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 I agree, so why did it take a thousand times as many and you still haven’t understood it?
Thanks for that textbook case of revisionism. You literally argued that phylogenetics must be wrong, because you thought it implied the ancestor was a jaw. In your own words:
“A jaw as the physical ancestor of perch, salamander, lizards, pigeon, mouse, chimp wouldn’t be a viable physical ancestor, but it is a viable conceptual ancestor!”
The implication being, that a jaw could not exist as a living organism. It would just be a jaw
But now you’re trying to make it seem as if you meant a creature with a jaw. But then your whole argument against phylogenetics collapses, because a creature with a jaw is an entirely reasonable and viable living organism.
But back to Rumraket demanding I show the conflict in nested hierarchies, particularly the conflict in the nested hierarchies of taxonomies vs. the multiple conflicted nested of phylogeny:
So there you have it taxonomy based on structure doesn’t agree with the ever changing phylogenetic trees. They said exactly what I’ve been saying in this discussion.
Now Rumraket demanded I give statistical significance to my claims. A duck is 100% a bird, it is 100% not a Sarcopterigian fish. A duck is as much a fish as a 52-year old man named Paul Wolscht is the six-year-old girl he claims he is. Eesh!
But not if it’s a jawed creature with fins when you need to get a jawed creatures with feathered wings instead.
Rumraket,
Rum, you presume people don’t understand because they disagree with you. Just because you are convinced in your own mind does not mean you are right. There are real counter arguments that you seem to be dismissing without a solid reason.
Exactly.
Now back to Rumraket demanding I demonstrate conflicts in the nested hierarchical trees. Here is nested hierarchical tree relating the organisms we talked about based solely on the defining characterstics mentioned earlier:
Sarcopterygii fish: lobed-fins
Birds: beaks, feathered wings
Marsupial mammals: mammary gland, pouch, primitive placentas
Placental mammals: mammary gland, sophisticated placenta, no pouch
I will show in a subsequent comment how this taxnomic nested hierarchy differs from the prevailing phylogenetic nested hierarchy.
Click for larger image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/12/vetebrates_based_on_structure.png
So I just showed a nested hierarchy based on taxonomy. Now I’ll show one of the buzzillion possible phylogenetic nested hierarchies.
The following is from
https://en.wikipedia.org/wiki/Actinopterygii#Classification
It should be quite evident the two nested hierarchies do not agree at all! Why? The phylogenetic tree is based on cherry picked data. When genes are put into the algorithms, they only uses genes that are in the species they want to build a tree on. This obviously doesn’t account for the genes and features that are in one group and missing in another! It’s cherry picking!
It fails to acknowledge fish don’t have feathered wings! This willful suppression of data in phylogenetic methods helps constructs phylogenies that accord with foregone conclusions. The claim that phylogenies agree with predictions is nothing more than saying “the phylogeny that we predicted was the phylogeny we created by cherry picking and fudging data”. They claim 100% agreement, or close to it. I learned how to fudge and cherry pick just like they did. I did so with the BMP2 protein which was in conflict with the more honest tree I built with the Cox1 protein.
Click below for larger image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/12/the_stupid_phylogenetic_tree.png
There’s no conflict between those trees. Does Salvador think that conflict means choosing different organisms to make one tree or another?
Classified as a wooden duck. It’s nesting is best explained by common design.
I’ve about given up on responding to Sal. He doesn’t listen, he runs a Gish Gallop, and he assumes he knows much more than the actual people in the field (any field). Also, he’s starting to remind me of Captain Queeg’s breakdown on the witness stand. Ohno = strawberries; you do the rest.
But anyway. As Entropy points out, there is no conflict between the two trees he’s just posted. Sal, I recommend you read a text on the subject, Tree Thinking, which among other things will teach you how to interpret a tree. Sal, are birds and mammals both amniotes? What about dinosaurs with beaks and feathers? Where do they go? What about Panderichthys, Tiktaalik, Ichthyotega, etc.; are they fish or tetrapods?
But seriously, I don’t know why I bother. Depressing.
They aren’t the same tree John. Birds and mammals may be amniotes, but they aren’t fish. You have’t figured that out yet? Ostheicthes are fish. The diagram doesn’t agree with structural similarities.
A fish is not morphologically a bird. Birds have feathered wings, fish don’t. Haven’t you figured that out yet?
From wiki:
Yes, recently published phylogenetic equivocations treat the Osteichthyes as a clade that includes birds.. It’s not like the data actually agree with the phylogeny since it is built on cherry pick features. Did it ever occur to you with the way you fudge and cherry pick data you could get the fish to be descended from the birds? Those phylogenetic trees would also be “conflict-free” from your definition since you cherry picked it from the same data set.
There’s a certain YEC who didn’t get his nickname “the human shit-stain” for nothing. Just sayin’.
