Yet I was trying to get a definition that would be more acceptable to you, and still would reflect what I’ve read of Bechly’s view. That’s why I started with the Wikipedia definition.
Ah, so would you agree that either the transitions aren’t there, or that they do not overturn Bechly’s view of whale evolution?
There actually is evidence, that I’ve quoted from Nature, they say it’s doubtful a tree of life can be constructed, because of such difficulties as they mention. And what I said is plain, no theory is adopted if it has significant difficulties, how is this unclear?
I got off track a bit, different than modern whales.
Which is why people also call giraffe legs flippers! When they look at the actual anatomy.
No, I’m saying that something is behind the names, people do recognize significant differences.
Really? You can be an atheist, and allow that God exists?!
But you did say that organisms each having a parent was just what common descent means! And Bechly’s view that external input is needed does take him outside of naturalism.
Alright, but do you accept their conclusion that concerning orphan genes, “we can’t build family trees for them”? If so, this is even more of a difficulty than different genes generating different trees, for orphan genes, we cannot generate a tree at all.
That’s fine.
Well, this illustrates the problem: “Orphan genes are ‘the hard problem’ for evolutionary genomics. Because we can’t find other genes similar to them in other species, we can’t build family trees for them. We cannot hypothesise their gradual evolution; instead they seem to appear out of nowhere. Various attempts have been made at explaining their origins but – as Paul and I describe in our book chapter – the problem remains unsolved.”
Genes should have origins that fit the model of common descent, and orphan genes don’t seem to, at all.
Well, arms and legs, the same could be said for them too. But no one calls an arm a leg, or vice versa. Not even biologists do that.
I’m not sure why you mention design blueprints, the discussion was about body plans, and how to classify a limb as different enough to say it means a new body plan.
By saying “amount of genetic material”, I also include changes in the amount. But either way, it has nothing to do with Bechly’s argument.
Once again! “Genome comparisons indicate that horizontal gene transfer and differential gene loss are major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the majority, of genes. The extent of these events casts doubt on the feasibility of constructing a ‘Tree of Life’, because the trees for different genes often tell different stories.”
Note, what they are discussing casts doubt on the feasibility of constructing a tree of life! Not a prokaryotic tree, nor a cetacean tree, the whole tree is in doubt. And “different genes often tell different stories” supports a previous point I was making saying, just that.
So I can discount what you say? It’s not evidence, because “someone says it”?
Certainly! I wasn’t claiming they should. I claim they are not as rare as the ones we can count.
Wow. Again I must discard something because “someone said it.” Your logic is absurd here. I assume you believe in Napolean? In Julius Caesar? You know the only evidence we have for these is “someone said it”…
I am aware of them, and I expect you need to choose a gene, and generate a tree. But I already know this can be done, so what would that prove? And I have it on good authority (I know, somebody said it) that different genes often generate different trees, so what is the point of doing that? If I’ve already seen that conclusion, what would I learn?
But Nature articles and papers aren’t properly categorized as “hearsay.” Apparently you don’t read such articles and papers, though, that’s not evidence, no point in going there.
I did look up a definition, when you challenged me on that, and what I found agreed with what I understood it to be.
Not anymore! Epigenetic material is critical to body development.
That’s what James Tour has been asking biologists for some time now, “Show me the chemistry”, for major new structures to arrive. They can’t. You seem to assume this is demonstrated in general. Where is that? Again I bring up the Third Way concerns, one of which was phenotypic novelty. You seem unconcerned, like this is a settled issue. It is not.
I would accept Bechlyt’s definition for the sake of dealing with his challenge. The problem isn’t that it doesn’t fit the standard definition, but that it’s too vague and self-contradictory to be applied.
It’s hard to tell what Bechly’s view of whale evolution is, because he never quite says. But if his view is that a land animal turns into a whale by saltation, the transitional forms kill off that notion. If his view that each of the transitional forms arises by saltation, sequentially until we eventually arrive at a whale, that’s fine. But that means that the saltations are much smaller and the time allowed for them is much less clear. This is a common creationist complaint: every time a fossil gap is filled, it just creates two more gaps. Unless you can produce a movie showing every little step of the evolution, a creationist can just claim that the evidence is against it. Of course the transitional forms exist. Are you unaware of the fossil record of whales?
