Moderator’s remark: this post is long enough to need a “more” tag. But the wordpress editor will only allow me to add that at the very beginning or the very end. So here it is at the very beginning.
Do you want to be my cousin?
Sure. If not me, then who?
- “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
- No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
- Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
- The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
- The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
- The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
- A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”
Problem is you constantly challenge the scientific arguments for common descent. You sound like one massively confused guy
I would take that as a “no” if you did. So what more would you need to be convinced?
Let me think on it and review some past posts and some books I have on phylogenetic reconstruction. It’s a deep and complex subject. Perhaps I will start an OP on the Origin of HigherTaxa book I linked earlier.
Even better might be an OP or a series of OPs where I myself try to lay out a case for common descent based on the phylogenetic methods that I could have other people review and critique. That would be a better measure of whether I understood the material.
You criticize me for being a skeptic, dazz? Better I should take them on faith?
What? You believe in common descent but you doubt the evidence for it. How is that not taking it on blind faith?
Have you looked at my papers on crocodiles and ratites? Either of those would be examples of the strong evidence for common descent within those groups.
I really am excited by the prospect of Neil creating a new thread and there being an extensive discussion of this there.
Especially since it will get the “according to philosophers, what is truth anyway” stuff out of this thread.
I don’t recall any arguments about the “standards for truth”. Let’s take the example of phylogenetic classification again. For evolutionary biologists the standard would be that it accurately reflects the branching order of the species involved (if any at all). Although I appreciate that it is inconvenient if your pet theory fails the acid test, I usually assume that creationists / IDers adopt that standard as well. Is that mistaken? Do you think they prioritize other standards? Not sure I understand your position.
Oh, and I also would like to know when something “works well”. Not entirely clear either.
That’s a major issue. It is not surprising that when you run a phylogeny program, it comes up with “a tree”. Not some particular tree that you have focused on, but one of the large number of possible trees that could connect the organisms you are studying.
For example, with 10 species, there are over 282 million possible trees (trees with labeled tips and unlabeled interior nodes). When we run a phylogeny program we will come up with one of those 282 million. Now we take another region of the genome (say another gene) and consider its sequences for the same set of 10 species.
Does nonlin.org really think that, for that second set of sequences, it is not surprising if it comes up with the same tree, or with a tree that is closely similar?
I do think that it is not surprising, but that is because the pattern of differences between sequences reflects evolution on the same underlying genealogy, the same phylogeny. But nonlin.org thinks that the similarity of these two trees is not evidence of there being a common underlying genealogy. Because, implicitly, what nonlin.org is saying is that there is some reason other than shared genealogy that those two trees would be the same, or nearly the same.
What is that reason?
Ooh! Ooh! I know that one! Pick me! Pick me!: Because Jesus chose to make it look that way. Or maybe because similar species have similar genomes, because that’s only logical.
But it now seems apparent that nonlin accepts common descent; he just insists that random mutation and natural selection just have nothing to do with differences among species. As long as Jesus directly causes mutation and fixation, he’s cool. When he said otherwise, he was just being incoherent.
Don’t you mean Jebus?
Paternity tests aren’t evidence for common descent.
No, but I’d be happy to take a look. Links?
Mung,
Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003; 52:386-402.
Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K., Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D., Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences 2008; 105:13462-13467.
Joe Felsenstein,
If you are comparing with the common design hypothesis I would expect this in both if the design is done at different times. For example if we are comparing sharks and humans separated by 400 million years in fossil age I would expect an older sequence and we were comparing two genes if the design was 400 million years apart I would expect the mutational change to reflect the allotted time. Lets add mice at 100 million years if they were also a separate design I would expect both genes to follow the tree pattern.
Why would ancestry have a different pattern then common design if parts were being reused?
Once again you have not successfully communicated your hypothesis. Lots of word salad. You appear to be talking about different, independent creation of species. Or is it classes (i.e. sharks = Chondrichthyes)? And so on. Try to clarify what you are claiming.
John Harshman,
Joe is claiming that two genes in a group of species will create the same or similar trees is evidence of common descent.
I don’t think this eliminates common design as a hypothesis as long as the species were designed at different times and reusing genes, which is a logical possibility.
