New Book on Arguing for Evolution

BTW when have we observed any fixation rates? Hint- never. Joe

Unfortunately you don't have anything to support your claim that non-functional genetic markers can stay around for 50-100 million years. The problem is there isn't any genetic data to link to the transformations required. And common descent is baraminology.

A parent, or a progenitor, in biology, would have to provide some genetic material directly to its offspring or recipient, to be such.

Right the designer provided the gentic material directly to the giraffes. Also read "Why is a Fly Not a Horse?" by geneticist Giuseppe Sermonti. Joe

And a progenitor does not have to be a direct ancestor.

Grief, you still wriggling round on that one? Yes, it does. A parent, or a progenitor, in biology, would have to provide some genetic material directly to its offspring or recipient, to be such. In all other senses, it is just you wriggling around on a semantic hook of your own design.

And your position cannot explain non-functional genetic markers staying around for eons of generations.

Yes it can, Joe. Neutral fixation and a mutation rate gentle enough to ensure that these things hang around over the timeframe that these things are used for. Obviously, we can't use degraded markers, so we use the ones that aren't. They don't last forever, but 50-100 million years, no problem.

The concept of universal common descent is useless to science because all it is is throwing vast amounts of time at slight variations.

Whatever use UNIVERSAL common descent may be to science, the concept of common descent is extremely useful. And "massively empirically confirmed", comme on dit. If I saw the word "outragei=ous" in a text, and then saw it again elsewhere, it would be a compelling indicator of common descent - copying, rather than separate origin. And that's what a lot of the nonfunctional markers amount to. It is desperation to deny this evidence, either by shouting "common design" or by insisting "they would have degraded". They haven't degraded, because we can detect them. Or, what is it we are detecting in our naivete? It can't ALL be common design. Speling erers. Repeats repeats repeats. snoisrevnI. Disconxxxxxtinuities. Transionposits. Lot's of 'em. Shedloads. Chas D

Evidence Chas- Endosymbiosis only explains mitochaondria nad chloroplasts. And tehn still isn't any way to test that claim. So no, I don't deny it. It is just that it is an untestable claim. As for dreaming up, well that is all your position has. And a progenitor does not have to be a direct ancestor. And your position cannot explain non-functional genetic markers staying around for eons of generations. The concept of universal common descent is useless to science because all it is is throwing vast amounts of time at slight variations. Joe

From those 8 that got off the boat, you mean?

Before Joe goes off on one (not that it makes much difference), I will admit that this is a bit of a nonsequitur! Chas D

Umm long term descent of humans has only led to more humans.

From those 8 that got off the boat, you mean? I think ID is trying to be taken seriously, Joe.

Long term descent of prokaryotes only leads to more prokaryotes.

And? We sit and stare at prokaryotes and they never give rise to giraffes. Well hoo-ey sir, I think you've just found a fatal flaw in the theory of evolution. Endosymbiosis. Major discontinuity in the history of life and - arguably - non-Darwinian (as in "not gradual", and "messes up the naive Tree of Life"). A one-off association of genomes at the base of the whole eukaryote clade. This does not, routinely, throw up giraffes, but the keyword is progression. We don't see it before our very eyes. We don't see the continents move or the stars recede either. I could have sworn it took the same time to fly to the States last year as it did 10 years previously. Continental drift - huh! I know you don't buy endosymbiosis - Denial-of-the-Month for November, I recall - but then you don't really accept anything other than what you can dream up.

And the current consensus can’t support its claims.

The claim that all giraffes had parents needs support? Isn't it kind of obvious? If you think about how giraffes happen. There's this mummy and daddy giraffe, ya see, and they love each other very much, and ... but no, that process being responsible for all of giraffe-kind and many, many generations prior is far too much of a stretch. We need a 'poof' and Zarg magics a fully grown diploid organism into being. Or, creates a zygote from genes that have never tried making a giraffe before and nurtures it in a surrogate. Ouch.

The current consensus holds the outragei=ous position that our existence is nothing more than accumulations of accidents.

