I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.
Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.
If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.
One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.
That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).
Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.
The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”
So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.
So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.
I’m wondering, idly, if Erik is confusing model theory and model selection theory?
He keeps saying the former. On the latter:
Others are free to propose other models.
Because you suggested that I think the methodology has no merit. I hoped you would indicate why you think I think so. Nevermind.
I know the implications are stunning. This is all the more reason to make sure if they are correct.
Does model selection have a context and a purpose in your world or not? Is the researcher trying to prove something or not? If “others are free to propose other models” then are they not doing model selection and thus they can be said to be researchers too?
What Theobald did was take on the role of researcher and select models. But he did so irresponsibly, ending up with irrelevant results to real life.
John claims it’s a conclusion. Apparently evolutionists can’t even agree.
It is a conclusion. You can conclude, from testing the predictions of a hypothesis, that the hypothesis is true.
And in order to test the predictions of the hypothesis, you have to find out what it predicts, and to do that, you have to assume it is true so you can work out what would follow.
Nature is naturally parsimonious. So who needs philosophy, that most unparsimonious discipline of them all?
What would make them orthologous if they weren’t already?
It seems to me that the best way to demonstrate the truth of your claim here would be to state the models that Theobald should have considered but did not, and that you can’t know Theobald failed to consider the proper models unless you know what those models are. So why not say what they are?
What would make that a stupid question if it wasn’t already?
Nice philosophy
I gave a list of reasons for my evaluation of Theobald, not just the one that you keep jumping on. And you are not refuting even that one reason, you are only asking an irrelevant question about it that I already answered.
To repeat, the answer is: Any theory held by some actual person. Theobald is a biologist. Surely he knows a different biologist that has a profound disagreement with Darwinian common descent and has something alternative to propose. This would be a good start.
It would be completely senseless to stoop to Theobald’s level and to make stuff up on the fly. Let’s stay relevant, shall we?
And why don’t you answer any of my questions in return for a change? Pick one or some: Where did I say that the fact that children resemble parents is evidence against speciation? Based on what were Theobald’s alternative hypotheses “obvious” to you? Isn’t it more important that the hypotheses were relevant to the data, because then they would be real alternatives and the testing would have some actual meaning? In its current state, what exactly do you think Theobald’s test demonstrates?
For instance?
It is strange ,in all the other sciences people are in complete agreement.
It isn’t irrelevant at all. It’s the only way you could support your claim. That’s not a refutation, merely pointing out that you have no argument so far and suggesting the way you could make one.
That isn’t an answer. It’s a placeholder for an answer. I can’t think of any biologist with a profound disagreement about common descent. (Not sure what the adjective “Darwinian” is doing there.) If you can, what would that person’s alternative be? As far as I can tell, Theobald proposed all the reasonable possibilities of separate descent. You are the only one here who can tell us what he missed.
Relevant how? What other hypotheses does anyone, anywhere entertain that Theobald did not consider?
You said that reproduction within a species is evidence against speciation. I think that means the same thing. But if you disagree, never mind. Why is reproduction within a species evidence against speciation?
Here’s the direct quote: “Organisms reproduce along the lines of species. Always have, as far as observation is concerned. In order for (macro)evolution to be true, you have to demonstrate something that obviates this fact.” If you disagree with my summary of what that meant, then explain why what you said is evidence against “(macro)evolution”.
If one is testing common descent, one must test it against the alternative, separate descent. Theobald created models of a number of different forms of separate descent. I don’t know what else he could have done. I’m not sure what you mean by “hypotheses that were relevant to the data”; it should be the other way around, that the data are relevant to the hypotheses. I think his test demonstrates that the data are much more likely given a hypothesis of universal common descent than given any hypothesis of multiple separate descents.
Why not just come out and tell me at least one other hypothesis he should have tested?
As usual, the claim is that evolutionary theory just has to be wrong, and that there has to be something better. The anti-evolutionist doesn’t know what is wrong (just denies the evidence that would destroy evolution if it didn’t exist), and doesn’t know of anything better (that is actually meaningful), but there’s just got to be something better that some biologist has come up with.
So, no meaningful criticisms of evolutionary theory, and certainly no better alternative. Erik just doesn’t like it, never has. Understood, but that hardly matters.
Glen Davidson
The only way? By what logic? Feel like supporting your claim? I guess not.
So you know of no alternative hypotheses. So you cannot construct a test that is relevant to real life, only a meaningless hypothetical for pastime.
Yes, by positing that separate descent would imply a different data. You see no basic problem with it? Of course you don’t. I should know you by now.
Therefore let’s conjure up another test here on the spot.
The data: The sun rises and sets regularly.
Hypothesis #1: The sun orbits the earth.
Hypothesis #2: The earth orbits the sun.
So far so good? Do you spot the difference with the layout of this test compared to Theobald’s?
I see that you can carry on the conversation without me. Perhaps I should leave you to it? It’s the only way I can think of. If there’s another way, please say what it is.
It may not be relevant to real life, whatever that means, but it’s certainly relevant to creationism. Isn’t separate ancestry the actual claim of creationism?
