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.
Your complaint UPGMA (the idealized simple tree) is moot, because runs with ML, ME, NJ yield the same essential results.
The main issue is the outgroup. I pointed out why Sharks are inappropriate. The Sarcopterygiian have supposedly 3 extant lines: Coelecanths, Lungfisgh, Tetrapods.
If you assume tetrapods are Sacropterygiians, then this results in the small distances between Lungfish and Coelecanths only explainable by slow molecular clocks, or equivalently tetrapods having very fast clocks. I confirmed this inference by referencing appropriate works, but it should have been plain as day to interested parties long ago.
But the Distance matrix tables, be they Dayhoof, JTT, whatever show tetrapods have slightly slower clocks the Lungfish and Coelecanths relative groups outside vertebrates. That means one has to simultaneously invoke fast and slow clocks for Lungfish and Coelecanths. This is an absurdity, which means the claims about tetrapods being in the Sarcopterygiian clade are bogus, and so are all the beautiful cladograms and phylogenies that can be built with such bogus inference. You yourself unwittingly admitted how easy it is to build bogus phylogenies:
You kick the shark out as an out group, and use a better one, or better yet use mid-rooting, and you get the Linnaen hierarchy restored, and the clocks, even by evolutionary standards, look more coherent.
But I smelled this skunk a long while back, and reading the Smithosian article about the astonishingly slow clocks on Ceolecanth’s confirmed to me my instincts were right. You weren’t the one who pointed out the problem of slow clocks in the Ceolecanth, I figured it out all by myself, not you. And now I also have papers by researchers who independently arrived at the same conclusion as I did.
So, you’ve got a serious problem using sharks as an outgroup. Sharks don’t qualify, unless you want to impose a foregone conclusion.
But beyond all this, the readers can easily see the powerful effect of changing the outgroup on the nested hierarchy that is generated. Looks to me like outgroups were chosen to conform to a foregone conclusion, the outgroup choice wasn’t based on coherency, as I’ve demonstrated with the distance matrices above.
Sharks as an outgroup leads to numerous incoherencies, but hey, it supports the idea that this mangled piece of mud is our ancestor:
It’s what keeps the universe in balance.
Glen Davidson
I’m hoping God agrees with me, that’s all that matters. Or better yet, I agree with God.
Anyway, nice to see you. Hugs.
A very religious man was once caught in rising floodwaters. He climbed onto the roof of his house and trusted God to rescue him. A neighbour came by in a canoe and said, “The waters will soon be above your house. Hop in and we’ll paddle to safety.”
“No thanks” replied the religious man. “I’ve prayed to God and I’m sure he will save me”
A short time later the police came by in a boat. “The waters will soon be above your house. Hop in and we’ll take you to safety.”
“No thanks” replied the religious man. “I’ve prayed to God and I’m sure he will save me”
A little time later a rescue services helicopter hovered overhead, let down a rope ladder and said. “The waters will soon be above your house. Climb the ladder and we’ll fly you to safety.”
“No thanks” replied the religious man. “I’ve prayed to God and I’m sure he will save me”
All this time the floodwaters continued to rise, until soon they reached above the roof and the religious man drowned. When he arrived at heaven he demanded an audience with God. Ushered into God’s throne room he said, “Lord, why am I here in heaven? I prayed for you to save me, I trusted you to save me from that flood.”
“Yes you did my child” replied the Lord. “And I sent you a canoe, a boat and a helicopter. But you never got in.”.
If Tiktaalik ain’t yo’ daddy, then who is? Maybe this man can help:
It’s never too late Sal.
Sadly he has.
stcordova,
Yebbut, if you pick a certain outgroup, you retrieve the ‘taxonomic tree’! Using cytochrome c friggin’ oxidase! That’s pretty remarkable, especially since this is not a morphological gene at all; it’s central respiration. And yet, it doesn’t vary according to respiratory demand at all; it coincides with the Linnaean tree built on ‘shared characteristics’. (I know an ace way of getting a clade to share characteristics BTW. Ask me how).
I still don’t know why there should be a squid way of passing on electrons to O2, and a shark way, and a squirrel way, and the squirrel way needs to be less different from the whale way than the hagfish way …
Allan,
Thanks for you response. I looked at a list of genes that were used in the 2014 paper on the topic. They used RAG2 which is an immune system gene. Do you have problems with that? Should they have not used that? How about if I used Topoisomerases?
