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

[glipsnort (Steve Schaffner)]

@Jon_Garvey

That’s the rub, surely: the definition of “fitness” is normally related to differential survival/reproduction.

It is defined as the expected, not actual, reproductive success of the trait in question. (Either the absolute success, or success relative to an alternative trait – one can define both absolute and relative fitness.)

@Jon_Garvey

“This trait would have been successful if only it hadn’t failed through bad luck.” On what measure?

Measuring fitness is quite a different thing than fitness itself, and you seem to be confusing them. The fitness of a trait is how reproductively successful it would be if you could generate identical populations many times and measure its average success. Any particular history of reproductive success provides an estimate – a measurement – of the fitness; it isn’t the fitness itself. In the case of a trait at an appreciable frequency in a very large population, like a lab flask of bacteria, the actual history provides a very good estimate of the real fitness. For a new mutation or for a small population, the actual history provides a very noisy measurement.

@Jon_Garvey

Virtually any trait, including loss of function, can increase survival of the phenotype, in the right circumstances.

I’m pretty sure that’s false and it’s certainly irrelevant. False, because I think most possible traits are unconditionally deleterious or (often) nonviable. Irrelevant because fitness is defined on a particular genetic background and in a particular environment. It’s perfectly well understood that the same trait may be beneficial in one environment or on one genetic background and deleterious in another situation.

@Jon_Garvey

To define fitness apart from measuring reproductibe success would seem to require a complete knowledge of each and every circumstance relevant to the organism and its environment, and then to make a value judgement about the value of the trait in question - which would require being God. You surely can’t usefully define a supposedly scientific term like “fitness” on the basis of what an omniscient being would deem advantageous!

Again, you’re confusing the fitness itself with accurate measurement of the fitness. Just because I sometimes have no good way of measuring something doesn’t make that something a scientifically useless concept. According to statistical mechanics, the temperature of the air around me is a measure of the average kinetic energy of all of the gas molecules in it. Calculating that average would seem to require a complete knowledge of the velocity of each and every one of septillions of molecules, which is utterly impossible. And yet “momentum” continues to be useful scientific concept anyway, as does the microscopic definition of temperature.

[gbrooks9 (George Brooks)]

“Survival of the Fittest” can be measured in an equation, where everything is held equal except as few variables as possible. What is being measured? The absolute number of offspring (over time) vs. the percentage of offspring as a ratio of total offspring produced in the population (over time).

Like offspring produced over time is just like cash disbursements being generated by an investment project … some years are big… some years are low … but the Net Present Value of all these cash outflows can be quantified - - and compared against other projects.

In measuring survival of the fittest - - or really, Natural Selection (still a much better phrase, even though I’m defending survival of the fittest at the moment!) - - each Ancestor represents a PROJECT … and each new descendant (over time) is a variable cash flow.

These various rates of offspring over time can be quantified, and compared back to Year Zero (whatever year you want to make zero).

Assuming you run the experiment (or study) long enough, you can generate statistically significant results … and literally Quantify the most fit individuals!

Ancestors

[Sy_Garte]

@glipsnort

People often point that out, but they’re mistaken when they do. Tautologies are always true. When a new mutation creates a fitter phenotype (and thus a fitter genotype(*)), the fitter phenotype usually does not survive, as I’m sure you know. So survival of the fittest can’t be a tautology.

Of course, but my point was that saying survival of the fittest is a tautology does not remove natural selection from the realm of science. I was not agreeing with the saying. But while the distinction you make between expected and actual measured fitness is valid, it doesnt really answer @Jon_Garvey’s point about predictability of the fitness of any particular phenotype apart from a priori knowledge of the contingent factors interacting with the phenotype. In other words the use of expected fitness in population genetics equations is a theoretical construct that is very useful, but does not address this point of predictability. At least that I can see.

[GJDS]

@glipsnort

According to statistical mechanics, the temperature of the air around me is a measure of the average kinetic energy of all of the gas molecules in it. Calculating that average would seem to require a complete knowledge of the velocity of each and every one of septillions of molecules, which is utterly impossible. And yet “momentum” continues to be useful scientific concept anyway, as does the microscopic definition of temperature.

