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.
And if we couldn’t, would you be without a clue regarding their relationships?
We wouldn’t be.
The fit of theory and its entailments with what is observed is typically how theory is confirmed. The moving goalposts in by critics of one area of science indicates a lack of regard for the standards of evidence.
Glen Davidson
Allan Miller,
The paper experimentally shows different interaction between species.
colewd,
This still does not demonstrate a functional association with the amino acid changes in cytochrome c. When you get binding of two molecules, the association is the subject of selection, not simply one of them in isolation. The binder evolves in the presence of the bindee, and vice versa.
There are also the clades with no variation in cytochrome c, and those with no cyt-c apoptosis pathway, to consider, if you are demanding a species-specific functional reason for the Dayhoff differences.
Allan Miller,
In one case the mutation is speeding up the reaction (humans) and in another it is slowing down the reaction (mice) and another (frog) no reaction at all. One mutation! This is evidence that the apoptosis “circuit” is custom to each animal.
I do like your claim that binder evolves with the bindee 🙂
Except for a complete lack of any explanation, this could have been an accurate statement…
One would not expect a theory to be composed of parts that don’t fit into a coherent whole.
Sort of like keiths then? God is very bad, but he doesn’t exist. You’re going to let keiths get away with it but not Erik?
🙂
He’s got you there Allan. Should have just said “I don’t know.”
colewd,
Sure, interactions are complex, and the huge numbers of gene differences must play a role in the function of any one. Nonetheless, I’m not seeing evidence that the reason for variation in cytochrome c sequence is Design.
Worth a mention at this juncture that chimp and human cytochrome c’s are identical. We all know it’s there that ‘UCD’ is found most objectionable! No-one really gives a stuff about the relationship between bacteria and archaea.
Mung,
Still struggling with this most simple of subjects? Poor fella.
Mung,
No, I’m much more happy with the answer I gave. The mechanism that predicts the actual data is vastly to be preferred to the one that does not.
“So, Holmes, what is your preferred hypothesis – that the miscreant exited through the door, or just kind of went ‘kaboom’ and disappeared on a wave of dark energy?”
“Observe the footprints, Watson, then tell me which I should prefer”.
No, the cutoff is not arbitrary. It is specific, i.e. to do with the species, so that the claimed speciation can be observed. And I don’t need to see the moment of partition. All that’s needed is the evidence that species do that. You know, like in linguistics you can follow the paper trail from Latin to French and Spanish and that’s how you know that languages evolve and diverge like that. The pinpoint when Vulgar Latin became Old French is debatable, but the fact that the one became the other is not debatable, and this way it’s justified to look for bigger groupings and other language families based on similar evidence (at the same time knowing that, based on such evidence, e.g. Semitic and Indo-European cannot be grouped together).
Unfortunately, Darwinian evolution seems to be based on “we can draw a tree, therefore species evolve like that” instead of the right way, “we know that species evolve like that, therefore we can draw a tree”. Soon I will give up. If there were any appropriate evidence, Harshman would not be urging me “down the tree” or himself “up the tree”. Such silly bargaining would be unnecessary, if the theory had anything tangible speaking for itself.
You haven’t provided a mechanism that predicts the actual data yet. And the mechanism of common design actually does predict the actual data.
Erik,
You missed out the first bit of the reasoning – if descent (genetic copying, with changes) were the only process in operation, we would expect to be able to draw a tree. We can draw such a tree, and it is corroborated by including multiple character states in the analysis. With caveats, of course, because there are good reasons for imperfections which flow from the operation.
If ‘design’ were the only process in operation, we would not expect to be able to draw a tree and have multiple characters converge on the same tree.
Your approach would have languages deemed separately created by the simple expedient of destroying all books documenting the transition. If you were consistent, as soon as that exercise had been completed, no-one could persuade you, by any means, that languages diverge.
Mung,
Template copying of DNA.
That mechanism being? Oh, that IS the mechanism! Hahahaha.
