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.
Actually Theobald makes no assumptions about the number of functions of cytochrome c. Rather, Theobald simply uses the demonstrable fact that there is an unfathomably large ensemble of known cytochrome c sequences which can do each other’s job. Whether that is one or several jobs is irrelevant. Heck, Theobald doesn’t even need to assume it has any function at all. It could be ten, one hundred million, or it could be zero. The only thing that matter is the branching order the diversity of sequences yields when you use a phylogenetic algorithm to sort them.
What you fail to comprehend, and have failed to comprehend now for years, is why the tree derived from cytochrome c molecular data, matches the tree derived from morphological data with an extremely high degree of statistical significance.
There’s absolutely no reason why an algorithm that simply tries to explain the data set using the smallest number of evolutionary events, should produce a particular cytochrome c tree that matches the tree drawn from morphological character states using the sample principle, if common descent isn’t true.
Don’t be scared, Bill. Keep reading.
Stephen J. Gould’s creationist PhD protégé Kurt Wise explains that the fossil record is at variance with evolutionary theory. He even uses nice cladograms. Go to 20:20 in the video:
https://www.youtube.com/watch?v=Gy1zy5ddMS4&t=1621s
Wise even studied geology at University of Chicago, where Jerry Coyne now teaches and where John Harshman got is PhD in evolutionary biology.
And since you are now following this course on phylogenetics, you should be able to explain why the branching order in the cladogram does not predict order of appearance in the fossil record.
stcordova,
You are saying that the patterns are the same, or roughly so, in a thread on Common Design vs Common Descent. So I’m guessing you are proposing Common Design of the pattern, for common reasons. So now (maybe, who knows what you are ever really saying?), you think its 2 different functions that just happen to follow the same distribution pattern because [message becomes garbled].
You are getting confusing/confused on this one. I’m not really sure what you are trying to say the pattern indicates. To me, it indicates a common (commonly descended) pattern of euchromatin, and reflects the known mechanistic constraint on distribution of SINE inserts (transposons, in case you had forgotten) to euchromatin. What are you saying it indicates?
Jeez, another friggin’ squirrel.
stcordova,
You seem determined to make this a[nother] thread about junk vs function. Whether transposable sequences are functional or not is totally irrelevant to their use in phylogenetics. Many functional sequences are used in phylogenetics. Surely you know that, a 10-minute expert like yourself?
Reading on, both Sal and Bill seem to have run away with the idea that function renders phylogenetic analysis suspect – in the former case, the possibility of not-being-junk; in the latter, not-being-junk for 2 reasons … Ay caramba.
Rumraket,
The multi function of cytochrome c is relevant because evolution needs to explain the origin of these new functions by inheritance alone. How does a cytochrome c that exists in a single cell become a cytochrome c that now is part of an apoptosis circuit and therefor has to have the sequence integrity to bind and form a function with other proteins.
Credentialism again? Wise has a B.A. from UC. His ability to remain a YEC after such an academic career testifies to his determination and compartmentalization skills, though not to his wisdom. I find his supposed scientific publications to be no more than cargo cult science. But we could discuss them if you liked.
You’re confused as usual. This thread is not about how everything evolved, it’s about whether nesting hierarchical data is evidence for common descent, and how supposedly “common design” explains the same patterns either equally well or better with a testable predictive model.
The conclusion of this thread is: Common design does not explain it, at all. Only common descent does.
In nice contrast to basically every other geology, biology and paleontology PhD graduates ever, including Stephen Jay Gould himself, and Jerry Coyne.
This stupid argument from I-can-name-a-guy-with-a-PhD-who-disagrees will not get you closer to the conclusion you seek and it’s honestly pathetic to see you keep making it.
Get it through your skull: Credentials do not dictate to reality.
Rumraket,
The conclusion of this thread is that Creationists still don’t even understand the question …
Sal’s credential-mongering is all the more pitiful when you read how Wise arrived at his rejection of evolution:
colewd,
To the extent this is relevant at all (not much) it is an issue at a specific boundary: the unicellular-to-multicellular ‘transition’ in the lineage leading to animals.
Would one not expect some kind of a discontinuity in cytochrome c relatedness at this barrier? There isn’t. Almost as if it isn’t there.
Amazing how that works.
Yet there is no law of physics, chemistry, biology or any other science that requires that common descent produce a nested hierarchy.
You forgot logic
PS: you’re fucking deluded (or retarded, or both)
Mung,
That’s pure Joe G.
Too true. I am a bit disappointed that the common design proponents couldn’t put any meat on the concept. Sal came up with this ridiculous notion of a deceiving designer that deliberately fakes the nested hierarchy. Bill actually came close with lineages developing like computer systems building on previous legacy, which only works because it apes the phylogenetic process.
Hell, if I sit down for two minutes I can come up with a better explanation why design might result in a nested hierarchy.
I can’t find it in the US constitution either.
Man, who decides those things?
There are thousands of predictive scientific hypotheses that don’t have a “law” that “require” their predictions.
