Ariew and Lewontin, "Fitness Confusions"

[Tim]

@stcordova

Figures of Merit as David Snoke suggested, also Engineering Metrics.

Figures of merit would appear to be largely unidimensional and, where multidimensional, offer no guidance in terms of the optimal trade-off between competing figures.

Further, figures of merit would appear to be frequently environment-specific. Running speed for terrestrial creatures, and flight speed for flying creatures, would appear to be useful figures of merit, as they would measure the ease with which the creature can both chase down prey, and escape predators. However, as a lineage adapts to new environments, they become increasingly irrelevant – as is the case with the ancestors of whales and penguins.

@stcordova

When a medical doctor measures the fitness of an individual it is along a laundry list of several diagnostics alone, and reproductive success isn’t high on the list. Counting how many kids someone made does seem kind of irrelevant to someone’s vital signs.

A medical doctor is focused on the survival of an individual not a population.

It does not matter how perfect a creature’s other figures of merit might be, if it cannot reproduce its lineage will undergo complete ‘genetic entropy’ in a single generation.

It is in fact not uncommon to see trade-offs that clearly sacrifice the optimisation of a creature’s own survival in order to increase the probability of reproduction and/or the survival of the resultant offspring. Any measure that cannot account for such tradeoffs is valueless.

[Roy (34-year veteran)]

@stcordova

@Roy

How could functional compromise be measured without reference to some form of fitness?

How could functional compromise be measured without reference to some form of fitness?

Figures of Merit as David Snoke suggested, also Engineering Metrics.

Biophysicist William Bialek points out (without explicitly using the term “figure of merit”) what figures of merit are optimized.

That’s not a complete answer. You haven’t said how to convert multiple different figures of merit into “functional compromise”.

By way of extension, figures of merit for a variety of biological systems can be developed.

Then which figures of merit are used is environmentally dependent, which is what you were trying to avoid.

Either you haven’t thought this through, or you are inventing it on the fly.

[Roy (34-year veteran)]

@Tim

Further, figures of merit would appear to be frequently environment-specific. Running speed for terrestrial creatures, and flight speed for flying creatures, would appear to be useful figures of merit, as they would measure the ease with which the creature can both chase down prey, and escape predators. However, as a lineage adapts to new environments, they become increasingly irrelevant – as is the case with the ancestors of whales and penguins.

Neck length is a possible figure of merit. But is a long neck better or worse? It’s better for browsing and spotting predators (giraffes) or for catching prey (elasmosaurs) but not for hiding in or moving through forest undergrowth (chital) or tunnelling (moles) or speed through the water (tuna, sharks, dolphins).

Shoulder width is another. But should it be large for competing for mates (buffalo) or small for chasing prey in warrens (weasels)?

Running speed is a good figure of merit. But lions are better than cheetahs at bringing down prey they do catch up with, and they hunt in packs. They also take prey away from cheetahs. So do lions have more genetic entropy than cheetahs? Even within cheetahs the same compromise of speed v strength applies. There’s no environmental specificity here. Nor was there between sharks and elasmosaurs.

Meanwhile, penguins move very slowly on land - but there are no predators to escape from there, and moving quickly is counterproductive on icy or rocky surfaces.

So how can figures of merit be used as a proxy for functional compromise when a change in either direction can reflect either an increase or decrease in fitness and/or functionality?

[stcordova (Salvador Cordova)]

Non-environmental-dependent figures of merit were alluded to in our Springer-Nature reference work, specifically the works of Princeton Biophysicist William Bialek.

The original draft referenced an article Natalie Angier’s in the NY Times, even though accurate, since it was a newspaper aritcle, the editor struck it from our paper, and we had to reference primary work of Bialek or his colleagues. But Angier was accurate as she interviewed the physicists. This is what Angier had to say:

Photoreceptors exemplify the principle of optimization, an idea, gaining ever wider traction among researchers, that certain key features of the natural world have been honed by [sic] evolution to the highest possible peaks of performance, the legal limits of what Newton, Maxwell, Pauli, Planck et Albert will allow. Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them the superb efficiency with which bacterial cells will close in on a food source; the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head; and the way a shark can find its prey by measuring micro-fluxes of electricity in the water a tremulous millionth of a volt strong — which, as Douglas Fields observed in Scientific American, is like detecting an electrical field generated by a standard AA battery “with one pole dipped in the Long Island Sound and the other pole in waters of Jacksonville, Fla.” In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants.

