natural selection” isn’t even a statement, let alone a tautology, moron.

  30. #30 truth machine
    March 18, 2007

    There is absolutely no reason to do things like other commenters “ignorant dolts” and such.

    You’re wrong, there are reasons. And I didn’t call anyone an ignorant dolt — please work on your reading comprehension skills. I did, however, call tgibbs a moron, but that’s because he accused others of being morons.

  31. #31 truth machine
    March 18, 2007

    Damn the broken html parsing at scienceblogs. Try

    I hear that moronic “natural selection is a tautology” objection, and then get almost as annoyed when I hear defenders attempt to claim that it is not.

    Of course it is a tautology

    “natural selection” isn’t even a statement, let alone a tautology, [that insult that you apply to others].

  32. #32 Mark C. Chu-Carroll
    March 18, 2007

    tm:

    Second warning. (And playing semantic games is no excuse. We both know that the comment you directed at TomS *was* intended as an insult; pretending that just because you put it in quotes surrounded by weasel-phrasing doesn’t change that. Surely you’re capable of correcting other peoples errors without casting those errors into unnecesarily insulting terms?)

    Insult me all you want; but if you insist on insulting other commenters, I’m going to start editing out the insults. I’d really hate to do that; the only one I’ve ever done it to before is John Davidson.

  33. #33 Mark C. Chu-Carroll
    March 18, 2007

    To get back to substance:

    I think that the only way to characterize “tgibbs” comment in an insulting way is to pretend that when he talks about creationists and the “natural selection is a tautology”, that what he means is that the words “natural selection” are a tautology.

    But as pretty much anyone who even read the original post knows, “natural selection is a tautology” is a reference to an incredibly common and annoying creationist argument. The argument in full blown form is “Evolution is a meaningless theory, because it’s all based on a tautology: the fittest individuals are the ones that survive to reproduce. Why are they the fittest ones? Because they’re the ones that survive to reproduce. So the theory of evolution really says nothing more than ‘The individuals who survive to reproduce are the individuals who survive to reproduce’.”

    (And even that is a somewhat abbreviated form of the argument.)

    I don’t think that expecting other commenters to type out that whole thing is reasonable, when everyone reading it knows what “the natural selection is a tautology” argument refers to.

  34. #34 truth machine
    March 19, 2007

    We both know that the comment you directed at TomS *was* intended as an insult

    I didn’t deny that. You really have a problem with accuracy, which helps to explain your mistakes concerning Godel and tautologies, among others. But I didn’t call him an ignorant dolt; I pointed out that he wrote the sort of thing that we might expect such a person to write.

    As for tgibbs and what he meant, you’re clueless. He wrote “and then get almost as annoyed when I hear defenders attempt to claim that it is not”, which exactly what you (reasonably) just did. He wrote “Of course it is a tautology, which means that it has to be true. Living organisms are required to evolve by the nature of inheritance” — but that’s not a tautology; in case you already forgot,

    A tautology is a logical statement which is universally true, by nature of its fundamental structure. That is, even without knowing anything about what the statement means, you can infer that it must be true.

    I don’t think that expecting other commenters to type out that whole thing is reasonable

    I don’t it’s reasonable to assume that everything that some supporter of evolution writes is valid, without bothering to pay attention to what he actually did write.

    As for “warning” me that you might start editing things out of my comments, it’s rather silly. Why should I be concerned that you might edit out the very thing that you’re asking me not to include in the first place? If you’re going to make a threat in order to curtail some action, at least make the threat stronger than the action to be curtailed. Sheesh.

  35. #35 truth machine
    March 19, 2007

    Surely you’re capable of correcting other peoples errors without casting those errors into unnecesarily insulting terms?

    In this case, the error was arrogance. I’m capable of many things, but I actually consider what I wrote to be a rather effective way of expressing the nature of the error. You might want to go back and read it carefully, instead of being so reactive — ooh ooh, he used a bad word!

  36. #36 truth machine
    March 19, 2007

    BTW, isn’t “Pigheaded Egnorance” an insult? Surely you’re capable of correcting people’s errors without casting those errors into unnecesarily insulting terms? Would it be insulting for me to point out that you’re being hypocritical? Perhaps you want to argue that insulting members of the other tribe is ok, but those of our own tribe must be protected from the contempt they earn, and how that contributes to honest inquiry.

  37. #37 Prince Roy
    March 19, 2007

    Please tone down the personal insults. There is absolutely no reason to do things like other commenters “ignorant dolts” and such.

    This is quite the double standard, seeing as how you refer to Egnor as a ‘bastion of shitheaded ingnorance’ and refer to him as an ‘idiot’ numerous times.

    Of course, you are on the correct side of the argument here vis a vis evolution, but if you don’t employ a higher standard of civil discourse yourself, how can you expect that your commenters will act any differently?

