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.
Yes, soon after he said that he was not making any assumptions. The case is absolutely clear when you acknowledge the following: Theobald’s test is not a biology test. It’s a test of model theory. He starts out claiming he is not making any assumptions (absolutely essential in the model theory) and then he goes on and errs against this. Nothing more needs to be said, really.
What do you mean what do you mean? You mean you don’t know what species are? I have been suspecting this much, yeah.
Hint: “Resemble” has no significance whatsoever in this discussion. Yet still you have been arguing all along something like “Look how similar those genes are. Common ancestor!” I have been arguing nothing of the sort. “Resemble” is your argument, not mine. From my point of view, similarities are categorically irrelevant to the whole issue.
You are the one saying they don’t, necessarily. You say that bacteria reproduced to multicellulars and all multicellulars branched from there all by means of self-reproduction. There must be some evidence that makes you say it. Ah, it was inference. Okay.
“Obvious hypotheses”? In the sense that someone else before Theobald has employed those “obvious hypotheses” to explain the same data? You have evidently zero clue about model theory. Theobald’s test is a flat-out ridiculous hypothetical with no relevance to real life. Let his test be tested by an actual model theorist and see what you get.
No, you’re just wrong. He is giving a historical context. I have already explained why. How come it is not possible for you to fathom that he is merely giving a historical context?
Is the (historical) assumption of orthology a better explanation wrt parsimony and goodness of fit, than various different independent ancestry models? That is basically the test.
He tests the parsimony and the power to explain a set of protein sequences (that were historically thought to be orthologous) of several different models. But he himself does not make the assumption that they are orthologous. He just mentions that this has been the traditional assumption, and he’s now testing that assumption wrt to it’s degree of ability to account for the data and it’s simplicity, compared to a set of different independent ancestry-models.
Erik, you’re just plain fucking wrong. Take it like a grown up, as in accept it and deal with it, and move on.
Something about pearls before swine.
This is such a common theme hereabouts. Assume a hypothesis to be true, test it on the basis of expectations if it were. “But, but, you’re just assuming it’s true … you have no grounds!”. Face, meet palm.
“No” as in “It’s not a test of model theory”? Then we are done.
Yes Erik, we are done.
In Theobald’s case: Embed a hypothesis into the data, then make up incompatible hypotheses and test all the hypotheses. Voila, those incompatible hypotheses really are incompatible!
He was not simply assuming the so-called alternative theories to be less reconcilable with the data – he was visibly designing them to be that way. This done, the test procedure is a foregone conclusion. It would have some value of curiosity if those so-called alternative theories were held by some actual people, but since this is not the case, Theobald’s paper is an exercise in futility.
Poor Erik. Another of his crackpot positions meets cold reality.
Want to talk about the empty set?
Hvabehar?
What do you mean what do you mean what do you mean?
Erik,
Curious then that, despite Theobald’s method having been subject to criticisms, that was not among them.
When biologists criticize, that’s what you get. Just like when a biologist does model theory, that’s what you get. Pretty obvious.
Erik,
Yet your objection is so … well … obvious, you’d think a critic would just say it and have done, rather than go to the trouble of writing programs to generate test data, and all that science shit. Your apparent hatred of biologists and the study of biology may be getting in the way slightly. The argument is much more subtle than you appear to appreciate.
Erik,
‘Assuming a hypothesis to be true’ is not the same as ‘assuming a hypothesis to be less reconcilable with the data’. So you betray your misunderstanding of even that simple point.
What? I know Theobald is not testing the truth of the theories. He is testing their consistency with the data. Do you know this? Apparently not:
Erik,
Perhaps it’s a language thing, but ‘true’ and ‘less reconcilable with the data’ are not synonymous in my book.
Same here. So why are you bringing it up? You assume I am conflating the two somewhere? Then you can quote me on this. Stop being fuzzy.
By inference, the entire field of biology is poppycock, and I guess all of mathematics, all of physics, all of chemistry, even linguistics and so on.
Papers by physicists are reviewed by other physicists, so.. well gee I guess it must all be total shit as they’d all agree on stuff and never bother to properly think about and test it. A plummer fixed your pipes? Better get it reviewed by, I don’t know, a farmer or a medical doctor, as another plummer would just agree it was all done correctly. It’s the great plummer conspiracy.
