New Book on Arguing for Evolution

_{Cornelius Hunter

January 19, 2012

Intelligent Design}

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Did you know that helping is evidence for evolution? As Randy Moore and Sehoya Cotner explain in their new book Arguing for Evolution: An Encyclopedia for Understanding Science, this and most everything else in biology proves evolution to be an undeniable fact. Altruism, they explain, may seem to be a “problem” for evolution. (They put “problem” in quotes because, of course, there are no realproblems for evolution. All those false predictions are simply explained by adjusting the theory.) In this case, most acts of so-called altruism are “anything but.” If an individual sounds an alarm to warn the others or dies to save the group, it is really just another evolutionary calculation. Does not such risky behavior maximize the chances that the all important genes will be propagated to the next generation? And so falling on hand grenades may seem to be a noble, heroic act, but actually it is simply a product of natural selection. As John Haldane once put it, “I would lay down my life for two brothers or eight cousins.” Read more

Comments

I take it that Champignon is no longer talking to me. Oh, well. I believe I've shown more than once that you're cherry-picking your predictions. Evolutionary theory does not predict that a creature such as a tapir will, over generations, develop numerous complex, complementary, and coordinated adaptations so that it can have a long neck. Darwin himself alluded to falsification of his theory by things that could not have arisen by evolutionary mechanisms. In doing so he set a rather absurd standard, that such adaptations must be proven impossible. But you run with it any way. Even after complementing Darwin's original mechanisms with others, pretty much everything in biology defies even a hypothetical explanation using any of them. So you take your nested hierarchies (big thumbs up!) and who cares if what's in the hierarchies is inexplicable through any of the proposed mechanisms? Any theory can be a good fit if you keep the confirming evidence and gloss over everything that doesn't fit. And then you compare the vast sum of biological innovation that scientists spend their lives trying to understand and imitate and compare it to a pebble in a stream. No, Champignon, fluvial processes are just fine for pebbles in a stream. But if the pebbles are arranged to spell "Hello, world!" then you have to take that into account and reevaluate what may or may not have happened, not just ignore the part that doesn't fit.ScottAndrews2_{January 20, 2012
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It's untestable Peter- it is as good as any fairy-tale. Your position has nothing on how a metazoan will develop from the union of two single "cells" with 1/2 a genome.Joe_{January 20, 2012
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Scott's problem is that he doesn't seem to accept one of the most basic ways in which a theory can be corroborated -- or maybe he does accept it, just not when it is applied to evolutionary theory. It works like this. You gather up the competing theories. You ask yourself, "If theory X were operating in the world, what characteristics would the world have?" You also ask yourself, "What characteristics would the world have if competing theory Y were operating?" "Competing theory Z?" You look at the world and compare it to the predictions of each theory. If the evidence matches the predictions of theory X far, far better than it matches the predictions of the competing theories, then this counts as corroboration of theory X. Evolutionary theory matches the evidence far better than any competing theory. Yet Scott says he won't believe it if you can't show him exactly why giraffes evolved. Imagine if Scott applied the same skepticism to, say, geology. A geologist explains to Scott the theory behind fluvial deposits. He points out that stream deposits all over the world appear the way you would expect them to if the theory were true. Scott points to a pebble and asks, "Why did this pebble end up here and not a meter upstream? What good is your theory if it can't answer simple questions like that?"champignon_{January 20, 2012
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Elizabeth,
Darwin’s original theory doesn’t tell you why there are giraffes AND tapirs
Yes, the wording gets difficult, and I may have blown it again. I wasn't raising a "why are there still monkeys?" point. But rather, assuming that you have tapirs or any of their ancestors, Darwin's theory doesn't explain why now there's this thing with a really long neck and all the extra cardiovascular stuff that goes with it. Nothing Darwin ever wrote predicts that. I'm not saying that given a tapir, that Darwin should be able to predict a giraffe, specifically, in millions of years. But his theory doesn't predict that degree of variation. He offers no reason why the descendants of tapirs wouldn't be different tapirs.ScottAndrews2_{January 20, 2012
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You’re fond of pointing out that evolution is (loosely put) the change, not the mechanisms of change. That’s fine, but then why do so many seem to think of it as an explanation rather than an observation?
