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.
stcordova,
There must be a point, though, where [non-universal] common ancestry kicks in. Where is it?
I don’t appreciate the accusation of spamming. The data was provided so you could independently play with it. Problem nodes? I provided the data, you freaking figure it out if there are problem nodes!!!!!!!
I edited the comment so you can click on the diagram to enlarge.
The diagram looks pretty close to what it should be. The lungfish and coelcanths form a clade. Do you have a problem with that?
stcordova,
Why me? You are the one saying phylogeny is useless. You run an analysis on one sequence (I only guess from the title of the upload that it’s cytochrome c) and appear to have a complaint about what comes out. Me, I’d recommend increasing your coverage. By and large, the more genes you add the more likely you are to converge on the phylogeny.
Yeah, I know that accusations of ‘spamming’ are likely to offend, but you do have a tendency to obscure by sheer volume, and there are times this appears deliberate in itself. An ‘onlooker’ will see reams and reams of Sal sticking it to the evilutionists, is my suspicion of the intent.
Humans are also vertebrates, but they don’t “look like a spine”. They have one. They’re also multicellular eukaryotes, but they don’t look like Jellyfish, or sea-sponges. They’re bilaterally symmetrical, but don’t look like flatworms. And so on and so forth.
A clade is defined by the shared characters inherited from their common ancestor, not by “how they look”.
The defining characteristics of Sarcopterygii isn’t “looks like a fish”. It’s supposed to be about having paired, bony, flesh-covered limbs. It used to refer to fins, but since it includes tetrapods now more generally refers to limbs.
ffs. Is it even possible for your objections to get any more inane?
stcordova,
So the fact that a molecular comparison at a very low level recovers the morphological hierarchy does not seem in any way remarkable?
If we reroot Sal’s tree with the sharks as the outgroup, it looks pretty normal, except for the lungfish-coelacanth clade. That is nonstandard. Most other studies end up with a tetrapod-lungfish clade inside of a coelacanth-lungfish-tetrapod clade. Having the different coelacanths all in their own clade seems OK too.
So we have one clade with 80% bootstrap support backing a nonstandard topology, but all the others agreeing with the usual consensus. As we had a bunch of clades to look at, this does not seem abnormal.
Sal draws a tree from a specific sequence. Allan suggests increasing the coverage.
…and Sal has the indecency and hypocrisy of accusing evolutionary biologists of cherry picking data. heh
How is it determined they are inherited by their common ancestor? By calling them common ancestors?
For the evolutionist the answer is simple, when two organisms share so many characteristics, but are unrelated, CONVERGENT EVOLUTION, Voila!
Who needs nested hierarchies?
phoodoo,
Wrong. For an evolutionist, the answer, when organisms overwhelmingly share common characteristics against which these ‘orphan’ differences shine out, is common descent. Nobody proposes that extensive sequence identity is due to convergent evolution. You really seem to have a bit of a bee in the bonnet about it.
Thank you kindly for your response.
I should point out the following have 99% coverage and 93% identity coverage in default BLASTP parameters at the NCBI website (BLOSUM62, etc.)
[NOTE: I’m the one who added “Ceol3” or “LFish1” to the UNIPROT names.]
In contrast I got 98% coverage and 85 % identity when I did:
Regarding Shark as an outgroup, I got 99% coverage and 87% identity for
For shark and human, I got 100% coverage, 81% similarity
Shouldn’t the choice of outgroup that creates a phylogeny at least be consistent with the actual patterns of similarity and diversity? I presume MEGA 6.0 decided to make the mammals the outgroup computationally?
The Mammalian outgroup seems to capture the pattern of similarity better between coelacanths and lungfish and the actual distance between humans and lungfish.
Just for completeness, the Diagram is below was created using a Minimum Evolutionary Phylogeny using MEGA 6.0 ( MEGA 7.0 64 bit won’t run on this particular computer). SPECULATIVE question: wouldn’t “Minimum Evolution Phylogeny” be the best phylogeny for creationists to use for their Baraminology studies, given they think there is minimum (as in next to no) evolution? I though UPGMA would be best for creationists, but the tree it generated looked really bad.
Any way here is the diagram below with the immediate link something you can click on to enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/min_evolution_tree.png
The problem is with the tuna, which joins the coelacanth and lungfish to form a “fish” clade to the exclusion of the three mammals. But clearly Sal’s taxon sampling is calculated (though he probably doesn’t realize it) to produce a bad result: only one actinopterygian and no tetrapods other than mammals, and thus a recipe for long branch attraction. If I recall, the original cytochrome c analysis, many, many years ago, found a more plausible result.