I’m open to suggestions. Thanks in advance.
I’m not the only one pointing out problems with the molecular clocks. This could be a fun area of research now that I’m learning how to use phylogeny software.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC150674/
It’s also possible evolutionary rates are inaccurate AND present-day RNA viruses originated less than 50,000 years ago.
When all else fails just make up some stupid strawman to knock down (nobody claims Tiktaalik is a direct ancestor of anything alive today).
By the way, that “mangled piece of mud” (what are you saying, that the fossil doesn’t exist?) was predicted to exist in a geological strata of the age in which it was found. If evolutionary transitions did not take place, and if the chronology of strata is incorrect, there’d be zero reason for that fossil to exist.
Why did God decide to put the fossil of a clearly transitional tetrapod into a strata he also (apparently) faked to appear like a 375 million year old Devonian-period beach or flood-delta?
Quotemining like the best of them in the worst tradition of arch-charlatan and liar for doctrine Henry Morris, who penned the turgid screed That Their Words May Be Used Against Them. Expertly reviewed here A shining, inerrant masterwork. A pearl before swine.
Henry Morris who, by the way, seems to have fathered the doctrine in so-called “scientific creationism” that when reality and doctrine differ, reality is wrong and doctrine is right.
But don’t take my word for it:
“…the main reason for insisting on the universal Flood as a fact of history and as the primary vehicle for geological interpretation is that God’s Word plainly teaches it! No geologic difficulties, real or imagined, can be allowed to take precedence over the clear statements and necessary inferences of Scripture.”
– Henry Morris, Biblical Cosmology & Modern Science, pp 32-33 (1970)
So the “true” Tetrapodamorpha ancestor of us is still a missing link. Thank you very much.
I was just using a figure of speech regarding Tiktaalik.
If Tetrapodomorapa existed, my molecular analysis casts doubt on Tetrapodomorha having sequence similarity to the other Sacropterygian ancestors because the distance matrices that I’ve now learned to pump out en-masse show there is a real clocking problem.
There are two components to the clocking problem if one invokes Tetrapodamora:
1. Lungfish and Coelecanth clocks must be slow relative to Tetrapod clocks. I smelled that skunk a mile a way, a long time ago, but didn’t quite have the tools to show it. The point is moot however, Smithsonianmag in 2013 quoted researchers admitting as much! So now Rumraket and other suggested a fix like a variable clock running slow. The fix isn’t based on experiment, it’s just based on a foregone conclusion. But that fix won’t work for the reason below.
2. If Lungish and Coelecanths have supposedly slow clocks, this does not agree with the distance matrices that show the opposite when compared to Chordates that aren’t vertebrates. If anything they have equal or slightly faster clocks than tetrapods. Ooops.
Ergo, Tetrapodomorpha should be excluded from various clades with Lungfish and Coelecanths. The only clade the ancestor of Tetrapods might share with Lungfish and Coelcanths is the Vertebrate looking clade which Linnaeus conceived of long ago, and which really isn’t the spirit of what Tetrapodomorpha was meant to be.
stcordova,
I think you may have missed the point. Regardless what you use, you get something approaching the ‘taxonomic hierarchy’. Even in genes that, so far as we can reasonably ascertain, contribute little or nothing to the specific form of a specific species – topoisomerase, spo11, RAD51, lactate dehydrogenase, an intron, a SINE insert, whatever. That is a remarkable fact, but you don’t seem aware that it is remarkable.
If you want Design to be the ‘better explanation’, at some point you might have to tackle the issue of why all these ‘housekeeping’ or (possibly) nonfunctional genes have a design need to be different across taxa, in a way that is consistent with common descent.
stcordova,
Again, Sal, I thought you had promised to cut down on the megalomania. Instead you seem to be ratcheting it up.
Allan,
I actually posted a while back on Bone Morphgenetic Proteins. I lamented at the time I didn’t have the tools to make such pretty cladograms. But now, thanks to Masotoshi Ney and his MEGA6.0.
They even put in accession numbers! I need to add some lungfish and coelecanths.
I guess someone needs to get on the author’s case as he is using Linnaen-like groupings.
Click to enlarge:
http://ars.els-cdn.com/content/image/1-s2.0-S8756328206005618-gr1.jpg
Well I did get ahold MEGA software 3 days ago…..and it is MEGA awesome.