Because the word is used in both senses, Scott, and it isn't even always clear (and the writer isn't always clear!) which is meant! "Evolution", at least in the context of biology, usually means either "change in allele frequency in a population over time", which could be due to random drift, or biased drift (biased because some alleles tend to confer greater reproductive advantage than others in the current environment) aka natural selection, or, in the longer term, "adaptation" meaning change the phenotypic characteristics of a population over time in such a way that it thrives in its environment. The "theory of evolution" is a theory as to how that adaptation occurs. Despite Darwin's title, his theory doesn't really explain speciation, but rather longitudinal adaptation, and so the basic theory of evolution (sometimes called "evolution") has been hugely elaborated, and some of the elaborations have been falsified and replaced. So I think I would agree with you that Darwin's original theory doesn't tell you why there are giraffes AND tapirs! It only tells you why a giraffe might have evolved from a shorter-necked ancestor.Elizabeth Liddle_{January 20, 2012
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Chas, Poor choice of words on my part. It's not that an evolutionary mechanism must be provided - an explanation - for every phenomenon. But if any combination of these mechanisms is in fact the cause of such things then it logically follows that they must be capable of producing the effect whether or not the explanation is known or documented. There is no reason to think that they are. You're fond of pointing out that evolution is (loosely put) the change, not the mechanisms of change. That's fine, but then why do so many seem to think of it as an explanation rather than an observation? Even allowing for common descent, the conclusion that giraffes are descended from tapirs (or that both are descended from the same ancestor) tells us absolutely nothing about why there are giraffes. My objection is primarily to evolution as an explanation, since, while it may explain similarities, it doesn't scratch the surface of explaining the differences. If you take that out of the equation I don't have much to object to.ScottAndrews2_{January 20, 2012
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Darwininan evolution must explain every last bit of it from the ground up.
Must? All Darwinian evolution needs to do is concentrate or dilute genes in the population in relation to a differential between carriers and non-carriers in average reproductive output. If there is a consistent differential between X+ and X- in terms of reproductive success, then it does not matter a damn to Darwinian evolution how that reproductive effect is implemented. A whole bunch of Christ-knows-what goes on in the organism of possessors and non-possessors, and their interaction with the environment. Result: differential reproduction success. This is a typical misunderstanding of the role of reductionism in evolutionary biology. It's not a bottom-up explanation in terms of genes' activity in phenotype, but in terms of genes 'levering' themselves through the generations, by whatever means. The organism is ... ummm ... a black box. Input: genes. Output: more genes (or fewer). The same problem is encountered by any designer who attempts to determine the full consequences of his twiddling before trying it out, unless he has that kind of perfect knowledge that designers seem to suddenly acquire in certain asserted circumstances. Even a simple one-base change can radically alter a protein fold in a manner that takes massive calculation to evaluate; then factor in all epistatic and environmental interactions ... or, tell you what, let's just chuck a few variants at the wall and see what sticks. This is, of course, a strength and a weakness. It's an effective approach to design, intent-driven or no. But "what works, works" is an unsatisfactory evolutionary explanation for those interested in phenotypes. Add in the death of all those things that didn't work, which are rather crucial to the reasons why what remains remains... and you have a theory that the determined can deny till the cows come home, no matter how many demonstrations one can provide of the principles in action.Chas D_{January 20, 2012
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Peter, Why did I bother posting two quotes from the same blog entry one after the other? Did you not read them? Must I do so again? Okay
To those studying evolutionary theory, the result “is an expectation rather than a surprise”, says Michael Lynch, who carries out such studies at Indiana University in Bloomington.

The result challenges the assumption in biology that increased biological complexity evolves because it offers some kind of selective advantage.
Of course results don't always match expectations, and yes, that is why the experiments are necessary. But to say that they specifically expected the result to contradict their assumptions? Yes, that is a load of crap, even if you polish it.
Do you actually have anything to say about the substance of the work in question as it seems to be exactly what you have been asking for a while now – specific mechanism , specific changes and specific results.