So the consensus position on all giraffes having parents is invalidated by the fact that a consensus (which may or may not include all the individuals in the first consensus) holds another position about the mechanisms of change. The consensus is that we need oxygen to stay alive; is that wrong too?

As for “parent” obvioulsy you don’t know how to read a dictionary. Think “progenitor”….

A progenitor, certainly biologically speaking, is a direct ancestor. A direct genetic ancestor. One which, furthermore, would have to exist in order to explain the nonfunctional genetic markers that appear for all the world to have passed down lines of actual descent. There aren't any discontinuities in lines of descent at this level, Joe. If you think there are, find 'em. Chas D

Well the HUMAN falling on the grenade is a HUMAN too. So self-sacrifice is not an adequate purpose. In a Darwinian sense you should get out of there and allow those who can't to suffer the pain of death. That would be natural selection. Joe

Chas D- Your position does not have any explanation for meiosis. IOW biology is definitely the wrong subject for you as you think imagination = evidence. Ya see your position can't even explain cellular differentiation beyond saying "lookie thar". Joe

Umm long term descent of humans has only led to more humans. Long term descent of prokaryotes only leads to more prokaryotes. And the current consensus can't support its claims. The current consensus holds the outragei=ous position that our existence is nothing more than accumulations of accidents. As for "parent" obvioulsy you don't know how to read a dictionary. Think "progenitor".... Joe

Genetics is no friend of universal common descent.

It is hardly its enemy! Long-term descent is only a matter of genetics. Genes are passed from parent to offspring, not phenotypes. The "G" in HGT is gene transfer, even though it can scramble the vertical phylogeny. By both means - vertical and horizontal - genes commonly descend. The current consensus is that all giraffes had parents. This is not an outrageous position to hold. It would be the case for your imaginary "first giraffe" also - ie, there wasn't one. Nor is it giraffes all the way down. I know that only leaves one option in your mind, but there is another. Would you like me to tell you what it is? Chas D

Genetics is no friend of universal common descent. Joe

Your understanding of things appears to be lacking any understanding. Perhaps you should invest in a dictionary…

OK, will do. I think I might struggle to find a definition of 'parent', in any biological sense, if no DNA from it is replicated, but I'll give it a go. Zarg of Epsilon 6, the father of all giraffes, cooked 'em up in a petri dish. Can I suggest an elementary textbook of genetics, for your part? Chas D

It is true and you aren't anyone to doubt anyone's competence. As for the differences betweem ny PoV and Creationists- I do not accept the Bible as any kind of authority whereas their position relies solely on it. And aliens are just ONE possibilty. And a designer would be a parent…

Not in any sense that I understand the word...

Your understanding of things appears to be lacking any understanding. Perhaps you should invest in a dictionary... Joe

Well Chas D, there are geneticists who agree with me. There are developmental biologists who agree with me.

If this were true, I would severely doubt their competence. I do begin to wonder what distinguishes your position as ... umm ... an "ID guy" from that of a creationist. Is it the aliens?

And a designer would be a parent…

Not in any sense that I understand the word, unless you are suggesting something decidedly gross. Chas D

Well Chas D, there are geneticists who agree with me. There are developmental biologists who agree with me. And a designer would be a parent... Joe

One is more of a “cell” than the other. And neither is really a cell because neither can reproduce on its own. The main problem is every other cell in a metazoan divides via mitosis. So you need to explain the origin of meiosis via stochastic processes. Good luck with that.

Joe, you are seriously confused. You think the explanation has to start with anisogamy (sperm/egg size distinction) and obligate diploidy? Or we start with multicellularity, and THEN evolve meiosis? Gah. Seriously, I think biology is the wrong subject for you. Now, Tiddles, about this proof of congruent triangles ... Chas D

The problem is there isn’t any genetic data that shows the transformations required to get a giraffe from a non-giraffe) are even possible.

