starlarvae

Probably a cruel idea, but it would be interesting to see the outcome of artificial insemination -- testing the boundaries of phenotypic plasticity. If such an experiment produced fertile, viable offspring would we have to concede that the parents were of the same species? "Niche" has the same problem. The pattern seems to be that we get an idea (based on our preconceptions, biases and limited knowledge), then we coin a term for the idea, then we go looking around in nature for a target on which to pin the term.

Dog breeders have produced a broad range of morphological variation within the species variety Canis lupus familiaris . See attached chart from American Kennel Club. But no one, so far as I know, is claiming that selective breeding has produced a new species within the genus Canis. No natural environment would pull as much phenotypic plasticity out of a species genome as is shown in this chart. And yet, nature is credited with producing all the various species of creatures, despite nature's ability to produce only a much narrower range of phenotypic variability from a given species genome, If dog breeders haven't yet produced a new species (or if they have, please comment) then how does nature do it, given its much feebler ability to produce morphological variability from a genome?

http://www.sciencedirect.com/science/article/pii/S1571064513001188 You asking about consciousness or behavior? Having experiences per se (being conscious) need have nothing to do with any observable behavior & vice versa (as in zombies and robots). Above link presents papers pro and con the idea that the link between physical activity and mental activity is to be found at the quantum level. A quantum solution would be a big step toward resolving some of the philosophical issues involved.

In What Darwin Got Wrong, authors Jerry Fodor and Massimo Piattelli-Palmarini discuss "master genes" that regulate multiple traits and so force those traits to evolve together. In their example, the traits regulated by a particular master gene, designated Otxi, seem unrelated to each other, but as a group the linked traits are oddly suggestive of an aquatic episode in humankind’s past. The authors write, "[. . . ] in particular, since the Otxi ‘master’ gene controls the development of the larynx, inner ear, kidneys, and external genitalia and the thickness of the cerebral cortex, selective pressures sensitive to changes in the functions of the kidneys (due to bipedal station, or different liquid intake and excretion resulting from floods or droughts), or the fixation of different sexual patterns, may have had in turn secondary effects on the expansion of the cerebral cortex and the structure and function of the larynx.” This set of traits, under the control of the same master gene, plays a foundational role in the aquatic ape hypothesis. Fluid/salt regulation (kidneys), 3D proprioceptive orientation (inner ear), breath control and speech (larynx), ventro-ventral copulation (genitals) and development of a complex cerebral cortex turn out to be fated to travel together, all being regulated by the same master gene, and all being components of the aquatic ape scenario. Certainly not conclusive, but suggestive.

All good points. We're honing in on philosophy of science. Namely, when science articulates theories and mechanisms to explain observations -- to get underneath descriptions of what is observed and propose causes as to why the given observations occur and not others -- then is science making an ontological (or epistemological) claim, or is science making a pragmatic claim? Does science claim to tell us about reality and the way things actually are? Or does science claim only to figure out what observations will obtain in certain situations? Does science explain observations or just interpret them using vocabularies that scientists have agreed to use for such interpretations? Specific to the topic of evolution: Are we using "natural selection" with the claim that we're explaining a process that shapes allele distributions? Or do we just agree that "natural selection" is our shorthand term for allele distributions that conform to certain statistical parameters?

Deviation from the null is EXACTLY what differential reproductive success is. What causes differences in reproductive success? who knows?

Yes, the population is "by definition" under selection. The definition is derived statistically. It is a contrivance. If allele frequency deviates from null model, you can define the difference as due to "selection" or anything else you care to invent, but all you really know is that the frequency deviates. Who knows what's causing it? Statistics can't tell you. But wait. The deviation from the null model is a measurement, yes. BUT the attribution of the deviation to natural selection is precisely a confusion of causality and correlation. If thermometer reading goes up, it's getting hotter. That's all the thermometer can tell you. It says nothing about the source of the heat. Measuring deviation from the null model tells you how far the allele frequencies deviate. But that's it. It says nothing about the source/cause of the deviation. But you're not detecting selection. You're detecting only the deviation in allele frequency, then defining that as a measure of selection pressure. That's called Begging the Question: You assume that natural selection is responsible for the deviation, then you take the deviation to be evidence of selection.

