Specifically, what is the evidence for common descent?(Not quite) famously, Darwin mused about the similarities of taxonomic hierarchies in linguistics and biology and asserted that the hierarchies must ultimately point to common descent. (Chapter XIV, On the Origin of Species) That’s common descent as distinguished from microevolution.
The linguistic equivalent is the single origin of all languages (eminently unproven and deemed unprovable) as distinguished from a language family (with demonstrable relevant organic shared features).
Darwinists are welcome to present their evidence. From Rumraket, we have the observation that all organisms can reproduce, “Nesting hierarchies are evidence of common descent if you know that the entities sorted into hierarchies can reproduce themselves. And that particular fact is true of all living organisms.” Good start.
From Joe Felsenstein we have the doubt that the border between micro- and macroevolution can be determined, “OK, so for you the boundary between Macro/Micro is somewhere above the species level. How far above? Could all sparrows be the same “kind”? All birds?” Not very promising.
From Alan Fox, “Darwin predicted heritable traits. Later discoveries confirmed his prediction.” Questions: Which heritable traits specifically? Was there a principled improvement over Mendel? And how does this lend credence to common descent?
Thanks to all contributors.
Erik,
That’s a bit more, but not much. Instances of stasis (if such they be) do not dismantle a general trend to change. If one expressed an argument ‘change never happens because here is an instance where it did not’, one might see the logical flaw.
Erik,
There is much, much more to it than ‘all genes being made of the same material’. The digital sequence identity of these genes is a fact that needs explanation, along with the pattern of differences.
Including insertions/deletions. The missing material is not made of anything, yet these gaps align with phylogenies just as well as all other character states.
But they serve as counterexamples. They indicate that you have to amass quantitatively overwhelming evidence of macroevolution in order to have any justification to claim a general trend to change. Without such evidence, we should end up concluding that the evidence is inconclusive.
Erik,
Roughly how many narrow-strata species would you say we’d need to stick on one side of the scales to counterbalance every instance of apparent (morphological) stasis? Where are you setting the bar?
I thought that biologists already had a standard in place. So you are saying they don’t and it’s up to every individual?
But if they have a standard in place, then be open about it. Despite counterexamples, how does one conclude that there’s a general trend to change (as in macroevolution so that we would be further compelled to infer common descent from there)?
Erik,
You stated that the non-stasis instances must be ‘quantitatively overwhelming’. So I thought you might be able to enumerate that, since it seems a clear statement about numbers.
Biologists have absolutely no problem with stasis, and no need of a metric of how much of it would disprove evolution, since stasis in one lineage says nothing about evolution in any other. Stasis is not the rule.
Erik,
Gish Gallup it is then.
You might want to look up what Gish Gallop is. It’s a debate “where the creationist is allowed to run on for 45 minutes or an hour, spewing forth torrents of error that the evolutionist hasn’t a prayer of refuting in the format of a debate.”
First, if I did that, it would not even be a formal fallacy. Second, it does not apply to this discussion. You have all the time and space in the world to reply. The topic is narrow enough: Common descent.
Erik,
You are wrong about this. To be more accurate, it tends to actually be individual specific at first occurrence. Microevolution promotes some of these inserts through the lineage and on to fixation in the entire species. And on for as long as that lineage leaves descendants.
If you seriously think that people are using ERVs which are only found in one species as evolutionary markers, you might like to give them a fraction more credit.
We find the same ERV(s) at the same site(s) in Common and Spotted Sandpipers – what might that tell us?
You mean rationalwiki.org is wrong about this, because all I did was quote from there. This is yet another case of one evolution proponent debunking the other, like IDists do to each other at UD. And then some equivalent of Barry or KF steps in and causes even more confusion. Not fun, I tell you.
Nothing relevant to macroevolution, because some obscure website says, “The Spotted Sandpiper is a small shorebird that may interbreed with its sister species, the Common Sandpiper.” They are basically the same species inhabiting different locations. Debunk that.
Erik,
No, you are wrong about your interpretation of what was said. Like I said, not just species specific, it’s even lower than that. Right down to the individual. And yet it can be used as an interspecific marker. How ’bout that? How is that possible? Go on, put all those facts together. A particular transposition occurs in just one individual, and then …
Excellent. You did some work. You have discovered that gene flow occurs in that species, and are happy that accounts for their common ERVs.
Now the million dollar question: do you think there are therefore NO species that are mutually infertile yet have the same ERV at the same site? You are happy to accept common descent for Spotted and Common Sandpipers, supported by both the ERVs and the observation of occasional introgression.
So now what about a putative Species X and Species Y? True species (not interfertile). Where they have the same ERV(s), they cannot presently exchange them through gene flow. How did they get there?