I am uncertain that your description is correct. Temperature is a concept of heat, and devices have been constructed to obtain accurate measurements and these have been standardised. We may seek a theory to equate temperature of any substance, including a gas in an enclosed space, and this takes us to the nature of the particular substance. If we find a theory of gases that is superior to the kinetic theory you refer to, the measurements will not change nor be modified. Also science may deal with different molecular concepts; for example as we approach absolute zero, molecules exhibit differing behaviour.

It sounds as if you conflate NS with something that is measured (even as an approximation) and at other times as an explanation for observations in your field (populations and variations related to their behaviour in niche environment spaces). It is this that makes NS an arbitrary notion that kicks in when one may be unable to account for all of the data, or imo, when there is a lack reproducible data.

Discussions of genotype, and subsequent inferences of a phenotype, become even more obscure to my way of thinking (as a non-biologist), since even the concept of a gene is debated.

When we say God creates and sustains His creation, we refer to the entire creation, and we should treat biology as a portion within that larger framework. Semantics in ToE strike me more as statements of belief specific to biology - or as @Jon_Garvey argues, more of a philosophical commitment, instead of a testable scientific theory.

[Jon_Garvey]

@glipsnort

Just because I sometimes have no good way of measuring something doesn’t make that something a scientifically useless concept. According to statistical mechanics, the temperature of the air around me is a measure of the average kinetic energy of all of the gas molecules in it. Calculating that average would seem to require a complete knowledge of the velocity of each and every one of septillions of molecules, which is utterly impossible. And yet “momentum” continues to be useful scientific concept anyway, as does the microscopic definition of temperature.

Steve

This is very largely my point. The scientific aspect of natural selection is the quantifiable (and hence predictable) statistical aggregate of its effects - measured by reproductive success; just as the gas laws quantify the unquantifiable.

The individual movements of molecules in gas, or the individually conceivable usefulness of traits, or alleles, which in fact perish, or are linked inextricably to deleterious traits, or dependent on other variable traits, or all the other confounding factors that make them unmeasurable … these are conceptually useful to science, but are not science themselves, on the very basis that they must be conjectured, not measured. And Brownian motion is a lot easier to conceptualise than the nebulous concept of “fitness” in the abstract.

Statistical predictions about human populations make an assumption, perhaps, that individuals are acting for certain reasons (self interest, for example), but the science is entirely in the statistical pattern. True, you could isolate an individual and examine his motivations in lab conditions, as social psychologists do (perhaps the equivalent of fitness studies like Lenski’s), but then you’re observing an abstracted contingency, not behaviour in the real world. It may confirm that individual human behaviour (like natural selection) exists, but not what fitness is beyond the statistical proxy of reproductive success.

It’s analogous to the idea that scientific laws are the same in all times and places - it’s conceptually useful to science, but a philosophical assumption that is not, itself, part of science.

@glipsnort

The fitness of a trait is how reproductively successful it would be if…

I probably erred in my last post: it’s less Arminian and more Molinist: “How would X behave if the world were other than it is.” Or if we could do measurements that we can’t, in fact, do. And although in a brief comment I neglected the role of the utterly deleterious trait (unfit = dead), it’s still paradoxical to be working on a concept about traits that are selected by real environments, which can only be examined by mentally abstracting them from real environments to hypothetical conditions that can’t be actualised.

This would be less strange if one were dealing with something one believes to be specific and constant, though unmeasurable, such as the movements of molecules. But “fitness” is an interaction between constantly changing actual variations and a constantly changing actual environment. In other words, it’s contingent in every way, can’t be measured, and has no concrete existence other than a teleological estimate of potential value. Just like history.

[glipsnort (Steve Schaffner)]

@Sy_Garte

Of course, but my point was that saying survival of the fittest is a tautology does not remove natural selection from the realm of science. I was not agreeing with the saying.

Sorry – I wasn’t trying to suggest that you did think it was a tautology. But enough people are confused about this issue that I thought it worth clarifying. The fittest do not always survive, and what survives is sometimes not particularly fit. Until people understand this fact, they don’t understand the concept of “fitness”.

[gbrooks9 (George Brooks)]

@Jon_Garvey writes:

“If selection cannot be reduced to laws (ie it is not a lawlike process), then it would seem science can only (in the main) observe it in the same way that one can observe historical events, such as the results of wars or elections, without being able to formulate laws of history that explain reliably who will win any particular struggle and why.”