Common design is an embarrassment. Cytochrome c has 91% identity between human and mouse because …. those 91% of residues were commonly designed! Cytochrome c has 100% identity between human and chimp because …. those 100% of residues were commonly designed! I have 100% sequence identity with the sequence in my father and mother because … well … What a joke.
Template copying of DNA does not predict the actual data. It doesn’t even predict some hypothetical dataset. You’re hand-waving.
I don’t know what you are talking about. I am working towards my degree in common design. I assure you, it is a better explanation. Or at least equally as good.
It also works by template copying of DNA. In case you were wondering. So it explains exactly the same thing as the template copying of DNA.
Why? Tell me, expert of common design.
So, in addition to the ability of drawing a tree, evolution has also “common design is silly” and “creationists are stupid” on its side. Okay. As long as it was just the tree, it sounded a bit more positive. Insufficient, but sort of hopeful.
Mung,
Does though. Try taking a sheet of paper and making marks on it, then photocopying in multiple ‘lineages’, occasionally making more marks as you go, discarding ancestors (yeah, death, I forgot). I predict the sheets will arrange in a tree pattern when you collate sheets by marks shared.
Mung,
Awww! Riding the coattails of the evolutionary explanation! I bet you’ve got a lab coat and everything, just like the real thing.
Granting this, we can conclude that sheets of paper with marks on them replicate themselves into more sheets of paper with different marks on them?
Erik,
Perhaps you can tell me why common design would require everything to be arranged as if a process of descent were in operation. Preferably not by analogy.
Well, both very valid points …
Erik,
We can conclude that a process of copying predicts a tree pattern. Self-replication is not a requirement for the observation anticipated.
It would not require. It’s just that it would make sense as a part of the bigger picture. Anyway, between us two, you are the expert, so tell me why you expect something different.
OK, where in this continuum of cytochrome c sequence identity does common design kick in, as the alternative to common descent?
Me-my dad 100%
Me-Charlemagne 100% (I’m guessing a bit)
Me-chimp – 100%
Me-dog (specifically Sam the black Lab) – 94%
?
Self-replication is not required with sheets of paper, but the observation that copying occurs and that there’s occasional dashing of more marks is required. In case of speciation and common descent, also some minimal observation is required.
I suggest that cytochrome c doesn’t tell jack about ancestry.
Erik,
I would not expect a tree pattern from something that does not generate a tree pattern as an inevitable result of the mechanism. Therefore – since there are many more ways not to give a tree pattern than to give a tree pattern – I would expect one of those. Something that is not one helluva coincidence.
Erik,
All of the copying could take place behind closed doors, if it makes you more comfortable.
And you do know that mutations occur, right? That’s needed to generate a tree pattern in DNA. Speciation is not a strict requirement for this at all.
Erik,
I suggest that I got my cytochrome c by descent from mother/father, not by ‘common design’. This is why I laugh at the notion that common design is a useful alternative to common descent.
If cytochrome c ‘tells us jack’ about common descent, is there any stretch of DNA that does a better job? Or are all such analyses so easily dismissed? (No prizes for guessing where I’m going with this …),
Not one helluva coincidence? But on Darwinian evolution, the entire tree of life and its emergence is accidental. On creation, it is the plan of Creator.
On evolution, cytochrome c is incidental across species, just like clay is incidental to vases, regardless of whether they come from the same potter or not. On creation, it’s decisive what cytochrome c does, so it has a reason to be there.
Silly Allan. It would still be required to know that people can copy and dash sheets of paper. As a general knowledge of a fact of life. Otherwise your argument would not be an argument, not for common descent anyway.
Awww! Riding the coattails of the design explanation!
I love how in the end creationists wind up denying the kind of reasoning that science depends upon, while equivocating on terms like “coincidence.”
It’s what’s necessary to cling to their priors, after all.
Glen DAvidson
Given template copying of DNA, how many different tree patterns does common descent predict? How many are there given the actual data?