That’s not evidence against common descent. It just shows there are problems in prokaryotes due to horizontal transmission and various other departures from a strict tree. But you aren’t talking about prokaryotes. You’re questioning the common descent of animals. That’s more or less a form of quote-mining.
Well, for one thing, that’s not the same thing you said the first time. It does seem more interpretable. Still, you should know that all scientific knowledge is provisional, and we will gladly adopt a theory that isn’t perfect, for now, as long as it’s better than anything else we can come up with. There’s a scale from good to bad, and you’re trying to substitute an idea that’s incompatible with any data for one that’s pretty good.
So you agree that was off track. Back to the subject: what about Basilosaurus tells you it has a different body plan from other artiodactyls, and what about Bechly’s definition of “body plan” makes that true?
Notice that giraffe forelimbs are legs, not arms. Is that a change in body plan too? What makes a different body plan? Giraffe toenails are hooves, cat toenails are claws, and yours are just toenails. Different body plans? Whales, of course, don’t have toenails. Do they even have toes? Does a cat have both front toes and rear toes, or are the front ones fingers? This body plan by language thing is more difficult than you might think.
I really can’t help you, but you could try reading back through this line of argument, trying very hard to understand what is being said. That might possibly help.
See how you substituted “naturalism” for your previous “common descent”. That makes your sentence true by radically changing tht meaning. You do that a lot without seeming to notice, which makes it hard to talk to you. Again: Bechly rejected naturalism, but he didn’t reject common descent, and by that he did mean exactly what people mean by the term.
Asked and answered. We can build trees that end at their origin or sometimes before that. This doesn’t mean we can’t build trees for the species that contain those genes.
Note how Buggs explains how to deal with this problem: sequence closer relatives to determine when the genes arose. This may also tell you how they arose. Unfortunately, junk DNA sequences tend to evolve away from recognizable homology much faster than coding genes do, and thus if a gene arises from junk, after enough time passes there will be no way to recognize that homology in distant relatives. (By the way, it’s a bit disturbing that Buggs is collaborating on a book chapter with e young earth creationist.)
That seems like a claim that no new genes can arise within a species. Would you agree, or are you confused?
Got to hand it to you, it takes a lot of nerve to do a quote mine right after posting the context. They are clearly talking about prokaryotes, and the whole tree is in doubt only because prokaryotes are a part of such a whole tree. But that says nothing about any other parts of the tree. Note also that “different genes, different stories” is also about prokaryotes. Do you know what a plasmid is?
Rather, he is saying make 12 random mutations anywhere in the string, and it becomes unreadable. Nothing about 7 character fragments, or having the same 2 mutations in every 7 characters.
Just adding “new organs”? Now it’s self-contradictory? What does this contradict? What is vague, when nerves and gut are not?
But all Bechly needs is a new body plan every 5-10 million years, this fits just fine.
I’m aware of the claim, and of the various difficulties with it. But this is not of concern for Bechly.
No, they made a general statement about the difficulty of creating a tree of life, with the prokaryotes in view. If they only meant the prokaryotic tree, why didn’t they say that?
That isn’t what is being done with the origin of orphan genes, or the nature of gravity! Until we know more, we can’t make firm conclusions. We don’t just adopt the best proposal on the market. Epicycles should have been abandoned, when they became quite cumbersome, with more continually needed.
Even with serious difficulties? I think that’s on the bad side of the scale.
So carnivory (cetaceans) requires different stomachs than herbivores (camels!), so I’m calling that different organs, and thus (per Bechly) a different body plan.
But I thought all vertebrates had the same body plan! So legs, arms, what’s the difference? But whatever you call them, they are very different than flippers, so I do say a different body plan.
I agree that this involves judgement calls, like when biologists do comparative anatomy. That doesn’t mean it’s hopeless! So I’m trying to do that with whales, and their putative ancestors. I’m going to leave the cats and giraffes discussion for another time.
But you keep calling on me to clarify what you find unclear. Your turn!