Tiktaalik is poorly preserved mangled fossil. You’re going to build your case on this piece of mud (below). There ain’t a lot of soft tissue is there that can be examined in detail? That’s what I see evolutionists do. They appeal to the worst and most uncertain data points to defend their case because the can fill the uncertainties with any story they want.
A feathered dino doesn’t mean a bird is a morphologically a fish.
The problem is John, you have already conceded common descent doesn’t explain the emergence of novel complex features that have no ancestor. That’s blatantly apparent in the fact you build so many molecular phylogenies based on shared genes and thus cherry pick out the problem of genes not shared by the set of species under consideration. In the case of Tiktaalik and feathered dinosaurs, do you have gene sets to even look at? Nope.
So how do you deal with genes in birds that aren’t in fish and vice versa? You tell stories as to how they were lost and gained as the bird evolved from a fish, it’s not like the data actually show the evolutionary history outside of your cherry picking and fudging. I showed that with Cox1 vs. Bmp2. That pan-genomic diagram I provided earlier is amenable to almost any evolutionary story you want to tell depending on how you wish to cherry pick the pan-genome.
On the one hand you build these molecular phylogenies with the gene mostly being stable through out time with slight variations, and then you totally ignore the genes that sort of just pop up suddenly out of nowhere that don’t fit the model of gene evolution that works for your phylogentic algorithms! You totally ignore the genes that just popped up as well as the unique features.
So how do you account for the Lungfish and Coelecanth and Shark hardly evolving for hundreds of millions of years and yet one fish diversifies into frogs, giraffes, birds, and kangaroos? You don’t. You just tell stories. In that regard you’re little different from creationists.
Really? For starters, let’s just consider how arrange the tips of the tree beginning with Neighbor Joining. How do you Neighbor Join creatures based on genes and morphological features they actually don’t share? A lungfish doesn’t have feather or mammary glands, so on what basis do you put them so close to the Lungfish and Coelecanths?
That actually was a rhetorical question! 🙂
I’ll tell you how it’s done, you pick a gene or feature common to both and IGNORE the data that make the species look radically different. You do enough of that, and you can persuade yourself a giraffe is a fish.
So these molecular phylogenies that show we’re so similar to lungfish, were they don’t with genes that are shared between humans and lungfish or genes that were not shared. That’s another rhetorical question.
Sal, this isn’t working. There’s no point in talking to you. Maybe someone else wants to continue.
So how do you do Neighbor Joining with genes that exist in one species and not another. You shouldn’t, so you pick genes that are shared. So systemically you focus on similarities and ignore major red-flag differences. You don’t seem to see that as serious problem.
Instead you and Rumraket gave excuses like you can only do such gene trees if the genes are shared by all the species in question. True, but then that shows how illegitimate the method is.
Now that I asked a pointed technical question, you bail. Readers will be forever wondering then how John Harshman, professional phylogeneticist can do a Neighbor Joining in gene trees when the gene is missing in one of the species in question.
Getting too close to home of showing how professionals actually cherry pick and fudge the data eh? Of course you’ll bail now that it is blatantly obvious what’s going on.
It took me a while to figure it out, but the problem is now blatantly obvious enough.
Arrogance combined with willful ignorance is just to painful to try to deal with. I’m sorry.
Oh, you don’t have to respond for my sake, but maybe for the other readers here.
Of course you know that I know you got stumped. The rhetorical question again: “How do you do legitimate neighbor joining between species using genes that don’t exist in one species.” Answer: you shouldn’t!
So when you said the two trees don’t conflict, I simply called your bluff. But you come up with the excuse that you don’t want to respond to me rather than admit to the systemic cherry picking that has become such an industry standard now that you guys don’t even see it.
You could of course, if not for me, stand up for the other readers and set the straight by responding to the rhetorical question. If you’re honest with yourself, perhaps for the fist time in your professional career, you’ll admit there is systematic cherry picking for the simple fact you build gene tree phylogenies only on genes present in all the species under question. There is no problem doing this if you’re NOT trying to make the gene tree the same as the species trees — that is brutally obvious in the bacterial world where HGT is normative. It is a problem however if you try to extrapolate gene trees illegitimately to species trees. That’s how one will come up with absurd implications like Axel Meyer that tetrapods (like giraffes) are fish.
It took me a little pondering as I was reading Joe’s book and doing the molecular phylogenies from scratch to see the forest through the trees.
But lest you think I’m the only one who sees this problem, I’m not. I alluded to it with the reference to the conflict going on in botany between the phylogeneticists and the old school taxonomists.
And then that remarkable chapter 10 in Joe Felsenstein’s book where he provided competing perspectives by researchers who dismiss some of the statistical phylogenetic methods being used in practice.
