Eddie, take a deep breath. You are right that there is a confusion about words, and what is being discussed. I do not disagree in fact with anything that Steve has written, so the confusion is not between us. My example was about the effect of the allele on people’s health. I wanted to show that biologists are not totally in the woods when it comes to mathematical analysis of the effects of genetic changes.
We made a guess (based on the position of the SNP and the activity of the gene) that the new allele could possibly have a deleterious effect on the health of the carriers. If so, then we would have expected to see a loss of HW equilibrium due to negative selection (which is more common than positive selection, btw). We did not see that. By itself, this does not prove that the new allele is neutral, but it is consistent with that. And that “prediction” (used loosely) turned out to be correct.
Your comment about humans choosing (based on cultural factors) how many kids to have is quite right, and could overwhelm any strictly genetic factors. But strongly deleterious alleles, will still in many cases reduce survival (for example of newborns or children) and averaged over an entire population that will show up as a disequilibrium in allele frequencies as selection plays a role. I would suggest checking out the HW equilibrium and its relation to selection, online. Its a very simple equation, and very useful in population genetics.
No, that’s not quite right, Eddie. We did quantify the relative fitness of the new allele. It was 1.0. In other words it had no selective effect, either positive or negative. That was the result of the HW calculation. If we had found dysequilibrium, we could have quantified the relative fitness as being something like 1.2 or 0.95 etc. But note that my example is not related to evolutionary outcomes except tangentially, because I wasnt working on evolution at the time, but on population genetics in disease. Steve, who does work directly in evolutionary biology, uses far more sophisticated models to determine the quantitative fitness of genetic and phenotypic changes. My point was solely to illustrate that there are many ways to come up with numerical estimates of fitness. Which can then be used for various purposes. Im sorry if this isnt clear, but feel free to ask more questions.
Sorry about that, Eddie. I think some of us have been trying to keep the discussion as non-technical as possible, but that often involves leaving out some information. Steve mentioned that we can talk about relative and absolute fitness, with relative fitness being much more commonly used. I will leave further explanation of absolute fitness to Steve or someone else, since I know little about it. For relative fitness, the factor (usually denoted as “s” or sometimes “w”) for fitness is 1, when there is no selective effect, greater than 1 when the effect is positive (meaning that the allele in question will increase with time in the population) or less than 1 (when the allele frequency will decrease with time). Most beneficial alleles will have s values close to 1, although sometimes, like the lactose tolerant genotypes, that value can be as high as 2 or more. The higher the relative fitness value, the faster the allele will spread through the population. I am pretty sure this is covered in online basic articles on population genetics, though I havent checked.
Possibly, depending on how much is known about the phenotype (or even genotype) of the new population. We made a guess based on the new genotype, which turned out to be wrong, since we were wrong about the phenotype. But if, for example the new population of rodents have white fur, (like lab rats) we could estimate a pretty low value for relative fitness, based on their lack of camouflage. On the other hand if they were much bigger than the indigenous population, it would be hard to predict, since ecology, animal behavior, and and all other biological fields are too complex to be easily modeled. It might depend on the specific jungle, what else is living there, what is the temperature, what food sources exist, and so on.
As you know, there have been many natural experiments (often non deliberate) that have illustrated how hard it is to predict the consequences of ecological change or human environmental interventions.
I might point out, shifting the topic just a bit, that some theologians have noticed this amazing complexity of our natural world, and have seen it (as I do) as a sign of the majesty of God’s creation. Whenever I hear that any simple natural law has been found to be not so simple, or that some model we have made to fully understand any natural phenonemon turns out to be not always true, I say “Thank God”. So getting back to @Jon_Garvey’s point, the fact that contingency is so universal in the natural world is to me a wonderful, indeed a holy thing. It doesnt mean that science is useless or that some things we call science arent really scientific. It means that (as Jon has said for some time now) we need to expand our definition of science to include the omnipresent fact of contingency in nature, and somehow (I have no idea how) to consider God’s providence in our naturalistic worldview. But that could be a topic for another thread.
Fitness is not a scientific concept as you have defined it, because we have not theory to explain what makes a particular organism fit. We know what creates heat, We do not know what creates fitness per Darwinism.
Almost, but not quite, Sy. In this case I’m trying to work with Joshua’s concept of science as a discipline with a good, but definitionally limited, set of tools and purposes. And if we ask why it should be that acts of God should be properly excluded from science, it’s because science has to do with the patterns that are reproducible and “lawlike” in nature. As Asa Gray wrote, favourably quoting Bishop Butler, “The only distinct meaning of the word ‘natural’ is stated, fixed or settled.”