But of course I meant to include common descent as part of naturalism. But I can restate what I said, “Bechly’s view that external input is needed does take him outside of what naturalists mean by common descent,”
So orphan genes don’t fall into the paradigm of “genes belong in a tree.” Why is that? We have no idea. So again, serious problems mean a theory is not yet ready for publication.
I don’t see this in what he says, though. What I see is this: “It may be that little funding finds its way to the origin of orphan genes because it appears to be an insoluble problem.” Insoluble? That doesn’t sound like we know how to deal with this problem.
I agree they arise, but my point remains, “genes should have origins that fit the model of common descent, and orphan genes don’t seem to, at all.”
Ah, so the whole tree is in doubt, then? That was my point, and that wasn’t quote mining.
No, this was also a general statement, not specifically and just about prokaryotes. And yes, I have looked into plasmids a bit, how does this apply to the discussion?
No, Bechly’s own definition is self-contradictory. And let’s remember that Basilosaurus had no new organs as far as we know.
Great. Which of the transitions in whales features a new body plan?
Which difficulties? And of course it’s a concern for Bechly, because it makes it even more difficult to determine where this new body plan is supposed to happen.
They did, but you don’t understand what they were saying. They were talking about the prokaryote tree as a part of the tree of life. If you can’t get a prokaryote tree you can’t get a complete tree of life. But you can still get the other parts of it, which isn’t what they were talking about.
We do if it’s pretty good. Common descent is very good, and all your objections are either misunderstood or trivial.
You fail to comprehend the bits you raise as difficulties. And again, even if it were bad, separate creation would be much, much worse. Your fallback position, if anything, should be “we don’t know” rather than that. Of course we do know, so much the worse for you.
Good try. But some artiodactyls are omnivorous. The ones with the different stomachs are the ruminants. And we don’t really know the diets of early artiodactyls that well, but the transition to carnivory, if that wasn’t the primitive state, likely happened before whales took to the water. So that transition has nothing to do with Basilosaurus and anyway did not feature the appearance of a new stomach.
No you didn’t. That’s what I think, and your little plays with words doesn’t change any of that. Also, my little plays with words were intended to communicate to you how silly you are being. But it’s impossible to communicate anything to you, apparently.
You are doing it very badly, since you know nothing about whale anatomy. Judgment calls require judgment, which you lack.
Can’t. Pass.
Bechly didn’t, and it would be a nonsensical thing to do.
Doesn’t make it better. I don’t think you know what “naturalist” means. And even if we guess at your private definition, it’s still not true. Naturalists, and even “naturalists”, mean the same thing by common descent that I do and Bechly did.
No idea what you’re trying to say there, but you really shouldn’t start with “so” as if it follows from something I said. Orphan genes are not evidence against common descent, and you can’t turn them into evidence no matter how much you repeat the same crap.
Sure. You’re not equipped to see it.
What sort of gene origin would fit the model of common descent, and what would not?
Again, you appear unable to read for comprehension. Perhaps it would have been better to say “a complete tree” rather than a "the whole tree”. The question is whether all parts of the whole tree can be determined, and maybe some of those parts are more like a network than a tree. The majority of the tree is not in doubt. The animal tree is not in doubt. And yes, you were quote mining, though you may not know that because of your ability to misread so much of what you see.
Suit yourself. You have no idea how plasmids apply? More evidence that you don’t understand what you’re reading. Plasmids are common vectors of horizontal transfer in Eubacteria, and a major contributor to differences between gene phylogenies and organismal phylogenies. Nothing to do with absence of common descent.
Are you blind, or perhaps dyslexic? My question isn’t rhetorical. If you are please say so. “The same” here simply means in number. The same in number. Two. Two mutations for every 7 characters. You really have to try harder with this comprehension stuff.
I quote Axe to you directly. Here it is again with the 2 in 7 part bolded:
Here’s how he begins his explanation with the seven character fragments:
Axe: Returning to Venema’s subtitle, suppose we want to estimate the proportion of 42-character strings that can replace it. One way to approach this is to generate a large collection of strings that are randomized at the first seven positions, and another randomized at the second run of seven positions, and so on, for a total of six collections.