From page 144, Joe quotes an opinion contrary to the practitioners of statistical phylogeny:
and from page 139 from Eldredge and Cracraft (1980, p. 69):
Synapomophies? Hmm, like mammary glands or the placenta that are on the life critical path of features of placental mammals? Synapomorphies that distinguish mammals from fish? That’s one reason a giraffe isn’t a fish.
So why would Axel Meyer think “we’re Sarcopterygiian fish”. The cherry picking is built into statistical methodologies that require phylogeneticists to use only genes present in both species to build their gene trees. Of course the inferences from such will be skewed as a result, and one can persuade oneself a giraffe is a fish — after all the calculus of probability and statistical molecular phylogeny demonstrate that to be the case from cherry picked genes, backed up with bootstrapped Maximum Likelihood computational algorithms.
Of course, John, you could admit I have a point, but you won’t do that, so you’ll bail out of this discussion on the pretense that I’m arrogant. Forget the readers who actually might want to hear your counter argument to what I just said.
Neil and Alan must love Adapa. He hardly ever posts links to parts of the human anatomy.
And he NEVER makes claims about evolution being falsified.
Nope. That is not what readers will be left wondering. I, for one, am left in awe of John’s incredible patience and kindness in the face of Sal’s…errr…. “behavior”.
DNA_Jock,
Yep.
In Sal World, the only legitimate phylogenetic inference would be one in which there are no differences. All differences are a ‘red flag’, and we can just cheerfully ignore those pesky runs of genetic identity – yea, even unto the 99th percentile. Pick those cherries, Sal! Pick ’em good!
He has been guanoed often. That particular comment didn’t hit my threshold.
It’s not arrogant nor ignorant on my part to point out a giraffe isn’t a fish and the reasons why.
Moved a comment to guano.
That one did meet my threshold.
it’s not that you shouldn’t, it’s that you couldn’t. The trees you’re talking about are based on the similarities and differences among shared genes. If you cannot align the sequences, then the methods won’t work. You’ll get nonsense. You might as well take random sequences.
Using shared genes is not cherry-picking, it’s taking the sequences that have information to tell you the relative divergences between the organisms under analysis.
Nope. The method does what the method is supposed to do. If you want to do trees with other kinds of information, then don’t use one that’s based on aligned sequences.
It doesn’t make sense Sal. Aligned non-shared genes would give essentially random distances. Do you really not see this?
No Sal, what’s obvious is that you don’t understand what you’re doing. When we choose a measure stick for an experiment we choose the stick that has the proper resolution to the problem we want to approach.
Completely different genes aligned to each other will not give you relative divergences between the organisms that have them. They’re nonsense in that regard. We choose shared genes because, by being present in all organisms, their differences should have some relationship with the times since divergence between those organisms. It’s obvious!
The problem is that you really don’t understand what you’re doing, and you don’t understand that it doesn’t make sense to try and align unrelated sequences. I find that blatantly obvious. So much so that I’m lost as to why you don’t see the problem.
Actually phylogenetic methods ought to be quite powerful when the Neighbor Joining is legitimate. On what grounds can we establish the Neighbor joining is legitimate? When the members of a group can breed with each other, as in humans with other humans.
It’s not legitimate to cherry pick and thus create an illegitimate Neighbor Joining when one group of speices has placentas and the other lays eggs. Sheesh! But systematic cherry picking has become so much the norm the problem is not even given a second thought, and the result is people believe giraffes are fish! With the amount of ad hoc rationalizations used to justify that, one could easily concoct another set of ad hoc rationalizations and argue fish are giraffes!
As Matzke rightly said:
I told him that over a decade ago. He disagreed in 2006, then in 2013 he finally saw the light.
Because Sal doesn’t believe in it. The yolk protein pseudogenes in mammals mean nothing to him, because they indicate evolution, and he ignores any evidence for evolution except for whatever he thinks his ignorance deconstructs.
For Sal, cherry-picking to fit his pseudoscience is the main rule. It’s why the Job-like patience of even John Harshman wears thin over time.
Glen Davidson
I actually have this book and can see that Joe quote-mined them.
stcordova,
I keep forgetting that Salvador put me on ignore. Seems to be his method for ending discussion. When he looks rather wrong, he ignores. Now he must be right!
Now some tidying up of things John Harshman raised. He asked how does Common Design predict the nested hierarchy?
Common Design doesn’t predict the nested hierarchy will be there, but it doesn’t predict it will not be there either! The same could be said for the theory of celestial mechanics. Celestial mechanics doesn’t predict a nested hierarchy of life will be there but it does not predict it will not be there either.
John, like so many things in this discussion, is making a false assumption that a claim of common design must necessarily make predictions about the presence or absence of a nested hierarchy. The fact it doesn’t make one prediction either way doesn’t falsify the notion of common design.
The evidence of common design is simple: “God must have done it because evolution can’t.”