  38. #38 truth machine
    March 19, 2007

    how can you expect that your commenters will act any differently?

    Actually, I did act differently; my insults weren’t gratuitous. My “ignorant dolt” played a critical role in a lengthy pedagogical comment, the content of which seems to have completely escaped Mark. And tgibbs complained about “that moronic ‘natural selection is a tautology’ objection”, and yet his claims were at least as moronic; I simply applied his standard to himself, as opposed Mark’s dishonest application of different standards to those who support and those who deny evolution. tgibbs thinks that “natural selection” or evolution actually are tautologies: “it has to be true. Living organisms are required to evolve by the nature of inheritance” — but that’s not a tautology at all, as it isn’t a logical necessity that living organisms evolve due to “the nature of inheritance”, whatever the heck that is. Aside from how different things would be with different laws of physics, put a bunch of living things in the middle of the sun and see whether they evolve — “the nature of inheritance”, whatever it is, doesn’t have the logical force to cause them to evolve. At least what creationists claim is a tautology (spelled out by Mark) is one — while being a strawman that has nothing to do with the basis of the theory of evolution, unlike the quite non-tautological, observable fact that natural selection plus random mutation results in evolution due to the contingencies of biochemistry on Earth.

  39. #39 truth machine
    March 19, 2007

    And actually, it’s more than just biochemistry; cell metabolism and reproduction are heavily dependent on the non-organic environment, chemical and physical. If “it has to be true. Living organisms are required to evolve by the nature of inheritance”, if that were a tautology, then we would see living things on every planet, on the sun, floating in empty space, everywhere. There wouldn’t be a single square inch, in this world or any other possible world, where living things would not evolve, if that were a tautology — a logical necessity. One the other hand, “The individuals who survive to reproduce are the individuals who survive to reproduce” is a tautology, it is logically necessary, but it doesn’t imply that evolution occurs — the creationists are right about that. What they are wrong about is whether that is what Darwin meant by “survival of the fittest”; he of course did not. He was talking about the fittest individuals — those most likely to produce offspring — passing (with modification) the traits that made them the fittest on to their offspring. That isn’t a tautology at all, as it depends on a mechanism for passing traits that was quite unknown to Darwin and that certainly is not logically necessary.

  40. #40 David Marjanović
    March 19, 2007

    My favorite tautology is “The Bible says it is the word of God. The Word of God is Truth. Therefore the Bible is Truth”.

    That’s not a tautology. It’s an invalid two-step logical conclusion. Here is the first step:

    1. The Bible says it is the Word of God.
    2. The Word of God is Truth.
    3. Therefore the Bible says it is Truth.

    We could quibble with the second premise — after all, the only “evidence” we have for it is the Bible itself, so this premise is based on the conclusion — but for the sake of the argument let’s accept it. The conclusion is drawn and used as a premise for the second step:

    1. The Bible says it is Truth.
    2. If something claims to be X, it is X.
    3. Therefore the Bible is Truth.

    The second premise of this argument is obviously wrong, which invalidates the conclusion; there’s no tautology involved.

  41. #41 Torbjörn Larsson
    March 19, 2007

    but if you don’t employ a higher standard of civil discourse yourself, how can you expect that your commenters will act any differently?

    Actually, Mark has explained his comment policy before, and IIRC it amounts to just that. I.e. the posts may be expressive to drive the point home, but the comments should be a normal measured discussion. I think; I can’t find the comments right now, and I expect that Mark may explain this himself and correct my vague memories.

    When bounded logics hounds such as truth machine or Caledonian on Pharyngula enters, exchange of information will become difficult and it will often be more about the truthiness of the ways the discussion is made than about the truth in it. Especially when they go into rant mode.

    And that is the truth. :-)

  42. #42 Torbjörn Larsson
    March 19, 2007

    exchange of information will become difficult

    Obviously, I forgot a ‘will “often” become difficult’. And seeing that tm contributes well and good in another thread here, the mistake stands out the more.

  43. #43 mgarelick
    March 19, 2007

    A strain which is the result of an evolutionary process, where non-resistant bacteria were wiped out, and resistant bacteria filled the niche left behind. Where that simple tautological statement: “if an antibiotic doesn’t kill a bacteria, then it doesn’t kill the bacteria” is a precise description of how the bacteria that paralyzed my father came into being.

    OK, this is where I don’t understand exactly what’s happening. If “resistant bacteria filled the niche left behind,” then it seems that, although the resistant bacteria flourished and took on a significance that they did not have before, they did not really “come into being”. I think there must be another step here that I don’t know about. Anyone have a simple (or at least accessible to a history major) explanation?

    (My guess: several iterations of mutation and selection produce a strain that literally did not exist at step one.)