This is fairly melodramatic. There are lots of examples where Evolutionary principles help predict the kind of fossils we will find, or the kinds of animals we will find together.

In the modern press, we have become familiar with “gluten” and the plausible idea that eating less gluten is healthier. The gluten found in modern wheat is particularly active. Gluten evolved in wheat (and other plants) as a self-defense against insects. And of course, insects evolved to be able to tolerate more and more active forms of gluten!

I am no Evolutionary scientist… but having read about the use of gluten by the “grasses” that specialize in producing plump seeds, I can formulate my own prediction about Evolution!:

If gluten was developed to defend grasses from insect predation, the fossil remains of the first plants on dry land should show that high-gluten grasses didn’t evolve until after insects on dry land evolved to the point where feeding on grasses became a profitable business for the insects!

I’ll come back later with what I find about the timing of the evolution of grasses…

If anyone has information on that, I encourage you to leave it here … whether it supports or destroys my “amateur evolutionist” theories!

George

[Jon_Garvey]

A nice traditional adaptationist tale, George - told with customary teleological relish (gluten strives to solve problem of insects, insects work to solve their coeliac problems.

But how does it fit with neutral theory?

[glipsnort (Steve Schaffner)]

@Jon_Garvey

The individual movements of molecules in gas, or the individually conceivable usefulness of traits, or alleles, which in fact perish, or are linked inextricably to deleterious traits, or dependent on other variable traits, or all the other confounding factors that make them unmeasurable … these are conceptually useful to science, but are not science themselves,

I can’t see how a scientific model (which is what both natural selection and statistical mechanics are) can be conceptually useful to science but not be science themselves. Science consists largely of making conceptually useful models of phenomena. If you have a criterion that declares natural selection and the kinematic model of temperature to not be part of science, then you need to reevaluate your criterion.[quote=“Jon_Garvey, post:65, topic:5784”]
I probably erred in my last post: it’s less Arminian and more Molinist: “How would X behave if the world were other than it is.” Or if we could do measurements that we can’t, in fact, do
[/quote]
Except that in many cases we can do a measurement that is an excellent approximation to the ideal measurement. In no science dealing with macroscopic phenomena do we ever make repeated measurements of identical systems; they always differ in some respect. That doesn’t prevent us from creating successful models and testing them.

@Jon_Garvey

it’s still paradoxical to be working on a concept about traits that are selected by real environments, which can only be examined by mentally abstracting them from real environments to hypothetical conditions that can’t be actualised.

I don’t understand your complaint here. Let’s move past generalities to a specific case. 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. From this I conclude that the trait in question (the ability to digest lactose as an adult) conferred greater fitness on people who had it. In other words, they had more kids on average. That conclusion is a fact about the world that I did not know previously. Now, is there something wrong with my inference here? Is my conclusion not scientific? Is there some other conceptual framework that would yield the same conclusion?

[glipsnort (Steve Schaffner)]

@GJDS

I am uncertain that your description is correct. Temperature is a concept of heat, and devices have been constructed to obtain accurate measurements and these have been standardised. We may seek a theory to equate temperature of any substance, including a gas in an enclosed space, and this takes us to the nature of the particular substance. If we find a theory of gases that is superior to the kinetic theory you refer to, the measurements will not change nor be modified. Also science may deal with different molecular concepts; for example as we approach absolute zero, molecules exhibit differing behaviour.

I am uncertain as to your point here. My point was that a theoretical construct can be scientifically useful even if it is not measurable under all circumstances.

@GJDS

It sounds as if you conflate NS with something that is measured (even as an approximation) and at other times as an explanation for observations in your field (populations and variations related to their behaviour in niche environment spaces). It is this that makes NS an arbitrary notion that kicks in when you cannot account for all of the data, or imo, when you lack reproducible data.

Fitness is something that can (sometimes) be measured. Natural selection is a process that can be inferred to be occurring or to have occurred. If we can conclude from observations that NS has occurred, then we can also conclude an allele had greater fitness. I’ve made this kind of argument, with greater or less certainty, multiple times in the literature. If you have objections to how I deploy the concepts of fitness and NS in science, by all means raise them. Your vague insinuations here of scientific incompetence are a little difficulty to rebut otherwise.