John bailed out when I challenged him on the mechanistic feasibility of mutation and selection to create complex novel features when he said common descent doesn’t explain the origin of new features.
Since complex novel features with no mechanistically feasible ancestors are incompatible with common descent, there was no common descent. Simple as that. Since there was no common descent, this implies the patterns of similarity must then be explained by common design.
I think The Evolution of Phylogenetic Systematics would be better.
You’re actually off my ignore list now that John has bailed out. So you must be wrong! 🙂
In any case, welcome back. Hugs.
Mung,
Mung is off now off my ignore list too. Merry Christmas!
Sal can’t come up with sound evidence for common design, so he resorts to the false dilemma fallacy without even managing to show that “evolution can’t.” He, of course, can repeat this garbage much longer than we can stand to point out its idiocy and dishonesty.
Meanwhile, he ignores all of the evidence against design, like the absurd journey of the testes from their ancestral position in mammals, while birds manage to keep testes within their body cavities. The stupidity of the brilliant designer?
Sal never explains anything, just runs through the ID fallacies as if they were ever anything but BS for the rubes. Which suggests that he’s really only here to impress whatever rubes he might send this way.
Glen Davidson
Thanks Sal. Merry Christmas to you too.
In case you’ve missed it, I’ve been arguing that you have a point.
🙂
A theory that doesn’t explain the differences can’t claim to explain the nested hierarchy because it is the differences that create the nesting in the first place.
Glen is off now off my ignore list. Merry Christmas Glen!
stcordova,
Interesting. OK, then please read my answer. I doubt it can be clearer than that. There’s no cherry-picking.
Let me know if it’s still not clear to you, and point to the main thing that looks unclear to you.
Exactly. Especially the radical ones like placentas and mammary glands or anything on the critical path of survivability.
The phylogenetic gene trees that are built with statistical algorithms don’t have a model for how the genes arose in the first place. It’s kind of a POOF and go model without admitting that it is!
Next they model the genes as slowly evolving with point mutations and an insertion or deletion here and there. The problem is, right there in that model, there is not much of a consistent way to create radically new genes!
Phylogenetic methods work well on things that can actually breed together, it doesn’t work well when for explaining radically new features.
Well, that would put an enormous amount of work on your shoulders. Of course, there’s the false dilemma. But then, you are claiming a universal negative, as if you knew and understood every possible thing that could happen, or not, in evolution. I don’t think you want to go there.
stcordova,
Don’t forget to check my comment above Salvador. Please check for what you don’t understand so that we can solve this issue.
The problem is with the method, not the data that says the species are dis-similar with respect to that gene. Not accounting for the fact a gene is missing in one species and present in another is cherry picking. This is analogous to ignoring the fact placental mammals have placentas and fish don’t. You ignore all the features that aren’t shared by a creature, and you can aggregate them in not very proper ways — such as claiming giraffes are fish.
Entropy,
Of course I could point to a protein that confirms my argument, Cox1. I can re-do this one any number of ways, but it will be about the same result because the distance matrixes show that it’s a good approximation of what creature should be NEIGHBORED with another in this diagram of vertebrates. This is one protein that will likely cherry picked out in publications because it doesn’t agree with the cherry picking of the prevailing viewpoints.
Click to Enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2017/10/nj_differnces_circled2-11.png
Based on the description, I don’t think so. A simple education on what phylogenetic trees mean and how to interpret them is the first thing Sal needs. Why do you think that book would be better? Have you read it?
It looks to me like the book covers a simple education on what phylogenetic trees mean and how to interpret them.
I have not read it but am seriously considering purchasing it.
It’s less expensive then Tree Thinking and it’s available on Kindle. It appears to have a broader scope and to include coverage of just the sort of questions Salvador is raising. To me, historical background is always important.
Plus, the single review on Amazon say’s it’s great. 😉
So why would you say it’s better than Tree Thinking, given that you are not familiar with either? Sal’s issues arise from incomprehension. The clearer and more focused the explanation, the better, and extraneous material would only confuse him. Not that reading anything does him any good, as he has shown by his reading of Inferring Phylogenies. He’ll just pick the bits he can misunderstand as supporting his position and ignore the rest.
Added note: I’ve just read the introduction, which describes the structure of the book, and the book doesn’t discuss anything that would help Sal understand phylogenetic trees.
Yeah, Darwin’s theory was a theory of “descent with modification,” not a theory of “decent without modification.” If it doesn’t explain the modifications it may as well be a theory of creationism.
Now you’re describing a theory of evolutionary change, as opposed to a theory that explains why there is a nested hiarchy.
You keep confusing these two. They’re related and in combination explains both the nested hiearchy in the patterns of similarities and differences among species, and how these differences arise in the first place. But they’re not identical, and they actually have different areas of explanatory scope.