  44. #44 Mark C. Chu-Carroll
    March 19, 2007

    mgarelick:

    Evolution isn’t a simple one-step process. Naive descriptions of it often make it sound like mutations occur in response to some kind of selective pressure. That’s not, in general, the way that it works. Selective pressures can only select from genes that exist in the population. Mutation is a separate process.

    In the course of normal reproduction, mutations occur. If those mutations aren’t lethal, then they’ll be passed on to some part of the population.

    So things like antibiotic resistance don’t come into being in response to selective pressures. Bacteria are constantly mutating, and the ones with the traits that allow them to reproduce most successfully in their environment are the ones that survive.

    What antibiotic use does is change things so that individuals which might have been less fit in an antibiotic free environment can become a dominant strain. For example, in an antibiotic free environment, bacteria that produce β-lactamase are less fit, because they devote significant amounts of its energy/resources to the production of β-lactamase, which is useless in that environment. It won’t die off – nothing about producing β-lactamase will kill it – but since it wastes energy and resources, other bacteria will out-reproduce it, and it will remain a very small part of the population.

    But put it into an environment where it’s likely to be exposed to penicillin – and the bacteria that don’t produce β-lactamase become the less fit ones – whenever penicillin is introduced, they die, but the β-lactamase producers survive. So the population changes: the mutation to produce β-lactamase, which was a negative in the prior environment becomes a strong positive in the new environment.

    Most antibiotic resistance occurs this way – the resistant variants occur naturally, but they tend to remain a small part of the population. But widespread use of antibiotics changes the picture, so that the small part of the population that is resistant becomes a much larger – or even dominant – part of the population.

  45. #45 mgarelick
    March 19, 2007

    Mark: thank you for your answer. I hope you don’t mind if I ask another question. As I read your answer, it seems that the widespread use of antibiotics affects the characteristics of the population, i.e., the proportion of bacteria that is resistant to the antibiotics, but it doesn’t change the characteristics of any individuals (by which I mean individual descendants, not existing individuals). In other words, every strain of bacteria that exists after the introduction of antibiotics also existed prior to the introduction. It’s hard for me to see how this constitutes evolution, except in the plain vanilla “change over time” sense. OTOH, if this happens more than once, then there will be strains which are different from any strain that existed before the process started. Make sense?

    And as long as I’m here: do you have a quick answer to why Ralph Seelke’s experiment (purporting to demonstrate irreducible complexity by showing inability of evolution to do two things at once) is wrong?

  46. #46 Mark C. Chu-Carroll
    March 19, 2007

    MGarelick:

    As I said – evolution isn’t a one-step process.

    Focusing on bacteria:

    You have a population in which mutations are steadily occuring. That’s a key piece of the puzzle. You also have selective pressures, causing some individuals to reproduce, and some to die.

    You can start with a single bacteria in a culture dish. Let it reproduce for a while, and you’ll have billions of individuals. And those billions of individuals will not be identical: mutations will have altered parts of many of them. Some of the mutation are immediately fatal – any individual with the mutation just dies. Other mutations are not fatal, but are slightly harmful – there will be fewer of those individuals in the population. There will be some with mutations that are beneficial – meaning that the individuals with that mutation will reproduce more often and more successfully.

    So you’ll wind up with a population of diverse individuals derived by mutation from a single original parent.

    Now – if you drop penicillin into the dish, some of the bacteria in the dish will die – in particular, those like the original parent that don’t posess antibiotic resistance will die. Some in the population will have the trait that allows them to survive in the presence of penicillin. Those will now be the more successful strain – and so the population will change – it will become mostly penicillin resistant.

    Wait a while again, and the dish will once again be full of bacteria. Only they’ll be different than the ones that were in the dish before you put in antibiotics – they will mostly be derived from the ones that had a mutation that allowed them to survive in the presence of pencillin. That population will still not be homogeneous: as the penicillin-resistant bacteria reproduced, mutations continued to happen. So after some time, you’ll have a new diverse population of bacteria – most of which posess some trait that makes them immune to penicillin – and some of which will have other traits.

    Now, douse the dish with a cephalosporin. Again, you’ll get a massive die-off. Most of the bacteria in the dish won’t be resistant to cephalosporins. So you’ll wipe out a lot of them – but the ones that had a mutation that happened to let them survive in the presence of cephalosporins will survive and reproduce, and as they reproduce, they’ll continue to accumulate mutations.

    Repeat this process 20 times, alternating penicillin and cephalosporin. By the time you’re done, the dish will contain a population of bacteria that is essentially completely immune to both penicillin and cephalosporins.

    The bacteria that you started culturing in the dish didn’t posess any traits that made it antibiotic resistant. But by the time you’re done, you’ll have bacteria that are highly resistant to both penicillin an cephs.