Rationalwiki.org should have answered this. They were presenting evidence for common descent, yet they ended up saying “This rare event is usually species specific.” This is categorically insufficient as evidence for common descent. So let’s have some relevant evidence now, finally. How long do I have to wait?
Not at all. There’s a better explanation. I gave it and you ignored it.
Erik,
Like I say … if you think they are saying that something which is only found in one species is evidence for common descent among species, you may conceivably have got it wrong. Indeed, I explained why. The use of ERVs in phylogeny is not based upon anything in Rationalwiki. The reverse, I think you will find, is the case. How can that paper exist if ERVs are taxonomically restricted to single species? Huh?
Hahaha. Denial bot.
You didn’t give it me actually, although I did see something about souls and planes of consciousness, if I recall my brief scan. You have evidence?
Again. “We haven’t seen it in real time” doesn’t describe any barrier to processes that can take many thousands of years. Your childish excuse making is getting rather tiring.
I’ll accept your admission you have zero evidence for any magic barrier to macroevolution and are just being the usual Creationist blowhard.
As a slight tangent to this, I confess I’ve always been perplexed and amazed by the idea that some ancient shrew-like creature gave rise to multitudes of different mammal groups we have and have had. Don’t get me wrong, I understand in principle how it occurred, but it’s still astounding to think of all the branching that had to occur to get everything from mice to mammoths. Oddly, the different groups of fish and birds don’t seem nearly as remarkable to me.
ETA: Just to add, conceptually I have no problem with envisioning some ancestor to both bears and dogs and some ancestor to all rodents, lagamorphs, and chiropters. But elephants? How do you get elephants??? So very cool, but difficult to grasp.
Erik,
What useful purpose do they serve?
You are looking in the wrong place.
I said that those sandpipers are the same species. They interbreed. So “common ancestor” does not apply, at least not in the sense relevant to the theory of evolution.
Thanks for the paper and thanks for being very emphatic about how very wrong rationalwiki is. I don’t enjoy evolutionists beating each other up, but evidently you do.
Erik,
The individual in which an ERV transposition event occurs is the common ancestor of all individuals that possess that. So yes, it applies. In order for that to happen, individuals in the two groups have the same ancestor (an individual in this instance). I’ve just had Mung ragging me that species can’t have common ancestors, now you would have it they are the only things that can (or could, were it not for the fact that they never do!). You are both wrong.
You do realise RW is edited by people like you and me, don’t you? In fact, see what it says now!
As I explained, Rationalwiki was not wrong in the sense you want it to be wrong – that ERVs cannot be used as taxonomic markers across species. The phrase was ‘usually species specific’. See that first word there? Concepts of intermediate quantity are a real problem for creationists, who seem to prefer ‘all’ or ‘nothing’ depending on circumstance.
Yes, I saw it. But you should understand that only broader than species counts as evidence for macroevolution, and even then it doesn’t count as evidence for specifically common descent, which the page was supposed to be about. Given that, I was correct in complaining about lack of relevant evidence.
I took a glance at your link. It’s not about endogenous retroviral insertions. It’s about SINE insertions. Those are not retroviral.
In addition, I found this https://www.ncbi.nlm.nih.gov/pubmed/11404340
Genetics is all you have, but it’s way over our respective heads. We won’t get anywhere with this.
Erik,
Correct. I don’t know why you feel the need to make this point.
So something whose known mechanism is to insert in an individual, and whose only known route into other individuals is by inheritance, is not evidence of common descent of two other individuals that share it? We’ve been here before, but these inserts are extensively used in forensics and genealogical testing. So have a word with them. They are basing their analysis on something that does not work.
What? They play exactly the same role, phylogenetically: a one-off event in an individual leaving a unique signal in descendants. Do you have any, like, meaningful objections?
I just quoted a reason to be skeptical about this.
Erik,
1) It would be unreasonable to assume that all transposons are at hotspots because some are. As I said, it’s not just common descent of species that uses these.
2) More damagingly for your case, the paper is is based upon phylogenetic analysis between species. If you wish to cast doubt upon phylogenetic analysis by using results from phylogenetic analysis, you will have your work cut out.
This actually illustrates the neatness of the whole enterprise. Cross-check the assumption of sound freedom from homoplasy using non-SINE methods of phylogenetic analysis, find it in need of revision, refine techniques to correct for it.
In other words, they have determined that two SINE insertions are not homologous because the distribution of that insertion is not congruent with the distribution of lots of DNA sequence characters. See? It all relates.
My experience is somewhat different but has parallels. Darwinian evolution didn’t really cross my path at school so I went to university to study biochemistry thinking the differences we observe in living organisms would hold at the biochemical level. Imagine my surprise when I found out that it almost didn’t matter what organism you used to study a particular biochemical reaction or pathway; the universality of, say, the Krebs cycle was across the board.