No I did not. TAXNOMIC nested hierarchies are real, it just makes it easy for evolutionists to concoct PHYLOGENETIC nested hierarchies if they close their eyes to orphan systems. It’s not like the data actually confirms evolution without miracles if you look at it objectively.
The designer made it easy for Darwinists to ignore evidence, and difficult for the truth to be perceived. Those wanting the truth have to examine the data with less bias.
There, that’s a more accurate description of the view I actually hold vs. the strawman mis representation you attributed to me.
Regarding Cornee’s misrepresentation of my hypothesis, I’ve said the data actually do tell the story if evolutionists won’t cherry pick it.
For example, the photo below is an optical illusion of Snell’s Law. If you cherry pick the data rather than carefully examine it, you could delude yourself to believe the pencil actually got bent. The truth is more subtle than what it looks like superficially, but the data is there, you just have to stop cherry picking, which is mostly what the assertion of Universal Common Descent is.
So, basically, you create an artificial distinction, and then you deny that there really is a nested hierarchy in the parts of the data you have an irrational prejudice against. Sorry, that isn’t an explanation. Nor have you even explained why this “taxonomic nested hierarchy”, the one you accept, exists.
And we have never managed to establish just what you mean by “orphan systems”.
Now why would he do that? Why is the designer deceitful such that he counterfeits common descent?
The strawman misrepresentation actually makes more sense.
stcordova,
Phylogenetic nested hierarchies are based upon similarities and differences, but the point at which the difference arises is key.
In essence, a specific SINE insert is an ‘orphan system’, or a Taxonomically Restricted Gene, or whatever. It is phylogenetically informative by virtue of its ‘orphanness’, forming a synapomorphy not shared by outgroups. Why is that invalid?
Perhaps you could confront some of the phylogenetics literature and explain just how it was cherry-picked. I invite you to have a go at some of my publications. I have in fact invited you several times, but you have never chosen to pick up the invitation. Do I need to post links again?
Probably yes.
Thank you Sal and Mung for proving my point!
QED
John Harshman:
Perhaps you could confront some of the phylogenetics literature and explain just how it was cherry-picked. I invite you to have a go at some of my publications. I have in fact invited you several times, but you have never chosen to pick up the invitation. Do I need to post links again?
No because you blindly ignore the problem of Orphan Systems, many of which I have posted in some detail. In view of that, your publications aren’t worth my time regarding the topic at hand.
I do, despite our sharp disagreements, have very high regard for Joe Felsenstein’s work. Ironically his work is revered in creationist circles, especially his mutational load arguments.
I just purchased Joe’s Felsenstein’s classic book on phylogenies, it retails at Amazon for as much as $119. I have much gratitude toward him for him making his text on Theoretical Evolutionary Genetics available for free and taking my questions on his classic, so I didn’t mind buying his other book on Phylogenies.
Here is Joe’s bio. I didn’t know Joe was a member of the National Academy of Science until now!
Now who’s cherry-picking?
stcordova,
… but you think Inferring Phylogenies is hogwash?
Go on then, why are ‘orphan systems’ and TRGs a problem for Common Descent? Bear in mind that without differences, restricted to some taxonomic level, no phylogenetic work could be done at all. So even if we have no account of the cause of the difference when it first pops up, its presence in a wider clade is reasonably accounted for by Common Descent … isn’t it?
It is literally mindboggling to seem them not get this again and again. There would be no phylogenetic signal if there were no differences at all. If they weren’t merely similar to some extend, but identical, then there’d be no way to categorize them. Taxonomically restricted character states, at every level from single nucleotide mutations, to gene/protein/structure/organ absense or presence, is the very thing that makes phylogenetics possible.
HOW can they not get this? How is it even possible to not get this?
I hate to be accused of misrepresenting your position but, by golly, you’re not making it easy for me.
1) If you deny the existence of objective nested hierarchies, then why on earth are we discussing common design as an explanation for them?
2) You faked an artificial nested hierarchy in PHYLIP to prove … what exactly, if not to prove that this is what the designer could have done as well?
3) When asked why God has chosen to be oblique about the evidence of design you quote this at me:
AND you tell us God likes to play cruel pranks at people he wants to condemn. AND you tell us that “the designer made it easy for Darwinists to ignore evidence, and difficult for the truth to be perceived.”
How is this not a deceiving God / designer?
Now, I really do try not to misrepresent other people’s position but you could be a bit more cooperative by actually choosing one.
They have no ancestors barring a miracle. Something without an ancestor falsifies universal common descent. Duh!
Hey, he paid for it, and if it was bought new, I made a nice royalty off of that. So he can have whatever opinion of it he wants, I’m happy.
I recommend your books and works to all my creationist friends with interest in these topics.
I bought your book NEW. So yes, I’m glad you got a nice royalty, it is very very well deserved. I look forward to paging through it. My professor refers to your works often.
Joe’s got some dang beautiful math, it’s good for the soul just to read it whatever one thinks about phylogenies. If not for phylogenies, that math is too beautiful not be meaningful in some other application.