    As I said – a lot of common explanations of evolution are oversimplified. They make it sound like mutations happen because of a change in selective pressures. So they’ll say things like “the use of antibiotics caused bacteria to develop mutations to make them resistant”. That’s not an accurate phrasing – mutations don’t happen because of some selective pressure. Mutations just happen. But populations change in response to selective pressures – and the change in the population changes the root stock – the individuals that will produce the future generations. Because of a selective pressure, the “basic model” from which variants are produced via mutation are changed over time. Just like in the example above – the second generation of bacteria – the ones produced after dousing the dish with penicillin – were different from the ones before the penicillin. And mutation introduces variation into the population; selection “chooses” the part of the population that survives – and then mutations happen to the subset of the population that survived the selection event.

    So getting back to the topic of how antibiotic resistance develops: there are many mutations occuring in bacteria all the time. But a bacteria that contains mutations that make it resistant to multiple antibiotics is very unlikely to develop unless it’s in an environment where the population of bacteria is constantly being exposed to antibiotics.

    One more metaphor, and I’ll stop.

    Suppose the original bacteria is A. You’ll start with a population of A bacteria, and let them reproduce:

    A A A A Ap A A A Aq A Ax A

    Ap is one that just happened to have a mutation that makes it resistant to penicillin. Aq and Ax are other mutation. Now let it keep reproducing for a while:

    A A A A Ac Ac A A A A A A A A
    A A A A A A Ap Ap Ap A A A A
    Ax Ax Ax A A Ax A A A A A A A

    Most of the bacteria are As; a few are Acs, Aps or Axs, and the Aqs ahve just died out. Now add penicillin:

    A Ap Ap Ap Ap Ap Ap Ap Ap Ap

    One of the non-resistant ones surivives out of luck,
    the Axs all die out, and the Aps survive. Now let them reproduce for a while:

    A A A A A Ap Ap Ap Ap Ap Ap Ap Ap Ap A
    AP AP Ap Ap Ap Ap Ap Ap Ap Ap Ap Ac Ac
    Ac Ac Ac Ax Ax Ax Ax

    You get mostly Aps; a few original As, and a couple of new variants – Ac and Ax. Now add cephalosporin:

    Ap Ap Ac Ac Ac Ac Ac Ac Ap Ap Ac Ac A

    Now you’ve got mostly Acs, with some Aps and some original As. But your population is *very* different from what you started with. It’s now full of penicillin and cephalosporin resistance genes.

    Now, for future exposures to antibiotics, your starting point in the bacterial population is very different. Instead of most of the members of the population
    being non-resistant, with a few having resistance mutations, now the population is almost entirely made up of bacteria with at least one kind of antibiotic resistant. As this population reproduces, it will be adding mutations “on top of” the new basis – the p/c resistant bacteria.

  47. #47 mgarelick
    March 19, 2007

    Mark: That’s great, thank you very much.

    Do any of the individuals in the population have resistance to both penicillin and cephalosporin, or is the population as such that is multi-resistant? (Sorry if I’m being a pest, but this is very interesting to me.) It seems that it would be great if we could ascertain a bacterial population’s resistance before introducing an antibiotic, but I guess that’s the holy grail of medical research.

    BTW, my wife suffered from two different multi-resistant pneumonias in the course of chemotherapy, so I’m very sympathetic to your father’s situation and wish you the best.

    And, I really dig your blog’s motto — not many people I know use “fun” and “math” in a sentence.

  48. #48 Mark C. Chu-Carroll
    March 19, 2007

    mgarelick:

    The way that it works is yes, you’ll typically see individuals that are resistant to multiple antibiotics. The way that it develops is often a step-wise process – a given population is repeatedly exposed to the same two or three antibiotics, and eventually, they’ll be resistant to all of them. Again, its a matter of that two-step process: the members of the population reproduce with mutations; some get killed by exposure to an antibiotic; the ones that surive reproduce with more mutations; some get killed by exposure, etc. The survivors of each step are the ones where the next set of mutations occur.

    In general (not always, but in general), the mutations that make bacteria resistant to different antibiotics are not mutually exclusive. You can have a bacteria that produces β-lactamase (which makes it resistant to penicillin), and also use a variant enzyme during the process of replicating its DNA (which makes it resistant to flouroquinolones). So when a bacteria which already posesses a trait which makes it resistant to one antibiotic goes through that process of mutation and then selection for resistance to a different antibiotic, the result is a strain of bacteria that’s resistant to more than one antibiotic.

    Repeat lots of times, and you start getting what people call superbugs – bacteria that are resistant to damn near everything. Things like MRSA. (MRSA stands for “methicillin resistant staphylococcus aureus, but it isn’t just resistant to methicillin; it’s a catchall term for bacteria that are resistant to all of the lactam antibiotics.)

  49. #49 indifferent
    March 27, 2007

    Don’t really care one way or the other about this topic…. came across this site by accident.
    But this Mark Chu-Carroll looks like a complete nerd.

