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

I have edited my previous remarks, as I can see how one may draw the wrong impression from the use of “you” in my sentence - there was no intention to question your competence.

My remarks were based on your comparison of NS or fitness with temperature - the former, as you concede, is something that can sometimes be measured - temperature is routinely and accurately measured, so your analogy with NS is clearly inappropriate. I am aware of inferences of fitness, and I recall some papers use a numerical value in calculations, but I cannot, as yet, find any basis in data for these values. You may be in a position to make a clear statement if you wish, but if my recollection is correct, other workers have reported attempts at correlating fitness, or NS, with data, and they report a very poor correlation. Again, this can hardly be compared to measurements of temperature.

Since theory and experimental data need to be shown to provide a clear and accurate correlation, I suggest to you that this criterial has not been met with NS or fitness, and so it is clear to me that your argument regarding some similarity of NS/fitness with temperature is flawed.

I mentioned the concept of a gene to show that even at the basic level (mutations causing novelty, followed by some type of selection) seems to be based on an uncertain foundation. Surely the notions related to ToE must include events involving genes.

You misunderstand what I said on this: the kinematic model of temperature is science, because it works with the repeatable, since statistically the individual movements of molecules can be averaged: it is the individual movements of the molecules that are unpredictable.[quote=“glipsnort, post:73, topic:5784”]

I can observe that genetic variants that confer lactase persistence increased in frequency in humans much more quickly than can be explained by genetic drift, that this happened multiple times, and that it only happened in populations that were practicing herding.
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This really (once more) makes my point: lactose tolerance is almost a model system in its simplicity, and population genetics can therefore predict it well. Without reading up on it specifically, I assume that the tolerance depends on one or a very few alleles, which were fortuitously (and, perhaps inexplicably: contingency waves its hand for attention) present in some proportion of the pre-pastoral population - presumably a sufficiently high proporion to make drinking animal milk customary, rather than taboo: populations don’t keep on trying to drink stuff that makes them ill in the hope of a mutation arising at some stage.

A population geneticist could hardly imagine a simpler case: a single, entirely new, food source appears amongst humans (whose love of manipulating the world makes them almost the only species one can envisage trying such a thing), which because of the advantages of pastoralism spreads steadily across the world. The genetics are, I assume, simple - certainly the phenotypic trait is. Pastoralism, clinical tolerance and allele frequency are all easily tracked both now and from historical records, and the scientific population genetics model works. Likewise, in other restricted cases such as genetic bacterial resistance, Lenski’s E. coli citrate tolerance etc. One can also add that the unusually vast interbreeding population of H sapiens not only assists the maths, but also buffers other evolutionary change.

But in the case of macroevolution in the wild, multiply up the number of genes (and non-coding elements) all undergoing unpredictable change at once, their mutual interactions, the wide range of phenotype changes they mediate, the additional mechanisms like neutral change - and in many cases the complexities of understanding what role any gene really plays in a trait, and what role any trait plays in survival (one common and much studied, and disputed, example - the stripes of the zebra). And then multiply up all the myriads of factors in an ever changing environment. And factor in the likelihood that the organism creates its own environmental niche. And then add in the difficulty that, for past events, much or most of that information is unavailable.

What one is left with is a mass of contingencies which cannot possibly be known individually, and which exhibit far more variables than the movements of individual molecules in a gas. Remember, firstly, that the original claim I challenged was that natural selection is not random, and I still argue that it is, as far as the scientific definition of randomness is concerned, that is, “unpredictability”.

Secondly the principle I suggested was that randomness (and hence contingency, which is random because unrepeatable and irregular) is the point at which science must cease to comment about efficient causation, because “unpredictability” is not an efficient cause, but an admission of ignorance of the causal chain.

James Clerk Maxwell, the father of statistical science, was well aware of this, separating the science that could be done statistically from the unknowable contingencies, which he placed in the realm of divine providence rather than science, by saying:

Would it not be more profound and feasible to determine the general constraints within which the deity must act than to track each event the divine will enacts?

So you see, I am not completely at odds with a historical understanding of the philosophy and theology of science in raising this.

According to neutral theorists it’s the substance of evolution on which natural selection applies a gloss. But in any research, noise is sufficiently important pootentially to swamp signal.

Your sentence itself is a little difficult to make sense of - but the the mathematics of evolution, in terms of population genetics, at least, is the mathematics of simplified modelling. Some of the time the modelling is good enough to make some useful predictions - Steve’s lactose tolerance being a case in point. But statistical maths does not explain individual interacting contingencies, and that’s my point. “Fitness” in natural selection, beyond the formal definitions applied to the simple case, is an intuitive concept rather than anything of which one can make sense, let alone mathematical sense.