He ostensibly solved the problem of suffering, via the Four Noble Truths: 1) All is suffering (We are born into this world) 2) Suffering is caused by unfulfilled desires (not getting what you want, or getting what you don't want) 3) To eliminate suffering, just get rid of your desires (then you'll have none unfulfilled) 4) The eightfold path: Right Living, Right Speech, etc. -- essentially a boy scout manual on clean living, a way to shed your desires.

Don't bother about defining truth. You'll spin your wheels forever. It's enough that we know how to use the word. That's all. We continue to use the word in certain agreed-upon ways, and that's it. There's no "the way the world actually is" lurking around at some "deeper" level. We just compare our experiences, and then come up with rules about how to use the various words that we use.

Right. Life creates a diversity of environments. The whole planet has been made over by the presence of life, made over to support diverse life. So, do environments select adapted organisms? Or do organisms select/create favorable environments? Do environments shape phenotypes, or do phenotypes shape environments? It's a little artificial to say that environments "select" when environments themselves get made over to meet the needs of their inhabitants. Anytime you interact with anything, I could say that that thing "selected" whatever behaviors your interaction with it consisted of. But that wouldn't tell us anything useful. Likewise, neither does the theory of natural selection tell us anything useful. Ok, how far back do you want to trace the causal chain? Organisms are able to do what they do only because the Earth is a certain distance from a sun of the requisite size, and that's possible because we're the right distance from galactic center. and so on. I suppose you could say that organisms are "adapted" to the mass of the proton. After all, look at how well the creatures operate in this world in which the mass of the proton is whatever it is. Maybe we need to tackle the Anthropic Principle.

It's not clear how much "environment" should be credited with the diversity of life. Early photosynthesizers dramatically reconstituted the proportions of gases that composed the atmoshphere. Bacteria nucleate raindrops and fix nitrogen in the soil. Calcium sea shells help regulate the ph of the oceans. Beaver dams. And so on. Creatures construct their niches, and those of neighbors and descendants, as much as they adapt to whatever situation they're born into.

I think they're talking about similarities, not differences. Their point is that genomes across species are so strikingly similar, relative to the diversity of phenotypes. Epigenetic gene regulatory mechanisms allow a shared set of genes to produce a variety of phenotypes. This is what happens when cells differentiate in a developing body. Reading up on this topic, I keep coming across the phrase, "non-genetic inheritance," to describe epigenetic inheritance, and even ecological (niche) inheritance. You think that's legit usage?

Here's a summary of such studies: http://www.scientificamerican.com/article/regulating-evolution/ In it the authors Sean B. Carroll, Nicolas Gompel and Benjamin Prudhomme elaborate on the findings coming out of comparative genomics: "For a long time, scientists certainly expected the anatomical differences among animals to be reflected in clear differences among the contents of their genomes. When we compare mammalian genomes such as those of the mouse, rat, dog, human and chimpanzee, however, we see that their respective gene catalogues are remarkably similar. [. . . .] When comparing mouse and human genomes, for example, biologists are able to identify a mouse counterpart of at least 99 percent of all our genes." "The discovery that body-building proteins are even more alike on average than other proteins was especially intriguing because of the paradox it seemed to pose: animals as different as a mouse and an elephant are shaped by a common set of very similar, functionally indistinguishable body-building proteins." "The preservation of coding sequences over evolutionary time is especially puzzling when one considers the genes involved in body building and body patterning." ". . . to our surprise, it has turned out that differences in appearance are deceiving: very different animals have very similar sets of genes." Similar observations are presented in this article, http://www.tandfonline.com/doi/abs/10.4161/cc.6.15.4557#preview , and here: http://www.nature.com/nature/journal/v402/n6761supp/full/402c41a0.html , in which the author says, "So many examples of [DNA] conservation have now been found that it is no longer considered surprising. We can now state with confidence that most animal phyla possess essentially the same genes, and that some (but not all) of these genes change their developmental roles infrequently in evolution [emphasis added]." So are these guys off the mark? They give the impression that DNA is highly conserved across species. And that phenotypic diversity is due largely to adjustments in gene regulation, particularly involving genes that guide development and the timing of developmental stages, rather than to genetic novelty via mutation.