Sal, let me suggest that if you want to discuss geology, young earth, or young life, you start a new thread. Though I will add that everything you mention here is a PRATT.
You’re the one that brought it up and started asking me and then whining as to why I didn’t respond. Now I get around to responding in this thread and you want me to start another thread. Well, Young Fossils is part of the OP. Young life implies no Universal Common Descent. So this is relevant.
You calling it PRATT doesn’t change the facts, like the Coloroado school of mines experiment, C14 invariant in strata and the faint young sun paradox. It suggests the pattern which you call phylogeny is a designed nested hierarchy.
stcordova,
Considering that you have never managed to say anything on-topic so far in this thread, including the OP, I regret ever asking you about geology. But in addition to being PRATTs, your objections are also cherry-picked and ignore all the basic facts of geology. Why not start a new thread to discuss geology? I would appreciate a coherent theory of earth history that fits the facts.
And here, I would appreciate a coherent theory of the nested hierarchy of life. All we have so far is “it must be true”.
For completeness I got 99% coverage 86% identity when I did:
so referring to earlier results: I got 98% coverage and 85 % identity when I did:
and 99% coverage and 93% identity coverage for
So for the gene tree (not species tree), it is perfectly sane to say Lungfish and Coelacanths are close to each other and each are distant from humans with respect to the cytochrome in question. One might get a different tree using different genes. We expect as much.
I should point out, there is not uniform agreement. Tree Of Life arranges its phylogeny this way without the Rhipdistia clade:
http://www.tolweb.org/Sarcopterygii/14922
and wiki this way that include Rhipidistia:
http://www.tolweb.org/Sarcopterygii/14922
But well, you can’t run away from the pattern of similarity and diversity I just demonstrated. I’ve shown, at least as far as cytochrome is concerned, the very protein the evolutionists are touting in this discussion, a human isn’t a lungfish- like creature, it isn’t a coelecanth-like creature, it is a mammal.
Compare also the morphology of the three creatures in question that form representatives of Sarcopterygii:
https://en.wikipedia.org/wiki/Coelacanth
https://en.wikipedia.org/wiki/Lungfish
and human
http://3.bp.blogspot.com/-GbqH_4K7G8M/TVSBf_171qI/AAAAAAAAA68/WhiakNgRA7M/s1600/fabio_lanzoni_fabio.jpg
It should be clear which two creatures are closer to each other. It’s not human and lungfish. It is confirmed morphologically and is consistent with the cytochrome data. A mammal is a mammal, it is not lungfish like nor coelacanth-e, it is mammal-like. Exactly what I said in the OP.
This clade:
https://en.wikipedia.org/wiki/Rhipidistia
doesn’t agree with the cytochrome-C differences. Not at all. Neither does it agree with the morphology as shown above. It is a narrative that is force fit. I just demonstrated it both in terms of molecules and morphology.
At least someone agrees with my assessment:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3069939/
And John Harshman is questioning that I rigged my samples of data. Nope, it is consistent with other researchers, unless John wants to accuse them of rigging too.
Goodbye Rhipdistia!
Oh, so you mean all nested hierarchies are simply based on sequence similarity? Is that it? Why look at characteristics at all?
phoodoo,
You’re making yourself look like an idiot. Read what Allan actually wrote:
keiths,
You are making yourself look like keiths.
I asked, why do we need to look at characteristics at all, just look at gene sequences, shouldn’t that be all we need?
Now you don’t get this of course, because, well, you are a keiths.
Allan, to Sal:
It’s just like Sal’s credential-mongering. He figures that whatever dazzles him will dazzle his intended audience, too. Unfortunately for Sal, the brighter folks see right through it.
phoodoo:
If you’re talking about morphological characteristics, then the answer is just as obvious: we don’t always have DNA sequences to go by. Care to point us to the trilobite genome?
keiths,
No, I am talking about nested hierarchies keiths, try to pay attention. If we don’t have the DNA sequences, then we should just say we don’t know the relationship, because it should all be based on sequences.
But that’s not the case is it, we also take into account what they look like. But since we claim convergent evolution can make any similarities, we better give up on morphology. Because morphological similarity is thus established as meaningless.