Six fragments of 7 characters. It’s a 42 character string. This is supposed to be analogous to his experiment with the enzyme, though in the enzyme experiment he mutates four 10-residue fragments instead of six 7-character fragments.
He goes on to state:
Axe: Here’s the problem, though. In calculating this higher P value, we have effectively assumed that the typo rate we found to be tolerable in the individual collections (two typos per seven positions) remains tolerable when we apply it to the full 42-character string. However, when we try this by generating full-length strings with twelve typos (maintaining the 2-in-7 ratio), we get completely unreadable gibberish:
Does it begin to click for you now?
Yep! That is in fact his point. I’m starting to think your failures of comprehension have become intentional because you don’t want to go through with this exercise.
They were a correct description of the motion of the stars, fit to predict some of it centuries in advance. In fact, they still are. The universe being magicked up by an infinite being, as people at the time believed, there was no expectation that much of any of it should be fundamentally simple, what ever exactly that even means. Nature is under no obligation to behave in accord with any theory our intellects are well-suited to grasp. If anything, it is on us to come up with a theory that is as simple as we can make it, not because nature is simple, but because we want a simple theory so predicting the future is all the easier for us. Nature has no such wants.
For all anybody knew, maybe the epicycles were the actual fundamental mechanism behind planetary motion, and things like the precession of Mercury’s perihelion would certainly suggest that even Kepler’s much simpler laws of planetary motion or Newton’s law of universal gravitation were not the whole story just yet.
But regardless, if one believed that the planets have some influence over human affairs, one would naturally feel better off having some idea of how to predict their motion over having none at all. We do, as a matter of fact, adopt the best we have at the time, even knowing of flaws with it, because the alternatives are either adopting something even worse or being without a predictive clue whatsoever. We still do this today, and there is nothing wrong with that.
Wrong would be to commit to a theory ideologically, and resist any suggestions of a theory’s flaws instead of recognizing them, all on the grounds that taking it as written is a matter of tradition, or key to the salvation of one’s soul. There are no such theories in science. We do not have “scriptures” like that.
We are talking about body plans, not body development. Not even the most optimistic member of the EES would suggest large scale, permanent changes such as the development of new body plans can be attributed to epigenetics.
And, in any event, that “epigenetic material” can, itself, be reduced to underlying genetics. So my point still stands.
Yeah, well, it should be clear by now that Tour is just a bullshit artist and an ignoramus to boot. As Larry Moran responded to that insipid challenge:
Does (Tour) really think that evolutionary biologists are obliged to supply “chemical details” proving that whales evolved from land animals or that humans and chimpanzees share a common ancestor? Are all chemists this stupid?
I wonder if he is equally skeptical about whether the Earth goes around the sun given that we can’t supply chemical details? I wonder what he thinks about plate tectonics?
Well, how so? He lists other items than Wikipedia, but that’s not contradictory.
Well, maybe the heat-exchange net came in then, maybe not. We don’t know. And then there’s those pesky flippers! Which I call new limbs.
Heat-exchange nets? Flippers? Stomachs for carnivory?
For one, Bechly points out that whales are claimed to have developed on one species lifetime!
I agree, but it doesn’t overturn his challenge somehow.
They certainly didn’t, please quote that part!
I agree, and you seem to have just changed your conclusion here, they didn’t mean just the prokaryotic tree.
Well, sure, but that is not what you had said.
I refer now to our agreement that a complete tree of life cannot be constructed. And the other issues I raised, such as the EES concern about phenotypic novelty. These are quite comprehendible.
But we do know agents can create language, such as a billions-word DNA string! In fact, that’s the only way we know this can happen, and we always conclude agency when we see a Rosetta Stone, etc. So this is not a desperate expedient, this is assigning a known cause, and the best and only cause we know of.
Wikipedia says: “Molecular and morphological analyses suggest Cetacea share a relatively recent closest common ancestor with hippopotamuses and that they are sister groups.” So I have reason to doubt that the transition to carnivory happened as early as you say.
Ah. The double standard appears.
I have argued that Bechly did, and I think it makes excellent sense to combine the two. Along these lines: “Although atheism might have been logically tenable before Darwin," writes Richard Dawkins, “Darwin made it possible to be an intellectually fulfilled atheist.”