Again, I must ask - do you actually read this stuff before you post it? The research shows not the addition of a new component, but a duplication of an existing component which the organism doesn't seem to need. What was the title of the article again? "Evolution of increased complexity in a molecular machine." These must be the same guys who sold me that remote-controlled flying bat out of the back of a comic book when I was a kid. (It was a rubber bat attached to a rubber band.) Let's file this earth-shattering discovery right next to four-leaf clovers. Seriously, if this is what you dig up when you really want to make a point then I think we're done.ScottAndrews2_{January 20, 2012
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tjguy,
How could a male and female of the same species evolve concurrently, at the same geographical location in such a way for them to connect, and evolve in a way that is complementary?
I'm afraid that's "not even wrong" as a question. PZ addresses this at length, as it's a common misunderstanding among creationists. http://scienceblogs.com/pharyngula/2009/03/elephantine_errors_from_ray_co.php
First, let's clear one thing off the table: males and females do not represent separate evolutionary phenomena. I know, that seems like it ought to be obvious, but one shouldn't take anything for granted in a discussion with people like Ray. Men and women are essentially identical in their genetic complement — with very few exceptions, we carry the same suite of genes — and all of the obvious differences are the result of simple switches. A female embryo can be induced to develop into a male by the presence of the appropriate hormones, and a male embryo can be born looking female with the right blockers or receptor errors. As for the appearance of those male and female sexes, their origin lies far back in the pre-Cambrian. The differences arose gradually. The distant ancestor of all those animals Ray rattled off, and including insects, clams, squid, starfish, and leeches, was a pre-Cambrian worm, and it was most likely a hermaphrodite, producing both sperm and eggs. The sexual differences Ray finds so difficult to comprehend arose by progressive specialization: genetic switches that could turn off either male or female gamete production were already present, and some individuals in the population turned off the making of eggs and made sperm, while others did vice versa. It happened in worms, worms that have contemporary relatives that live fruitful lives of sexual ambiguity.
Worth the read, and follow the links. Honestly...Peter Griffin_{January 20, 2012
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SCott
Darwininan evolution must explain every last bit of it from the ground up.
It does already. Robots have been shown to evolve complex behaviors that were not programmed in in advance.
These intricately coordinated changes are far more specific than the generalized “evidence” from which they are inferred and extrapolated.
It only seems that way because if it don't work you die. What's left then gives that impression.Peter Griffin_{January 20, 2012
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Scott,
So biologists expected the results to challenge their assumptions about how complexity evolves? Do you critically read any of this? Pardon me, but what a load of crap.
Where does it say that? It says (and you quoted it)
The result challenges the assumption in biology that increased biological complexity evolves because it offers some kind of selective advantage.
Personally I would have expected that. But it turns out it's not the case. It's how science works! Nobody expected the results they got, or why bother doing the experiments if you know what the result will be? Do you actually have anything to say about the substance of the work in question as it seems to be exactly what you have been asking for a while now - specific mechanism , specific changes and specific results. If you don't choose to actually address the substantive point and instead focus on the periphery of "what scientists expected" then I can only conclude your stated position is not held in good faith.Peter Griffin_{January 20, 2012
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Peter, Wow, how fast they spin this stuff. From the blog:
To those studying evolutionary theory, the result “is an expectation rather than a surprise”, says Michael Lynch, who carries out such studies at Indiana University in Bloomington.
From the very same article:
The result challenges the assumption in biology that increased biological complexity evolves because it offers some kind of selective advantage.
So biologists expected the results to challenge their assumptions about how complexity evolves? Do you critically read any of this? Pardon me, but what a load of crap.ScottAndrews2_{January 20, 2012
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Elizabeth,
Well, if you are convinced that behaviours can be genetically determined, then your objections, surely, is no different to your general objection to Darwinian mechanisms?