But you have to admit, I’ve identified a paradox with the molecular clocking of the Sarcopterygiian clade.
So, is the clock of Lungfish slow or fast relative to tetrapods? If you say slow, then how does that square with the distance matrices with non-vertebrate chordates?
stcordova,
Did you miss the point again?
Allan Miller,
Yes, I missed your point because I was looking for some gene name suggestions, since I didn’t see any seriously provided, I ignored whatever else you said.
I’m presently more interested in finding more formal confirmation for the clocking anomaly. There are some clock testing modules in MEGA6.0 like Tajima, etc. This seems like an interesting question relative to the OP regarding my revulsion toward putting Tetrapods in the Sarcopterygian clade.
stcordova,
Fair enough I suppose, since I barely skim your lengthy posts. It’s an important point, nonetheless, in view of the subject that is supposed to be being discussed – that ‘versus’ thing.
Why should he, just three weeks with the software and Sal has already overturned both biology and geology.
On the point about clocks, an obvious point that can be made is that at best if you look at one gene you only get a clock rate for that one gene. Wouldn’t want to cherry pick.
Guess there ain’t much point talking to people who aren’t interested in listening. Hey ho. Back to Busty Bertha, just a tab to the left. She’s not listening either, but somehow I don’t mind.
You have to rub shoulders with famous scientists and publish in a prestigious journal.
Mung,
Hey, my degree is from the most prestigious university in North Wales. Also the only university in North Wales.
I suspect the distances you are using are non-metric due to lots of multiple hits, likely resulting in saturation at many positions in the most distant comparisons. If you want to continue investigations with mitochondrial genes, you need to get a much bigger and better designed taxon sample.
😀
Has anyone been cataloging the number of ways common design is a better explanation than common descent?
For example, the most recent case seems to be that there are some questions about molecular clocks, therefore common design is a better explanation than common descent.
Haha. I think I am going to turn “smelling the skunk” or “smelled the skunk” into a euphemism. Just think of all the things it could be applied to.
Yes.
Time to adopt the Design terminology and call them molecular quacks instead
Think I smelled a skunk on that
I smelled the skunk. It’s why Salvador has me on Ignore. 🙂
I think we need a thread on the evolution of skunk smell.
At first it must have started off as just mildly offensive hygiene to the first non-skunk that got the mutation to become a skunk. Then this was a reproductive advantage, which int turn helped guide its ancestors towards skunks that smelled even worse. Eventually if you weren’t able to smell really bad, it became very hard to find a mate, so only the worst smelling ones survived on.
I can see the same thing evolving in humans one day.
And one on how skunk smell proves that God does not exist.
ETA: That “The Christian God” does not exist. “The Islamic God” and “The Jewish God” and “The Viking God” etc., are perfectly compatible with skunk smell.
I think I smelt another skunk
“Vultures and skunks will police the streets; owls and crows will feel at home there. God will reverse creation. Chaos! He will cancel fertility. Emptiness! 12 Leaders will have no one to lead. They’ll name it No Kingdom There, A country where all kings and princes are unemployed. 13 Thistles will take over, covering the castles, fortresses conquered by weeds and thornbushes. Wild dogs will prowl the ruins, ostriches have the run of the place. 14 Wildcats and hyenas will hunt together, demons and devils dance through the night. The night-demon Lilith, evil and rapacious, will establish permanent quarters.“
This is where the Bible foreshadows Donald Trump who supported by True Christians and is also smelly, therefore the Christian God is compatible with smelly things
Thanks for the suggestions. I tried the Tajima test with Ciona as outgroup and Lunfish and Coelecanth as the clock comparisons. The clock was fast on Coelecanth, humans a bit slower. This is a small sample size however and only one gene, so it’s premature to make a generalization.
Just for grins I tried the ML clock test on my UPGMA tree with Ciona as natural outgroup, it did not reject the constant clock hypothesis on that tree.
I will try some nuclear genes.
FWIW, creationists do accept some phylogeny, it is of interest to those tracking human genealogies and certain genealogies within Baramin. So I don’t have a lot of objection to applying phylogenetic techniques if we’re not looking too many generations back in time for the same created kind.
The bioinformatics techniques developed in the course of phylogenetics, particularly sequence alignment are very good. They were quite helpful in identifying critical catalytic sites.