From https://www.nytimes.com/2010/11/02/science/02angier.html

You may want to watch Bialek’s Hans Bethe 2015 Memorial Lecture with my commentary:

NERD'S CORNER: Perfection in Biology, Evidence of Intelligent Design

Greedy algorithms of optomization toward reproductive efficiency do not guarantee and may acually prevent organization of molecules toward figures of merit, at the very least, systems operating with figures of merit at the limit of physics may be NP hard problems that cannot be evolved by genetic algorithms in the life of the universe. Postulated example is creating a tetrameric potassium ion channel that is optimized to “perfect” shape and diameter to only allow potassium ion.

[Tim]

@stcordova

Non-environmental-dependent figures of merit were alluded to in our Springer-Nature reference work, specifically the works of Princeton Biophysicist William Bialek.

Photoreceptors exemplify the principle of optimization …

Photoreceptors are only useful in sunlit environments.

… and the way a shark can find its prey by measuring micro-fluxes of electricity in the water …

So many of these examples seem environmental-dependent, on closer examination.

And all this ignores the problem of adjudicating the trade-offs between overlapping/competing figures of merit.

[stcordova (Salvador Cordova)]

The limits of what physics allow, i.e. Heisenberg Principle, smallest detectable quantized energy for a given frequency of light, etc. are not subject to environmental conditions, they are theoretical and experimentally confirmable figures of merit. And in fact, environmental conditions are subject to the limits of physics.

Environments where light travels through space don’t create fractional photons of light. Therefore the smallest detectable amount of light for a given frequency is one photon. That is a figure of merit, as in, how sensitive an optical device can be as a matter of principle in terms of the number of photons it takes for the device to say it is detecting photons.

A voltage meter is rated for certain voltage ranges, that rating is independent of whether the meter is actually actively measuring something. So it is NOT environmentally dependent (except for the fact it is an environment that allows operation).

Angier, and more importantly, Bialek made that clear.

[RonSewell (RonS)]

@stcordova

Figures of Merit as David Snoke suggested, also Engineering Metrics.

You are abstracting in order to obfuscate. This is not so complicated. Environmental factors can favor traits, including the degree of expression. In that context, of course those traits can be comparatively measured.

[Rumraket (Mikkel R.)]

@stcordova

Greedy algorithms of optomization toward reproductive efficiency do not guarantee and may acually prevent organization of molecules toward figures of merit

So what? Nobody says natural selection has to guarantee perfection, and it isn’t a fundamental premise of the theory that it will always be able to achieve the perfect/best possible solution.

Once again you’re falling victim to this strange black-white thinking.

@stcordova

Postulated example is creating a tetrameric potassium ion channel that is optimized to “perfect” shape and diameter to only allow potassium ion.

Do you have some sort of secret information that this is one of those examples where natural selection definitely would not be able to achieve that result?

It is no use merely pointing out that natural selection can not guarantee an optimal solution, then finding an example of a putatively optimal solution, and to pretend your work is now done.
Now you need to do the work of showing that this is one of those instances where natural selection definitely wouldn’t be able to find this solution.

But you have not done this work. Many things that can’t be guaranteed can still have appreciably high probability of obtaining.

There’s even a role for self-organizing principles that don’t have to do with natural selection. Think of how liquid in zero gravity will naturally assume the optimal shape of a sphere that has the least amount of surface area per volume. Or how clusters of soap bubbles will naturally tend to organize into a honeycomb grid to distribute the overall surface tension and load. Many materials have these intrinsic properties (to organize themselves into certain shapes with optimal attributes) that natural selection strictly don’t have to “invent”.