What is the problem? Nobody posited that separate descent would imply different data. What was posited was separate descent. It turns out, as a result, that separate descent makes the data much more unlikely than common descent does. All the positing is in the structure of the hypothesized trees. If you would just suggest what alternative hypothesis should have been entertained, this would be a lot clearer.
No. The data do not differentiate among between hypotheses, since it’s equally likely (in fact a simple prediction) of both, at least if you incorporate earth’s rotation into hypothesis 2.
Why not make your point rather than offering vague hints? One difference I see is that the test is not actually a test, but I do wonder if that’s the difference you intended.
Okay. Like Theobald, you insist that the hypotheses are distinguishable in the light of the data on the very outset prior to the test. You demand that one of the hypotheses must be in ridiculously obvious conflict with the data.
Basic questions: If one of the hypotheses is in obvious conflict with the data, then in what sense is it a hypothesis at all? If the outcome is predictable at the outset, then what is the test for?
These are some of the reasons why I say Theobald’s paper is worthless. You are still entitled to your unreasoned opinion.
Regarding John Harshman’s recommendation of Speciation, and Erik not having easy access (no ebook version and 68€), Jerry Coyne covers speciation in chapter seven of Why Evolution is True. I find it very readable and it covers the ground, notwithstanding a distinct bias towards fruit flies. If Erik has an ebook reader, I’m happy to send him a copy.
You need to take this up with all the world’s scientists, not just with me. If the data are incapable of choosing among hypotheses, there is no test. Theobald’s test is a real test precisely because his different hypotheses predict different data. That’s not a flaw but a necessary condition of science. And of course the data are examined after coming up with the hypotheses; the data aren’t gathered to fit one hypothesis and the hypotheses aren’t chosen to fit the data. It certainly turns out to have been a better test if one of the hypotheses is a much better fit to the data than the other. But that’s not something you know until you actually do the test.
Again, if some other hypothesis would have been better to test against, what would that hypothesis have been? How do you know there is any such possible hypothesis?
Alan Fox,
I suspect the discussion of speciation is not going to be as complete and well referenced. How could it be, if we’re comparing one chapter in a popularization with an entire technical book?
I do wonder, though, whether Erik has access to any interlibrary loans. I would also think that any large university library, whatever the home language, would stock major works in English, which is currently the international language of science, so if he has access to such a library, Coyne & Orr is likely to be there. Where does he live?
Sure, but it is very clear with basic ideas and there are references. Looking at the Amazon blurb and reviews for Speciation I’m not convinced Erik falls within the target audience.
ETA not sure I do, either 🙂
I seem to think Erik has hinted somewhere in Eastern Europe but I could be wrong.
Could be, but I found it unusually easy to understand for a technical work, to the extend that I imagine an interested layman ought to be able to get through it. My imagination may be incorrect.
I would suspect that to be something else he doesn’t want to tell anyone. He likes to hold all his cards close to his chest, including birthday cards, business cards, and baseball cards.
And place cards.
Not a bad idea to hold credit/debit cards close to one’s chest.
Glen Davidson
I prefer a wallet, but to each his own.
Common descent explains the data far better than Baby Jebus does.
Mung,
Apparently you can just string a few sentences together that show you have not grasped something. SOP. Where is the conflict between ‘assume the hypothesis is true (for testing purposes) and ‘conclude the hypothesis is supported’ (after the test)?
Erik,
If one wants someone to indicate why one thinks a methodology has no merit, one would typically ask the question “what makes you think I think the methodology has no merit?”, rather than the question “Which is…?”. You were asking for the methodology. And, quite clearly, you think the methodology (phylogenetic inference) has no merit above the species level, since you say that again and again.
But Doolittle, like James Shapiro, Venter, Kurland and every other Creationist glove-puppet, becomes the darling of the Creationist world as soon as they say something vaguely out of whack with the mainstream.
Erik,
If one is criticising someone’s model selection, one would, I’d think, mention models they should have included.
Among the host of peer reviewed articles that respond to Theobald 2010 you can find online, there are several that constitute rebuttals and criticisms. Strangely enough, not a single one of those has the particular problem with Theobald’s choice of models to test common descent against, that Erik seems to think is the main issue.
The technical details are well outside of my understanding, but some articles are rather scathing of Theobald 2010. See for example:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823899/
Infinitely long branches and an informal test of common ancestry
Leonardo de Oliveira Martins and David Posada
Biol Direct. 2016, Apr 7. doi: 10.1186/s13062-016-0120-y
Rumraket,
This, incidentally, being the thing-that-never-happens: ‘Darwinists’ criticising other Darwinists. Except, of course, that no two ‘Darwinists’ are supposed to ever agree on anything! It’s traditional at this point to feign complete confusion.
Rumraket,
If that’s a valid criticism of Theobald’s test, there’s a simple way to fix it. Just determine if the likelihood differences between one tree and multiple trees with the infinite-branch-length data are significantly less than the differences using Theobald’s data. Thus we eliminate compositional bias as a factor.
Precisely because the (biological) technicalities are outside of our (mine and yours) understanding, we notice different things in the article(s) than the reviewers do. My approach is the philosophy of science approach, yours isn’t and never will be, and any attempt to reconcile these approaches will just create a mess. Already has.