@GJDS

Discussions of genotype, and subsequent inferences of a phenotype, become even more obscure to my way of thinking (as a non-biologist), since even the concept of a gene is debated.

Neither genotype nor phenotype depend upon any concept of a gene.

[Sy_Garte]

@gbrooks9

Biological arms races (between insects and plants, predators and prey) are indeed good examples of more predictable changes during evolutionary history. But I dont think you chose a very good example. The current anti- gluten fad is not based on scientifically valid health concerns for people who dont have gluten intolerance. Also I havent seen anything before about gluten being a defense against insects. (Not a terribly important point, just thought I would try to set the record straight on this).

[Sy_Garte]

Having pretty much agreed with @Jon_Garvey about the non predictable and non mathematical nature of natural selection, I need to walk back from that view and expand a bit on the arguments that Steve @glipsnort is making. As he points out in several comments, there are some fairly rigorous ways to assess natural selection mathematically, using known laws of biology. For example, signatures of selection can be seen in the equations of population genetics, and in one of the fundamental biological laws of biology - the Hardy Weinberg equilibrium which predicts allele frequencies.

This is different from the argument that Jon is making about predicting effects of specific phenotypic changes on NS, but it does refute (in my view) the claim that NS is outside of science.

[glipsnort (Steve Schaffner)]

@Eddie

How reproductively successful it would be … if you could generate identical populations many times and measure?

Science done in the subjunctive mood!

Correct. The subjunctive mood, which is quite often used when talking about probabilities in frequentist terms.

@Eddie

What if you can’t generate identical populations many times and measure? How do you come up with a number then?

As I suggested previously, you often don’t have to do that. If a variant is at an appreciable frequency in a large population, then the reproductive success of every individual with the variant is effectively another low-information measurement of the fitness. Taken together, they can give a very good estimate of the true fitness.

On the other hand, sometimes we don’t have that kind of information. For a mutation that occurs in a single individual and is then lost, we have very little information. So in cases where we can’t measure the fitness, we don’t know what the fitness is. Why is that a problem?

@Eddie

I’m also curious to know where your definition of “fitness” first appeared in the biology literature. Will I first find it in Darwin? In Fisher? In Dobzhansky? In Gaylord Simpson? Or only in much more recent literature?

I have no idea, and very little interest in finding out.

[glipsnort (Steve Schaffner)]

@Sy_Garte

Having pretty much agreed with @Jon_Garvey about the non predictable and non mathematical nature of natural selection, I need to walk back from that view and expand a bit on the arguments that Steve @glipsnort is making. As he points out in several comments, there are some fairly rigorous ways to assess natural selection mathematically, using known laws of biology. For example, signatures of selection can be seen in the equations of population genetics, and in one of the fundamental biological laws of biology - the Hardy Weinberg equilibrium which predicts allele frequencies.

This is different from the argument that Jon is making about predicting effects of specific phenotypic changes on NS, but it does refute (in my view) the claim that NS is outside of science.

I’ll agree completely that much in biology, including fitness in most cases, is not predictable in any practical sense. This is a frustrating fact that sometimes confuses physicists and the like into thinking biology is not a science.

[gbrooks9 (George Brooks)]

@Jon_Garvey

But how does it fit with neutral theory?

@Jon_Garvey

Isn’t neutral theory just “background noise” that goes on all the time?

Natural Selection, even in an Atheistic Universe is still “doing” something … based on environmental and competitive circumstances.

If Evolutionary forces didn’t respond to mathematical probabilities … one couldn’t make sense out of any of it.

[gbrooks9 (George Brooks)]

@glipsnort

I’ll agree completely that much in biology, including fitness in most cases, is not predictable in any practical sense. This is a frustrating fact that sometimes confuses physicists and the like into thinking biology is not a science.

@glipsnort @Sy_Garte and @Jon_Garvey

What are you folks disputing? Are you actually going to complain about the amorphous mathematics that surrounds the Evolutionary process?

It’s not like the math is impossible … or fallacious … it’s just a combination of processes that frequently take thousands of years to “net out”.

Naturally, the length of time for some of this to be measurable within a useful degree of confidence does get in the way of people’s lives that rarely exceed 100 years.

Considering these limitations, the amount of analysis that evolutionary researchers have been able to pull together from multiple fields is rather inspiring - - don’t you think?