[Tim]

What is made “clear” Salvador, is that post was written from a very narrow physics viewpoint, with little if any relevance to biology.

“The number of photons it takes for the device to say it is detecting photons” might, biologically, be the only relevant figure of merit in a few, very narrow environments – e.g. very low light environments. However, in most environments, other figures of merit are likely to compete, including:

1. Breadth of spectrum that they are able to detect photons of

2. Accuracy of differentiating between photons of different wavelengths.

3. Depth perception.

4. Ability to cope with changing light intensities without being blinded.

5. Energy cost of building and maintaining the visual system.

Etc, etc.

I would suspect that, even within physics and engineering, many of these competing figures of merit would be relevant, and that in these fields, just like in biology, the optimal balance between these figures would be environment-dependent – the photoreceptor arrays you use in a research telescope would not be the same as those in a cellphone camera, or in a optic fibre network.

As you have presented no articulation of how these figures of merit may be aggregated, even in theory, to provide an optimal tradeoff, this entire line of inquiry would seem to be a dead end, and of little practical interest.

[Roy (34-year veteran)]

@stcordova

The limits of what physics allow, i.e. Heisenberg Principle, smallest detectable quantized energy for a given frequency of light, etc. are not subject to environmental conditions, they are theoretical and experimentally confirmable figures of merit. And in fact, environmental conditions are subject to the limits of physics.

Environments where light travels through space don’t create fractional photons of light. Therefore the smallest detectable amount of light for a given frequency is one photon. That is a figure of merit, as in, how sensitive an optical device can be as a matter of principle in terms of the number of photons it takes for the device to say it is detecting photons.

Ok, so the number of photons required for an eye to respond to light is a figure of merit.

Now (as I asked earlier), how can figures of merit be used as a proxy for functional compromise when a change in either direction can reflect either an increase or decrease in fitness and/or functionality?

If an eye that responds to a single photon evolves into an eye that only responds to e,g, 10 photons in close succession, is that an increase or decrease in functionality? Is it functional compromise?

If two species or individuals differ in the number of photons required for their eyes to detect light, does that mean one has more genetic entropy?

I predict these questions will never be answered, because genetic entropy is just a sham intended to shore up creationism, and not a serious research proposal.

[Roy (34-year veteran)]

@stcordova

A voltage meter is rated for certain voltage ranges, that rating is independent of whether the meter is actually actively measuring something. So it is NOT environmentally dependent (except for the fact it is an environment that allows operation).

Voltmeters are environmentally dependent. They can be designed for different ranges of temperature^[1], humidity, atmospheric pressure; for use in air, underwater or in vacuum; for low light conditions^[2]. They may operate outside the recommended ranges of temperature, illumination, etc, but give inaccurate or no readings.

This applies to sharks and other electrosensitive fish too. Electrical conductivity of water is affected by temperature, pressure and salinity. Individual species have electrosensitive organs adapted to their normal environments.^[3]

So these supposedly “Non-environmental-dependent figures of merit” are nothing of the kind, and cannot be used to measure functional compromise and hence genetic entropy, since variation in the length of epidermal canals that decreases electrosensitivity in the Indian Ocean conditions could also increase electrosensitivity in Mediterranean waters.

Functional change is not functional compromise, genetic change is not genetic decay, and genetic entropy is unworkable even using the examples provided by it’s proponents. I have no expectation that Cordova and his co-authors have any intent whatsoever to collect data on fish electrosensitivity to back up their armchair speculations, not least because doing so would zap their claims out of the water. Genetic entropy is pseudoscientific garbage.