No, they're pretty much the same. But it seems like an oversimplification to reason that the same process that determines what an organism has also determines what it does, just because both are determined by genes. Hopefully the answer is not that it seems intuitive, because it shouldn't, and for at least two reasons. First, I suspect that many underestimate the complex requirements of even simple behaviors. Which takes more effort, building a robot that models an animal with legs, or programming it to walk or run several steps on a safe, flat surface without falling over? Or getting a floor robot to navigate a living room without getting stuck? Even the very simplest movements and motions must be mastered to near-perfection before anything more complex can be added. I suspect that we take lower-level motor functions for granted, such as the ease with which we place a finger on a selected key and press it. Darwininan evolution must explain every last bit of it from the ground up. Second is the coordination between behaviors and physical adaptations. Evolutionary narratives of physical adaptations invariably omit the required corresponding behavioral adaptations. Of what benefits are incremental steps toward the ability to camouflage by changing color when the organism is unaware that it does so or can does so and has no reason to to do? Or does the physical adaptation conveniently associate to the correct neural signals so that it changes color when it becomes stressed rather than when it must expel waste? I've seen no indication that either the physical or the behavioral adaptations are ever considered in terms of actual evolutionary mechanisms such as genetic variation and selection, let alone the precise coordination required between the two. Even if described in darwinians terms it begins to resemble a precisely orchestrated march toward increased and varied function rather than an unintended result of differential reproduction. These intricately coordinated changes are far more specific than the generalized "evidence" from which they are inferred and extrapolated. So yes, my objections are the same, but the problems which darwinism fails to explain are multiplied and squared at the very least.ScottAndrews2_{January 20, 2012
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Scott,
without addressing the underlying incremental genetic variation and selection.
Perhaps this will interest you then: http://blogs.nature.com/news/2012/01/resurrecting-extinct-proteins-shows-how-a-machine-evolves.html
By bringing long-dead proteins back to life, researchers have worked out the process by which evolution added a component to a cellular machine. The result, they say, is a challenge to proponents of intelligent design who maintain that complex biological systems can only have been created by a divine force.

The work, published online in Nature, reveals the pathway by which the two-component ancestral protein (let’s call the components A and B) became a three-component one (A, B and C). The gene encoding protein A duplicated, and two identical copies of the gene started making proteins A1 and A2. Then, A1 and A2 started to accumulate mutations so that they could no longer substitute for each other in the ring. To work out the exact sequence of events, the team identified the likely historical mutations and engineered them, one by one, into their version of ancestral A. They found that just one key mutation in each of A1 and A2 created proteins that could no longer bind promiscuously with neighbouring proteins in the ring, and instead had to occupy specific spots. The proteins “went from being a generalist to a specialist,” Thornton says. And A2 eventually became C, the third part of the three-component ring now made up of A1, B and C. The result challenges the assumption in biology that increased biological complexity evolves because it offers some kind of selective advantage. In this case, the more complex version doesn’t seem to work better or have any other obvious advantage compared with the simpler one; it is more likely that A1 and A2 proteins were just corrupted by random mutation. (The yeast didn’t seem worse off when they were stripped of their own three-protein ring and instead used one built of two ancestral proteins.) “What’s surprising to me is the idea that greater complexity doesn’t require acquisition of new functions. It can come from partial degeneration of the ancestor,” Thornton says.
The article itself can be found here: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10724.html
We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
Plausible mechanism for the evolution of complexity to the authors, but is it for you Scott?Peter Griffin_{January 20, 2012
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Well, if you are convinced that behaviours can be genetically determined, then your objections, surely, is no different to your general objection to Darwinian mechanisms? There's a mechanism for inheritance, a phenotypic effect, and the potential for variance in the reproductive advantage of different behaviours. The trifecta. As usual, I find myself asking: how can Darwinian evolution NOT happen? :)Elizabeth Liddle_{January 20, 2012
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Elizabeth,
Well, you are assuming that behavioiur has no genetic determinants. That is demonstrably untrue.