Alan Fox,
To add my testimony, as a fellow biochemist I was particularly struck by the cytochrome c phylogeny – all there was in those days. I am fascinated, though unsurprised, that relationships are writ so deep in the genes.
Thanks for reminding how long ago it all was! 🙁
Where you see phylogenetic analysis, I see merely genetic analysis. How to interpret genes, if their configuration really indicates the causes of the same configuration, is an overly specialized topic.
At least we can agree, perhaps, that macroevolution and common descent inevitably come down to debating genes. Everything else is inconclusive and tangential, including everything ever written by Darwin.
Erik,
Whatever it pleases you to call it, the paper that you invoked to counter the notion that SINEs are a reliable binary signal was itself based upon analysis between different species and different insert instances in the tree-building manner that John has elsewhere been patiently explaining. So if you think that paper causes one to doubt SINE/ERV data, one is trying to use a macroevolutionary phylogenetic analysis to try and defeat macroevolutionary phylogenetic analysis in toto. Even if one is ignorant of the fact.
It’s as easy as pie in this case; no need to feign ignorance. The DNA ‘bases’ you’ve queried are simply strings, closely analogous to a string of bits but with 4 states instead of a binary 2. They are copied with reasonable fidelity by DNA polymerase during reproduction.
I’ve said this before; you need know nothing more about genetics than this to grasp the basics of analysing gene trees and understanding the way lineages transform. Higher order grasp of genetics is not required.
Let’s feign expertise then. Earlier in this thread, pages ago:
Phylogenetic analysis supposedly finds common ancestors, but cannot find mother or father. Explain.
Bootstrapping isn’t phylogenetic analysis. It’s a way to test the reliability of a phylogenetic analysis. I can’t imagine that it would be needed in a paternity test or what data you would bootstrap. Paternity tests are similar in some ways to phylogenetic analyses but different in other ways. This is not a line of questioning that’s going to help you.
No, we can’t agree on that. I debate genes because that’s my specialty. A paleontologist would probably debate fossils. Every evolutionary biologist probably thinks the strongest evidence for common descent comes from his or her specialty. Of course we know a lot more today than Darwin did. But Darwin knew enough for many purposes. He certainly knew enough to discern that humans were apes. Of course so did Linnaeus.
Erik,
Bootstrapping is not relevant to the issue at hand and its reintroduction is, I suspect, a diversion to avoid acknowledging even the most basic concepts. It’s not a means of finding a parent, but of finding the best tree. Even then, it is not applicable to paternity testing, nor SINE data, nor small datasets in general.
But first things first, eh?
Not even that. It’s a means of finding whether the best tree is much better than some other tree, or to put it another way, of assessing how strongly the data prefer various parts of the best tree to other trees.
This was sort of my point. Allan thinks I am feigning ignorance about genetics. In reality, I can’t make sense of absolutely anything you are talking about. You are taking genes as indicating some specific causes for granted, as an article of faith, as a dogma without any need of explanation, but this is a point where I seriously need explanations.
A bootstrap on the ground does not tell me how it got there. It only tells me what it’s made of, if I inspect closer. Now, how do you make genes tell how they got to where they are and how they came to be in the configuration or pattern that they display? I’m pretty sure your answer is short: “Trust me, I’m an expert.”
Then perhaps you should try being less arrogant. You don’t know anything about it, but you know other people are wrong. How?
Just the basic method of science. The pattern of similarities and differences among species fits one explanation, common descent, and doesn’t fit any other that we can think of. Descent with inheritance, occasional changes, and branching is expected to produce a particular pattern, which matches what we observe. Nothing else is expected to produce such a pattern. Thus we infer descent.
This is no different from the way we infer that a carbon atom has 6 protons; experimental data fit that idea and don’t fit 5 protons, 7 protons, or gum drops.
It reminds me of something. I remember reading Darwin, how he compared biological taxonomy and linguistic analysis. He was profoundly wrong.
You see, there are similarities between things. One thing is similar to another and that’s how I know something about the other even though I may be seeing it for the first time.
What other explanations have you thought of?
No, in fact he wasn’t. But there’s no point in getting into that now. That linguistic thing was just an analogy, tossed off in the hope that you would understand his point. If you don’t like that analogy, would you consider the analysis of scribal errors in illuminated manuscripts? That one works quite well. See Howe C.J., Barbrook A.C., Spencer M., Robinson P., Bordalejo B., Mooney L.R. Manuscript evolution. Trends in Genetics 2001; 17:147-152.
Not sure what you intended to convey there.