Anyway, Joe Felsenstein’s book arrived in the mail. I already started reading it.
You are stealing his mail?
To visualize the clocking problem with the Sacrcopterygii clade whereby approximately 3 extant lines diverged about the same time (not exactly, but close enough) I depict the actual distances under the Jones-Taylor-Thornton (JTT) model for the Cox1 protein (from cox1 gene). One could use other distance models like Dayhoff, or whatever, but the same problem will show itself.
Below on the left (NOT TO SCALE) is a non-equilateral triangle where the lengths of each side are the measure of differences between the Cox1 proteins of human, coelacanth, and lungfish. That is the actual difference under the JTT metric, and as I said, it should be materially similar for any other reasonable metric.
This is in contrast to the expected idealized situation on the triangle on the right where the distances should all be equal under a constant clock hypothesis. I put in 16.05% since that is the average between the distances from human-to-lungfish and human-to-coelacanth distances, but one can put whatever figure should be appropriate for a constant clock. The point is that’s what an equilateral triangle looks like and that’s what the constant clock hypothesis should yield.
Ok, so the kluge that is needed to account for the discrepancy between the expected ideal is to assume the humans are evolving more than twice as fast as the Lungfish and Coelecanth, or equivalently the Lungfish and Coelecanth are evolving less than half as fast as the human.
I saw this problem years ago when people were criticizing Denton’s chapter “Biochemical Echo of Typology”. Denton’s critics said to the effect, “the constant clock would give the pattern’s we actually see. We shouldn’t be surprised humans are as divergent from bacteria as fish even if humans evolved from fish, therefore Denton is wrong.” But I eventually smelled the skunk in the criticism of Denton by the Darwinists. The fish were too close to each other in similarity, just like the triangle on the left.
The Kluge of invoking a slow clock for Lungfish and Coelecanths may fix one problem, but it creates another problem which I’ll elaborate later, and which I believe is fatal to the hypothesis that we evolved from some tiktaalik-like Tetrapodamorpha.
But anyway, I provide the diagram below to visualize the first part of the problem.
Click below to see enlarged image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/triangles_actual_expected.png
Now if we take Ciona, a non-vertebrate chordate as an outgroup for chordate vertebrates, we have a independent line of reasoning to estimate actual relative clock rates of lungfish, coelecanths, and tetrapods like humans. We might be able to confirm or falsify the klugde of slow clocks claims for Coelecanths which other researchers claim (for different reasons than the one I gave) to be the case for Coelecanths.
https://www.smithsonianmag.com/science-nature/dna-sequencing-reveals-that-coelacanths-werent-the-missing-link-between-sea-and-land-25025860/
As I have objected before, no one actually measured the clock rate with a stopwatch! It’s all by inference by assumptions that I believe are wrong. But, nonetheless it shows the sort of evolutionary Kludges that are often in play.
Anyway, when looking at the Jones-Taylor-Thornton (JTT) matrix on Cox1 , a copy of which I provided here:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/tunicata_jtt.txt
I saw evidences against those Kludges of slow clocks. If anything the Coelecanth looked like it was evolving faster than humans relative to the non-vertebrate Tunicate Chordate, Ciona.
Because the software MEGA 6.0 created by National Academy of Science Member Masotoshi Nei is freely available and user friendly it was one of the recommended tools for phylogenetic analysis. It included the Tajima clock test, which also has some interesting outputs.
So I ran the clock test on human, lung fish, and coelacanth. The clocks of the Coelecanth was slightly faster than human and human faster than lungfish. In any case, one can see if the preliminary data from this tiny sample size is genereralized, the assumption of slow clocks for the Coelecanth is falsified, and so is the spirit of the Sarcopterygiian clade. One can still assume for the sake of argument all vertebrates share a common ancestor, but it’s not like what the mainstream is claiming regarding Tiktaalik like tetrapodomorpha ancestors, it has to be something else. But since I believe the fossil record is young, I think such searches for the hypothetical vertebrate ancestor are in vain since the ancestor is only conceptual in God’s mind just as Richard Owen hypothesized, the vertebrate ancestor was never an actual physical creature.
I have depicted in rough form the way I interpret the Tajima test, but one could also glean this from the JTT matrix, with slightly different lengths (the lungfish longer than the human in the JTT analysis). But the if these data points hold in general (which is yet to be seen) then that is evidence against the spirit of the Sarcopterygii clade being the ancestor of tetrapods.
