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.
colewd,
I submit that you have never, ever, had a gap filled by a definitive instance of ‘outside-space-time-causality’. So your understanding of indiuctive reasoning is probably faulty.
Good point. I thought the same thing when reading him. But somehow he thinks his article constitutes formal proof for common descent, and Harshman agrees.
Rumraket,
Or the degree came before the dementia set in 🙂
Allan Miller,
Are you claiming the Aquinas 5 proofs are not from inductive reasoning based on cause and effect?
Are you saying you will accept nothing less than 100% reproductive isolation as evidence that speciation can happen? But many species are not separated by 100% reproductive isolation. The family Anatidae, for example, has scarcely any species that aren’t connected by a chain of occasional hybridization with every other species. Do you deny that there are multiple species of ducks? Or are you willing to say, on the basis of hybridization, that ducks are all related and that speciation can happen?
It’s true that no experiment I know of has produced 100% complete isolation. But experiments don’t last as long as populations do in nature. Why is the inference invalid?
Not proof. That’s not a word used in science. But very good evidence, yes. It seems that the only thing you would be wiling to accept as evidence of universal common descent would be a movie of the common ancestral species changing into all the others. Is that true? If not, what would you accept?
colewd,
I think that anyone who talks about cause and effect outside of spacetime probably doesn’t have a clear conception of at least one of those concepts.
Erik,
I think you may be close to asking someone to prove the negative. If one feels there is a constraint, that would be a positive claim one could test. But to prove there is no constraint, across all species, would be something of a challenge, like proving there are no orbiting teapots. I’m not sure why I have to shoulder the burden of proof on this one.
The other thing to consider is mechanism, as I said. If there is a constraint, how does it access genomes in order to limit the serial extent of their change? Because all a cell has access to is its current genome.
You are asking me to prove that there is not some vague force outside of genomes that limits the range of microevolution explored by them, it appears. And yet, two species that cannot interbreed have near-identical genomes (say 99%). So, they didn’t just need a bit of a shove over this invisible barrier, their entire genome needed copying outside the normal run of template copying, just because that 1% difference was supposedly inaccessible to microevolution. Or, some fraction of it was. Hmmmm …
That isn’t what you said. You said you were assuming that humans were all related. Now you’re changing your story. But organisms with quite large genetic distances can have the ability to interbreed. Ducks, for example. Genetic distance is only very weakly correlated with ability to interbreed.
Let me suggest that you are not equipped to spot the reasoning in a paper and to judge whether it’s circular. Again, descent is a conclusion, not an assumption.
Well of course you think he’s right. You’re both creationists. But the objective criterion is nested hierarchy.
I don’t quite know what you mean by “connected solely by reproductive mechanisms”. Why is the inability of two species to interbreed evidence against orthodox common descent? Is the inability of Spanish and French speakers to understand each other evidence against orthodox common descent of languages? The fact is that inability to interbreed can arise gradually. We see it right now, as there are groups with all possible degrees of interbreeding and lack thereof. And, as I mentioned to Erik, reproductive barriers have been observed to evolve in the laboratory.
Allan Miller,
Of course, there are forces that constrain variation. Natural selection, for starters. But I doubt that’s what springs immediately to the Creationist’s mind.
No, you may have read it, but apparently you didn’t understand it. It isn’t sequence similarity that’s being judged statistically significant, but the difference in fit of the data to one tree or to separate trees. The single tree explains the data much better than any combination of separate trees. Now why should that be?
[G1, G2, G3, G4, (G5, G6, G7, G8, G9], G10, G11, G12, G13) …
Gn is generation.
[G1-G9] is when species A exists. (G5-G13) is when species B exists.
A member from G1, G2, G3, and G4 can interbreed with a member from G5, G6, G7, G8 and G9, but not with a member from G10 or later.
At no point does an organism give birth to an offspring that isn’t a member of it’s own species, and interfertile with it.