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1. e.g. Maximum operating temperature of +50°C, minimum operating temperature of -25°C ↩︎

2. Luminous displays. A standard voltmeter will operate in complete darkness, but it’s no use if the readout isn’t visible. ↩︎

3. The length of the canals leading to the crypt varies greatly across fishes of both primitive and teleost organs. Canal morphology is adaptively matched to the resistance of the environment of each species, with longer canals in marine and brackish environments to increase the voltage gradient between the pore surface and the receptors in the ampulla (Collin and Whitehead, 2004), and shorter canals in freshwaters (Gauthier et al., 2015). (source) ↩︎

[Roy (34-year veteran)]

@stcordova

The Springer-Nature Switzerland AG Reference publication that I mentioned earlier is here in a book that used to be priced at $1500. It’s on university shelves now:

Dynamical Systems and Fitness Maximization in Evolutionary Biology | SpringerLink

The abstract:

Five years after Charles Darwin put forward his theory of Natural Selection, Herbert Spencer coined the phrase “survival of the fittest.” Survival of the fittest implies that individuals with highest fitness will survive and will pass on their traits – as required for evolution. Since then, scholars have struggled to mathematically model genetic change, inheritance, and selection, and further to define “fitness” to understand how fitness changes in a population over time. For about 90 years, the goal has been to prove that fitness continually increases – fitness maximization – in line with traditional expectation.

That isn’t the traditional expectation, let alone the current one, so it’s not a goal to prove it.

Anyone who understands that fitness is dependent on the environment, and that environments change, knows that fitness cannot continually increase. The idea that fitness remains roughly constant as a result of opposition between evolution and environmental change was named the Red Queen hypothesis some 50 of those 90 years ago.

This chapter presents the history of this issue to date, including proving a new simple and elegant formula for the fundamental theorem of natural selection with mutations, and a new application of the fundamental theorem of dynamical systems to evolutionary models which constrains the possible concept of fitness maximization.

A new formula sounds exciting, until recalling Sanford’s previous efforts at modelling and deriving formulae.

Taking a mathematical modeling perspective, we present both experimental genetics and mathematical models. Field biology researchers have observed that generally populations are either in stasis or are in fitness decline, and many mathematicians modeling genetics have rejected the very idea of general fitness maximization. We consider a variety of mutation-selection models, from Fisher’s early work, mutation-limited models that consider one mutation at a time, models that consider a distribution of simultaneous mutations, to the most comprehensive numerical simulations. We conclude that fitness is best understood in terms of net functionality (not just reproduction rate), and that fitness maximization is not a robust biological principle.

I conclude that Basener et al. don’t understand what ‘fitness’ is, since they’re saying that reproductive success should not be understood in terms of reproductive success.

I pity any institution that paid $1500 for this.

[stcordova (Salvador Cordova)]

@Roy

I conclude that Basener et al. don’t understand what ‘fitness’ is, since they’re saying that reproductive success should not be understood in terms of reproductive success.

No, we represented the pop gen understanding (or should I say misunderstanding) of the issues. Ariew and Lewontin only drove the point home in their essay fitness confusions.

No concept in evolutionary biology has been more
confusing and has produced such a rich philosophical literature
as that of fitness. The confusions have arisen because a concept,
originally introduced as an inexact metaphor by Darwin, has come
to play an analytic role in the formal quantitative dynamics of
evolutionary biology. The confusion has arisen from the mistaken
belief that a single coherent definition of fitness is required by
and can be applied over all dynamics of evolutionary genetics.
There is a conviction among philosophers and biologists that
somehow a property of fitness must be included in dynamical
explanations of evolution through natural selection. Our purpose
in this essay is to show that
(1) The concept of “fit” as introduced by Darwin both in the
explanandum and the explanans of his theory does not appear in
quantitative dynamical theories of genetic change in evolution;
(2) Any attempt to introduce a unitary analogous concept of
“reproductive fitness” into dynamical models as a scalar ordinal
which will explain or predict quantitative changes in the
frequency of types must fail;
(3) This failure is a consequence of the fact that in
different biological situations different algorithms must be used
to connect temporal changes in type frequencies with quantitative
information about reproduction and that in an important fraction
of cases even complete information on reproductive rates is
insufficient to determine whether a type will increase or decrease
relative to others in the population.

As far as the most fit being that which reproduces, and that which reproduces being the most fit, that is a useless tautology (analytic statement) as far as trying to prove Darwinism.

