Biological Information and Intelligent Design: Meyer, Yarus, and the Direct Templating Hypothesis

Faith & Science Conversation
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Not at all. My claim is that it’s reasonable to describe Valentino as “attractive” even if he never attracted any women. If he’d been raised in a monastery and no women ever laid eye on him, for example. Frankly, your entire argument makes no sense to me.

Well, no, what you say doesn’t make sense – which is why I wouldn’t say it. What I’m saying is that a
cheetah who can run 10% faster is more fit to hunt gazelles, even if any particular cheetah who is faster doesn’t end up catching more gazelles than a slower cheetah (because she’s killed by a hunter in her youth, for example). The slower cheetah is not “selected”. Where did you get that idea?[quote=“Eddie, post:113, topic:5784”]
Note that this last complaint is not Waddington’s. It’s mine. Waddington was complaining that the simpler conception of fitness was tautologous, not incoherent.
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Yes, I know. Waddington’s complaint makes sense in terms of “fitness” as it was then conceived. Not surprising, since he was a highly competent biologist. You will note the response of evolutionary biologists when the propensity definition of fitness was proposed: it was accepted. As far as I can tell, it was immediately and universally accepted, with no controversy. This tells me that it was recognized as capturing the right way to think about fitness, something that was already implicit in the way biologists were deploying the term. As the paper proposing the definition noted, researchers’ emphasis on statistically significant measurements of fitness meant that they were already had some such notion in mind, without having fully articulated it. I’ll note that a probabilistic definition was also implicit in Kimura’s work using diffusion theory. I’m pretty sure he’d already derived an expression for the probability that a beneficial allele is lost by chance, a concept that makes no sense if “beneficial” simply means “survives”. [quote=“Eddie, post:113, topic:5784”]
Look, I know I am not going to get a profession to change its ways. I’m just giving you reasons why that profession sometimes fails to communicate itself to others, and does not succeed in winning over the public. In popular expositions of evolution, the profession gladly teaches the public that what is “fit” will be “selected”; but then out of the other side of its mouth, as here, it says that what is fit is not necessarily selected – but gives no plain-language examples, and no plain-language reason, for saying so.
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Your complaints have been all over the map here, and have certainly included that charge that the concept of fitness doesn’t have content. In any case, none of this is exactly kept secret. If you look at the Wikipedia entry on biological fitness, the very first section is titled “Fitness is a propensity”, and it includes exactly the kind of plain language example that you say we don’t offer.

You might consider modifying your approach. Rather than telling experts in a field that one of their central concepts is without value, you might start by asking questions: What exactly do you mean by that term? Why is it defined that way and not some other way? How do you find the concept useful?

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Perhaps I’ve missed it, but I haven’t noticed any of the critics of “fitness” present an alternative formulation, even though I’ve asked multiple times. Describe using some other conceptual framework why genetic variants that produce lactose tolerance have risen to high frequency in populations that practice herding.

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Yes, that’s fine. (When dealing with organisms with a well-defined lifecycle, you can specify any point in the cycle for comparison, e.g. the average number of offspring that a newborn will produce).

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Half-life.

“Expectation” just means “mean”. There’s nothing teleological about the concept.

Sure you can. You can define and estimate absolute fitness, and even compare between species if you wish. It’s rarely at all a useful thing to do though. We’re much more likely to be interested in (and able to estimate) relative fitness, which is defined between alleles, which by definition occur within the same species. (Also, you might note that if the panda and polychaete populations are both constant in size, they have identical absolute fitnesses.)

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This sentiment is deeply misguided. What distinguishes highly predictive scientific fields from ones where prediction is difficult is not the quality of the science, but the intractability of the systems being studied. Complex systems are harder to predict than simpler ones. That’s all – that’s the entire difference. Are you suggesting we stop studying complex phenomena?

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This is a meaningless tautology. It cannot be falsified, while adaptability can be falsified. Fitness can be measured by a measure of survival and reproducibility, but it cannot ne defined by this. One cannot say that organisms are fit because they are fit.

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Then it’s good that we don’t say that. We say that some organisms are more likely to leave offspring, and we define that quality as “more fit”.

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How does one identify those organisms who are more likely to leave offspring? Let us say that we can say that fat organisms are more likely to leave offspring (and to verify this statement), then we can say that fat organisms are fit.

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Usually, you identify traits that are more or less fit, by counting offspring or by looking for rapidly increasing allele frequencies. You can define the fitness of an individual organism by averaging over their traits, but that’s only a realistic exercise for artificial strains with minimal genetic variation.

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Exactly. There are objective things about a man that make him attractive – whether or not we’ve figured out what they are.

Did you see what you just did there? You went from “There must be objective features that make him attractive” to “I should be able to determine…” Those are not analogous statements at all. The analogous statement is, “There must be objective features that determine the fitness of a cheetah.” And there are, whether we understand them or not.

Now, in both cases, we understand some of the objective features, but not all of them. I can tell you with little doubt that a lame cheetah, or one with bad eyesight, or a bad digestive system, will be less fit; I can’t tell you whether a 2% faster cheetah will be less fit. I can tell you that I’m less attractive than Valentino; I can’t tell you whether Tom Cruise is less attractive than Valentino.