    You’ve gotta be careful of what any nerd (especially one advanced in age like Mark) says. They’re bitter. Lockers got stacked, books slapped out of their hands while they were walking down the hallway, sitting alone during lunch, hanging out with other nerds and making fun of the cool kids.
    It’s upsetting, but in my experience nerds bring these situations upon themselves.
    I’ve grown out of my nerd bashing years. But when I see a guy like Mark Chu-Carroll, sitting there with his balding head and nerd-like features I get that urge again.

  50. #50 indifferent
    March 27, 2007

    now don’t go getting all science-y on me talking about this proton, that squirrel, these ribonucleotides, those pancake stacks.

    In today’s age there is absolutely nothing wrong with being a nerd. Which in my mind is a shame, kind of helped keep things in line. But these days you have boys smooching boys…. girls kanoodling with girls…. nerds acting like they’re ‘cock of the walk’.
    The way half of the people on this board talk I don’t think I’d be incorrect in throwing around the labels: nerd, geek, dweeb, dingus, loser. This would have all been fine to say back in 1985. Back then we had guys like William Zabka, from Karate Kid – the guy who swept Daniel Sons leg (Sweep the Leg, Johnny!!!), to keep all you dweebs in line.

  51. #51 Xanthir, FCD
    March 27, 2007

    Hokay…

  52. #52 Jonathan Vos Post
    March 27, 2007

    And that’s why my son skipped high school. Just went from 8th grade to university. Really.

  53. #53 indifferent
    March 28, 2007

    Jonathan….
    you really should have sent your son to high school.
    Us cool kids toughen nerds up, seriously. We help give them thicker skin. So when someone picks on him later in life he can be like, “phwwww, whatever…. I’ve been through worse”.

    People look at the cool and think ‘jerks’, ‘idols’ or ‘helpers’.
    We’re helpers, give me 2 weeks with an unconfident nerd and I’ll turn him into a confident nerd.

  54. #54 Mark C. Chu-Carroll
    March 28, 2007

    And there you see a shining example of why my 4yo son is already learning karate. By the time the assholes who think they’re cool are ready to start bullying him, he’ll be ready to defend himself.

    As for the bitterness thing… I just started working for Google this week. I’ve never seen a space with such a high density of geekish people; and I’ve never seen a workplace where people in general seem so *happy*. Far from being bitter, I’m proud of my geekiness, and I think that’s become pretty common. Here at SBs, we even had a “Biggest Nerd/Geek” competition, which I’m proud to say I won.

  55. #55 Jonathan Vos Post
    March 28, 2007

    Once again, this time as a father, I agree completely with Mark C. Chu-Carroll.

    My son earned his brown belt in Karate, and won various medals and trophies. He was coached in classical sword by the #2 master in the world.

    Skipping high school was the right thing for him. At his university, he was an elected member of the Student Government — the representative for Engineering, Technology, and Computer Science. He was elected because the Jocks knew he was a jock (brown belt, Little League All Star, skiing), the Cool knew he was Cool (he did stand-up at Hollywood coffeehouses, and plays bass in a local Rock group, for example), and the Nerds knew he was a nerd (professionally published in Mathematical Physics and in poetry and in fiction).

    Thus, at the age of 15, he had his own office on campus, supervised a multimillion dollar budget, received a regular paycheck from the state government, and had a faculty parking pass. SInce he could not yet drive, he auctioned off the faculty parking pass and used the money to clean up in college poker games.

    Meanwhile, people of “indifferent” abilities reached their lifetime peak in High School, and began their long, slow, sad decline.

    Best to your son, Mark. I predict a bright and joyful future for him, and the ability to kick ass numerically, verbally, and — when necessary with complete jerks — physically.

  56. #56 Tyler DiPietro
    March 28, 2007

    How much you wanna bet indifferent came here from Casey Luskin’s latest ignorant rant on “Evolution News & Views”, which links to this very post as an example of the evilness of the Darwinists?

    But anyway indifferent, a lot of nerds used to think like you, but most decided pretty early on that they didn’t want a job mixing concrete. Be a good chap and bugger off, we have work to do that people actually give a shit about.

  57. #57 Norm Breyfogle
    March 28, 2007

    Mark CC: I’d pay good money to see your son kick indifferent’s son’s ass.

    I wonder if indifferent sees the irony in his screen name? He’s certainy not indifferent when it comes to what he calls nerds. And what’s with his nonsequitur equating a sexual preferences with intellectualism? Oh, wait, I know: he saw “Revenge of the Nerds” as a doctoral thesis.

  58. #58 Xanthir, FCD
    March 28, 2007

    Now, now, Norm, we have no way of knowing whether indifferent’s potential children will also be jackasses. What I would pay money for, though, is seeing Mark’s kid kick indifferent’s ass. ^_^

  59. #59 Jonathan Vos Post
    March 28, 2007

    Once again, this time as a father, I agree completely with Mark C. Chu-Carroll.