Therefore they are impossible? I think the problem may be your shaky species concept and grasp of genetics. I wonder how you envisage the creation of the 'first giraffe', from a mechanistic standpoint? If we follow the lineage from giraffe backwards, what do we come to? A giraffe with no parents? Chas D

Chas D, There isn't any evidence that a giraffe "evolved" from anything other than a giraffe. The problem is there isn't any genetic data that shows the transformations required to get a giraffe from a non-giraffe) are even possible. Joe

Chas D:

A better way to look at it is two cells with a genome each.

One is more of a "cell" than the other. And neither is really a cell because neither can reproduce on its own. The main problem is every other cell in a metazoan divides via mitosis. So you need to explain the origin of meiosis via stochastic processes. Good luck with that. Joe

And ... (in what may be my final post on the matter, since I'm not really after that toaster!) one could try looking at it from this angle: Suppose we have a time-teleporter. First we are able to teleport to the giraffe/tapir split. We see this organism that (through DNA testing) we determine to be the common ancestor. Is there any prediction we can make about what it will NOT evolve into, left to its own devices? Can we, for example, exclude the giraffe on any grounds? Or, for that matter, the tapir? We can then teleport to any point between then and now, and try and establish what went on. There are now two (probably more) lineages, one of which seems to be lengthening in the neck in a variant manner in the population. By exhaustive experimentation, we identify a gene, necklen1, that functions in development to lengthen the neck. There must be other genes, since this must have an effect on the birth canal, but we focus on this gene and determine its selective advantage in the population. We try and determine the source of that advantage ... and can't. Every time we run the experiment, necklen1+ individuals produce more offspring than necklen1-. Yet can we establish causation? It is a statistical effect. All the details of individual lives that necklen1+ individuals encounter must factor in. We could look at high trees, or better luck with the ladies, or spotting predators ... It's a bit of each, it's all and none of them. We come rushing back to the future: "Scott! Scott! We found one of the genes!". "Really? And what was its advantage?" "Errr ... 1.001". Chas D

Your position has nothing on how a metazoan will develop from the union of two single “cells” with 1/2 a genome.

A better way to look at it is two cells with a genome each. Nonetheless, I suspect the time spent outlining a detailed analysis of a path from haploidy to cyclic haploid/diploidy, and beyond to metazoan haploid/diploid asymmetry and gender differentiation, might actually be better spent teaching geometry to my cat. Chas D

Scott: It is not both an observation and an explanation, because it does not explain. Sorry, when I said "it's both", I meant "evolution is (loosely put) the change and the mechanisms of change". But actually it does explain, even if that explanation is not the kind you'd like. Evolution explains in general terms how species cannot avoid changing, and also how such change may be constrained into certain kinds of 'adaptive channel'. But again, you want some reconstruction of history. Can a geneticist explain why Hitler had the genetic makeup he did? Half the genes each from mum and dad, recombination, linkage blah de blah. No, explain something about his genetic makeup! So genetics is bunk, it has no explanatory power then. Tapirs and giraffes descended from a common ancestor, not a tapir. Chance is a legitimate explanation for divergence, and for anaganesis (change in a lineage). Why giraffes rather than some other form descended from the giraffe/tapir common ancestor? I don't know what other forms are possible. Why you rather than one of the billions of possible combinations of your genes (half of them girls)? Chance. You allow chance to operate without dismissing genetics for its failure to explain that little conundrum. But evolution must have a step by step explanation for THIS form. Evolution derives from genetics. It is constrained - it doesn't start from random points and leap round phase space like a mad bastard. But it is mostly governed by chance - chance mutation, chance meetings with predators and mates, stochastic fixation. Chance IS an explanation. As is contingency. But we don't know the structure of the adaptive landscapes that giraffes could have explored, and we don't know why the dead giraffes died or the survivors survived. We only have the form of the survivors, not the detail of the lives their ancestors led and the threats they survived and succumbed to. Chas D

Scott, Since you seem to be avoiding my central point, let me stress it:

Who, for example, would postulate a magic barrier to the pebble’s motion, and suggest that an intelligent pebble mover must have been involved in order to overcome the magic barrier? And not just any intelligent pebble mover, but one who moves pebbles exactly as they would have been moved according to the original theory, had the magic barrier not been there?