The rest of your argument founders on this basic confusion.

I will also note that there’s nothing at all unusual about distinguishing between a propensity for success and actual success; it’s part of how we interpret the world. As has already been noted, the superior army does not always win the battle. The most attractive man does not always attract the most women. The best team does not always win the World Cup. Sometimes VHS beats Betamax. The race is not to the swift nor the battle to the strong.

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Your statement still has some issues that need unpacking. “Barring accidents, the most fit individual will be selected” is not a statement I can assign a meaning to in this framework. I would say that, including accidents, the most fit individual is more likely to reproduce. Success at reproduction is a random process, i.e. it is nothing but accidents; all fitness tells you is how likely an individual is to have more of the successful accidents. There’s no deterministic process that goes on in the absence of accidents.

As is happens, we’re typically more interested in the fate of fitter traits, rather than fitter individuals. We can say, for example, that a newly arisen trait (specifically an additive trait, i.e. neither dominant nor recessive) that gives a 1% fitness advantage has a 2% probability of spreading throughout the population. That’s an unusually large selective advantage, and you see that it’s still easily swamped by the noise of random reproductive success. That’s why viewing success as the normal result – the thing that happens barring accidents – is not likely to give you a good picture of the situation. Fitness is usually a modest bias in a stochastic process.

Even with this clarification, though, there is an additional, subtler complication. If we agree to define the fitter trait as the one that causes the individual to have more offspring on average, then natural selection is the idea that fitter traits will be more likely to increase in frequency than less fit traits (note that this is again a propensity), all other things being equal. The kicker is that sometimes all other things aren’t equal. It sometimes happens that the less fit variant also has the effect of increasing its own inclusion in gametes, so that it’s more likely to be passed on. (Cartoon example: sperm that have the variant kill sperm that don’t have it.) In this case, the less fit trait can still spread and take over the population. To properly handle this kind of situation, you have to treat natural selection as operating on multiple levels, i.e. both the genetic and the organismal level. So a single simple statement about natural selection isn’t adequate.

It’s useful in a variety of contexts. Often it’s estimated retrospectively. It is of some biological interest, for example, that lactose tolerance provided a very large fitness advantage. It’s surprising and puzzling that this simple trait should be such an outlier in selection strength, and scientists like surprises and puzzles.

For another kind of use, consider this paper, which uses a rough guess at the fitness cost of a disease to give practical guidance on how to design genetic association studies. Such association studies are a big deal in the world of human disease genetics at present.

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Hi Eddie -

You seem to be advocating that scientists stop using Bayesian methods. Given the remarkable success of Bayesian methods across the sciences, I don’t think your campaign is going to succeed. I give it a 1% chance of success.

But of course, your campaign could in fact go viral, knock out the competition, and sweep the field of philosophy of science, even if it’s not very “fit” in this competition between methods…

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Interesting how the widespread use of contraceptives has made that statement problematic in humans.

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Bayesian methods are precisely (or I suppose one should really say “approximately”!) as good as the scientific model into which they’re plugged. And are still vulnerable to the number of variables and how well they can be defined.

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@glipsnort
@Eddie
@Jon_Garvey
@Chris_Falter
@Jonathan_Burke

I haven’t commented here for a while, but I have caught up on most of the comments, and I think I see a pattern that might be worth mentioning.

The argument seems to boil down to whether or not its possible to predict the results of natural selection, without a priori (or a posteriori for that matter) knowledge of some quantitative estimate of fitness (which I think Steve has pretty well defined).

The answer is no, for the reason that Steve has given, it is extremely difficult to make accurate predictions in very complex scenarios. Since all of biology sets the standard for complexity among the sciences, it isn’t surprising that the central theory of biology, evolution by natural selection, would suffer from this problem. But biology is not alone. The three body problem in physics suffers similarly, and the solution of the Schrodinger equation for elements much larger than hydrogen does also.

This lack of predictability is not a hallmark of a bad science. The old idea that science always makes testable predictions has been modified greatly over the past century, ever since the uncertainty principle showed that in some cases, non-predictability is the rule. Chaos theory treats the idea of non-predictability in mathematical terms, and demonstrates its application to a large number of deterministic processes throughout the physical and social sciences.

So what all of this means is that yes, natural selection is a highly complex phenomenon whose outcomes cannot be predicted on empirical grounds based on quantitative assessments of fitness measures. But, again as Steve has shown, this doesn’t mean that such measures don’t exist, both absolute and relative fitness can be measured quantitatively and used in population genetics and Hardy Weinberg calculations to make useful predictions about how evolution works.

Here is an illustration from my own work. My group discovered a new allele of a human metabolic gene. We assessed its frequency in several populations. We found that it followed Hardy Weinberg equilibrium, which implied that it was not undergoing natural selection. We therefore predicted that it might not have any effect on fitness. After some further study, we found that indeed, as predicted, this allele had no effect on the health of the population (because of the activity of the gene in question, we thought it might)… So, while we never actually measured the fitness of the allele, the genotype, or the phenotype of the people who had the allele, it was still possible to make predictions about its role in natural selection based on biological law.

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In other words, Bayesian