Our chapter highlighted the absurdity of using the accepted definition of fitness in evolutionary biology.

See RH Brady

Natural Selection and the Criteria by Which a Theory Is Judged — The Nature...

Since tautology is fatal for any sort of causal explanation, it is somewhat mysterious to find a number of authors advancing an admittedly tautologous formulation of natural selection. Waddington, for example, published the following passage in 1960:

Natural selection, which was at first considered as though it were a hypothesis that was in need of experimental or observational confirmation, turns out on closer inspection to be a tautology, a statement of an inevitable although previously unrecognized relation. It states that the fittest individuals in a population (defined as those which leave the most offspring) will leave the most offspring. Once the statement is made, its truth is apparent. This fact in no way reduces the magnitude of Darwin’s achievement; only after it was clearly formulated, could biologists realize the enormous power of the principle as a weapon of explanation.

YIKES!

the fittest individuals in a population (defined as those which leave the most offspring) will leave the most offspring.

We only represented the way evolutionists conceive of fitness. We suggested Bialek because the problem that evolutionism tries to solve is evolving “organs of extreme perefection and complication” not evolving that which makes more offspring. We took some pains to show that so-called natural selection favors gene loss, not accumulation of complexity.

“Genomes decay despite sustained fitness gains” – Richard Lenski

Nuff said.

[John_Harshman]

As predicted, Sal never communicates his intended point and ignores requests to do so.

[Roy (34-year veteran)]

Context restored:

@stcordova

@Roy

… We conclude that fitness is best understood in terms of net functionality (not just reproduction rate), and that fitness maximization is not a robust biological principle.

I conclude that Basener et al. don’t understand what ‘fitness’ is, since they’re saying that reproductive success should not be understood in terms of reproductive success.

No, we represented the pop gen understanding (or should I say misunderstanding) of the issues.

Then you should have said that ‘the pop gen (mis)understanding of fitness is best understood in terms of net functionality.’ Though that wouldn’t have looked as impressive a conclusion.

As far as the most fit being that which reproduces, and that which reproduces being the most fit, that is a useless tautology (analytic statement) as far as trying to prove Darwinism.

Our chapter highlighted the absurdity of using the accepted definition of fitness in evolutionary biology.

You haven’t come close to the accepted definition of fitness in evolutionary biology. I don’t think you know what it is.

We only represented the way evolutionists conceive of fitness. We suggested Bialek because the problem that evolutionism tries to solve is evolving “organs of extreme perefection and complication” not evolving that which makes more offspring.

Evolution favours organisms that make more offspring (that themselves reproduce). ‘Evolutionism’ doesn’t try to solve anything.

“Genomes decay despite sustained fitness gains” – Richard Lenski

Nuff said.

No creationist post is complete without a quote-mine, and this is a doozy.

1. It’s missing the first word. The actual text^[1] is “Mutator genomes decay, despite sustained fitness gains, …” It’s only referring to genomes of organisms undergoing hypermutation, not to genomes of all organisms. This omission has been deliberately concealed by capitalizing the ‘g’ in ‘genomes’.

2. It’s missing the context. The title continues “… in a long-term experiment with bacteria”. So this is about what happened with some of the bacteria in Lenski’s LTEE, under restricted laboratory conditions. It doesn’t even apply to all bacteria in the LTEE, let alone other bacteria or other organisms, and it doesn’t apply permanently, only during periods of hypermutation.

3. It’s misattributed. Lenski was only one of 9 authors of the paper, and wasn’t even the lead author. While Lenski clearly endorses those words (in context, anyway), it’s unlikely he wrote them.

Extracting those words from their limiting context, fiddling with the capitalization to hide the omission, and attributing the text to Lenski alone are all dishonest acts. So the question that needs to be answered - the first and only question that needs to be answered right now - is:

Where did you get that ‘quote’ from?