That’s why I said, about a million posts back, that what is contingent and NOT reducible to lawlike processes may certainly be observed and recorded within science (like the endless lists of Enlightenment naturalists) or else there would be no data on which to form new theories. But contingent causes properly belong outside the scientific method. They will be termed “random”, which is proper if everyone recognises that word as meaning always (in science) “unknown and beyond the scientific method”, rather than vaguely allowing ideas of ontological randomness like “undirected” or “purposeless” into scientific discourse.
A classic example was Steve’s mention of half-life, in which the statistical pattern is pretty precise and absolutely measurable: element A decays to element B, and experiments measuring the proportions over time will determine the half-life. Science rules, OK.
But decay of the individual particles is absolutely unpredictable, to the extent that someone like Lou Jost used to say it was “uncaused”. But that is not a scientific, but a philosophical or theological statement, as would be any idea that it is “undirected”, “spontaneous”, or any other explanation beyond “cause unknown and unrepeatable, ergo beyond science’s purview - ask a philosopher or theologian.”
The philosopher might well comment that “no cause” is incoherent. The theologian might well invoke the doctrine of providence. Neither would need to apologise for not providing empirical data for their view, because empirical data has only to do with repeatable causes - and contingency ain’t one.
For “quantum events”, you can substitute any “random” contingency, such as the hyper-mutation of the immune cells, neutral changes in genes, or anything (in fact) that does not yield a lawlike set of causes at the level under consideration. And that’s where, theologically speaking, God is making choices, just as where lawlike process occur, that’s where God is creating dependable regularity.
The question is not whether God is active in nature (if one is an EC that ought to be a given), but in what manner : science discerns the patterns in nature (or as George D rightly points out, constructs patterns it hopes match the real ones), but cannot do more than record contingencies - and look to other disciplines for causation, even though the causes are not necessarily supernatural.
As you rightly say, contingency is a “holy thing”: possibly science could be expanded to include it (but not without changing its groundrules against final and formal causes): or if that’s not useful perhaps scientists could just learn to do more than science, recognising and stating if they are crossing the boundaries, or at least being more aware that science does not in any way exhaust the understanding of creation.
Ohno gave a figure of 30K genes that could, in the nature of things, be the maximum under selection at any one time (presumably meaning in any one population). I understand that to be one basis on which Kimura founded neutral theory: most genes would be fixed or perish completely independently of natural selection.
Since Ohno’s time, the knowledge of the number of genomic features undergoing evolution has vastly expanded through non-coding elements, overlapping genes and so on (though perhaps the number of coding genes has shrunk since HGP). Either way, those like Eugene Koonin suggest that selection necessarily remains blind to many beneficial and moderately deleterious mutations simply because of the elements that are under stronger selection. Hence, in the small populations of most higher species, most selection is said to be purifying, and most change neutral.
On the face of it, then, selection seems to be as much due to the other 30K (or whatever figure is now accepted) elements under selection, but mostly not under study, as to the value or otherwise of the particular gene being researched. This appears to me to break any clear correlation, in many cases, between tangible benefits or detriments of a trait and their being selected (and hence the idea of “reproductive success”).
Do population genetics fitness considerations take the limited capacity of natural selection into consideration in some way?
Bayesian analysis can move in either direction in time. If I know that a new allele confers resistance to streptomycin, for example, I can predict that it will provide greater fitness to a bacteria population in my body when I’m taking antibiotics. If a new allele reduces the leg-to-body ratio in male humans, I can predict that it will provide greater fitness to the lucky Valentinos who have it.
That said, any predictions would be probabilistic rather than binary. The overall fitness of a trait in a population in a particular environment is highly complex. And as our friend Steve stated earlier,
Not the entire difference, as Hayek pointed out in his Nobel lecture. The complexity of physical systems nevertheless remains tractable to science because the variables are geberally independent, and most can be safely ignored in an experimental or modelling situation.
However, the complexity of human systems (he was an economist) is not so because the complexity is what he called “organised”, in that all the variables affect all the others. In that case, unless one knows all the individual factors completely (impossible), one can intrinsically only make generalised approximations, rather than predictions: in other words, it’s not “more difficult”, but “qualitatively dissimilar”.
The problem is, one cannot know for sure just how approximate ones conclusions are: you don’t know what you don’t know until you know it, and so even Bayesian procedures don’t protect one from being wildly wrong.