Thanks for detailed reply. Please set me straight on something. My understanding is that one surprising result coming out of all the comparative genomics studies is that DNA is highly conserved across species -- that genomic variation across species is not proportional to the phenotypic diversity that we observe across species, but is far less that was expected, based on the vast phenotypic variation that we observe. This disparity, or apparent paradox, (little genetic variation, but lots of phenotypic variation) gets explained in terms of epigenetic regulatory mechanisms. A largely shared set of genes can produce highly diverse phenotypes, in this case, because epigenetic mechanisms regulate when during the life cycle and where in the body various genes are turned on or off. The various regulatory regimes, in turn, determine, to a significant degree, phenotypic differences across species. It's that whole evo-devo thing. If this varying-by-species epigenetic regulation gets turned into genetic differences (somewhere down the line) as you suggest, then why are these epigenetically induced gene differences not more prevalent in the comparative genomics studies? Why does it look like DNA remains highly conserved through evolution if the epigenetic differences get translated into genetic differences? Shouldn't those genetic differences -- to a degree proportional to the phenotypic differences -- show up in the comparative genomics work?

Thanks for the links to references. If selection is a quantifiable "force," and its unit of measure is a change in allele frequency, and the signifcance of that change is statistical (does it exceed or not some statistically defined threshold relative to the null hypothesis?), then the question remains as to cause and effect. The difference between natural selection and genetic drift rests on a statistical threshold. The assignment of causation (selection or drift) is done by convention (by defining statistical thresholds and seeing whether the thresholds are exceeded or not). Statistics is a descriptive tool, and useful for that. It can produce suggestive correlations. But causality is something else. Quite.

Wrong. Differential reproductive success is observationally verifiable. You can count offspring. You can tally up their traits. You can do all kinds of statistical analyses on their genes. But you cannot observe natural selection. The most you can do is observe differential reproductive success, and once you've observed it, then you can dance around chanting, "Natural selection."

You are way off. You ever come across references to epigenetics? This is an growing field in molecular biology and evolutionary biology. Some stresses and other environmental effects produce epigenetic changes that regulate gene expression and are heritable and that therefore can participate in evolution. Here is one of many papers on this topic: http://onlinelibrary.wiley.com/store/10.1113/jphysiol.2014.272096/asset/tjp6184.pdf?v=1&t=i2qjfhim&s=03d1cc76a24527cb58bd2df8e3c7c34ea29b1b9a If that link doesn't work, the paper is in J Physiol 592.11 (2014) pp 2307–2317 2307 The Journal of Physiology title : Inheritance is where physiology meets evolution authors : Etienne Danchin and Arnaud Pocheville the authors make their case that "non-genetic inheritance shatters the frontier between physiology and evolution, and leads to the coupling of physiological and evolutionary processes to a point where there exists a continuum between accommodation by phenotypic plasticity and adaptation by natural selection." Thanks for that contribution. Epigenetics is central to the new evolutionary paradigm, but as yet underappreciated by those members of the olde guard preoccupied with rooting out creationists.

Yow. Don't get your undies in a bundle. The comment you quote goes back to my characterizing the whiteness of bones as a trait, and I was informed that the bones are a trait and the whiteness merely an aspect of that trait. Nothing in a dictionary is going to settle that indeterminacy of usage. And your explanation of natural selection just makes the point I've made several times already -- namely, that natural selection is a superfluous concept and we can just drop it. Because, what we actually observe is differential reproductive success and its consequences on the genotypes and phenotypes of succeeding generations. That's all you've said. Nobody's arguing with that. The dispute enters when we try to explain the observation. Many people invoke something that they call "natural selection" to explain it. But, as your comments above illustrate, "natural selection" is just a synonym for differential reproductive success. So, all I'm doing is trying to be a good scientist and stick with what is empirically verifiable: differential reproductive success. Occam's razor cautions against inviting superfluous ingredients into our theorizing, which I think is sound advice. So, let's drop "natural selection".