To make this less abstract, you can imagine that what changes from one generation to the next, is the average size of the members of the population. So while at any one time an organism gives birth to one that is sliiightly bigger or smaller, that difference isn’t big enough to cause reproductive problems. But over a sufficient number of generations, they literally can’t mate because of accumulated size differences.
This is why reproductive isolation logically cannot be evidence against common descent.
Yes I did.
I’m not quite sure what to make of this. What does “replicate across species” mean? New species arise (mostly) by one species splitting into two species, after populations of the ancestral species (usually) become geographically isolated from each other. Reproductive isolation happens gradually, and one generation is never a different species from the previous generation, but eventually the two populations pile up enough differences that if given the opportunity they will not or cannot interbreed. What part of that is “replicate across species”? What would prevent the scenario I describe from happening? What allows you to discount the copious evidence that it does happen, has happened, and is happening now?
Rumraket,
Youch. I missed that – may have been added to the post after I started my reply. It’s … I …. I mean what … I can’t even understand why someone would ask that, having seen the scenario of divergence sketched many times. “Don’t understand biology but it’s all shite!”.
That’s what you get when you have such a degree of similarity in the data. Isn’t it obvious?
By the way, if the assumption is that alternative theories must involve separate trees, then sorry, wrong assumption. The creationist can easily answer: One creator, therefore the same genes. Very similar to evolutionist logic.
The worst about Theobald isn’t the way he treats the data. It’s the way he treats the alternative theories – he doesn’t even lay them out!
A contradiction in terms. It means it cannot logically happen. That’s my theory.
In theory, yes. We will continue this discussion when someone tests the theory. Until then, your theory is as good as mine.
Erik,
I’d say not. Your theory doesn’t even make sense.
A whopping 16 proteins iirc.
I thought we were talking evidence. Now it turns out you were talking inference. What a waste of time.
I don’t like ID for the exact same reason. Their evidence for “design detection” is just “design inference”.
Or, if the genes are different, one creator who made different genes.
Which, by the way, is the “explanation” for very different forms of life that lack homologies, save very “deep” homologies, like cephalopods. One creator, different genes.
Real explanations make sense of that, and evolutionary theory makes sense of the differences by long-term divergence, according to the evidence of homologies in developmental genes and lack of much homology in something like eye development.
Creationists, and Erik, just say one creator. Not surprising that Erik has nothing but creationist twaddle to fail to explain a damned thing.
Glen Davidson
Erik,
Well, that’s another one throwing ID under the bus!
What a failure of comprehension.
Glen Davidson
“The data set consists of a subset of the protein alignment data from ref. 27, containing 23 universally conserved proteins for 12 taxa from all three domains of life, including nine proteins thought to have been horizontally transferred early in evolution27.” – Theobald 2010
“Here I report tests of the theory of UCA using model selection theory, without assuming that sequence similarity indicates a genealogical relationship.” – D Theobald, A formal test of the theory of universal common ancestry, doi:10.1038/nature09014 May 2010
John Harshman,
Can you give an example where the range of the same species DNA is wider then two separate species?
How much wider can the same species DNA be as compared to humans 99.9% similarity?
PFM
So there can’t be evidence to convict a criminal without direct observation?
His blood on a broken store window. His knucles have scratches on them. A nearby intersection camera has a snapshot of his car close the time of the robbery. The stolen goods were found in his garage. He doesn’t have an alibi. He has a history of robberies. He is in debt to some powerful organized crime gangs.
“Your honor, there’s no evidence he robbed the store, it’s all inference.” – Eric, 2017
Mung,
Award-winning Marconi bakery?
Rumraket,
Yes, we seem to visit this area quite often!
The DNA in this hair found at the scene matches that in a cheek swab taken from my client. But I submit that, since the sources cannot interbreed, you must dismiss all charges.
But it’s so much more parsimonious!