Biology, of course, lacking willful humans, is somewhere in between physical and humans science, but is closer in its complexity to the human than the physical science situation. That’s been my point all along.
This example appears another case where direct comparison with human history in the form of war makes the point I started with. Imagine in a war that some boffin stupidly suggests painting some of their warplanes white, and some stupid politician agrees to a study to check if it will save money on camouflage. The outcome, if not a foregone conclusion, is easily ascertained by the losses that would occur to the white planes. Science rules, OK.
But another boffin questions - more usefully - whether, say, USAF or RAF decals detract from camouflage and should be removed. If they attempt a trial, the multiple confounding factors of minor advantage, losses from friendly fire and especially the fact that even effective camouflage has a marginal role in overall success make the trial inconclusive in principle. In fact, the effect of removing decals would be a black box because of the nature of the real world: the fitness of decals is outside science… or if not that example, there is a level of complexity beyond which science cannot go.
The best that could be modelled is, perhaps, some experiment in which pilots’ ability to spot decaled and undecaled planes in a photograph is tested - but the model is so far from reality that it cannot help the war effort.
In other words, the slam dunk cases for selection like lactase persistence may demonstrate the existence of a mechanism, and may in certain cases be of practical value. But as soon as one knows that multiple causes are in operation - many of them entirely contingent - other competing traits, neutral retention of traits, ecology, animal behaviour, forest fires, cold winters, predation of young etc etc, there will come a point where all models give increasingly unreliable answers.
If that point is unrecognised, there is a danger of treating a black box as if it were science, rather than the stuff of theology, philosophy - or just imagination.
Jon, I fully agree with everything you wrote except for the last sentence quoted above. I think its a matter of degree, and that it makes no sense to postulate boxes called science (where predictability is the rule), other non scientific boxes like theology, philosophy and imagination. So there are highly complex systems in scientific models, (and yes, I mean the models themselves, not just the reality) which are difficult to allow predictions. I gave some examples in a previous comment. A great deal of biology, but not all of it, fits into this category, as does the vast majority of humanities like history, literature, art. But not all of it. As a musician, you know that the beauty of music can derive partly from contingency but also from some fairly rigourous rules of harmony, dissonance, melodic scales, and so on. I remember learning the laws of harmony (as practiced by JS Bach) as if they were laws of physics (parallel fifths are forbidden comes to mind).
Even your warfare model is a mix of contingency (just think of the weather issue during the Battle of the Ardennes) and some pretty useful and predictive modeling. I would cite Tolstoy’s long treatment of the laws of war in War and Peace, the curriculum of military academies that include a great deal of theoretical principles based on empirical observations (these can get extremely technical, like positioning of naval forces, and use of artillery). Yes, there are always exceptions. Even Tolstoy’s dictum that larger armies defeat smaller ones does not always hold. But the same is true in all of biology, and to a lesser extent in chemistry as well.
My point is mostly semantic. We agree on the nature of science and other fields of study, and we agree on the role of contingency and complexity. My point is simply that its a mistake to label highly contingent, complex, non predictable phenomena (or the models we construct to study them) not “scientific” a priori. In fact treating black boxes as they were science is often the first step to a better understanding of the natural word.
Eddie asked a while ago when the propensity definition of fitness came into play. I ran into this pretty clear statement of that conceptual approach from Thomas Hunt Morgan in 1916:
[quote]
If through a mutation a character appears that is neither advantageous nor disadvantageous, but indifferent, the chance that it may become established in the race is extremely small, although by good luck such a thing may occur rarely. It makes no difference whether the character in question is a dominant or a recessive one, the chance of its becoming established is exactly the same. If through a mutation a character appears that has an injurious effect, however slight this may be, it has practically no chance of becoming established. If through a mutation a character appears that has a beneficial influence on the individual, the chance that the individual will survive is increased, not only for itself, but for all of its descendants that come to inherit this character. [/quote]
What’s notable is that Morgan is considered a mutationist, rather than a Darwinian, and this understanding of the probabilistic nature of fitness was largely lost in the Modern Synthesis.
I do find it a little odd that Eddie has been defending the Darwinian and Neo-Darwinian understanding of fitness against its critics, given his usual embrace of those critics.
“What work does the word ‘advantageous’ do that isn’t already covered by discussing ‘fit,’ ‘unfit,’ and ‘neutral’?”
I don’t see the utility of quibbling over roughly synonymous terminology in someone else’s discipline. But if I’m blind to a crucial difference between “fitter” and “more advantageous,” do carry on.