"Best" evidence for evolution.

Well, the same basic chemistry makes a human hand and a human foot. Why don't they look the same? Because regulatory genes adjust the expression of genes at different places and times in development. We know that another family of transcription factors are involved in this - the T-box genes. Tbx4 is mostly expressed in the leg and Tbx5 in the arm.Arms and legs are, of course, made of the same proteins, and also the same structures - the basic pattern of bones in the arms and leg is clearly the same; they just develop different relative sizes and shapes. And that's because of the genetic pathways (of which the T-box genes are an important part) causing different genes to be expressed more or less at different times of development. That causes bone to be laid down at different speeds at different places and thus they form different shapes.And that's not much difference here with chimp feet and human feet. They also have the same pattern of bones, just these are of different sizes and shapes - just as they are between the human hand and foot, and between the chimp hand a foot. Slight changes in the behaviour of transcription factors and signalling molecules will cause changes in the expression of genes at different times during development, causing different bones to grow at different rates and thus assume different shapes - making a chimp's foot look different to a human foot.But this is where conversation with you gets weird. Because you don't find this process mysterious at all. You think it's perfectly normal for the same structures to grow at different rates and into quite different shapes, as long as it happens on trilobites. I can't understand why you think this change in the size and shape of bones is impossible: while the obviously much greater difference in size of shape (and, for that matter, presence and absence) of carapace elements here is not at all problematic:

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You say this as if it seems obvious to you that such a mechanism must exist, but as you describe all these processes I get the opposite impression: that why and how the same basic chemistry produces such different animals as you say it does remains a huge mystery. If the processes themselves determined the particular structure or phenotypic expression then these would not be different for different species and yet they are VERY different.

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Well the processes don’t seem to be that different at the basic levels. The same gene sequence will translate to the same protein sequence in almost any living thing. There are some variations but they are small and rare. The important thing is time timing and location - when and where a gene is active.

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If, say, a certain gene or gene complex or whatever in chimps makes a particular protein that contributes to the hand-like feet of the chimp, while the same or analogous gene with the same protein product makes the human foot, then it's not about the basic chemistry in DNA, it's about something else that you haven't yet defined.

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Mostly that will be timing - when genes (and they will be pretty much the same genes) are active and when they aren’t. Not that the differences are that big. Indeed, I would suggest that you might as well talk about the differences between a human hand and a human foot.

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I don't know what all the relevant comparisons and analogies are, but if the same basic chemistry makes a hoof in a horse but a flipper in a dolphin, how do you account for the difference?

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Aside from the fact that the horse has a very large toenail and the dolphin has (as far as I know) none I doubt that there are huge differences at the level of the proteins present. The same elements are present, just arranged rather differently - although we can still identify the bones as being basically the same bones.

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And all this makes it even more unlikely that you could ever get the evolution of say a mammal from a reptile by any known genetic processes, or normal genetic processes or whatever the terminology should be. The very fact that the same basic chemistry makes such very different structures makes evolution impossible.

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The very fact that the same basic chemistry underlies them all makes an evolutionary explanation very much easier. Bigger differences would be harder to explain. And you are overstating the differences - both a horse’s leg - hoof included - and a dolphin’s flipper are variations of the same basic structure (indeed, this is true for all vertebrate limbs).

Well, the genetic stuff that makes the chimp foot will ALWAYS make a chimp foot and NEVER a human foot, right? So although there are so many similarities you can refer to, in actual fact you are NEVER going to get a human foot from the chemistry that makes a chimp foot in a chimp genome. So although it seems the changes needed to get from the one to the other are very small, as a matter of simple fact they never occur and what it would take to cause them to occur seems to be beyond anyone's ability to imagine and spell out. And as usual you have to find a pathway for hundreds or thousands of other equally small-seeming changes to occur to get the whole human out of the whole chimp. It SEEMS so simple because the changes SEEM so small, but I don't even see you trying to imagine it.(Just as a mental exercise, what sort of mutations would have to occur to move that thumb-like toe of the chimp into the position we find the big toe in the human foot? Is there anything in the chimp genome that ever produces that variation, or are we having to imagine mutations bringing about the changes in position? This is where the "trial and error" comes in that I keep saying has to happen when you don't have the built in variations. You have to get certain kinds of mutations in a certain sequence to make the changes and mutations being random and most often producing something neutral or utterly useless, I don't see how you are ever going to get to the human toe at all: i.e. it's impossible even though in this case it looks like such a very simple matter of making a very simple small set of changes (as opposed to the case of getting from a reptilian to a mammalian ear design)I get your objection to my view of trilobite variation but I'm not going to try to spell that out here. Well, no, I'll just say that if you can get Great Danes and chihuahuas and golden retrievers and dachshunds out of the same Dog Genome that's how I figure you get the different variations of the trilobite because it's all nothing but a rearrangement of exactly the same parts. The chimp versus the human foot are not just a matter of rearranging the exact same parts even though it looks like such a simple matter of such simple tiny changes. But I'll have to try to get into this issue later.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