Right now I am reading Theobald’s response to K&W and he (Theobald) is saying that phylogenetic inference is something distinguishable from sequence similarities, a distinction that K&W apparently said was missing in Theobald’s test at first. I must take my time to read both sides to figure out who is (more) right and then I will get back on the topic (if still relevant).
Oh okay, cool story bro.
I’m not a certified mind-reader, like you and keiths. John should say what he means.
I understand little of why. Not that this is an argument, we have just gone beyond where I get how these things affect the test. I don’t understand what is meant by infinite branch length and it’s relation to compositional bias. Sorry 🙂
No problem. If you’re interested, “infinite branch length” just means that every site in the sequence has had time for enough successive mutations that the sequence is randomized with respect to the ancestral sequence, so the only information remaining is compositional bias, i.e. some amino acids are more common than others. There may even be some domain conservation, so that, for example, part of the sequence may be biased toward hydrophilic amino acids and part toward hydrophobic. At any rate, given infinite branch length, the only information remaining is compositional bias, not phylogeny.
Looks like Sal found a friend over at Evolution News.
The notion of an eye is driven more by common architectural themes rather than exact heritable details. Thus there are common designs among eyes. In fact, trying to define the notion of eye by phylogeny alone is kind of ridiculous.
Why then define much of any function by phylogeny? If a functional trait is inherited, then fine, but if there is a gap in one species giving rise to another, why insist on common descent. We don’t need the assumption of common descent to assume the eye exists in many lines of species.
The eye evolved 40 times independently. How did the human eye with backward wiring become so similar to the octopus eye with forward wiring?
No need to assume common descent as an explanation. Common design through special creation a better explanation. Common design (as in similar architectural features) is evident in the octopus vs. human eye. No need to assume the similarities are via common descent. It’s a next to useless and likely wrong inference to assume common descent.
How does that work as any sort of explanation, Sal?
Sal:
We don’t assume common descent. It’s a conclusion based on overwhelming evidence, unlike “common design”.
Evolutionists simply lack the stupidity that is required to ignore the evidence and accept common design over common descent. Creationists possess that stupidity, whether it comes naturally or as a gift from the Holy Spirit.
The idea of “common design” is flat-earth dumb as a substitute for common descent.
Evolutionists are as naturally stupid as Creationists.
How big of a gap of feasibility would be required before you find creation to be an explanation?
If you say there is no gap big enough for evolution to bridge, then even if special creation were true, you would never be able to recognize the truth.
You finding an explanation convincing isn’t the same as an explanation being true or false. You could after all be wrong. All you are saying isn’t you aren’t convinced of special creation, that’s not the same as saying special creation is wrong.
If a miracle is needed to make something happen, then that’s an explanation. What evidence do you have that the numerous mechanistic gaps in evolving the features of life ordinarily emerge, especially at the biochemical level. Phylogenetics doesn’t explain the origin orphan systems!!!!!!!!!!!
John Harshman already confirmed the possibility of the many miraculous insertion of genes into the “tree of life”…Why not miraculous appearance of orphan systems?
After you open the door to miracles in evolutionary theory, why stop at gene level if whole systems can’t be accounted for? Miraclevolution it is… 😉
Look at this miraclevolution; land walking rat turning into 150 ton whale; No body plans change required! lol
Can’t argue with that because miracles like that happen everyday… 😉
Do you get a cut each time you recommend him Alan? Or just a Grumpy
Old Whiny Atheists member badge?
Probably Jerry will let you post on his blog without trying to censor you. For such a complainer he has really thin skin though, so don’t make any jokes about cats.
Every tub must stand on its own bottom. Accepting for the moment that evolutionary theory, due to some new evidence, became untenable, that would not give strength to another theory. Only a better fit to the evidence would do that for me.
Special creation may be true, though an awful lot of factual evidence to the contrary needs to be waved away. If there’s some evidence that supports special creation, I might find it persuasive. Depends what it might be.
As I said, for me, there needs to be better alternative theories with supporting evidence to persuade me that evolutionary theory is not, at the very least, on the right track.
How does one read the following.
Does it read to you as “God is Nowhere” or “God is Now Here”? There is obviously ambiguity. But depending on how one perceives the gaps (spaces) one will read the letters one way or another.
We have a similar issue with the debate over common descent vs. common design. Where do you place the gaps? I’ve tried to demonstrate there are substantial gaps that show the need for God to be there at the origination of orphan systems.
God makes it very easy for people not wanting to believe to do just that if they choose.
If you choose not to see the gaps in evolution of species, nothing will ever convince you.
The way I characterize Allan Miller’s words, if he saw a miracle of special creation with his own eyes, it wouldn’t convince him evolution was wrong but rather that it shows God can work a miracle that evolution already worked! 🙄
Biology is intelligently designed with gaps that would persuade someone willing to see the gaps, but gaps that are not so apparent that if someone wanted to disbelieve, they could easily delude themselves that there is no God.
Neither.
I’m sure he would. In fact I’ve commented there in the past. What are you getting at?