The diagram below represents the relative clock rates, the triangle represents some supposed mean. The diagram is not to scale. This is all preliminary, so some of the argument is qualitative at this time. But the diagrams attempt to depict visually the problems I claim exist.
click to see enlarged image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/tajima_text_preliminary.png
Why’s there a clock at all, if it only started ticking 6,000 years ago? As with the en masse insertion of imperfect phylogenetic information (which subterfuge True Believers can see right through), there has been en masse insertion of imperfect rate information. I bet if you looked at synonymous vs nonsynonymous sites you’d see an imperfect difference there too. For some reason.
A Creationist worth his salt ought to be able to pinpoint the moment the clock started ticking, just as they ought to be abe to use phylogenetics to pinpoint the roots of the baramins. Positive evidence. Instead, as ever, it’s all about undermining evolution, in hopes of being the only paradigm left standing.
My argument is in the classic form of a Proof by Contradiction. We assume the thing we believe to be false in order to demonstrate its absurdity.
Google Reductio Ad Abusrubdum to see what I mean.
stcordova,
A twofold difference in clock rate makes the clock absurd?
Abusrubdum? Wasn’t that a spell in Harry Potter?
What other paradigm could there be, if evolution is false? Some OTHER unguided process?
I realize believing in evolution requires some suspension of disbelief, but come on.
Unless God shows up like He did to Paul on the Road to Damascus, for you and me there is no positive evidence. You just have to play the hand you’re dealt.
If we’re playing blackjack and the dealer is showing an Ace, do you take insurance or not? Well, you make the decision based on inference, not because you have positive direct evidence.
So yeah, all I have are anti-evolution arguments. You probably won’t accept the testimony of a Moon Walking astronaut who prayed for a blind girl in the name of Jesus and she got healed, but I believe it, despite James Randi’s challenge:
For people like that blind girl that was healed by a Moon Walking Astronaut Charles Duke, it echoes something in the gospel, “One thing I do know, that though I was blind, now I see.” John 9:25.
Maybe you haven’t seen such miracles in your life, so you’re less inclined to believe. I accept that is one of the reasons you don’t believe. I respect that. But I also accept the testimony of people like Charles Duke plus what I think were miracles in my own life, some are too personal to talk about.
So maybe no positive evidence for you for creation. But you don’t exactly have positive evidence either we evolved from the mythical Tetrapodomorpha sister of Lungfish and Coelecanths.
My argument attempts to show Tetrapodomorpha as ancestors of humans is a myth of evolution, the name is just a pejorative name against creationism, it’s doesn’t reflect reality. The molecular data doesn’t agree that Tetrapodomorpha is our ancestor even though that mangled piece of mud called Tiktaalik is called a Tetrapodomorpha member. Tiktaalik’s existence doesn’t make Tetrapodomorpha our ancestor, that claim is likely a myth, or at the very least there is no positive evidence to that effect because fish give rise to other fish, and that will be true for N-generations and hundreds of millions of years. The Lungfish and Coelecanths and Sharks are proof of that claim (that is if you cling to the Old Fossil Record hypothesis).
So no positive evidence from me to you, only negative anti-evolution arguments. If you hang around here, as you have for 3,400 comments, you’ll just get more of the same. So don’t bother demanding positive evidence from me. I already said so long ago and many times, so why do you pretend that I ever promised positive evidence?
See here: ID Falisifiable, NOT science, NOT positive, NOT directly testable:
Yes because it doesn’t square with the data in the JTT distance matrix or the Tajima clock test that I described in the very next comment which says the clocks are equal to faster for the Coelecanth. You can’t have a slow clock and more-than-twice-as-fast clock simultaneously in the same inertial rest frame unless you have at least one or maybe two broken bogus clocks!
So you mischaracterized my argument.
phoodoo,
I don’t believe the stated possibilities are exhaustive. After all, you are not a YEC., so would presumably not support the contention that disproving evolution leaves YEC as the only other option, which is Sal’s apparent contention.
It doesn’t require me to suspend disbelief in some magic bloke in the sky making it all look just like evolution, which seems on the face of it rather preposterous.
stcordova,
I’m suggesting positive evidence based upon scientific tools, not testimony or scripture.