    My son earned his brown belt in Karate, and won various medals and trophies. He was coached in classical sword by the #2 master in the world.

    Skipping high school was the right thing for him. At his university, he was an elected member of the Student Government — the representative for Engineering, Technology, and Computer Science. He was elected because the Jocks knew he was a jock (brown belt, Little League All Star, skiing), the Cool knew he was Cool (he did stand-up at Hollywood coffeehouses, and plays bass in a local Rock group, for example), and the Nerds knew he was a nerd (professionally published in Mathematical Physics and in poetry and in fiction).

    Thus, at the age of 15, he had his own office on campus, supervised a multimillion dollar budget, received a regular paycheck from the state government, and had a faculty parking pass. SInce he could not yet drive, he auctioned off the faculty parking pass and used the money to clean up in college poker games.

    Meanwhile, people of “indifferent” abilities reached their lifetime peak in High School, and began their long, slow, sad decline.

    Best to your son, Mark. I predict a bright and joyful future for him, and the ability to kick ass numerically, verbally, and — when necessary with complete jerks — physically.

  60. #60 Norm Breyfogle
    March 28, 2007

    JVP: Your son sounds like an ideal general purpose biocomputer in a sound body. Color me impressed, truly. What is it with you and yours? Is such balanced profundity caused more by genetics or environment?

    Just some rhetorical gushing; you don’t need to answer.

  61. #61 Jonathan Vos Post
    March 28, 2007

    I am an ignorant and stupid man with no common sense. So my son must have inherited his gifts from my wife.

  62. #62 Norm Breyfogle
    March 28, 2007

    Modest, too, eh?

  63. #63 Greg
    April 9, 2007

    Um … How did a post about tautologies — presumably a “Basics” post which, I would have guessed, was supposed to discuss, you know, math, degenerate into a discussion about sons kicking the asses of other sons and picking on nerds and yadda yadda yadda. Come on, guys, do let’s give a solid effort to being adults. I mean, this “indifferent” guy called someone a nerd and it got a reaction? Give me a break. What is this? High school? Obviously, the guy just needs a big nerd hug.

    MarkCC, it’s your blog, man, and I do sympathize with your feelings about your father. I would point out, though, that not linking to the podcast, refusing to allow for an examination of the viewpoint you attack, is, well, not exactly “good math”. Or at least it’s not good science. Now maybe you’re not going for good science, nor any kind of science at all, except that, again, this is the “Good Math, Bad Math” blog, and the post is titled “Tautologies”, so … hmm …

  64. #64 Mark C. Chu-Carroll
    April 9, 2007

    Greg:

    I see the not linking as not being a big deal. I provided enough information to easily locate the article I was discussing.

    To me, it’s like the difference between citing something in a bibliography of an online paper: you can do a text-only cite, or you can include a direct link in the citation. There’s nothing wrong with text-only citations. It’s a lot more convenient when there’s a link, but it’s not necessary so long as you provide a proper citation.

    I think it would have been inappropriate if I wrote the post, and deliberately obfuscated things so that you couldn’t easily identify or locate the article I was discussing. But that’s not what I did: I clearly identified the source – I just made it a tiny bit more effort to go to the original article, because I’d rather not help increase the hit-count for the DI when they’re promoting dangerous stuff like this.

  65. #65 Chris
    July 3, 2007

    The anthropic view of the universe is best summed up in the old British Army song (to the tune of Auld Lang Syne)
    “We’re here because we’re here because we’re here because we’re here -
    We’re here because we’re here because we’re here because we’re here.”

  66. #66 Norm Breyfogle
    July 7, 2007

    All of philosophy is motivated by amazement over the inexplicable fact that there’s something instead of nothing.

    Wouldn’t absolute nothingness be simpler than this immense complexity in which we find ourselves immersed? How do we harmonize the search for the simplest explanation of everything (the holy grail GUT) with the fact that everything is definitely NOT as simple as it would be if nothing existed at all? isn’t Occams’ Razor (and therefore logic and science) in some sense at odds with the fundamental fact of existence?

    Just posing the question. I’d really be fascinated by any responses.

  67. #67 Xanthir, FCD
    July 7, 2007

    Philosophy might have problems with it, but logic, science, and Occam’s Razor don’t. OR, especially, isn’t about finding the simplest solution (as that’s often wrong), it’s about finding the simplest correct solution.

    Nothing is simpler than something, yes. But since something exists, the simplest theory must discard the possibility of nothing.

  68. #68 Torbjörn Larsson, OM
    July 8, 2007

    Wouldn’t absolute nothingness be simpler than this immense complexity in which we find ourselves immersed?