People who believe in naturalism, of course.
All but Bechly certainly don’t believe in external input to nature! I think you may be the one who doesn’t know what “naturalist” means.
I think what I am saying is clear, the expectation when biologists started decoding genomes was that this would (finally!) provide a clear way to create the tree of life. Orphan genes do not fit in this paradigm. If you can’t create a complete tree of life, then common descent is not demonstrably true.
Genes should be related, genes should have evident ancestors, you should be able to point out likely ancestors, likely origins, for genes.
I think “complete” or “whole” are basically synonyms, though. But “network” and “tree” are not. That’s a problem.
So what was the actual meaning, please explain this, along with the extra context that changes the meaning.
Yes, I understand that about plasmids. I do not, alas, understand your next statement, the abstract made a general statement, are they not allowed to do that? I don’t see how your statement addresses what I said. I agree that they are not talking about the absence (or presence!) of common descent, they are talking about different genes generating different trees, which is the point I was trying to defend.
Right, that’s what I’m saying, he proposes the same proportion of mutations to the entire 42-character string, distributed randomly throughout the string. You were saying something quite different.
You quoted what I am arguing for! It’s very clear, first he mutated selected portions of the string, then he mutated throughout the whole string. What you are saying is not what he did: “If we allow the full sequence to have the same 2 mutations in every 7 characters”. Nope, that’s not it.
Can you stop this utterly pathetic attempt at stalling and just move on? What I wrote made perfectly logical sense and was an entirely comprehensible paraphrasing of Axe to any cognitively healthy, normal-functioning individual.
Since you don’t seem to suffer cognitive overload at being challenged to perform normal breathing operations, I must conclude your obtuseness here is deliberate.
You’re a forking coward and you’re a fraid of where this discussion is going. Man the fork up, grow a pair, and let’s proceed to the meat. Shall we?
That was suggested, actually, by a scientist who (finally!) responded in a journal note to Douglas Axe’s 2004 paper.
To DNA? I don’t think anyone says that.
Ah, Larry Moran. I used to follow his blog, and I just checked, and junk DNA is still his hill to die on, ENCODE results notwithstanding. He’s holding his flag, and science kind of goes on without him! And if he has a great response to James Tour, why does he need to prop it up with straw men? Like implying Tour doesn’t subscribe to heliocentrism, or plate tectonics. And why haven’t the people Tour actually challenged enlightened him by pointing out that his requiring chemical details is inappropriate? They just haven’t answered him, as I have heard.
But enough questions about Dr. Moran, surely Tour means details like how do we get the needed changes in DNA? DNA is a chemical. This question was raised by Stephen Meyer in Darwin’s Doubt, in reference to the Cambrian Explosion, how did all the needed DNA changes happen? And nobody said this was somehow an absurd request.
It’s not at all obvious that Copernicus’ model was all that superior to Ptolemy’s. It also did not fully do away with epicycles. It may ultimately be a matter of taste, now that we (well, some of us, let’s say) understand gravitation and the consequent planetary motion so much better than our predecessors did, but between Copernican heliocentrism and Kepler’s laws, if I were to pick which was incremental and which a significant improvement over the paradigm of its day, I’d say Kepler’s was more revolutionary.
Either an explanation should be abandoned for being too cumbersome (how ever much that is, in retrospect) or incomplete, or it should be provisionally accepted until something that makes yet more accurate predictions or is simpler at comparable accuracy – or, as the case may be, is both simpler and more accurate – is available to replace it. Did you change your mind between then and now, or do you actually both agree with me on the latter and also hold to the former as you expressed in the message I was replying to, all at the same time?
On that note: Considering what ever alternative to whale evolution you would propose to explain their genetics, anatomy, and the fossil sequence unambiguously linking them to land-dwelling precursors, how well do you reckon would your hypothesis fare in terms of its experimentally testable implications? Since you agree that models that best fit and predict data should be the ones we go with, how ever well that may be, what exactly do you have in mind that actually exceeds in these metrics the evolutionary account for the origin and diversification of cetatians?
