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.
First the neighbor joining tree, shark rooted. The computed caption:
click link to see enlarged image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/shark_rooted_nj_tree_v1.png
Next the ML tree, with computed caption:
Click link below to see enlarged image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/shark_rooted_tree_ml_tree_v1.png
Exactly. I was taking Sal’s definition of orphan as something “not present in everything else” or “taxonomically restricted to group/species X”.This can be applied even to single nucleotide mutations.
I would venture a strong guess that a gene or even organ/bio-system absense-presence-based phylogeny would correlate with phylogenies derived from orthologous genes.
To the extent the “organ/bio-system absense-presence-based phylogeny” agrees with the Linnaen style typological taxonomies, the phylogenies computed for orthologous genes I expect should generally match.
But as I’m trying to show, with the cytochrome-c, the “organ/bio-system absense-presence-based phylogeny” of the paleontologists does NOT agree with either the Linnaen style typological taxonomy NOR even the computed molecular phylogeny of cytochrome-c orthologs. The Typological Taxonomy agrees more with the computed molecular phylogeny than the narrative that we evolved from a lungfish-like, coelacanth-like creature.
Yeah good luck with that. Try including more species btw. Do it with fifty, or a hundred (okay maybe that’s extreme). And get a wider coverage of the eukaryotes. Get some fungi, mulluscs, crustaceans, a couple of primates, some whales, some felines perhaps, some birds, some reptiles, your fish, and so on and so forth.
Stop cherry picking.
It is an observational fact that it varies.
You understand what “observational fact” means right?
Mung,
This is far easier than you seem to be making it. You, who accept common descent, don’t even understand the rationale for it.
Differences aren’t indicative of common descent. But a difference, when inherited by an entire clade, becomes a similarity in that clade.
Species 1: AAAAA
Species 2: AAAAB
Species 3: AAAAB
B is a difference when considering all 3, but a similarity when considering the latter 2. The simple inference is that all share a common ancestor which did not have B, and that 2 and 3 have a common ancestor which is not an ancestor of 1.Of course other scenarios – other phylogenies – may in fact be the reality, which is why one is better off looking at more data. But, I don’t see why the basic logic of this causes Creationists to blink so furiously.
Mung,
You choose. I mean, you could probably make a reasonable estimate yourself using basic statistical inference – how likely is it that a particular alignment would result from common descent rather than ‘random’ factors. This is bog standard stuff – the kind of threshold decision scientists in many fields make all the time without Creationists getting all haughty with ’em.
Rumraket,
Yeah, and specifically-located SINE inserts 🙂
The constant molecular clock assumption is particularly unwarranted when it comes to something like cytochrome c. What’s remarkable, though, is that you can take a gene that has precious little to do with the ‘form’ of the organism (yeah, I know, apoptosis; irrelevant), and recover anything even close to the morphological tree. And do it again with another gene. Try an intron, or functional RNA, you’ll get the same. Curious, innit?
I don’t now, but that is the quote that Sal cited at me when I asked why God was being oblique about the evidence for design. So I guess he thinks it has some relevance in this context.
I thought the job of common descent was to explain how the actual distribution of distinguishing characters among species came about. You’ll get the correct phylogenetic tree as an added bonus.
BTW, I do not see what unguided evolution has to do with this.
Could you put whales in there? I am really curious where whales end up. Whales are fish in the real TAXONOMY right?
It’s unwarranted because outgroup comparisons show that it is. You can’t just assume a clock. You have to first show a reason to believe it.
No it doesn’t. That study shows a monophyletic Sarcopterygii that includes tetrapods.
Why, it’s downright miraculous!
If you’re opposed to a certain inference, anyhow.
Glen Davidson
stcordova,
Interesting. I don’t know what’s happening here, but note that when you include the outgroup you can see that mammals are evolving faster than other taxa, so there goes the clock.
It isn’t clear to me why you are still not recovering the same tree that your favorite 43-locus paper does. Perhaps, despite all your BLAST skills, you are using non-orthologous sequences. Perhaps you still don’t have enough taxa. I sincerely doubt that it’s because cytochrome c is different from all other genes.
OK, Sal, I’ve spotted one of your problems. At least some of your sequences, probably all of them, aren’t cytochrome c at all. They’re cytochrome c oxidase I. You do know that’s a different protein, right?
No, it doesn’t. Your inability to read a tree is getting in your way here.
Yes I do, and apparently you’re in denial. You whined about the me dropping the shark gene. Well I put a shark back in, and even higher quality sequence to boot. You whined about more tetrapods. Well I added one, I could add more, but how about you tell the readers if you think such changes will somehow put the tetrapods into the Teleostomi clade?
