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.
Here is some info on Jeanson and some of his publications including an article in the prestigious scientific journal Nature:
Jeanson made some arguments regarding MRCA’s a variety of animals. His writings are very technical, I’m still trying to slug through them.
Rumraket,
So now you are making the claim that echolocation evolved. Are you aware there are different types of echolocation in bats?
How far back can these MRCAs be traced, i.e. what is a “kind”? How do you recognize when a phylogenetic analysis has passed beyond a “kind” boundary?
stcordova,
Most of those publications seem irrelevant to the claim you made for them. Did you just cut and paste from a CV?
Rumraket,
Yet you have to use these mechanisms to explain echolocation in Whales and not the ancestors.
How many times does it have to be explained to you that the origin of innovation is a completely separate question from the origin of the nested hierarchy of life?
Incidentally, are there in fact any “echolocation genes”? If so, do they have no homologs in related species? And are you aware that many mammals are capable of echolocation, including humans?
John Harshman,
How do you claim a nested hierarchy when innovations are not inherited but skip generations? You like Rum are sweeping contradictory data under the carpet.
Quit making shit up.
You manage to sweep all of the data of relatedness plus the evidence of evolution from the geologic record under the rug based on your unsupported claims that convergence is contrary to common descent along with idiotic BS like innovations skipping generations (I don’t even know what stupid idea lies behind that moronic claim, although I think it goes back to some of Sal’s nonsense).
Have you ever even considered the evidence as anything but the enemy to be fought with all of your ignorance?
Glen Davidson
petrushka,
I would say ‘no’. There’s nothing about the horizontal/vertical distinction that precludes treating the gene as the unit of selection.
What exactly do you mean by “skip generations”? Where do you find any such thing?
colewd,
What the fuck?
We can analyze accepted species for MRCAs. Example: coeleacanth and lungfish, certain bacteria.
I don’t know precise boundaries, but a cow doesn’t belong in the fish clade. But exact precision of the boundary isn’t necessary. Example: several bacteria share the same aaRS genes. Therefore, based on accepted clocks and INTRA-species (intraspecific) divergence, when was their aaRS MRCA.
I’m interested in plotting the extant Sarcopterygii genes with that of mammals, it may or may not state the point I’m trying to get across in the OP, namely, we don’t belong in Clades defined by Sarcopterygii or Teleostomi. As Nick Matzke said and which I called him on:
In the diagram below it describes half-correctly the work of creationist and ID proponent Linnaeus:
http://universe-review.ca/I10-02-Taxonomy.jpg
This was right:
this was wrong:
Primates don’t belong in a fish taxonomy, neither morphologicially nor in molecular taxonomies, it only appears there in phylogenies and that is one of the many reasons I reject mainstream phylogenies.
I believe in an Orchard model of created kinds and phylogeny is valid there, but don’t know the precise boundaries save to say, a cow doesn’t belong in the fish grouping, etc. I would not expect a fish to give rise to a bat (which is what evolutionary phylogenists claim), but I would expect a fish kind to give rise to another fish, that is what creationist “phylogenists” would claim. The main difference is that creationists have much higher regard for Orphan systems precluding Universal Common Ancestry.
But back to more technical matters, starting with PHYLIP or whatever, do you create radial diagrams like the one I made? What software do you use? I don’t like the cladogram representation as much as the radial or axial representations.
Or at the very least, the cladograms I get don’t look as symmetric as the radial diagram for what I consider symmetric distances. I may elaborate later on that complaint.
I should point this out:
https://academic.oup.com/mbe/article/19/9/1637/996854/The-Paradox-of-the-Ancient-Bacterium-Which
This is evidence again of Young Life Creation (YLC) not necessarily Young Earth Creation (YEC). All YECs are YLC’s but not vice versa.
This geological issue can be applied to extant bacteria. If a species of bacteria is 250 million years old, then why should their genes be so similar between species and also between individual members? It shouldn’t using mainstream assumptions of neutral theory. That is if one says certain sections are subject to neutral mutation between species, then the same should be true between individuals of the same species.
The problem of lack of similarity in the above referenced paper is a big red flag for individuals of extant bacteria within the same species.
Less of an issue, but still an issue is that of cycads, lungfish, coelacanths, horseshoe crabs and other “living” fossils that should have so much more intra-specific divergence.