Sal:
Okay, let’s pretend they require miracles. The 10^38 pound elephant is still in the room:
You can squirm all you want, Sal, but that elephant ain’t gonna disappear, unless you (successfully) pray for a miracle. Duh!
To deny common descent is flat-earth stupid.
Rumraket,
Never underestimate the power of the Jebus Effect.
keiths:
phoodoo:
phoodoo, one comment earlier:
Derp.
Truthfully speaking we are mammals, we aren’t Sarcopterygian fish. I just demonstrated it.
I said in the OP:
From Wiki:
“though a strict cladistic view includes the terrestrial vertebrates.” Ahem, not strict cladistics view, but a loose the view to say a kangaroo is a lobe finned fish! The creatures have different architectures.
I expect a fish to give birth to a fish. After N-generations the descendant of a fish will be a fish, not a Kangaroo.
Evoutionists tried to justify their claims with rather fishy evidence (pun intended). This is a photo of what the real tiktallik fossil looks like. It may be fair to say, some imagination could be in play as to what the living creature actually looked like.
Quality of the specimen poor? No Shitake Mushroom Sherlock!
phoodoo:
So according to you, it’s ridiculous to infer that the trilobites below are related.
This sort of thing is why we laugh at you, phoodoo.
Sal:
Yes, and I responded to that bit of idiocy two weeks ago:
Rumraket made the same point to you earlier today:
Will you ever learn, Sal?
The rest of my comment summed it up nicely:
No, no keiths, this is where your limited reasoning skills fail you.
I am saying that if we listen to evolutionists, then this would be the reasonable logic we must apply. Morphological similarities no longer matter, because you see, convergent evolution of course can create any morphological similarities. I mean heck, if we listen to evolutionists, this is pretty much expected, almost downright guaranteed. At least it is guaranteed, now that we found it it must have happened. Its like a prediction of the theory, an after the fact prediction sure, but still.
So now that we know evolution can do pretty much anything, we can predict it can do pretty much anything.
You’re confusing “evolutionist logic” with “phoodoo logic”.
If evolutionary biologists were stupid enough to follow phoodoo logic, then yes, phylogenetics would be a hopeless mess. Luckily, they are far smarter than that, and they have figured out ways to distinguish homology from homoplasy.
It is unlikely that you will ever understand those methods, because you’re a phoodoo. But don’t mistake your incompetence for a flaw in the science.
Cellular Biologist Change Laura Tan, University of Missouri offer the creationist orchard view vs. the universal tree of life view:
https://answersingenesis.org/creation-science/baraminology/taxonomically-restricted-essential-genes-organisms-family-tree/
phoodoo,
Are you withdrawing this goofy statement?
You think it should be based only on sequences, but that’s because you are a phoodoo. Evolutionary biologists aren’t phoodoos, thankfully.
You really are embarrassing yourself, or would be if you were capable of embarrassment. I doubt you rigged your sample; you just chose it very poorly. No, it isn’t consistent with other researchers. Take the paper you cited in support: it included a much better taxon sample than yours; though it had only 7 taxa, there were 4 tetrapods while you had only 3, and more importantly only one of them was a mammal. Nor is the main issue under contention the relationships among coelacanths, lungfish, and tetrapods; it’s whether tetrapods are sarcopterygians. You tree is not compatible with this entirely because it puts the tuna cladistically closer to lungfish and coelacanths than they are to tetrapods. The paper you cited recovers a monophyetic sarcopterygii, with the sole actinopterygian outside the group. And that’s what data generally do.
Your problem in finding the correct phylogeny has nothing to do with different gene trees. It has everything to do with a poor analysis, and almost certainly with the taxon sample. If you would like to experiment, add another teleost or three, or some additional actinopterygian like a sturgeon or paddlefish, an amphibian, a bird or crocodile, and a lizard to the sample, and see how that comes out.
Sal,
You forgot to emphasize that her “paper” appeared in the prestigious Answers Research Journal, published by the creationists at Answers in Genesis.
Bwahahaha.
Ooh, it looks so sciencey, with all the graphs and tables. And the colors! Sal is impressed. But what does it actually mean?
Sal,
Have you explained to Behe, whom you fawned over in this segment of the “Apologetics Academy” Youtube video, that he needs to examine the data with less bias?
Since he is not a Darwinist, how do you explain his acceptance of common descent? Why is he ignoring the Designer’s message? Why doesn’t he “want the truth”, like you and Bill? (LMAO)
Some of the worst crap I have seen in my life. This “there is an upper limit to how unlikely an event that can happen in the universe because only 10^140 events can take place” is demonstrably false.