We could give you an exact list of mutations that would turn a chimp into a human, because we have both genomes in full. But that wouldn't be instructive. It would also be overkill, since it would include much that was unnecessary, and wouldn't actually tell you which changes were necessary to get a human looking foot.But I'm baffled why you expect me to be able to give you the specific mutations necessary. Do you know the genetic developmental pathway that causes the chimp genome to produce a chimp foot? Me neither. This does not reflect badly on us - the details of this are not understood by professional geneticists either. Development is extremely complicated, and there are people who've spent careers unraveling the genetics behind the development of the vulva of a tiny little roundworm - a microscopic organ that consists of about 20 cells.If we don't understand how the pathway currently works, how can we describe how it could change?If you're just looking for hypothetical ideas of the type of mutations, then of course we can speculate. Since the feet of chimpanzees and humans are so similar and consist of all the same parts, all that you need to move the relative positions of the parts is for bits to change the rate and/or timing at which certain bits grow during development. We even have some clues where to look here, since we do know the genes which set the patterning which makes toes develop in different ways - shh and certain Hoxa and Hoxd genes. But you probably don't want to change these, as they're fundamental to all sorts, but the some of the genes which they transcribe are clearly setting in place processes that cause different toes to develop in different ways.So those genes, or the ones they in turn transcribe, or inhibit, are the ones you'd need to change. A point mutation which reduced the activity of a specific gene, for example, would mean that it produced less of it's protein - if that protein is what's causing bone to develop at a particular speed in a particular location, then this would mean that would happen slower, and you'd end up with a differently shaped foot.Or you could have the same effect not by changing the activity of the gene itself, but by recruiting another gene into the process which inhibits how that gene work. Development is full of genes that inhibit the activity of others and this is one of the reasons developmental genetics is so complex. You can change a process one way by inhibiting a gene, then change it a different way by inhibiting the inhibitor, then change it back by inhibiting the inhibitor of the inhibitor. And so on. Yes they are. Of course they are. I'm not sure how to respond to such an odd statement except with 'look' (note to avoid confusion that that's a right chimp foot and a left human foot):

Oh good. I wasn't sure of that/ OK, but the thing is you have to have the necessary mutations occur in the right sequence at the right time don't you, and that's what I think has to be impossible, especially since the whole body would have to be changing at the same time also with mutations in the right sequence and the right timing. You aren't going to get, say, half a human foot and nothing else, you're going to get a whole human foot and get it WHEN you get all the other human body parts, all at the same time.I want to get into more of what you wrote but have to stop for now.

We also have hominid feet that are intermediate between these two, many of them. Which is precisely what we would expect if they each evolved from a common ancestor, and as the hominid foot evolved for upright walking.Enjoy

What the hell are you talking about? What is your misunderstanding of evolution? How do you think that evolution would have to occur? That is very important for all of us, including you, to know because that is what your assertions are all based on and if they're completely wrong then your conclusions will be completely worthless.For a working example, let's say that there's a physical change that requires six genetic mutations: A, B, C, D, E, and F.Why would the necessary mutations have to be in a single possible sequence (AKA your "right sequence")? Why would A have to happen before B and not the other way around. The only mutations where that would be necessary would be base substitutions or codon insertions/deletions in a duplicated sequence, such that the duplication would have to have happened first, but in most situations there is no "right sequence" involved. It would be like insisting that a cake recipe could not possibly work if you obtained the ingredients outside the "right sequence"; all that's required is that you have all the ingredients together in the end.And what's this "at the right time" nonsense? Mutations can be acquired at any time with most of them being neutral for many generations. Are you thinking that they all have to happen in a single generation? That makes absolutely no sense whatsoever. Why would you think such a thing?For that matter, do you think that there has to be a sudden massive single-step change within a single generation from Form A (eg, chimp foot) to Form B (eg, human foot)? That is saltation which is the opposite of evolution -- Natura non salta! (Lat. "Nature does not make leaps!"). Is that how you think it must work? Well, that isn't how it works, never has been, never will be.And as for the characteristics of the rest of body also evolving, yes, they are, even when they're not changing (evolutionary processes also cause stasis, so evolution never stops). But all changes do not happen at the same time, nor is there any reason for them to. That's how you can get "chimerae" like Archaeopteryx in which (comparing 27 features of birds, Archaeopteryx, and Coelurosaurs) we find:

• In two features, all three groups were the same (eyes having sclerotic ring and scapulae having same shape).
• In two other features, birds and Archaeopteryx were the same and different from Coelurosaurs (body covered with feathers and fused clavicles [wishbone]).
• In 17 other features, Archaeopteryx is different from birds and the same as the coelurosaurs (femur, fibula, sternum, ribs, gastralia, cervical vertebra type, caudals, vertebral column, humerus, ulna, carpometacarpus, teeth, palate, snout (instead of a beak), occipital condyle and foramen magnum, anteorbital and external mandibular skull openings, and external nostril openings near the tip of the snout (instead of near the eyes).
• In 6 other features, Archaeopteryx is intermediate between birds and Coelurosaurs; those features are:
  • Metatarsals -- Partly fused
  • Bones -- Hollow, not pneumatic
  • Coracoids -- Wider, rounded, fused to scapula
  • Pelvis -- Unfused, simple, triradiate. Pubis slightly forward-projecting
  • Orbits -- Smaller. Bony surround complete (?)
  • Braincase -- Moderately expanded fusion less complete

So then, not all characteristics change at the same time nor at the same rate! If you think that they have to, then you are wrong yet again.This is why we keep asking you how you think evolution is supposed to work. And because you refuse to ever tell us that, we are left having to constantly ask you just what the hell you are talking about. Complete and utter nonsense! "half a human foot and nothing else" WHAT THE F*CK!?!?! You have lots of 'splainin' to do about that particular piece of crap. It's "gems" like that which prove conclusively to us that you have no clue whatsoever about evolution.As a result of the behavior change to walking upright, the "chimp" foot (actually, the foot of the common ancestor between chimps and humans) would change over many generations. These changes would be the lengths and subtly in their orientation with each other, but all the bones would still be present every single generation, every single step of the way. There would never a situation of half a foot and nothing else! There would always be a complete foot, just slightly different from the previous generation's foot. Uh, no, not necessarily. Different parts can evolve at different rates; remember Archaeopteryx?Australopithecus afarensis (Lucy's species) was bipedal though not completely human-like. Still their foot was very similar to the human foot, much closer to the human foot than to the chimp foot. Their pelvis was strongly intermediate, which affected their gait -- in comparing chimp, australopithecine, and human pelvises from two distinguishing angles, you could identify the pelvis as chimp or human from both angles, but from one angle the australopithecine pelvis had the human characteristic and from the other angle it was definitely chimp. And of course the cranial development was pretty much the last "human" characteristic to evolve, long after the feet and pelvis had completed their evolution.So your baseless assertion is complete nonsense and contrary to reality. Furthermore, there is no possible mechanism for forcing all characteristics to evolve in lock-step at exactly the same rate. And there's that nonsense again! What the f*ck are you talking about? 
If you are going to try to deal with evolution, then please at the very least learn something about it first!

Exact same parts: no, the digits are shaped differently and the DNA is only going to make that shape digit it's designed to make: chimp genome, chimp digits. Yes the chimp and human have the same number of digits but if mutations manage to move the "thumb" of the chimp to the position of the human big toe (which seems impossible to me because mutations aren't that organized) it's not going to look like a human big toe becauase it's not the right shape. It's a different digit and the DNA knows the difference.

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Exact same parts: no, the digits are shaped differently and the DNA is only going to make that shape digit it's designed to make: chimp genome, chimp digits.

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Are you really claiming that when you meant that the parts were the same shape when you wrote (in Message 333): Even in dogs, flat-faced breeds like pugs or bulldogs have a different shape of skull from an alsatian or a collie. With trilobites, it’s even more extreme.