Creationists have referenced Joe Felsenstein’s work, even PHYLIP, even though Joe isn’t a creationist.
Here was a thread on one matter of particular interest to creationists who use Joe’s Phylogenetic methods:
Actually it has significance to the issue of YLC and hence indirectly to Common Design vs. Common Descent.
Anyway Wiki wrote (back then):
Joe was kind enough to respond:
The irony is, creationists have some eagerness to learn and use some of the tools Joe has created, perhaps even his PHYLIP suite, but definitely not in the way he intended!
No, it isn’t.
It’s independent of evolutionary mechanisms. It certainly is not independent of mechanisms of inheritance/heredity.
And that’s why evolution does not predict a nested hierarchy.
Not a Chance
I have no idea what you meant by that. How did it answer my question? Are you claiming that “kinds” are species, in contradiction of your source, Jeanson?
So, in other words, you have no idea.
[not clear what Matzke said, what Sal said, or what someone else said]
However, it’s true that phylogenetic analysis doesn’t determine direct ancestry, i.e. real species are at tips, not internal nodes. What you think that means is unclear, but I think it’s something incorrect. It’s simply a limitation of our ability to draw certain conclusions from data. But not other conclusions.
I don’t think Matzke acknowledges what you think he does, since what he said (if I can pick his statement out of the mess) seems uncontroversial.
In the next bit, you are confused by words. The phylogenetic species concept has little to do with phylogenetic analysis or phylogenetic systematics.
And yet you accept that there is such a thing as a vertebrate, right? Don’t vertebrates include both fish and primates? What’s the conceptual difference between Vertebrata and Osteichthyes? And the fact that counting primates and carp in a common group offends you is not evidence against that group’s validity. If primates and carp don’t belong in the same group, why are they consistently put together in phylogenies constructed from different data?
In other words, you are completely unable to say where valid phylogenetic analysis ends and invalid analysis begins. If there were real created kinds, wouldn’t we expect some kind of sharp and obvious dividing line?
It hardly matters, as you will misinterpret the display either way. Better to concentrate on meaning than graphics.
I thought DNA-Jock won the “Darwin Award” for trying to explain to Salvador how temperature affects heat capacity.
If only Sal had read Denton’s new book.
The Wonder of Water
You have still not managed to figure out that the amount of intraspecies divergence doesn’t reflect the time of formation of the species (remember coalescence?), and that none of these so-called “living fossils” is unchanged from its ancient relatives, either morphologically or (especially) molecularly.
How do you determine how much intra-species divergence a species should have?
Allan probably didn’t mean what you think he meant. Didn’t he already try to explain that to you?
Why can’t genes acquired by HGT be inherited just like any other gene? In fact, how would we even know HGT took place if that were not the case? And that inheritance is vertical.
Allan is probably using “descent” in two difference senses, and you seem to be convinced that just isn’t possible. I beseech you, in the bowels of Christ, think it possible that you may be mistaken.
You’re the one who forgets that I pointed out situations it’s absurd to apply coalescence theory, like when Ne is large and unstirred.
Yeah, like between Eukaryotes and Prokaryotes, between crabs and giraffes. Flowering plants and gymnosperms.
Enough data, we might see the dividing line in doubtful cases like say in cats.
As far as humans go, I think I can tell a human from most other primates, can you? 🙄
You persist in bringing up irrelevant points that you think are zingers. This is at least closer than your attacks on Nick Matzke, who isn’t even here. I don’t think you really should be building up your ego at others’ expense. It’s immoral. And, which may be of more concern to you, transparently futile.
Do you understand that divergence within the species you mentioned depends on coalescence, not the age of the species or lineage?
Are you claiming that eukaryotes are a created kind? That prokaryotes are a creates kind? That crabs and giraffes are created kinds? That flowering plants and gymnosperms are created kinds? If not, they aren’t relevant. You really aren’t very good at this “argumentation” thing.
What sort of data would be required? How would you recognize that line? And do you think cats (presumably you mean Felidae there) are multiple kinds?
Ah, so if you can tell them apart, they’re different kinds? Great. I can tell a lion from a tiger, therefore they’re different kinds, right? Or does the emoji indicate that this sally actually meant nothing? When will you make real arguments?