No, within the context of evolution my expectation would be exactly the opposite - behavior must be genetically determined. Either it's genetic or every generation of every species has "that talk" with its offspring to ensure continuation of the species. I do some digging around before I throw these questions out, but as usual it seems no one wishes to lead with their most compelling evidence. Cited examples include - variations in cricket songs - differences between nesting habits - lion infanticide - behaviors of offspring when parents with differing behaviors are bred Most of the research paints in broad strokes, discussing gradual changes in behavior and the potential selective benefits without addressing the underlying incremental genetic variation and selection. Other research seeks to identify the genes associated with behaviors, which is interesting but does nothing to explain their origins. What's lacking is the underlying basis for concluding that the genetic determinants for behaviors themselves result from variation and selection of existing genes. There appears to be no evidence that the behaviors of living things, from the complex ones we marvel at to the simplest ones we take for granted, arose by darwinian mechansisms.ScottAndrews2_{January 20, 2012
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The male and female reproductive systems are irreducibly complex and complementary systems. How could a male and female of the same species evolve concurrently, at the same geographical location in such a way for them to connect, and evolve in a way that is complementary?
Invented difficulty, I am afraid. "Male" and "Female" are categories relating to differentiation of multicellular bodies, or more specifically the size of the gametes they produce. You don't get this size distinction in single-celled organisms (it is an interesting exercise to try and understand why). Sex is found throughout eukaryotes, including unicellulars. Even those that no longer do it have the critical enzymes that are unique to the sexual process - they descend from sexual ancestors (if you accept that anything descends from anything else, that is! :0) All that is really needed to kick off a sexual process is a free-living haploid population. Fusion of these haploids creates diploids. And that's where all the trouble starts. No, I don't have the organisms to hand. But confusion about what sex is, at heart, is confounded if you think the world only consists of plants, fungi and animals, and sex had to evolve in them, with gender on day 1, rather than them evolving from single-celled sexual ancestors. Sex, on the evidence, pre-dated them all. The modern system is a classic example of one whose 'irreducibility', in evolutionary terms, is illusory. There is a biologically plausible stepwise path right from end to end. I won't spell it out - it is, after all, an evolutionary explanation, and we don't go for them, do we? :0) You're not alone, a lot of biologists get this one wrong too.Chas D_{January 20, 2012
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Are there any real darwinian explanations for any behaviors? I’ve harped to the point of boredom on the lack of darwinian explanations for physical attributes, only to get bogged down over what is or isn’t a significant change. Fair enough. What about behaviors? Assuming that sexual reproduction evolves somehow, the organisms have to actually do it. But why would they? It’s not as if they can reason on the need to perpetuate themselves. Well, you are assuming that behavioiur has no genetic determinants. That is demonstrably untrue.
Why would anything ever evade a predator, as being eaten or not makes no difference to an organism with no awareness of or concern for its own existence?
Not sure what you are saying here. But organisms with a reflexive evasion response to threat will tend leave more offspring than one without, so the principle of natural selection should work just as well for genetically influenced behaviours as for physical attributes. Behaviour is part of the phenotype.
Is there any behavior simple enough to take for granted? Birds building nests? Walking on legs? Behaviors are typically omitted from darwinian narratives even though they are absolutely critical aspect of evolution. Did lizards cast of their tails for no apparent reason until the behavior of doing so to evade predators took hold?
Well, I'm not sure what narratives you are reading, but there is plenty of research into the genetic (i.e. heritable, and thus selectable) determinants of behaviour.
How many adaptations require a corresponding behavior to confer benefit? What is the darwinian pathway for the evolution of bird migration across oceans to destinations where the bird has never been? The increments of change are genetic, so what is the behavioral expression of a single mutation? Is it selectable? What evolutionary explanations are available for behaviors?