Take a bowl of 150 ten-sided dies and throw them. You have just done something more unlikely than creationist calculations claim are even physically possible.
Under the creationist view, there are miracle-generators on the internet. Here’s one: Random Letter Sequence Generator.
Put in 10 and 10 in the fields, leave the alphabet as-is. Press [Click to generate letter sequence]. You’ve just performed a miracle. Creationist “calculations” claim that what just took place should not be physically possible in this universe.
How utterly fatuous and inane.
Let’s remind ourselves about the stated mission and beliefs of the Answers in Genesis organization:
“By definition, no apparent, percieved, or claimed evidence in any field, including history and chronology, can be valid if it contradicts the Scriptural record.” – answersingenesis.org
This is INSTANT DISQUALIFICATION in science. You NEVER put your conclusion first. This PROVES by their own admission that they never can or will admit to anything other than what they already believe.
What happened to “follow the evidence whereever it leads?”. They poured it down the drain.
Done. Case closed. Game over.
Incorrect. I think evolutionists have no idea how they should make their groupings. However, if they really believe in convergent evolution, that would be the only honest conclusion.
But then they would have to desire to make honest conclusions, not cherry picked ones-so that is unlikely.
So keiths, what about the pregnant woman, when are you going to answer? You seem to have time now. Why are you so afraid?
phoodoo,
I’ve answered your question here, in the appropriate thread.
Now, when are you going to get around to answering mine? And Timothy’s?
As usual you just rant cluelessly about things you don’t understand. Why do you feel this need to pontificate on matters beyond your comprehension?
It is obvious that it is reall you who is afraid.
phoodoo,
Because if a characteristic (eg sequence similarity) is shared by a clade, that is indicative of its common descent from an original sequence in an ancestor.
WTF? You are unbelievable Sal!
You reject “phylogenetic” nested hierarchies remember? So why are you telling us the designer created one? And why would he do that, if not to trick us? Or is the truth more subtle again?
Powerful retort Rumraket.
Amongst your finest! You are quite a poetic wordsmith to boot.
Before molecular biology became fashionable, taxonomists had to go by morphological characters. For those who were interested in establishing evolutionary relationships, a considerable problem was indeed figuring out which characters are ancestral and which derived. Phylogeneticists were well aware of this problem and had several tricks up their sleeve for dealing with this, and with convergent characters. Morphological and molecular trees are mostly congruent.
BTW, I assumed from your absence from this thread so far that you, like Mung, accepted common descent. Was I mistaken?
‘Convergence’ seems to be the latest one from Creationist Seminary – several have tried to make something of it, to varying degrees of understanding of what it means. It’s often accompanied by ‘ain’t evolution grand?’. I tried to get a thread going on it, but no nibbles.
phoodoo seems to think that evolutionists argue (or, perhaps, should argue) that extensive sequence similarity is due to convergence. They don’t. What makes convergence convergence is the fact that it stands out from the overwhelming pattern of (apparent) common descent, not that it looks just like it.
Marsupial moles are identified as convergent with moles because everything else about them says ‘marsupial’. At the molecular level (something Creationists seem even more unwilling to comprehend), there are virtually no examples of convergence beyond a few residues in length. The ‘similarities’ we are talking of here are billions of bases in total length, and convergence could not come close to supplanting common descent as the more likely explanation.
Right Allan, because the whole concept of totally different DNA sequences making almost the same animal is a preposterous notion for evolution, and one that evolutionists would NEVER have predicted or considered possible, until…oops.
So their predictable reply of course was, “Its not a problem for evolution! Never was! Of course nature will find similar solutions! Its obvious!..”
First it was that the evolving of an eye was an unlikely event, that if you could unwind the clock, would never occur the same again, then next it was, “Oh, it happens all the time, what’s the big deal??”
This is the pattern of evolutionist propaganda. As soon as you discover a hole in your theory, just claim you knew it all along. Or as you famously proclaimed:
“Its not true.
Prove its true.
Even if it were so what.
We always knew it was true
Its not a problem for evolution
Changes to the theory show how true it is.
We predicted it.”
phoodoo,
You’re getting excitable again. What’s your beef? There is virtually nothing in large-scale molecular sequence data [eta: meaning more than a handful of bases in length] that could reasonably be ascribed to convergence. Common descent is far the likelier cause of such extensive commonality. So no, not a problem for evolution. This seems to annoy you.