Mung,
Who said they couldn’t? I made that very point here:
Mung:
Um, no. I addressed that possibility here:
No, I’m claiming that kinds within prokaryotes and kinds within eukaryotes can’t be the same kinds. So there is a dividing line which you seem to insinuate can’t be readily determined.
But anyway, what phylogeny software would you recommend to TSZ readers. Surely we don’t need some gigantic system for certain phylogenetic questions.
Nope, because they can interbreed today.
You think humans and chimp ancestors interbred, fine, how about a detailed description of the architecture of such a creature which would resolve the serious morphologocial differences.
Do you understand coalescence is inapplicable for large unstirred populations like say where the number of individuals (as in bacterial) could be in the pentillions spread around the globe and unstirred?
Refer to equations 4 and 5 to see the point I’m trying to explain, if not exactly, close enough:
https://qgsp.jouy.inra.fr/archives/vareff/vareff.pdf
I also pointed out, unless there is stirring of the population, coalescence can’t take place. See the diagram in Dave Carlson’s paper as that shows the problem I refer to if you’re willing to see it.
Jeanson and I have different views on species, but his work (started by Rob Carter) on the genetic clocking issues I think is highly promising.
I talked briefly with him about the aaRS genes. That work has not yet begun by anyone, so like the nylonase project, some of the early foray into the subject is explored on the internet in places like TSZ.
And btw, the nylonase project is now highly regarded by creationists that would actually understand the manuscript I and John Sanford co-authored, not to mention I think it is good enough for secular publication after some overhaul. I see no major errors in the fundamental points.
No, that’s not the dividing line. I’m talking about the dividing line between within-kind and between-kind similarities/differences. The fact that you can’t identify such a line is evidence that there isn’t one, since it ought to be obvious.
PHYLIP works just fine for many questions. And it’s free. It would be nice if there were a nice GUI-based, user-friendly program. But there isn’t. I have most frequently used PAUP.
That doesn’t answer the question. Jeanson (with no expressed justification) appears to think that kinds are mostly families. What do you think? Can you in fact identify any kinds at all?
No, but I think I can identify what sets of species are not kinds, and that is good enough for my purposes, but not for yours. I hope that answers your question directly.
Thanks for the info on PAUP. Thank you for taking the time to dialogue. I hope you got something of value out of the discussion.
As for myself, I need the phylogeny stuff to beef up my nylonase paper, so this is immediately relevant. So thank you for the pointers. Much appreciated.
No, I don’t. Coalescence happens in “unstirred” populations, if I understand what you mean by the term. It certainly depends on population size, but bacterial populations are not of constant size and certainly experience both bottlenecks and selective sweeps.
I don’t see what point you are trying to make with those equations. You will have to say what you think the point is.
What is Dave Carlson’s paper? More importantly, how is any of this relevant to cycads, lungfish, coelacanths, and horseshoe crabs, which are the subject in case you have forgotten?
So your whole thing about being able to tell humans from other species was meaningless. OK.
No, I think human and chimp ancestors were a single population at one time. What serious morphological differences are you talking about? Why aren’t australopithecines good intermediates? What does any of this have to do with how you would identify kinds?
Your hope is in vain. I don’t think you’re capable of answering questions directly. You can’t identify what sets of species aren’t kinds either, because that would be exactly the same as identifying kinds. What you really mean is that you know some particular species belong to different kinds from other particular species, but those species are so far from each other that this supposed knowledge is operationally useless.
If you want me to get anything of value of the discussion, start answering my questions rather than ignoring most of them and dodging the rest.
I said, “NO”! How is that not a direct answer?
The part after “but” obfuscated to the point that “no” was meaningless. Perhaps you intended otherwise, but that was the result. So why can’t you identify any kinds? Shouldn’t they be obvious?
Sal,
The elephant.
I can’t identify them to your satisfaction, but not having a detailed description doesn’t mean they don’t exist, people familiar with math understand this, and FWIW, you believe in ancestors that you don’t have a description for either!
The existence of orphan systems is what I would consider delineation of what sets of creatures cannot be of the same kind (like fish and butterflies), therefore the kinds by way of inference exist even if we don’t know exactly what they are.
There are two creationists schools of thought and neither school gets along that well with the other.