In case translation is necessary:

Who, for example, would postulate a magic barrier to accumulated microevolutionary change, and suggest that an intelligent designer must have been involved in order to overcome the magic barrier? And not just any intelligent designer, but one who operates in exactly the same way that evolution would have operated, had the magic barrier not been there?

champignon

Scott, I wish I could take credit for the 'Rumpelstiltskin dance' comment, but that was Chas D's memorable description. I see it hit a nerve. champignon

Champignon,

it’s clear that the pebble’s location is compatible with the theory. And since the theory does such a splendid job of explaining the arrangement of this fluvial deposit, as well as deposits all over the world, why challenge it?

You're begging the question. You're asserting that the giraffe, for example, fits the theory just like the pebble in the river is compatible with its respective theory. Except that's your conclusion. You're just reasserting it, begging the question. The giraffe does fit the theory, within reason, if you're talking common descent. There may be something to debate there, but it doesn't interest me. If you're not talking about common descent, but rather an explanation of how giraffes descended from an ancestor similar to a tapir, then no, none of the mechanisms proposed to explain such things do in fact explain it. I mean that in two ways. There is no specific pathway of variations and selections. You may think I'm harping on that, but that's not really my point at all. Primarily what I mean is that there is no basis for considering such mechanisms adequate to explain the giraffe's neck and its associated cardiovascular developments. There's no empirical basis for concluding, even provisionally, that an incremental process of variation and selection could produce such an extensive series of coordinated, cooperating modifications. There's also no reason why they should. You can and will assert repeatedly that such mechanisms effect such results. Over the course of several weeks you have offered every imaginable objection, excuse, or distraction to avoid explaining what empirical evidence would influence someone to share this belief. Occasionally you even accuse me of being unreasonable, as if there should be some charitable basis, some special pleading to justify the acceptance of your premise. I'm pretty sure you've appealed to authority. Come to think of it, I even declared victory on this matter some time back and accepted your implicit concession. I did, what was it you said, a Rumpelstiltskin dance. I suppose I'll just have to do it again. ScottAndrews2

Scott, Yes, most people wouldn't bother debating the reasons for the pebble's location. Even if they lacked a detailed scenario, it's clear that the pebble's location is compatible with the theory. And since the theory does such a splendid job of explaining the arrangement of this fluvial deposit, as well as deposits all over the world, why challenge it? Who, for example, would postulate a magic barrier to the pebble's motion, and suggest that an intelligent pebble mover must have been involved in order to overcome the magic barrier? And not just any intelligent pebble mover, but one who moves pebbles exactly as they would have been moved according to the original theory, had the magic barrier not been there? champignon

Champignon, If the only way you can rationalize this is to liken the genetic and functional difference between a tapir and a giraffe to the spatial difference between possible locations of a pebble then you're out of gas. This is a rhetorical question. I really hope you think about it rather than trying to answer it: Why isn't there a debate forum out there with a picture of a pebble in a stream, where people spend hours debating what precisely landed the pebble in that exact spot rather than several inches or feet away? Could it be because it's entirely unremarkable and everyone agrees that water moves pebbles, making it a useless illustration in a discussion of something that is remarkable and the cause of which is debatable? What were you hoping to illuminate with it? ScottAndrews2

Scott,

We can observe that giraffes are descended from tapirs and have not the slightest clue why some of the descendants of tapirs are giraffes. In fact, we don’t. It is unexplained. That is the difference between observation and explanation.

We can observe that the pebble is here and have not the slightest clue why it's not one meter upstream. It is unexplained. That is the difference between observation and explanation. Hydraulic theory is therefore not an explanation. champignon

Chas, It is not both an observation and an explanation, because it does not explain. Knowing that a giraffe is descended from a tapir or its cousin does not explain how the features it has came about.