---

1. No source was given, so it’s possible that Sal was quoting from some other work by Lenski, but I can’t find one. Nor can I find that text sans ‘Mutator’ anywhere. Maybe Sal can cite a different source, but I doubt it. ↩︎

[John_Harshman]

Warning: I’m not a population geneticist. But I think I can clarify Sal’s confusion nevertheless. Fitness is not defined tautologically if you think of it in a statistical framework. Fitness isn’t defined as differential reproduction. It’s defined as expected differential reproduction causally correlated with genotype. Differential reproduction is not a definition of fitness; it’s an estimate of fitness. That estimate may be confounded by “noise”, i.e. stochastic variation.

[Rumraket (Mikkel R.)]

@stcordova

@Roy

I conclude that Basener et al. don’t understand what ‘fitness’ is, since they’re saying that reproductive success should not be understood in terms of reproductive success.

No, we represented the pop gen understanding (or should I say misunderstanding) of the issues. Ariew and Lewontin only drove the point home in their essay fitness confusions.

Yes we all agreed the concept of fitness must be applied in the context of a specific circumstance (environmental and genetic). Once you do this, the concept works just fine.

Then you can say, for example, that the carrier of an allele that gives antibiotic resistance is more fit than a non-carrier in an environment where they are exposed to the relevant antibiotic.

@stcordova

As far as the most fit being that which reproduces, and that which reproduces being the most fit, that is a useless tautology

That’s because you invented it in your own head.

“The most fit” isn’t defined as “that which reproduces” anywhere in biology. Nor is “that which reproduces” defined as “the most fit”.

An organism somewhat less fit than the theoretically most fit organism can still reproduce, and probably very well.

@stcordova

Our chapter highlighted the absurdity of using the accepted definition of fitness in evolutionary biology.
(…)
the fittest individuals in a population (defined as those which leave the most offspring) will leave the most offspring.

The fastest individual (defined as that which runs the furthest distance in a set amount of time) will run the furthest distance in a set amount of time.

And running speed can be measured and compared. They hold regular running competitions where running speed is compared for different individuals on different distances, different terrains etc.

So just as we can make sense of, and even physically measure, how fast different runners are (and we can imagine the theoretically fastest possible runner who is faster than all other runners), we can make sense of and physically measure how good individual organisms are at surviving and reproducing under different circumstances.

@stcordova

We took some pains to show that so-called natural selection favors gene loss, not accumulation of complexity.

Depending on circumstance. In some circumstances it favors gene gain.

@stcordova

“Genomes decay despite sustained fitness gains” – Richard Lenski

The argument from a deliberately doctored paper title? That’s a little desperate even for you, mr. Cordova.

The correct title of the paper is actually “Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria”.

It talks about how in asexual organisms (bacteria) with unusually high mutation rates (mutator strains that evolved in the experiment), deleterious mutations of small fitness effects can hitchhike (linkage) with beneficial mutations of stronger effect.

Lenski isn’t talking about loss of complexity or loss of genes in that paper. He’s talking about the relationship between fitness, mutation rate, and population size in asexual organism.

[Joe_Felsenstein]

Fitness is not a tautology. See a my article at Pandas Thumb on that.

[RonSewell (RonS)]

@stcordova

As far as the most fit being that which reproduces, and that which reproduces being the most fit,

As far as the most fit being that which reproduces >> Generation One

that which reproduces being the most fit >> Next Generation

most fit being that which reproduces >> Generation next

And so forth. Was that so difficult?

@stcordova

Non-environmental-dependent figures of merit were alluded to in our Springer-Nature reference work

Is hydrodynamic efficiency not a figure of merit, as physical as it gets? Thus, aquatic mammals would be under strong selective pressure over the transition to an ocean going lifestyle. The change in environment determines the change in score weighting, and therefore what constitutes fitness in both senses of reproductive success and morphological ideal.

[Faizal_Ali]

@John_Harshman

As predicted, Sal never communicates his intended point and ignores requests to do so.

@stcordova and his collegues are used to communicating to the likes of @colewd, @Giltil. @Eddie, et al. It’s a bit much to ask him to suddenly change tact and start communicating in a manner suitable for people who actually understand this stuff and are not going to reflexively accept whatever BS he comes up.