The YEC Baraminologist Model Builders: Todd Wood, Kurt Wise, others
The YEC Anti-Evolutionists: typical creationists like me, John Sanford, others
The Anti-Evolutionsts believe in kinds, but we don’t focus our efforts on trying to identify them. We can identify gaps that would delineate groups of kinds. We don’t get along too well with the Baraminologists.
Btw, I just downloaded PAUP. Can’t say when I can get around to using it. I tried Trex and Clustal Omega. Clustal Omega creates cladograms I find hard to read relative to the radial diagrams, it doesn’t create radial diagrams.
Thanks for the pointers.
You mean to say you can’t identify them at all. Why not? Now, I believe in ancestors (and I can describe them in many particulars based on phylogenetic reconstruction, but that’s not relevant) because their existence is the only explanation for the nested hierarchy of life. Why do you believe in kinds? You can’t give me anything for that.
Sorry, that doesn’t work. You have to start by identifying particular “orphan systems” (a vague and deceptive term) as diagnostic of a particular kind. You have to explain why these also define groups larger than kinds, presumably, and perhaps also groups within kinds, if you ever get around to declaring any kinds.
Why do you believe in kinds, if you have no interest in the evidence that there are any?
Clustal is not a phylogenetic analysis program, though it will do quick and very dirty analyses on its alignments. You shouldn’t take them seriously. Then again, you don’t take any phylogenetic analyses seriously, do you?
A quick response to Salvador Cordova’s questions about use of PHYLIP. The PHYLIP file format for aligned sequences is actually rather tolerant of extra spaces, unless one makes a sequence name too short by having too few spaces at its end.
For sequences of unequal length, you need to align them. ClustalW will do that. Then you can tell it to produce the output file of aligned sequences in PHYLIP format.
Once the sequences are aligned, there are many programs that can analyze them, from PHYLIP, also PAUP*, MEGA, MrBayes, and RAxML.
Also, a comment on baraminology. I am in favor of it. Keep on building those trees, baraminologists! They will get bigger and bigger and bigger, until finally Noah will need on the Ark only one bacterium, one archaean, and one eukaryote. That will make the Ark easier to build …
Joe,
It’s even easier than that. Noah and his family are eukaryotes, and their gut flora can provide the bacteria and archaea. Once they load themselves onto the Ark, they’re set.
A bit of evolution after the Flud will take care of the rest.
@keiths: Problem with that is, the eukaryote has to be single-celled so they can hyper-evolve into all the other eukaryotes in the very short time available.
Thank you Joe, that was very helpful. I appreciate the info, especially form the author of PHYLIP himself. 🙂
Neither have you yet that seems of little concern
newton,
Theobald is trying to establish common descent independent of mechanism. Echolocation just happens to be a new feature that appears in both bats and whales. This is just one on many new features that appear, others are sight, and flight.
Since new features are not expected from inheritance how do you explain this anomaly as part of the model of common descent?
New features are not part of the model of common descent. It’s the nested hierarchy of new features that offers evidence for common descent. And new features aren’t anomalies. Almost all “new” features have precursors, and echolocation is no exception. Most mammals, notably including humans and shrews, have some capacity to echolocate. Bats and cetaceans have just developed this ability to a greater degree. How is that surprising? Sight and flight aren’t mysterious either.
Especially the nested hierarchy of orphan features with NO traceable ancestor. 🙂
No, not especially. They’re just as good as any other feature, but no better. And there aren’t very many such features. By the way, emoticons annoy me; words are better at communicating.
ID/creationism, the “science” of non-evidence and outliers.
It really is very nihilistic.
Glen Davidson
Ahem, enough such features to create Darwin’s abominiable mystery of flowering plants and the potential of large number of orphan genes and systems. We don’t know as much as you suggest we know. The more we learn, the more orphans we discover. In fact we have quite enough such orphans to create very nice nested taxonomic hierarchies.
In any case, it’s a non-sequitur to say orphans of any complexity prove common descent. That’s nonsense.
Sorry to annoy you, no disrespect intended, but well, that’s my communication style. I don’t fancy myself as a scholar, just a trouble maker.
That’s not to say I won’t try to meet you half-way as best as I can. But you can bail out of this discussion anytime if you find more enjoyable company.
But on a related note, I just got this pointer from someone at the NIH. Phylogeny for non-specialists:
http://phylogeny.lirmm.fr/phylo_cgi/simple_phylogeny.cgi
What do you think?