Forget about Wikipedia. Bechly doesn’t talk about it. His definition is self-contradictory because he mentions a lot of things, none of which apply to his major example, whales.
Since we can’t know about the rete mirabile, you can’t use it as evidence of a new body plan. And you calling flippers new limbs doesn’t make them new limbs. Again, definition of new body plan by different descriptive language is not useful.
Of these, we know only about flippers. Do you really think flippers can’t easily evolve from legs by known processes?
Claimed, but without good evidence. How is that a difficulty for the existence of transitional forms, even if true?
Yes it does, because it makes the difference that we need to show in demonstrating a new body plan much smaller. Of course that depends on where in the sequence you want to put the change, assuming it isn’t distributed over the whole series.
Already quoted. Understanding depends only on your ability to read.
I’m trying to clarify a point. You think I changed my conclusion because you have trouble with reading.
We don’t agree. Cannot now be constructed, and will not be fully bifurcating due to horizontal transfer, incomplete lineage sorting, hybrid speciation, etc. But outside prokaryotes, these are minor.
Those issues have nothing to do with common descent vs. separate creation.
DNA strings are not language and don’t have words. You may be thinking of codons as words. They aren’t, and most of the genome isn’t codons anyway. Most of it is in fact junk. And of course genomes evolve. We know that, and we even know some of the processes involved. If you want to add another process — God caused some mutations — that would be compatible with the data, though superfluous and without evidence. Still, that wouldn’t be separate creation. Separate creation is compatible with the data only if we allow that God is trying to deceive us by making it look as if there’s common descent.
Note that hippos are not ruminants. And they may descend from omnivorous ancestors, something similar to entelodonts. You’re thinking of cows, and that’s just not it.
Your argument was falsified by direct quotes from Bechly, and your Dawkins quote is irrelevant, as is so much of what you post.
Nope. Try a dictionary.
True, but not all things people believe are relevant to what they mean by “common descent”. Whether there is external input to nature is one of those irrelevant things. Note that Bechly expressly believes in both external input and common descent.
This is silly. Orphan genes, or new genes in general, are expected, as is gene loss. Nothing in that is a reason to doubt common descent or even tree-like descent. Nor do they prevent demonstration of common descent as long as there are parts of the genome that are found in all the organisms you’re looking at.
The problem here is that if a gene arises from junk DNA, it gets conserved by selection while the junk DNA doesn’t, so eventually the evidence connecting the new gene to the junk will be lost. Fortunately we don’t have to rely on orphan genes to determine phylogeny.
Still not reading for comprehension. When you say “the whole tree” I think you mean “each and every part of the tree” is in doubt, when only a few parts are in doubt. Yes, a tree is not a network (in ordinary usage, not mathematics). But it is a structure of common descent, so if parts of the pattern of descent are tree-like and others are network-like, that’s not a problem for the idea of universal common descent. Still, the tree parts outnumber the network parts overwhelmingly except, perhaps, in Eubacteria.
Been doing that for a while now. We’ve reached the point of diminishing returns unless you start paying attention.
That’s evident, but I’ve done everything I can.
And they’re talking about that happening in prokaryotes.
What needed changes? Meyer refers to new genes, and then cites a paper that says no new genes were needed. Typical incoherence.
I missed this post somehow, sorry. I say we can believe in the validity of our reasoning, if it comes from a self-existent reason. That’s different than saying God must give us infallible reasoning abilities.
No, the claim here was that survival results in valid reasoning, and counterexamples show this is not a necessary connection. As Plantiga wrote, “Clearly there are any number of belief-cum-desire systems that equally fit a given bit of behaviour.” Counterexamples can be multiplied, for any given behavior!
My answer is that we all acknowledge the principle that reasoning is to be rejected, if we see it comes from nonreason. We do this all the time, and without exception, when we evaluate what people tell us. Only now, in one case, at the very foundation of our reasoning, we are told to make an exception to this. And accept, as our foundation, just what everyone rejects, when they see it in people.
I never said you should, I only quote him because I expect you think him perceptive.
So you don’t accept conclusions from people you consider reliable? Who you think can reliably reason? That illustrates the principle.