    The argument I have seen is IIRC that, since theories aren’t about simplicity but elegance (roughly, expressive power), the simplicity of nothingness doesn’t mean anything. Simplicity is used when comparing equally powerful theories, and a priori a vacuum is as simple as nothing – one object vs one object (or perhaps ‘object’).

    But nature likes symmetries (perhaps because that too is elegant), and our physics contains a lot of them. Simply, our vacuum is much more symmetric and elegant than replacing it with nothing.

  69. #69 Jonathan Vos Post
    July 8, 2007

    Re #66: Norm, Simplicity is not that simples.

    Jonathan Post, Computer Futures, Inc.

    Philip Fellman, University of Southern New Hampshire

    Complexity in the Paradox of Simplicity

    Abstract

    David Hilbert’s long lost “24th problem” [Thiele] was intended to clarify the notion that for every theorem, there is a “simplest” proof. His grand program was demolished by Godel, but his problems, upon solution, bestow instant success and even immortality to the solver. His notion of “simplest” raises key questions for the 21st century (when computerized automated theorem proving has solved some famous problems but created debate as to what constitutes proof), these questions capable of analysis in the domains of Complexity and the Philosophy of Science. In particular, given multiple definitions of “simplest,” involving differing definitions of, usage of, and justifications for elegance and (qualitative and quantitative) parsimony, by what meta-criterion do we choose the simplest of those? And how are our hands tied by neurological and psychological limitations on our ability to introspect on how we choose (i.e. “choice blindness), and how automated theorem provers operate? Are we, in Zeilberger’s phrase, “slaves of Occam’s razor?”

    This paper surveys the literature of Philosophy as it pertains to Simplicity and Occam’s Razor in the abstract, in Mathematics, and in Science. This survey is essentially an annotation of a survey by Alan Baker. Several new branches of Proof Theory and the Theory of Complexity, particularly from Chaitin, Hutter, Kolmogorov, Martin-Lof, Matiyasevich, Rissanen, Solomonoff, and involving the “Minimum Description Length” (MDL) formalism are explored in this context, yielding some new axiomatic and computational approaches to Simplicity which avoid decidability and computability limits of the general problems of Complexity.

    Presentation at the 6th International Conference on Complex Systems (ICCS), June 25-30, 2006; Boston, MA

  70. #70 Norm Breyfogle
    July 9, 2007

    Excellent responses; thanks.

    A related question: isn’t the concept of a truly exhaustive grand unified theory a pipe dream motivated by a psychological need for control? (There’s really no need for a GUT, and a final one may in fact be impossible; science may very well continue to progress indefinitely without one.)

  71. #71 Torbjörn Larsson, OM
    July 10, 2007

    isn’t the concept of a truly exhaustive grand unified theory a pipe dream motivated by a psychological need for control?

    Partly, certainly. But IIRC the most part is a reasonable expectation, or rather at least five cooperating ones:

    - As data and theories expand, they resolve more detail.
    - As data and theories expand, they mix over larger areas.
    - Parsimony points to theories binding parameters (less free parameters) as the best, and the numbers of them does decrease, so why would not a GUT bind them all?
    - Gravity involves all forces implicitly, so a full QG theory is likely a basic GUT anyway.
    - AFAIU entropic, holographic and quantum principles points to that there is room for just one more layer beneath particles, such as strings. Then you run out of ‘information space’, if I understand it correctly you will not have enough bits of information for deeper mechanisms (theories).

    I’m a bit vague on the details of the last point, because I haven’t found these discussions and references again. I hope it isn’t a mistaken factoid – but it could simply be buried in old sci.physics.research usegroup discussions.

  72. #72 Jonathan Vos Post
    September 2, 2007

    By the way, here’s an extreme counteraxmple of Egnor et al claiming that evolution can only proceed one gene mutation at a time.

    Published online: 30 August 2007; Corrected online: 31 August 2007 | doi:10.1038/news070827-6

    Bacterial genome found within a fly’s
    DNA transfer from bacteria to animals is more common than thought.

    Ewen Callaway
    News @ Nature.com

    Researchers have found a surprise hidden in the DNA of a fruitfly: what seems to be the entire genome of a parasitic bacterium called Wolbachia. Smaller bits of the promiscuous parasite’s genetic material turned up in worms and wasps, too.

    The size of the Wolbachia insertion in the fruitfly Drosophila ananassae — more than 1 million base pairs — has caught researchers by surprise. If bacterial DNA is so common in other creatures, they caution, researchers should be careful not to mistake it for contamination and accidentally throw it away when doing genome sequencing.

    It has long been known that organisms can sop up foreign genes, the most usual example being bacteria swapping DNA with each other. DNA from mitochondria and chloroplasts — cell structures thought to have evolved from specialized bacteria — have also made their way into the genomes of multicellular eukaryotes (a category including plants and animals). And a worm parasite of plants has been found to contain a gene from nitrogen-fixing soil bacteria. But transfer of bacterial genes into animals has been thought rare.