Eddie, are you saying that you think all genotypes in a given environment will reproduce with equal frequency? If you think that genetic diseases that affect reproduction exist, then you agree that differences in fitness exist.

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Ha! @Sy_Garte… come on man… release the white knuckle grip!

  1. What gluten does to humans is completely irrelevant to the point I was making.

  2. What’s the point of reading about Gluten if you don’t find out why it exists to begin with ??

Here’s an old article … Before “hating gluten” became a fad!

@Jon_Garvey

Fitness … like everything in the science of Evolution … is a reference to populations… and sub-groups within populations.

Worrying about the fitness of a specific individual … or even its immediate family… is like trying to prove or disprove something because we can’t figure out where the P-level electrons in a molecule are going to be from moment to moment.

I don’t find this complaint to have much value in the overall scheme of things.

I’m not sure if Neutral Theory really means what you think it means. Isn’t it a little like implying that the environment doesn’t significantly change anything in a population? … that even as the climate becomes dryer, wetter, hotter, colder … populations don’t respond to it at all … they only do what genetic drift does to them?

I doubt if you’ll get @Relates Roger to agree to that kind of blasphemy!

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As I already said, the point of my comparison was that a theoretical construct can be scientifically useful even if it is not measurable under all circumstances. Do you disagree?

It depends on what you may mean by “useful” - normally what you seem to refer to would be considered by scientists as speculation.

@Eddie

Yep… that’s why I think some of the postings we’ve had on “fitness” aren’t doing anyone any favors!

“Fitness”" in terms of Evolution is mathematically derived… but difficult to observe in a single person’s lifetime.

Fitness is measured by a sub-population’s genotype long-term marginal superiority in producing offspring … where “long-term” almost always means 3 or 4 or more generations.

Though I’m sure there are scenarios where marginal superiority in producing offspring has to be netted into the 5th or 10th generation because of the complexity of the interactions in the cycling of the environment and the life cycle of the population being studied.

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George

Neutral theory arose largely because of the theoretical limits of natural selection. And drift is significant enough for at least some workers to believe that the pattern of lactose tolerance in Europe is consistent with neutral drift rather than adaptive selection (thus showing that even the simplest story has caveats). You can read that in the Wikipedia article on “lactase persistence”.

Neutral theorists, although they retain some apparently ill-defined role for adaptive selection, will say that most evolution in small populations (ie most advanced species) occurs through neutral change, that purifying selection simply weeds out the disasters, and that natural selection is overloaded and very incomplete.

Eugene Koonin’s 2009 overview of current ET is essential reading on that. Note that he says natural selection is “not quantitately dominant” in genome evolution. There seems to be sometimes a sense that genome evolution is driven by neutral drift, and phenotypes by NS - which is a little hard to comprehend if the phenotypes are the expression of genotypes. One suspects the reality is that neutral theorists, involved in genomics, simply pay lip service to adaptive selection by passing the buck to the people interested in phenotypes - but Joshua would be the person to comment on that, since he as a paid-up neutralist who strongly downplays Neodarwinian mechanisms.

GJDS

It’s perhaps relevant that in Steve’s lactose tolerance example, the historical evidence for the worldwide spread of pastoralism, ancient Roman records that northern Europeans drank raw milk, and so on, were not only useful, but essential, for the hypothesis that tolerance has spread through natural selection. The case would be much weaker if only current populations were studied. But I question whether that renders historical records as “science”.

Closer to your own discourse, the aether was a theoretical construct that was useful to science, though never observed, and eventually (like astrology), discounted. I would argue, though, that it was a scientific conception for the clear reason that it was definable, and explained regularities in nature. The difference from natural selection beyond model systems is that it evades definition and is held to account for contingencies.

@Jon_Garvey

I’m not too impressed with “Neutral Theory as Dominant Factor”. I just don’t believe one gets a whale from a land mammal by juggling existing alleles…

George

You and me both, but it’s the way things have gone. In Asa Gray’s day the problem was how advantageous variations actually occur to be acted on by selection. Now neutral theory takes away the bit that made sense of it… or at least, as a fortuitous process. Add in providence, and neutral theory is as good as any other divine action.

Jon,

I am somewhat sympathetic to the position put forward by @glipsnort, but my main point is valid, the NS is used in a nebulous manner, while unreasonable claims are made; i.e. that it represents a law of nature, which I firmly think it does not. The following quote from a PoS treatment is instructive (I have made a few minor editorial changes to try and reduce the length, but the message is clear. I have put points relevant to this discussion in bold.)

“…… these mathematical models are overly simple and are rarely used beyond introductory texts in population ecology. For example, …… the Lotka-Volterra equations treats the predators as specialists, incapable of eating anything other than the prey in question…. these assumptions are typically false. These models do, however, serve as the basis for many of the more realistic models used in population ecology. The more serious models add complications such as age structure, variable growth rates and the like. Even in these more complicated models, biological detail is deliberately omitted and yet the models are adequate for the purposes at hand.