What utter fucking bullshit. Erik has descended into the classic conspiracy nutter methodology: If the evidence is against me, the evidence is fake (news).
How should I read this:
O non-fuzzy one?
Rumraket,
Nope – just biology! Prove to me that there is any merit in biology, bearing in mind that I think all biologists are charlatans including you!
Allan Miller,
Elaborate.
Rumraket, to Erik:
Corneel:
Lol. Google translate isn’t much help:
I’m far more moderate here: That paper by Theobald where he does model theory (as opposed to biology) does not prove what you think it proves.
Oops — looks like I accidentally cut off the ‘S’. Let me try again.
Erik,
Explain.
Not much better:
Allan Miller,
The second half of the sentence that you omitted should explain it. What’s your problem?
Heh, it’s a common danish expression, can’t be directly translated in a way that makes sense.
But it’s like saying “get your shit together you are sleeping on your post”.
Erik,
Now spike the helmet you are standing and snot boils.
keiths,
You know. I used to live in Danmark for several years, but I don’t recall coming across this expression.
Erik,
My problem, such as it is, is that, in response to the statement ‘Assume X’, you said ‘he does not merely assume Y’. What you then go on to say is irrelevant; you show that you haven’t grasped the point about what one is ‘assuming’.
Anyway, as has already been said, what hypotheses should he have included? If he cherry-picked, what fruit was left ungathered?
Rumraket,
Awesome. Love the Danish language 🙂
To be fair, I heard it only in Jylland. So maybe it wasn’t all that Danish 😀
Rumraket,
Is it really about boiling snot?
That would be a literal translation of the words, yes. Snot koger = snot boils.
Heh, not the real Danmark right? Me and my family lived in Aarhus and learned some Danish there. Occasionaly we return there for holidays, and enjoy the opportunity to speak the language again. I doubt I will ever get to use that expression though. Pity.
Rumraket,
Thank you. I’ve heard enough. 🙂
Cherry-picking would have been a minor sin compared to what he did. Cherry-picking means pick the theories in a biased way, but instead of this, he made up theories on the fly that nobody ever held, without giving any reasons if anyone should hold them and why. In this way, his alternative theories are not really alternative. An alternative theory is an alternative explanation of the same data. His so-called alternative theories are various degrees of conflict with the data – and the degrees of conflict are trivially predictable already before the testing gets started. That’s not how any sort of testing works.
Moreover, I started looking at the other paper you linked to. Up front (pp1-2), the objection reads,
Isn’t this what I have been saying? And, apparently a reviewer addendum in the end concludes,
Damn right it’s a scientific philosophy thing, not a biology thing.
Anyway, this responses to criticism will likely be a far more interesting read than Theobald’s first paper. Also Doolittle’s “Uprooting the Tree of Life” that someone linked to earlier is interesting, about actually discovering the tree and evaluating its causal significance in a far more relevant way than anyone here has attempted.
Erik,
Now you’re just getting abusive without any other content. Bad day?
John Harshman,
You could fix this by adding content of your own. Nothing to add?
There was nothing in your comment to respond to other than to point out there was nothing to respond to.
Erik,
Careful – Doolittle is using a methodology you think has no merit. “Love the conclusions, hate the method” is a recurring theme among Creationists. As long as something appears to upset the presumed Darwinian apple-cart, that’s good enough for some.
Erik,
No.
John Harshman,
Let’s see. Theobald’s fundamental fail at model selection is no content according to you. When I point out your failure to define “species” (because, among other things, we are talking *origin of species*), this is no content according to you. When I correct your misrepresentation of my position (“How is the fact that children resemble their parents evidence against speciation?” Can you quote me on this? Go ahead.), that’s no content according to you.
Point taken. Looks like my next move should be to put you on ignore so you would not distract me from engaging with the topic.
Which is…?
Erik,
That sequence similarity is indicative of a phylogenetic relationship.
[eta – and by that I don’t just mean vertical descent. The phylogeny of a sequence does not necessarily align with the phylogeny of the rest of the genome in which it sits].
Erik,
That would be a curious move – John is better placed than any of us to discuss these matters.
Allan Miller,
We’ll see once I get there. When a thing is worth reading, I take my time.
Erik,
Why ask me, then?
Not to put you down, Erik, but the implications of the biochemistry are stunning and I feel you are dismissing them without appreciating the, well, beauty of the science here. It takes a little effort but I’m sure you’d find it worthwhile.