I have been noticing how Felsenstein and Harshman think probabilities and similarities are causes. This is what makes evolution work, seems like.
Regardless if coming from an atheist or believer, the science of biology would not be different. Just the background metaphysics would be. And maybe the philosophy of science.
Sometimes I forget just how utterly brilliant Glen is. Is he intentionally under-achieving by being here at TSZ?
You mistake me. I know that it’s nearly impossible to convince a creationist of anything. I’m just trying to figure out what sort of creationist you are and where we differ so I can focus my futile attempts on the right spots. If you don’t like “how far down the tree”, try to understand what I was trying to ask. I’m trying to find how much common descent you are wiling to accept. Is it worth trying to present evidence that Zonotrichia sparrows are related by common descent? Is it necessary? This is why I ask the questions you refuse to answer.
Not quite. The nested hierarchy might be considered the same thing, but the homologies are only suggested homologies until analysis on a tree shows them to be real. The suggested homologies are the raw data.
Nested hierarchy must be considered evidence for common descent until you can come up with another plausible hypothesis that explains the data as well or better. This is something else that the creationists here have always ignored, and I expect nothing better from you. Still, I’m sometimes surprised.
Please stop making up stuff that we supposedly think.
How does the knowledge that some people and dogs share common ancestors tell us that all people and all dogs share common ancestors? You don’t have any evidence that what you know can be extrapolated to cover an entire species.
I’m willing to accept that my siblings and I share the same parents. If I provide DNA samples, can you make a tree from it using your favorite phylogenetics software?
Why would it make sense?
Why would different bacterial species that live in the same environment, use different cytochrome c sequences, instead of identical ones? In what way does that “make sense as part of the bigger picture”?
I think you have little to no idea of what you’re being asked to make sense of with your common design rationalization. I think that, at the current level, it just exists as some vague ephemeral concept in your head (and all the various IDcreationists who like to regurgitate that term) that you haven’t really tried to seriously apply to actual data sets from the diversity of life. And only because you have it as this vague, foggy idea that never enters into the concrete, can it even be entertained.
If you really tried to apply it, you’d discover how utterly preposterous it would be.
Yes. But I don’t let that keep me from having some fun. 🙂
Well, I keep meaning to get to two books by Elliott Sober. Reconstructing the Past and Evidence and Evolution because I’d love to be able to make a better case for common descent than what I’ve seen to date.
Something that doesn’t end up being reduced to the claim that the creationists lack a better explanation, therefore I win. People often claim that design explains anything and everything. ok, well then, it explains the nested hierarchy too.
I find one big poof less preposterous than innumerable little poofs. Occam’s razor and all that.
I’m the sort of creationist to whom causes matter over probabilities and similarities. That’s why your questions are misguided. I may answer whichever way for the sake of the argument, the real question is if it matters, how and why.
You already conceded that from a little bit of common descent you cannot get more common descent, not to mention UCA. So why do you think your question about sparrows is relevant? Or if it is, then why my answer about dogs and wolves is not relevant? What difference does it make?
So the best evidence for common descent is “Come up with something better!”
That’s how “inference to best explanation” probably works for you, I guess, but I reject evolution and ID for similar reasons – shift of burden of proof and failure to point to causal links. You think that the ability to draw a tree demonstrates common descent. ID theorists think analogy from man-made artefacts demonstrates ID. Both are wrong.
John Harshman,
Your control can start where inheritance can be independently documented.
Mung,
When arguing for common descent how would you deal with the lost gene problem in Salvador’s diagram? Especially getting lost in two different lineages.
I don’t know what that means. Please pay greater attention to clarity. And I don’t think you answered the question, which was “How does the knowledge that some people and dogs share common ancestors tell us that all people and all dogs share common ancestors? You don’t have any evidence that what you know can be extrapolated to cover an entire species.”
colewd, to Mung:
Why are you asking Mung, of all people?