    The new work, published today in Science1, suggests that gene flow from bacteria to animal hosts happens on a larger scale and more commonly than suspected.

    The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. “You’re talking about a significant portion of its DNA that is now from Wolbachia,” says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. “There has to be some sort of selection to carry around that much extra DNA.”

    Genome within a genome

    One-fifth to three-quarters of all insect species are plagued by Wolbachia, which lives inside testes and ovaries and passes from one female generation to another through infected ova. To ensure its spread, Wolbachia can skew birth ratios towards females and even prevent infected males from successfully mating with disease-free females.

    The bacterium’s close association with egg cells means there’s ample chance for bacterial DNA to get permanently sewn into a host’s nuclear genome, says Dunning Hotopp, whose team expected to find just small stretches of parasite DNA in fruitflies. A Japanese team previously found a single Wolbachia gene in the adzuki bean beetle2, and Dunning Hotopp and her colleagues expected to find much the same.

    Instead, they found that the tropical fruitfly has sucked up the genome practically whole. The team looked at D. ananassae free of Wolbachia infection, and checked for 45 genes selected from across the bacterial genome. They found 44 of them. Because these test genes are so widely spread throughout Wolbachia DNA, this suggests that the rest of its genome is likely in fruitflies too.

    Many of the Wolbachia genes were infiltrated by strands of insect DNA that jump around the genome, and so are unlikely to be functional. But at least 28 of the bacterium’s 1206 genes are active in the flies, the researchers showed. They don’t yet know whether these genes are producing proteins or what effect they might have. “It could be quite profound,” says John Werren, a biologist at the University of Rochester, New York, and part of the team. If the genes weren’t doing anything, he says, they would have been dropped or mutated away.

    There’s no telling when the insertion occurred, but because the sequences are unique to D. ananassae, it probably happened after the species split from other fruitflies.

    The team found much shorter stretches of the Wolbachia genome in other insects, including several species of nematode worms, wasps and a mosquito — suggesting that this kind of DNA transfer is quite common.

    Not trash

    The work brings a note of caution for anyone doing genome sequencing, says Ulfar Bergthorsson, a geneticist at the University of New Mexico in Albuquerque.

    Traditionally, when genomes are sequenced, computer programs toss out any bacterial genes from the final code, assuming that it is simple contamination. But the existence of wide-spread gene flow from bacteria to insects suggests that sequencers should be more careful, says Bergthorsson. “It’s unwarranted to exclude bacteria-like genomes from sequences.”

    As yet more organisms get their DNA decoded, researchers are certain to find more genes that have seeped from bacteria into animals, says Werren, particularly in reptiles and amphibians. Finding bacterial genes in mammals, however, is unlikely, because no bacteria are known to infect their sperm and egg cells.

    Visit our newsblog to read and post comments about this story.

    * Correction: the article was amended to reflect the fact that 28 of 1206 bacterial genes, rather than 28 of 45, were active in the flies studied.

    References

    1. Dunning Hotopp, J. C., et al. Science doi:10.1126/science.1142490 (2007).
    2. Kondo, N., et al. Proc. Nat. Acad. Sci. 99 14280-14285 (2002).

  73. #73 Torbjörn Larsson, OM
    September 3, 2007

    The Wolbachia result is fascinating for many reasons:

    - This is not a unique mechanism. IIRC they found Wolbachia genome fragments in the genome of 11 of the species of flies, wasps and nematodes researched.

    - It is accidental and dramatic. Retroviruses do it on purpose (but of course, when they get stuck in cells such as the germline it is accidental) and assimilated organelles transfer their genome to the nucleus piecemeal during long times.

    - Researchers have excluded bacterial genomes from genome search earlier, thinking it is all contamination.

    - Some of the Wolbachia genes seems to be expressed in lieu of other promotors, stop transcripts et cetera used in eukaryotes than in the innate biochemistry.

    But there are also caveats:

    - The expressed genes are few (IIRC ~ 2 % of some hundred bacterial) and at low level (AFAIU ~ 10-6 of normal activity). This is reminding of the ENCODE results that also detects spurious transcription without known biological significance due to newer sensitive technique. Any benefits or possibility of selection for or against are still to be tested.

    - The benefit is a hypothesis. One author claimed in a blog that they have preliminary results that homozygosity of the Wolbachia genes are strongly non-beneficial in the fruit fly who got most of the entire genome. (D. ananassae.) Either insertion was recent, and/or it will presumably be selected out, or there are heterozygous benefits.

    That said, these “hybrids” are pretty @$#! cool.

    You are … a beautiful, beautiful butterfly. (From Alien: resurrection.)

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