In practice, one particular tree is tested against all the other particular trees. If one tree fits the data lots better than any of the other trees, that’s evidence favoring that tree. It’s unclear what sort of pattern would be expected from special creation. The best I can think of is that we might see no relationship at all among species (i.e. the same level of similarity expected by chance) or we might see what’s called a star tree, in which all the species share similarities in some subset of the data but the rest of the data are no more similar than expected by chance. The standard analyses implicitly test for both of these, because in either case no tree would be much better than any other tree. We would not expect, in other words, to find a nested hierarchy in the data.
Now, what explanations can you think of?
Wait a minute. You were supposed to know how science works. Then you should know that like has nothing to do with it.
With the analogy, Darwin was illustrating something about biology. The analogy was profoundly wrong. And my like has nothing to do with this. If you disagree on this point, then we shall get into it very deeply.
It’s a lesson about analogies. If you don’t know how analogies work, then this is another reason to get into it very deeply.
Resemblance all the way down. Species are of the same constituent elements and this explains it. Whereas inability to interbreed strongly suggests no deeper organic or genetic relation.
Erik,
That explains nothing; common descent explains it all. Common descent it is, then! Cheers, Erik, you’ve been very helpful.
Any reasonable theory would group stuff by similarities and yield the exact same tree as common descent. Similarities are the most obvious trivial common-sense feature to go by. The tree (taxonomy) would be the same, in fact it has been the same all along since before Darwin. Common descent is an unwarranted assumption projected on the taxonomy.
If common descent were a natural biological feature in the tree of life, something like this should be natural https://upload.wikimedia.org/wikipedia/commons/6/6f/Editorial_cartoon_depicting_Charles_Darwin_as_an_ape_%281871%29.jpg
As far as I can tell, the analogy is just fine. It’s just your attempt to make it be about universal common descent, which it wasn’t, that is giving you fits.
Wrong all the way. The elements (are you actually referring to chemical elements here?) don’t determine the genetics or phenotypes. As you point out, all species have the same elements. And yet they differ. Not only that, at the genetic level they differ in exactly the ways that can be explained by accumulation of the sorts of mutations we see happening within populations: point mutations, indels, inversions, chromosomal fission, fusion, and exchange.
As for inability to interbreed, that comes in all flavors, from no difficulty at all, through partial isolation, to complete sterility. It’s also been induced in the lab by selection experiments. That’s just as we would expect if one species gradually turns into two species. So no.
Your explanation is no explanation at all. It’s nonsensical, too.
Different elements – anatomy, cells, biochemistry. Things biologists always used. You see, the tree was there before Darwin. Positing common descent did not change the principle, only fueled detailed examination.
What does “induced” mean here? Was the ability to interbreed “induced” or inability? Among what species?
Erik,
Any reasonable theory would explain why the similarities (actually, nested identities) cluster in a tree-like pattern. You’re just saying it would ‘cos you say it would. Whatever the pattern, that’s what you’d say you expected. “Five of clubs. Yes, I know you just showed me, but it’s what I expected”.
Whereas a process of descent and population bifurcation would be expected to give tree-like phylogenies, as you can see by examining … well, a tree. If we see what our process would give, that is a substantial strike in our favour.
And no, a man-ape hybrid is not a sensible expectation if evolution were true. Divergence in two separate lineages does not lead to a hybrid between the end-points of those lineages. It is not a difficult concept to grasp.
Hmm. How about the fact that they are similarities? Wouldn’t a big cup and a small vase, amphoras and bottles also group like “nested identities” in the shape of a tree? Is there a way to avoid this?
So we agree that the tree is a real thing, not a human construct, and such in need of explanation. Common descent didn’t change the principle of nested hierarchy. What it did was provide an explanation of why that hierarchy exists. Once again, though you have always ignored me so far, I invite you to provide another explanation that fits the facts as well or better.
It’s inability that has been induced, meaning that by subdividing a single population in the lab and exposing both segments to selection of one sort or another, the two segments begin to show reproductive isolation from each other. It’s been done most often with everyone’s favorite genetics lab animal, Drosophila melanogaster. If you want further information, I invite you to read the book Speciation, by Jerry Coyne and H. Allen Orr, which lays out the experiments in great detail.
Erik,
Yes. Use molecular data. Then use more of it. That’s what I’ve been talking about all along.
It’s difficult for creationists. Hence the crocoduck.
Actually, what’s really striking about Erik’s claim is that it’s the old misconception (or simply strawman) that gradual divergence should lead to mythical chimeras. Creatures that are one half very distinct, intact traits from one parent and half very distinct traits from the other parent. Such folks really can’t wrap their head around trait blending or recessive vs dominant traits and the like.
And thus the canard of the “ape-man missing link” is perpetuated…
According to Rationalwiki, L-gulonolactone oxidase synthesizes vitamin C.