It’s hard to find good numbers that can be directly compared, and what I’ve found in a quick search compared mitochondrial genomes, not nuclear genomes. Mitochondria evolve several times faster in most taxa than nuclear genomes, somewhere around 5 times faster in mammals and birds. One study I looked at finds the maximum (not average) distance between two humans in mitochondrial DNA to be 0.5%, while other studies have put the maximum mitochondrial distance between two members of some mammal species at 6.5%. I know of duck species with even greater internal distances, though I strongly suspect in those cases that they aren’t really one species*. The distances between closely related species can be a little as 0.0% (i.e., identical haplotypes shared between species).
Pet peeve: it’s “than”, not “then”. Those are two different words.
*This depends on obscure details of species concepts.
Erik,
I wrote a long reply to that, but it disappeared into the ozone. I don’t have the heart to write another just now. Reminder: always copy before posting.
Theobald:
Yes, this is what he says. Then keep reading, and this is what he says,
What does it mean to say “conserved proteins”? It means *conserved when transferred on to other species in the course of evolution*. That’s the evolutionist presupposition projected on the data right there.
The conserved proteins “were identified based on significant sequence similarity“. What does this mean? It means that instead of any observation that the proteins are actually conserved (a causal proposition), they were tested for similarity (a correlative proposition). “Similar enough, therefore conserved.” Sorry, but correlations are not causes.
Such conserved proteins have therefore been “postulated to be orthologues”. That’s more evolutionist presuppositions already at the stage of preparing the data. Enough said.
But this is still not the worst thing. The worst is that, having laid out evolutionary expectations (a single ancestry) for the data due to the high degree of similarities already on the outset, he proceeds to test alternative theories, making the alternative theories claim *separate ancestries* at a few points. Why? Why would the alternative theories claim separate ancestries at those points in particular? He does not say. But he should realize full well what this does to the so-called alternative models’ relationship with the data. In effect, he clearly makes the so-called alternative models disagree with the data from the beginning and then ends up confirming that they disagree.
This is a formal travesty, not formal test.
That’s correct. Someone or something must directly observe the similarity in the DNA.
Observational evidence (e.g. that the dude was seen to be elsewhere at that time) trumps any amount of indirect evidence you may muster.
You place a misplaced faith in the reliability of eyewitness testimony.
What points would you prefer? You do not say.
John Harshman,
You really don’t get it, do you? There is always “evidence” both ways. Always. You have to actually argue your case so that it trumps the counterevidence. You are not even trying.
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. You demonstrated “inference”, something like: There’s variation and adaptation, no big leap from there to speciation.
Okay, if you think that’s superior…
LoL
Eyewitness testimony based on similarities.
Erik, he doesn’t MAKE the sequences be what they are. Theobald believing they are orthologous does not MAKE them orthologous. The paper is supposed to test this very assumption. All he’s saying here is that, yes, that has been the traditional view, and that is the one I am now going to test. That’s basically the gist of what he says.
If by “this” we mean your posts, yes. I agree.
It was Theobald’s test. It was up to him. For so-called alternative theories, he simply made up random stuff. Strawman fallacy. No amount of digital data can fix this.
He PROJECTS the explanation on the sequences. Based on this PROJECTION he tests the explanatory power of the theories.
Sure, the data is what it is. But the INTERPRETATION of the data is a totally different thing. At first he says he doesn’t assume that similarity indicates genealogical relationship, but a minute later he does exactly that,
Theories are about interpretation OF THE DATA, but he had the INTERPRETATION already embedded in the test, so the alternative theories were not alternative interpretations OF THE DATA. They were disagreements with the pre-selected interpretation.
The worst is that it’s blatantly obvious.
I got the gist when he first said that he doesn’t assume genealogical relationship based on similarities and then a little later he said that conserved proteins are orthologies because their similarity is statistically significant. You should have gotten that gist too.
What would make them orthologous if they weren’t already?
If you have someone who does not even accept that common sequence is good evidence for common descent at around the species level, there ain’t much point going beyond species and hoping for a better result. Especially to Theobald and UCD, which no-one on the opposition benches seems to be capable of grasping.