Time itself will create the tree pattern not descent or design as the mechanism. The sensitivity of the gene to mutation will also play a role.
Could we kindly drop the pretense that there is such a thing as a common design hypothesis? There was a lengthy thread on the subject here and no one ever explicated the hypothesis. Has something changed?
ETA:
It isn’t intended to eliminate common design as a hypothesis. It can’t do that anyways because the common design hypothesis is never stated (afiak).
Saying “the common design hypothesis” doesn’t mean there is one.
Thanks John.
I absolutely agree. It appears to have something to do with re-use. It’s unclear what constitutes re-use or how that qualifies as a common design hypothesis.
Does loss of use indicate uncommon design. Common undesign?
Is he talking homology (in the old sense of the term) or something else?
Mung,
What does it matter if it is an age old hypothesis or I made it up. Unless these guys just want to assume common descent design has been the competitor since Darwin. Do you think Joes argument eliminates design?
Mung,
Example: PRPF8 the central spliceosome gene is use in sharks and humans. If one sequence was inserted 400 million years ago and one 200 thousand years ago (same original sequence) I would expect as much mutational divergence as the gene would tolerate.
Of course not. How could it?
So because PRPF8 appears in both sharks and humans you take this to be a case of re-use, therefore one of common design?
How do you determine that this is a case of re-use. And then how does it follow from that, that it is a case of common design? There’s no logic here Bill, just words.
Mung,
First, I want to thank you for the constructive dialog here.:-)
I don’t know it is re-use. I only know that it is possible in this scenario. If we look at Winston’s model, it is making a case for modular re-use of genes as exists in the modular software world.
Additional data will either strengthen or weaken this hypothesis.
I don’t know that common design follows. I just don’t think Joe’s evidence can eliminate it as a possible explanation. Again, time is helping create the tree not just the change mechanisms.
I see you are incapable of articulating your ideas, probably even to yourself. Perhaps someone else can make something of it.
No, what this would show is that the older the insertion, the more the sequence would depart from the original condition. If you tried to build a tree from that, humans would end up quite close to the “root” of the illusory tree, and species would be arranged purely by recency of creation, without regard to taxa. But it’s worse than that: all living species are quite recent. Just because the first fossil shark is ancient, that says nothing about extant sharks. Your big problem here lies in assuming that “shark” is a unitary thing instead of hundreds of living and fossil species. Modern species do not reach back to the Devonian.
Last point first, I guess “consistent consilience of different data sets” is what makes your classification “objective”. This is not how the definition of “objective” works in any other science (and this is a fatal point that forces me to reject your explanation, but let this pass for now).
Classifying cars by colour, weight, power of engine, etc. is decidedly objective, because these are characteristics that every car has and everybody can independently determine these characteristics. The resultant classification has an objective basis.
The difference you are trying to make is not objective versus subjective. It’s consistently consilient versus not. Okay. But this does not by itself lend any evidence for common descent. Hint: Matryoshkas!
Look at the exact formulation you are giving – “the data provide strong evidence”. It’s the data, not the model, so not nested hierarchies, right? What is the data?
Everybody moderately observant about facts of biology notices the gaps in the data. According to the theory of (macro)evolution with its hypothesis of (universal) common descent, humans and apes are mighty close in the tree. Yet they don’t breed among each other. So why put them so close on the tree? Is this not an important piece of data? All along it looks like you simply glide over the gaps as if they were not there. You only enjoy the big picture and you assume it works by itself.
The gaps between matryoshkas don’t work by themselves and cannot be glided over. What justifies gliding over biological gaps?
*** facepalm ***
The way you are describing this design-process of re-using the same basic gene in new creations, and then just letting it accumulate mutations over some subsequent period of time, what you’d get is star-trees, as in not really a tree but a central point with lots of lines coming out of it, if you submit them to a phylogenetic algorithm.
As in all the branches would connect directly to a single node, there would not be any nested clades.
Wow. Let’s unpack this a little. colewd seems to be starting with sharks and humans having the same sequence. Then mutations change them.
We can compare this with the standard account of evolutionary biology. They start with the same sequence (having a common ancestor). Then mutations, plus other evolutionary forces, change each of them.