You whine about mid point rooting, and not having the shark as the outgroup. I put the shark in as the out group removed the midpoint rooting. Did it put tetrapods in the postion of the Teliostomi clade? NO NO NO!
For the readers benefit. This is the teleostomi clade:
https://en.wikipedia.org/wiki/Teleostomi
The clades under it are:
Actinopterygii (ray finned fishes)
Sarcopterygii (lobe finned fishes)
Actinopterygii (ray finned fishes) include salmon and strugeons. Now look where the salmon and strugeons are in the diagram!
Sarcopterygii (lobe finned fishes) include coelcanths and lungfish and supposedly the tetrapods. The Coelecanths and Lungfish are there but the tetrapods are — Yikes kind of in a sister relation under some vertebrate clade, just like the Linnaen taxnomy. Gee, that seemed to be comparable to the conclusion of a molecular study I cited with 43 genes, but that study didn’t come right out and point to the even more devastating conclusion.
Then Allan Miller weighs in on other matters rather than actually deal with the generated cladogram.
C’mon John, if you really wanted to refute what I’m saying, you’d do the data runs yourself with sequences of your choice, but you won’t. Maybe deep down you know that whatever you do, short of sketchy data manipulation, those tetrapods aren’t going to end up under the Teleostomi clade.
Posture and bluff all you want, but you and I know who is holding the stronger hand in this round.
It should be fairly evident in light of not just this data but studies that included the 43 genes that tetrapods don’t nest within Teleostomi nor should they belong in Sarcopterygii.
You can’t make this up.
You need to look at that study again. Try harder to read and understand the tree.
Well, how about that, I actually used a different gene than cytochrome C. Thanks for the fix and correcting my mistake.
But you know the hits are still likely homologous right, they are just a different gene. But now I will be more methodical. I’ll select high identity entries.
Any bets whether it will put Tetrapods into Sarcopterygii? One way to find out is to redo with Cytochrome C Oxidase I. This time, I realized I can leverage Entrez to get good orthologs.
Thank you for the free-of-charge technical corrections. I’ll do a run in short order. Then we can try some other genes.
For a change this was a good discussion.
stcordova,
Wha? I was responding to points made. Points made by, among others, you. There is no point me joining in on the cladistic detail; it’s John’s field.
But I like cherries.
LOL. Yeah, why can’ t you stay on topic, like Sal does 😀
Corneel,
Heh heh. Yes, that was a bit rich!
Since I’m rebuilding the first Cladogram on Cytochrome-C Oxidase rather than Cytochrome-C, here are some technical details. I chose the gene because it had some nice size, it coded for something with 520 residues.
Nothing is stopping me from also doing a cladogram with cytochrome-C or other genes like RAG1.
Anyway, thanks to John Harsman for his technical correction of my mistake as it will improve the quality of the discussion about my hypothesis that Tetrapods should not nest in the Teleostomi clade and that saying Tetrapods are Sarcopterygiians is an equivocation and abuse of labeling, it doesn’t match the spirit of what is actually represented in phylogenetic gene trees.
https://en.wikipedia.org/wiki/Cytochrome_c_oxidase#/media/File:Cytochrome_C_Oxidase_1OCC_in_Membrane_2.png
It’s actually a beautiful looking protein.
Allan Miller,
Sorry. My apologies.
stcordova,
Not a problem,. I don’t take this all that seriously!
This should be a wakeup call for you: you are not competent to do what you are trying to do. Ignorance is not a fault, but the arrogant assumption that you aren’t ignorant certainly is. You will have to learn a lot more before you’re capable of doing what you’ve been claiming to do here.
It’s not just a different gene, it’s a mitochondrial gene. In animals, mitochondria evolve much faster than nuclear genes. This means that in order to get a decent analysis you have to work much harder. You may need a better model, and you certainly need a much denser taxon sample, in order to achieve reasonable results.
Again, you need a much bigger taxon sample before you can hope for valid results when you’re using mitochondrial genes.
Unfortunately, you don’t seem to be drawing the proper lesson.
stcordova,
We might wonder why there’s a squid-specific way of passing an electron, and a rabbit way, and a shark way … as I’ve said before, I find it remarkable that low-level (albeit vital) function can get anywhere near convergence on the morphological tree – lactate dehydrogenase, DNA polymerase – as well as this intron, that SINE … they all vend to vary in this same curious way in taxa. And not just in ours.
“The spirit”?? What do you think you mean by that? Tetrapods are sarcopterygians because Sarcopterygia shows up as monophyletic on phylogenetic trees; pretty much all of them except for your little attempts here.