Well, migration is interesting - perhaps it's irreducibly complex! But there is certainly research on the subject. It's just not true that it has been ignored!Elizabeth Liddle_{January 20, 2012
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Are there any real darwinian explanations for any behaviors? I've harped to the point of boredom on the lack of darwinian explanations for physical attributes, only to get bogged down over what is or isn't a significant change. Fair enough. What about behaviors? Assuming that sexual reproduction evolves somehow, the organisms have to actually do it. But why would they? It's not as if they can reason on the need to perpetuate themselves. Why would anything ever evade a predator, as being eaten or not makes no difference to an organism with no awareness of or concern for its own existence? Is there any behavior simple enough to take for granted? Birds building nests? Walking on legs? Behaviors are typically omitted from darwinian narratives even though they are absolutely critical aspect of evolution. Did lizards cast of their tails for no apparent reason until the behavior of doing so to evade predators took hold? How many adaptations require a corresponding behavior to confer benefit? What is the darwinian pathway for the evolution of bird migration across oceans to destinations where the bird has never been? The increments of change are genetic, so what is the behavioral expression of a single mutation? Is it selectable? What evolutionary explanations are available for behaviors?ScottAndrews2_{January 20, 2012
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Why does there need to be an "ultimate" purpose? Why not the expressed purpose of wanting to save your fellow human beings? That's a perfectly adequate purpose.Elizabeth Liddle_{January 20, 2012
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I think it does. If there is no ultimate purpose, it is foolishness rather than a heroic act. There is no ultimate purpose in anything without God. I doubt very much that there could be anyone in the world in his right senses who would lay his life for the ideals of successful reproduction of progeny. Life is laid down for the eternal and transcendent.Eugene S_{January 20, 2012
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Choose as appropriate: (a) altruistically selfish genes or (b) selfishly atruistic genes. A nice Darwinian dilemma.Eugene S_{January 20, 2012
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Well, if that were true, I'm sure the evolutionists would come up with some clever just so story that purports to explain it. But I agree with Joe. Evolution doesn't predict sex reproduction at all. In fact it cannot explain how sexual reproduction evolved. Oh, I know there are just so stories to try and explain this problem, but it is just conjecture, not science. The male and female reproductive systems are irreducibly complex and complementary systems. How could a male and female of the same species evolve concurrently, at the same geographical location in such a way for them to connect, and evolve in a way that is complementary? I don't know what organism might be thought to have evolved the first sexual reproduction capability, but let's say it was an amoeba for example. What are the chances of two amoeba simultaneously and separate from each other evolving a complete and complementary reproductive system? Even if this did happen and the two amoeba were a mile apart, it would do no good as they would never meet. Imagine the amount of changes necessary for two asexual organisms to randomly evolve into complete functional complementary male/female organisms?! Talk about believing in miracles!tjguy_{January 20, 2012
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And so falling on hand grenades may seem to be a noble, heroic act, but actually it is simply a product of natural selection.
Cornelius - either you misunderstand or you misrepresent. Falling on hand grenades is a noble heroic act. Our tendency to do noble herioc acts may well be the result of natural selection. That doesn't make it any less noble or heroic.markf_{January 19, 2012
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Maus, You haven't thought this through. Not only did you invent a 'fact' out of thin air (massively greater pre-reproductive mortality among males versus females), but the 'fact' you invented doesn't help to explain a 15:2 ratio of males to females. Suppose the ratio is 15:2 and that mortality is much higher for males. Since females in your scenario are more likely to live long enough to reproduce, a parent that produces more female offspring than average will be more likely to get its genes into the next generation. A parent that produces more male offspring than average will be less likely to get its genes into the next generation. The 15:2 ratio is therefore not stable. Selection drives a decrease in the ratio. Your 'explanation' doesn't work. Want to try again?champignon_{January 19, 2012
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Sure, Champ. On seeing such an example in existence, or simply postulating one as a Gedanken, the immediate Evolutionist rationalization would be that this was due excess historical mortality in the males of the species. Whether due in-fighting amongst the males for mates or due mortality in defense against predators. And both have been variously offered to explain the 52:48 male favored gender split amongst humans. This is all, of course, under the Evolutionist idea that a future prediction is to predict that the past will remain the past.Maus_{January 19, 2012
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Sarcasm is not an argument. And in the context of what Barry said I would be right and wrong. :razz:Joe_{January 19, 2012
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Says Joe, not realizing that his statement undercuts Barry's argument. LOL.champignon_{January 19, 2012
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Except the theory doesn't predict sexual reproduction.Joe_{January 19, 2012
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Barry, Evolutionary theory predicts the 1:1 sex ratio that we see in most sexual species. Since you claim that it can be used to predict anything, let's hear your explanation, using evolutionary theory, of why the sex ratio should be 15 males for every 2 females.champignon_{January 19, 2012
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