But this exchange just highlights a problem with natural selection theory. There's no way to know if the survivors were cowardly and avoided precarious landscapes. Or if those killed were dumb and didn't sense the danger. You can make up all kinds of stories about why this one got killed and that one survived, about whether the event and its consequences for the gene pool were random or reflected some aspect of fitness. There's no way to know. And yet, we keep talking about fitness, adaptation and such as shapers of phenotypes, when we can't tease apart any such considerations from the endless contingencies that bear on the kinds of situations we're interested in.

Gulp. Aren't you afraid you're giving ammo to . . . the . . . dreaded . . . Creationists !!?? If Wilson is right, then what's up with the theory of natural selection? Why is it so central to evolution theory? I suspect he's right, to a point. I'd like to know how he thinks epigenetics ultimately will re-cast evolution theory. Plus, in the light of evo-devo, phenotypes might have far less to do with endogenous (environmental) forces than with endogenous (physiological) forces.

". . . . whatever aspect of a trait you have decided to label." Oh, brother. Here we go: What's qualifies as a "trait" and what qualifies as merely an "aspect" of a trait? You're just making it up as you go. Can you give me some logic, and not just a list of assertions? The fact that evolution occurred is plain from the fossil record. But the putative mechanism of natural selection is just plain incoherent.

Really? Its bones are white. Why would white bones be selected over some other color? Same with the blood being red. Also, its heart makes a faint noise while it beats. Why was that noise selected, and not some other one? This list could go on and on. EVERY trait has been selected, sayest thou. I think probably not. The favorable traits will spread? How can you recognize a favorable trait EXCEPT by watching it spread? The traits that spread are the ones that spread. That's all. There's no need to attribute to them mystical properties, such as their being "favorable" or "adaptive." The possessor of the deformed beak might just fly over to where the unique beak will enable it to exploit a new foodstuff, or attract a kinky mate. Look at all the beak variety among Darwin's finches. Which finch beaks are "deformed"?

It's akin to circular reasoning, like in Plato's Euthyphro, where, in a nutshell, "piety" is defined as that which pleases the gods. OK, so how do we know which things please the gods? Obviously, it is those things which embody piety. Which is what? That which pleases the gods, of course. And so on. Which traits contribute most to reproductive success (or "adaptation" or "fitness," etc.)? Those which are selected. OK, so how do we know which ones will be selected? Obviously, it is those traits that will contribute most to fitness. But which are those? They are the ones that get selected. And so on.

That's still part of the tautology problem. First they're "selected," and then they are dubbed "favorable," after the fact, for having been selected. Is there any distinction to be drawn between selected traits and favorable traits? If not, then let's drop the favorable business and just call them selected traits, because that's the more empirical term. We can count noses and talk about what got selected. "Favorable" just means selected. If a trait is anything within the phenotype, then a complex organism is made up of an astronomical number of traits. How in the world can we determine in that crow in the tree which of her traits were selected and which just came along for the ride? was the beak selected? or the beak plus the nerves and muscles that move it? or all that plus the geometry of the skull that supports the beak? or the whole bird?

What makes the traits favorable, other than their being selected? This is a longstanding criticism of natural selection theory: It is a tautology, as in "What gets selected?" "Favorable traits." "What makes a trait favorable?" "It's one that gets selected." BTW, what qualifies as a trait? A fingernail? A finger? A hand? An arm? The concept of trait is completely arbitrary. I'm not sure what this list proves, if anything. The finches descended from a common ancestral population on the mainland. Members of that population would have varied phenotypically. When the birds went to the islands, they just ended up wherever they found suitable accommodations, as far as edible food and whatever else they found to be agreeable. Shorter beaks took up residence here and longer beaks there. The peppered moths apparently are largely nocturnal, so the coloration/camouflage story doesn't carry much weight. At least some of the widely circulated photos of moths on light and dark trees were staged, and meant for illustrative purposes only. The gastropod shell research is interesting, but no more instructive than research into any other predator / prey relationship. Differential reproductive success can tune the piano, but it can't compose the melody.