We normally approximate the latter case by having the changes be random. (That’s an approximate description and does not get us into any deep issues of how much real randomness there is in nature). This underlies the statistical models we use.
colewd’s description sounds like it too can be approximated by having a statistical model of random changes. If so, it’s identical.
So we could use colewd’s scheme to infer common ancestors, and it sounds as if the inferrred trees would be the same as ours. I’m glad to hear that he agrees with our inferences.
And once again the discussion bumps against the refusal to acknowledge what biological entities actually do, as opposed to what they look like when abstracted to statistical data. With due respect, you are not a biologist, Dr. Felsenstein. You are a statistician (which is a great honour in itself, no irony here).
We just got rid of the “nested hierarchies are evidence for macroevolution” nonsense. It would be a great opportunity to review the biological facts to see if they really mean what evolutionists take them to mean.
Just look at that.
Those species don’t breed among each other and yet systematists insist on putting them close to each other on the tree. What?! Are they blind? Can’t they see the gaps? Why do they glide over this important piece of data?
Statisticians, the lot of them! (don’t take me wrong, that’s a great honour, they just suck at biology)
And in case you think I am exaggerating, the estimated divergence time between the species in the upper two panels is put at ~ 33 MYA. That’s 5 times as long as the split between chimps and humans. You are in no position to lecture Joe about biology, Erik.
Corneel,
I don’t dispute the data. I dispute the interpretation of the data, something like “nested hierarchies are evidence for macroevolution”.
I fully admit the nested hierarchies, wherever you place the species on the tree, etc. I only question if biological species are the sort of thing that can (macro)evolve as proposed.
To mention again the analogy with languages (something that is in Darwin’s work and in Theobald), a proto-language evolves into a language family because the historical record shows the gradual changes (important point: no gaps in between!) over generations. Human communities carry the language and provide the basis, motive cause, and mechanism for the changes.
What is the basis and mechanism for macroevolution that is causally capable of first generating the biosphere and then constantly regenerating it, crossing the gaps between animal species, genuses etc? Something non-causal like natural selection, differential survival or Very Long Time won’t do.
And therefore it evolved? Can you even hear what the question is?
Erik,
Let’s first get this out of the way: You were making a big fuss about the reproductive isolation between humans and other apes. But of course, all sexual species are reproductively isolated from other species (that is one of the ways we define them), and you were ignoring the fact that the species in Hominidae are united by a great number of morphological and molecular characters. I know that the gap between humans and apes is blown to enormous proportions in your mind’s eye, but there is no objective support for that position. The example of fruit flies was meant to demonstrate that creationists don’t give a damn about much larger divergence in any group outside of Hominidae.
No gaps? Really? Tell me, how was the gap between English and French crossed? Can you show me a manuscript with Proto-Indo-European writing to prove that those languages derive from a shared proto-language? Can you produce writing of all the intermediate steps leading to modern English and French? No, you can’t. Now imagine Nonlin smirking that this proto-language is a figment of linguist imagination. Unpleasant, no?
Linguistics is not my forte, but I am guessing that you people reconstruct bits and pieces of that precursor by comparitive methods of extant and documented languages, and that you extrapolate from how contemporary languages are known to have changed.
The “gaps” between species (and why only animals?) didn’t have to be crossed, because they didn’t exist at the time of speciation. Lineage branching and divergence are the only mechanisms that are required to explain the current biodiversity. Is that acceptable, or do you believe in species immutability?
I didn’t say that. Just pointing out that there are good biological reasons to put humans and apes together, no matter how large you perceive the “gaps” to be.
No objective support such as reproductive isolation? Are you saying that reproductive isolation is subjective, something in the eye of the beholder?
I get that for evolutionists any select point of similarity about fruit flies (or bacteria or parrots) provides a sweeping demonstration that humans are the same. May I operate similarly: Any tiny difference, e.g. reproductive isolation between humans and apes, conclusively demonstrates they are not the same at all, never were, and never will be! I guess I may not. So why can you?
Yes. But the comparative methods were developed based on and were closely informed by actual written records that show the nature of language evolution. It never was: Looks like a nested hierarchy, therefore evolution! It was: As demonstrated by written records, languages evolve in such-and-such manner over time. Therefore they do. It looks like a nested hierarchy, but this is just the manner of the evolution, not evidence for the evolution.