The point for tapir/giraffe divergence is that this mutation-fixation process is only anchored by the ability of a current population to ‘get at’ each other.

It is also "anchored" to the range of configurations that are accessible to a population of tapirs by means of evolutionary mechanisms. We can observe that giraffes are descended from tapirs and have not the slightest clue why some of the descendants of tapirs are giraffes. In fact, we don't. It is unexplained. That is the difference between observation and explanation. ScottAndrews2

Scott,

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?

Yep, it's both! I think the essence of all of it boils down to descent - one individual gives rise to others, which give rise to .... If that's all that happens - all the individuals are identical - then I guess there's no evolution, although there is common descent. But if we get some kind of change in the genetics of one individual, that in itself is evolution. A lot of people fight shy of that, because (as I have seen it put) it changes the game from "making evolution too big to see, to making it too small to miss". People would be right to suspect that, if it was some kind of trick, but technically, it is evolution, even that low-level. So that is one mechanism of evolution: mutation. Next we get the descendants of this first mutant. They could be snuffed out - it is deleterious, or just unlucky - or they could start to gain a toe-hold in the population. Descendants of the first mutant start to take over the population, in a wibbly random-walk kind of way. This can be both selection and drift - differential output and/or the influence of chance. As far as the lineage of any organism possessing the mutation is concerned, when an organism looks up its family tree, it 'sees' a series of ancestors all with the mutation, until it gets to that first mutant. That mutation in that ancestor was the moment the gene changed. Everything else is simply moving towards more and more of the population being descended from that ancestor, and fewer and fewer not. It's a process of elimination, not change per se. But it is commonly regarded as "evolution" - change in allele frequency. So ... clear as mud, sorry! The point for tapir/giraffe divergence is that this mutation-fixation process is only anchored by the ability of a current population to 'get at' each other. As soon as you get isolation - split a population in two - the mutations either side are not shared, and nor is the fixation process. This completely uncouples them, and divergence appears to be a common result. I think this is why Darwin did not explain the Origin of Species so well - he was looking for a role for Natural Selection, and could not find it. The real answer is chance. And that's why concrete answers are so elusive. Chance is everywhere, and that don't half mess with your causality! But chance is a legitimate explanation for why two things are divergent. Channelled chance, one could say. Selection keeps them from just disintegrating, genetically, while physical limitations on possible forms stop them from going just anywhere in genetic space. I think the final point - why not just keep on producing tapirs - relates to our love of categories. Current organisms are of a particular form, and we see that as "tapir-form". But that is a lateral compartment. Organisms are just produced sequentially, and the mechanism that holds a species round a current form - interbreeding - does not operate in time. Species aren't anchored in time - or not, at least, as far as can be detected! Chas D

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Choose as appropriate: (a) altruistically selfish genes or (b) selfishly atruistic genes. A nice Darwinian dilemma. Eugene S

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

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

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

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

Sarcasm is not an argument. And in the context of what Barry said I would be right and wrong. :razz: Joe

Says Joe, not realizing that his statement undercuts Barry's argument. LOL. champignon

Except the theory doesn't predict sexual reproduction. Joe

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

Elizabeth, altruism is not a false prediction of evolution (by which I suppose you mean the Neo-Darwinian Synthesis), because the NDS predicts absolutely everything that exists and its opposite too. For example, do you need gradualism? We’ve got plenty of gradualism. You need something to explain the absence of gradualism in the fossil record? Well, we’ve got that too! It turns out that evolution is gradual when it needs to be slow and extra speedy when it needs to be fast. NDE predicts altruism and genocide. You’ve gotta hand it to a theory that predicts a behavior and the opposite of the behavior with equal alacrity. Barry Arrington

In what sense is "altruism" a "false prediction" of evolution? Elizabeth Liddle

I would cite the Cambrian explosion, the general trend towards stasis, irreducible complexity and the existence of an unfathomably sophisticated information bearing DNA, code as powerful evidence for evolution. Alan