Sal, to John:
This is Sal’s go-to defense mechanism when someone corrects a stupid error of his. He should be thinking “I just got my ass handed to me”, but instead he tries to spin it as if he’s pulling one over on his opponents by getting “free-of-charge” corrections.
Hopefully ALL of them are cytochrome c oxidase, which means they are homolgous which means the diagram stands, I just mislabeled the gene, but a rose is a rose by any other name. The other proteins in the UNIPROT listing where I got them from were 5 times smaller, so it’s likely I did hit the actual homologs.
However, to that end, before I move onto creating cladograms of other genes, I’ll go through the Cytochrome-C Cox1 more methodically.
METHODS and MATERIALS
To find orthologues of the gene of interest I start with this Cox1 which was the first entry used to generate above cladograms:
Then it’s a matter of BLASTING it against individual species and confirming I get the orthologous Cytochrome-C Cox1. This time I will attach accession numbers that readers can use to confirm the entries in Genbank.
Here’s a cytochrome c-based phylogeny simply from the Uniprot “Tree” feature it makes when you get an alignment. I have no idea what kind of algorithm it uses to make the tree from the alignment.
But it all looks fine to me. I just found a host of (actual) cytochrome c sequences and asked it to do the alignment.
http://www.uniprot.org/align/A20171110F725F458AC8690F874DD868E4ED79B88D77E3EP
The bacteria are all the most distantly related to each other and to everything else. I suppose this could indicate they might not be cytochrome c’s. Some of the annotation is horrible for bacterial strains.
The fungi are together, but more closely related to the rest of the eukaryotes. The primates are together, and with the rat make up the mammals. The birds are together. The frog which makes up the amphibian, is the most distantly related tetrapod (from humans) so sits on a branch node closest to the tetrapod-defining node. Which is inside the Sarcopterygii together with the Coelacanth, with salmon (a ray finned fish) outside.
That’s how Uniprot sorted them, but again I have no idea what algorithm or settings it uses.
Picture is too small so here’s a link: https://i.imgur.com/ss71eSX.jpg.
Your tree has a weird thing happening at the crucial node, i.e. where the coelacanth, salmon, and tetrapods meet. I can’t figure out if it’s a graphic glitch or if it’s generating negative-length branches. But it certainly doesn’t clearly show a monophyletic Sarcopterygii.
Ok first, here is the cleaned up FASTA file of cytochrome-c COX1. I should mention I tried to put in Gallus gallus (chicken) and it mangled the phylogeny tree. Since John Harshman is and expert on birds maybe he can explain it. I assembled the orthologs according to my Methods and Material in the previous comment.
I post the following for interested readers to process the data and independently review my findings. This time I added accession numbers to enable duplication of any results which I claim.
stcordova,
Why don’t you just search GenBank for “Cytochrome c oxidase subunit I”?
Sal,
Why must you keep spamming the thread with sequences? Upload them somewhere else and link to them.
Ok, there are various trees that can be run. ML, NJ, minL, whatever. I’ll just post a few of them.
click the link below for a larger image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/cytochrome_c_cox1_v2.png
That would be the best way assuming the annotations are correct. Just for my own piece of mind I was just being thorough. The hits I got with my more painstaking method still returned “Cytochrome c oxidase subunit I”, so that was assuring.
Thanks for you help. Much appreciated.
Still, I can’t account for why my gallus gallus hit blew up the cladogram.
Rather than fix it, I could go on to another gene, like THE cytochrome-C. Other genes suggested were RAG1, or whatever.
Yes that does look weird. The same thing seem to be happening close to the mammal-alligator node. And all the way out at the three bacteria node there’s another glitch. How annoying.
See what I mean? After being shown that you’re incompetent, you just blow it off and blithely continue. Putting in a chicken shouldn’t mangle anything. You did something wrong, but I don’t know what it was.
Define “blew up”.
What your tree shows, incidentally, is that your data/method are incapable of resolving the four-way polytomy among lungfish, coelacanth, actinopterygians, and tetrapods. Do you know what the little numbers next to the nodes mean?
No kidding. No Shitake Mushrooms too.
Rumraket,
I just had a little play with one of your sequences, one of the Salmon sequences. BLAST found a few other paralogs in the salmon, and orthologs in rainbow trout but also among the top hits … Caligus rogercresseyi. Never heard of it, turns out it’s a sea louse. It’s a parasite of … wait for it … salmon, and rainbow trout. This looks like HGT to me. So here’s an example where common descent is reasonably inferred from sequence alignment – not of the entire organisms of course, but of the gene. Yet if we just looked at this gene, we might be misled into nesting sea lice with salmonids.
Some might think that destroys the entire enterprise. Anomalies? How dare there be anomalies!
Confidence level (interval).
But, there are other methods, and one can add more bootstrap support.