Even if one got them to accept that interbreeding can cease through divergence alone at species level, you’d just shift the problem to genus level, on the ‘evidential’ case.
“Show me a genus arising through divergence”. “How does a genome replicate across the genus when the genus can’t interbreed?”.
“Show me a family arising through divergence”. “How does a genome replicate across the family when the families can’t interbreed?”.
It’s laughable, but if you’re trying to get someone to see it’s laughable, when they clearly don’t mind saying dumb things … species is Erik’s line in the sand. I suspect he knows that if he caves on that, taxonomic ranks would tumble like ninepins. So, in go the heels.
No, he explains why he picks those proteins for the test, because they have been assumed to be orthologous. That’s what he intends to test, he’s just giving you context.
He is saying “I pick these proteins which are assumed to be orthologous and I intend to test whether that is actually the best (wrt parsimony and explanatory power) model for them”. And then he does that by using models that DON’T assume they share ancestry, and computing their parsimony and explanatory power (what he calls goodness of fit) and comparing their relative likelihoods.
That sentence doesn’t make logical sense.
Sure, the data is what it is. But the INTERPRETATION of the data is a totally different thing.
Yes, and he’s testing whether a previously held interpretation is a good one
He explains that he does the test without the test somehow assuming that similarity implies a genealogical relationship, and then he picks protein sequences that have been assumed to have gone through a common genealogical relationship in order to submit them to a test of that assumption using a method that does NOT make that assumption, by explicitly comparing the parsimony and explanatory power of different models that don’t make the assumption.
Spænd nu lige hjelmen du står og snot koger.
No, he simply didn’t. That is simply and plainly wrong. You are confusing a commentary on the historical context, with the actual models being compared for their parsimony and explanatory power.
Think about it for just one second. Several of the models he is testing UCA against are independent ancestry models. An independent ancestry model using similar sequences logically cannot be assuming that sequence similarity implies descent OR IT WOULDN’T BE AN INDEPENDENT ANCESTRY MODEL.
The independent ancestry models cannot somehow produce the result that the sequences arose by common descent. They’re models that literally assume the sequences do NOT come about by common descent. So what is being tested is their explanatory power and parsimony, compared to other models. One of which is a common ancestry model.
Did you even fucking read the paper?
Some of the models that are tested on their parsimony and explanatory power are INDEPENDENT ANCESTRY models. What they are invoked to explain are similar sequences, but the models ASSUME indpendent ancestry. What is computed is the degree of ad-hoc ness and simplicity, aka explanatory power and parsimony OF the independent ancestry models, compared both to each other, and tho a UCA model.
There isn’t anything in the test that intrinsically lowers the explanatory power and parsimony of independent ancestry-models, compared to UCA models.
Yes it is, it’s blatantly obvious, so why THE FUCK aren’t you getting it? it’s right fucking there in plain text.
Again, he is first explaining how his test is supposed to work, and later he gives a historical context for the proteins used in the test. The test itself does not make the similarity=>common ancestry assumption. Anywhere.
What do you mean by “organisms reproduce along the lines of species”? How would you tell if they didn’t? How in fact can you tell whether a lion from 5000 years ago is the same species as a lion today? How is the fact that children resemble their parents evidence against speciation?
You don’t apparently understand that all science, even linguistics, is inference from observations. Without the inference, all you have is raw data. I don’t think you have any idea what science is.
And I didn’t say “variation and adaptation”. The experiments I mentioned found evolving reproductive barriers, and that’s what speciation is. We can also see populations in nature with any desired degree of reproductive isolation from none to 100%, in a continuum. Isn’t that evidence? And yes, the nested hierarchy of life is evidence too; there is no other explanation for it.
He didn’t make up random stuff. He made up a number of obvious hypotheses. I ask again, what hypotheses should he have used instead? If you can’t back up your objection, you have nothing.