…… in a position to state the philosophical problem posed by mathematics in population ecology. Population abundance is completely determined by biological facts at the organism level – births, deaths, immigration and emigration – but the (standard) mathematical models leave out all the biological detail of which individuals are dying (and why), which are immigrating (and why), and so on. That is, the mathematical models ignore the only things that matter, namely, the biological facts. The mathematical models here – the relevant differential equations – seem to ignore the biology, and yet it is the biology that fully determines population abundances. How can ignoring that which is most important ever be a good strategy?

We might put the point in terms of explanation: the mathematical models are not explanatory because they ignore the causal detail.”

Thus it is understood that simulations may prove useful for some specific goals or studies, which I think is the point made by Steve, but this is far from discussing laws of nature, and NOTE the fact that causal details (as well as biological facts) are often ignored (or to echo your favourite theme, teleology and causality are ignored).

Hardly the case for ToE as a God-ordained notion of the sciences, what!:stuck_out_tongue_winking_eye:

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Thanks for the quotes, GJDS. For those finding good reasons not to invest in books on the philosophy of mathematics (of which there are several!), I recommend this very readable blog series on the shortcomings of modelling systems involving organised complexity (of which life is one) by Michael F. Flynn. It relates nicely to your point about maths trumping reality - or as Flynn puts it, regarding the output of models as data, whereas:

As the great statistician, George E. P. Box, once said, “All models are wrong, but some are useful; the practical question is how wrong do they have to be to not be useful.” (Robustness in the Strategy of Scientific Model Building)

I also like:

Significant problems in biology, economics, and so on can seldom be characterized by two to four variables. It is impossible hold all the other variables constant. We wind up with a half-dozen, or even several dozen quantities, varying simultaneously in interconnected ways. Genomes or economies have a wholeness to them that a mass of gas or even a mass of policyholders do not…

These problems are too complex to handle with the 19th century mathematical techniques that were so successful on problems with two-to-four elements. But neither can they be handled with the statistical mechanics of the 20th century that worked on problems of disorganized complexity. You cannot take an average of heterogenous data.

As an aside I wonder whether the modern preference for running computer models over making observations in the field represents some kind of reversion to the Greek approach to science, in which messy contingencies were safely ignored because the principles behind reality were pure and mathematical. So reality was a faulty approximation of mathematics, rather than mathematics a faulty approximation of truth.

In that case your distinction is simply wrong. The kinematic model of temperature works with the repeatable for some systems. For other systems, the measured temperature will fluctuate unpredictably, or depend on the size of your probe, or not even be defined. Plasmas may best be described by two temperatures, not one. Other systems can have a defined temperature that cannot be measured in practice, while for other systems competing definitions are being haggled over. None of that means that temperature has ceased to be a scientific or useful concept.

Meanwhile, back in genetics, for some systems fitness can readily be measured, while for other systems it can be defined but not measured, while for still other systems the simple definition breaks down and people haggle over whether to replace it with another one. None of which means that the concept has ceased to be scientific or useful.

I’ve omitted a great deal here – we can back to the details. First, though, what’s the answer to my questions? Was there something wrong with my inference about lactase? Was the inference scientific? Do you have a different conceptual framework that yields the same insight?

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Don’t be ridiculous, Eddie. Scientists are humans who speak natural languages. They routinely start with intuitive concepts and use the appropriate word in an existing language. As understanding of the concept is refined and modified over time, the definition of the word becomes quite diverged from the original. That happens all the time in all branches of science. “Force”, “mass”, “energy” and (yes) “temperature” all have highly technical meanings in physics that have only limited connection with their original meanings. The scientific definitions have also changed over time, and have sometimes been the subject of fierce debate among scientists. Yet you only complain about evolutionary biologists when they do the same thing. Why?

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You seem to be wobbling between the complaint that fitness is vacuous and that it has a misleading name. There’s nothing vacuous about the concept of “romantic fitness” (or, as most of us would call it, “attractiveness”). You can study what traits go into making someone attractive to the opposite sex and estimate it for an individual. And yes, it’s a perfectly sensible to say that someone was attractive but didn’t score with the ladies – for example, if the claims about Valentino being gay were true, or if he’d been hit by a truck when he was a teenager, or had become a monk.

Instead, you’re just complaining because you don’t like the name fitness? Seriously? Physicists define a quantity called “strangeness” that has nothing to do with strangeness, and have up and down quarks that have nothing to do with direction, and you’re complaining about biologists? At least “fitness” as currently defined has some real connection to the intuitive notion of being fit for an environment. Sheesh.

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