Again, to be methodologically sound, you should be able to tell the difference between what the big picture looks like when systematised (I fully acknowledge that it looks like diverging branches) and the actual mechanism for change (i.e. that species actually branch from plants to animals, bacteria to humans, not caring about the differences at all).
In linguistics, a language family tree is what a language family looks like when the data is synthesised into that form or shape. On the other hand, the mechanisms of linguistic change are sound shifts (over generations), semantic shifts, borrowing (linguistic contact), and cultural evolution/decay/disruption (extra-linguistic causes). Divergence (on the tree) is a categorically different thing from that which causes the divergence (mechanism). A language family tree is no evidence for anything. Instead, a language family tree is justified by tracking sound shifts, lexical and grammatical features, etc.
I will be waiting until you comprehend the relevant distinction and are able to employ it. Maybe.
In biology, the reason to emphasise reproductive isolation is that reproduction is the concrete link between generations of species.When the reproductive link is there, it’s undeniable that one species can/could evolve into the other and likely can evolve even further up to a point. But when the link is not there, how can you posit the same mechanism?
Reproduction has a limited range as a mechanism of evolution, as demonstrated by the fact of reproductive isolation. It gives you microevolution, but not macroevolution.
As long as you can just declare this I guess it’s game over. Oh wait, if you can just declare it won’t do, then I can just declare it will.
DNA Jock loves this rich content.
Rumraket,
Yup, non-causes are causes. Keep declaring.
Question is, do you think there’s any evidence for CD and is that why you believe it?
I had been wondering what field I was in, and what I had been doing, and whether I knew any biology. Now Erik has cleared that up. Where would I be without him?
Again, we did not know whether the 5,000-comment thread on common descent had resulted in the dramatic failure of the argument for common descent, and a definitive clarification of the argument for “common design”. We have been stuck in a situation where both sides argued that they have won. Now, Erik has spoken, and that decides the matter.
Our gratitude to him, The Decider.
I maintain that reproductive isolation, just like any other invariant character, is bloody useless for deciding branching order in phylogenetic analysis.
I agree with the “are not the same at all, and never will be”, but beg to differ on the “never were” part. How would that follow?
Then you guys are missing out on a solid demonstration of the fact that languages derive from common proto-languages 🙂
To be sure: the nested hierarchy is not the only indication of common descent, and there is plenty supporting evidence from paleontology and genetics (among others). Some people already discussed the example of the GULOP pseudogene in primates, for example. The pattern in its distribution is well explained by invoking the evolutionary mechanisms of mutation and genetic drift, in combination with common ancestry.
But these are not causes of language change, are they? Of course a change in the vocabulary or the way words are pronounced corresponds to language change, but this is a mere description, and tells us nothing about causes.
Ooooh, this is gonna be FUN!
I have never heard before that reproduction is a mechanism of evolution and I am not following what you are saying here at all. It looks as if you are confused about the distinction between speciation (lineage splitting) and within-lineage change (microevolution). Do I understand correctly that you view the requirement of an uninterupted chain of reproduction an impediment to the branching of evolutionary lineages?
Joe Felsenstein,
Please, Lizzie, take a look. I am sure that in any other forum this great man would have been motivated to say at least something related to his purported field of expertise. But here he descends to mere insults. I blame you for creating this environment, Lizzie.
I provided the causal background earlier: Human communities carry the language and provide the basis, motive cause, and mechanism for the changes.
Language evolves because human communities evolve over generations. In biology, species evolve because … (please fill in the gap so that it is relevant to macroevolution, thank you very much).
Since you can just declare them non-causes, I can do the opposite. You’re not arguing, you are just stating opinions. I think natural selection is a cause. Now what? Will you now proceed to just state that you think it isn’t? Surely there’s some other way for us to communicate than us taking turns stating our mutually contradictory views.
… Populations split and become reproductively isolated, suffer mutations, and those mutations affect the physical characteristics of the organism and thus their ability to survive and reproduce.
Rumraket,
Granted for microevolution. Anything specific to macroevolution?
The underlying process is the same. It’s just more time for accumulation of change of reproductively isolated populations.