The stuff with bootstrapping was incredible as it touches on topics in theoretical computer science.
1) Since you believe in miracles, why do you think “they have no ancestors barring a miracle” means “they have no ancestors”?
2) No, something without ancestors doesn’t falsify common descent unless that thing is a species. If some sequences within genomes within organisms are without ancestors, that doesn’t translate into the organisms being without ancestors.
3) You haven’t shown that anything you’re calling an “orphan system” actually is without ancestors. You have in fact shown no curiosity about the origins of genes or of anything else. Further, your definition of “orphan” seems to slide around freely, since you use it to refer to sequences that have clear relatives, either other members of a gene family or non-protein-coding sequences in other species.
Joe, you seem to have a new puppy-dog. Perhaps you could paper-train him.
That remark highlights our disagreement.
I was emphasizing missing ancestors in principle. A sufficiently complex orphan systems rules out a natural ancestor, it is more consistent with a miraculous origin. But if you don’t believe that there could even in principle be any system complex enough and different enough from other systems, then even if a miracle was the cause, you’d never arrive at the truth given your criteria. If you’re happy with your criteria, then you’re happy with it. I’m not.
One of us is closer to the truth. But if humanity is ending, what’s in it for you to stand for something you can’t formally prove anyway, even if you are right. Even if you are right, a million years from now, your argument with me will be pretty meaningless to you.
This is almost too crazy to reply to. Yet I will try. My argument with you will be meaningless to me within 30 years or so, optimistically speaking, but there are still reasons to pursue truth even if we derive no eternal benefit. Humanity is almost certainly not ending within the foreseeable future; these are not the End Times.
A sufficiently complex organ doesn’t rule out a natural ancestor, since we know of ways that complexity can arise gradually. Even if a natural ancestor were ruled out, that doesn’t tell us that the organisms containing the organ had no ancestors. As people have been trying to explain to you from day one, we are supposed to be talking about the reason for the nested hierarchy of life, not the causes of the features we use to discover that hierarchy. There is clearly no possibility that you will ever understand this. Yet I try.
Regarding why I believe the fossil record is young, I mentioned smooth contact domains and discrete changes in strata. That can clearly be seen below.
The bending of all strata is also telling. Perhaps more on that later. In the meantime, the colordo school of mines plus numerous actual laboratory experiments showed stratification is not created solely (if ever) by layering over millions of years, but by natural mixing and particle properties. Hence the layers become very disrete and distinct.
This video includes film from the Colorado school of mines. C14 levels in fossils is relatively invariant with depth, enough so to falsify the claim of Old Fossils.
When I joined the ID debate, I was a believer in Old Fossils. My views changed the more I pondered the matter. After studying General Relativity and Cosmology in grad school, YEC became personally more plausible as the Big Bang became hard to believe.
But, one can be a YLC (Young Life Creationist) without being a YEC. There are a few of these kinds of creationists. I was a Old Earth/Young Life Creationist for a while. Hermann Muller and Joe Felsenstein etc.’s work on mutational load added to my belief that at least for humanity, the human race is young. I began attending NIH conferences regarding ENCODE. Combined with Muller’s work and ENCODE and REMC/RoadmapEpigenomics, 4D Nulceome,etc. — many YLCs have become more adamant about the youth of humanity.
But not complexity such as the things I’ve described, starting with Spliceosomal introns. If you believe it, I acknowledge you believe it, but I don’t. I described what would make me find it believable, and so far no answers that would change my mind.
The fact I now think the fossil record is young really makes it unlikely I will ever accept the doctrine of Universal Common Ancestry. Common Design by an act of miraculous special creation seems the more accurate model of events.
In the OP and elsewhere I had complained about placing humans in the Sarcopterygii clade because humans don’t look like lungfish. Sure you can define the clade with Maximum Likelihood, whatever. After using MUSCLE alignment and boostrapping, the diagram generated by MEGA software on the following sequences is presented below. It accords with the complaint I made in the OP.
Anyway, first the sequences, then at the bottom the cladogram.
Click to enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2017/10/cytochrome_comparison.png
Makes sense, better to be consistently wrong. Next up why cigarettes are good for you .
stcordova,
Why do you keep sticking ‘universal’ in front of it? Surely we can talk of the phylogeny of finches, or terns, without getting bogged down in everything ever?
Anyways, if it has no ancestor, how come it shares so much else with the outgroup, barring the nominated differences? Duh?
stcordova,
What’s the point of spamming with an unformatted dump of sequences? Anyway, are we powerless to refine this picture? Is there nothing else we can look at that would resolve problem nodes? Anywhere?
Why does it need a miracle?
Below is the same data under a maximum parsimony tree (150 bootstraps) generated by MEGA software.
It looks to me like the arrangement a creationist Linnaean Taxnomy would have generated anyway in a Taxnomic Nested Hiearchy.
Click to enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2017/10/cytochrome_maximum_parsimony.png