No I didn't have the differences exactly in mind, just a general idea about them. I think it may come down to a matter of proportions mostly although even that can vary somewhat within a species genome, as the heavy jaws of the Mrcaru lizards demonstrates. But the trilobite spines all look EXACTLY alike despite being arranged in different positions. Some are missing in some varieties but otherwise they seem to be the same organ in every example I've seen. The pug and bulldog faces seem to fit with their general body proportions -- the long face of the greyhound goes with its long body. Also the Dachshund. etc.All that seems to me to be derivable from the same genome. POSSIBLY a mutation might have happened in the case of the flattened dog faces but I'm not sure that's even necessary.But the chimp body despite its basic structure reminding us of human beings, is proportionally completely different, as well as having completely different specific parts like the shapes of its fingers and toes, also soles and palms, position of "thumb" etc. Sure I'm guessing about all this but I'm reasoning about it too: it does seem to me that you couldn't get the human body AND the chimp body from the same genome, although you COULD get all the trilobites from the same genome and all the dogs, pugs and collies and all from their same genome.So to get a human from an ape body would require mutations galore and that's what requires trial and error, which I believe to be impossible because of the huge number of changes that would have to occur.Edited by Faith, : No reason given.

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No I didn't have the differences exactly in mind, just a general idea about them. I think it may come down to a matter of proportions mostly although even that can vary somewhat within a species genome, as the heavy jaws of the Mrcaru lizards demonstrates.

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The variation in muzzle length in dogs seems more appropriate here, since it is a larger difference and you insist on comparing the products of artificial selection with wild species. Or, if you just use the lizards, what about the caecal valve ?

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But the trilobite spines all look EXACTLY alike despite being arranged in different positions. Some are missing in some varieties but otherwise they seem to be the same organ in every example I've seen.

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There are a lot more and bigger variations than the spines - so this looks like deliberate obfuscation. And of course there are differences in shape. You might as well say that a toe bone is a toe bone, but that would sink your argument.

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The pug and bulldog faces seem to fit with their general body proportions -- the long face of the greyhound goes with its long body. Also the Dachshund. etc.All that seems to me to be derivable from the same genome

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No. They don’t. Not even close.

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But the chimp body despite its basic structure reminding us of human beings, is proportionally completely different, as well as having completely different specific parts like the shapes of its fingers and toes, also soles and palms, position of "thumb" etc.

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But those are mostly differences in proportion. Longer toes are not completely different - they are still toes. With the same arrangement of bones.

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it does seem to me that you couldn't get the human body AND the chimp body from the same genome, although you COULD get all the trilobites from the same genome and all the dogs, pugs and collies and all from their same genome.

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I guess that if the only differences you are prepared to see are the spines, you might manage to convince yourself of that. But if you have to blind yourself that much you aren’t even trying to get it right.

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So to get a human from an ape body would require mutations galore and that's what I call "trial and error" and believe to be impossible because of the huge number of changes that would have to occur

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I disagree, because most of the differences are in shape and proportion.

In the trilobite the spines determine the shape to a great degree.Yes the caecal valve in the lizards is interesting because it adapts the gut to the tougher foods the larger jaws can handle. Remember both these adaptations occurred within thirty years, and they are obviously interdependent. I'd say it must have something to do with design factors determined at the DNA level that work together somehow although that is a pretty mysterious possibility in itself. Otherwise you have to imagine the separate appearance of the caecal valve and the jaws in stages, which I believe is the usual evolutionary understanding, and thirty years doesn't seem to be anywhere near enough for that, and since that gets into the trial and error I've been mentioning, again I think it's simply impossible. Edited by Faith, : No reason given.

Still no response from you about your abject and gross misunderstanding of evolution (Message 337). Learn something about biology. Learn something about genetics. Learn something about mutations. Learn something about evolution.With such gross ignurnce of evolution et alles that you continue to display, none of your bald assertions can possibly have any meaning. And until you describe to us step by step in detail how you think evolution is supposed to work (ie, your misunderstanding that you base all your bald assertions and conclusions on), we can have no idea what the hell you are talking about.

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In the trilobite the spines determine the shape to a great degree

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There are plenty of differences in trilobites other than the spines. The trident organ in Walliserops is an especially dramatic example.

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Yes the caecal valve in the lizards is interesting because it adapts the gut to the tougher foods the larger jaws can handle. Remember both these adaptations occurred within thirty years, and they are obviously interdependent. I'd say it must have something to do with design factors determined at the DNA level that work together somehow although that is a pretty mysterious possibility in itself.

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I think that it is an environmental response. But if you are going to count longer toes as a big difference I think you have to count it, too.

"An environmental response?" Sounds rather Lamarckian though I guess all you mean is that a slight adaptation along those lines had survival value so it kept being selected. But that's pretty much what I said myself. it has to appeare in the first place though, that's the hard part to account for.