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.
Phoodoo just hates that his opponents — whatever the topic — won’t make the arguments he wants them to make.
How is he supposed to win debates if his opponents are being all intelligent and stuff?
phoodoo,
It was actually discussed in the Origin of Species (though obviously not down to DNA level). Before virtually anyone else had even encountered the subject. DNA was the icing on the cake.
And, you’ve got it backwards. We aren’t talking about totally different DNA sequences, we’re talking about largely identical DNA sequences – these are reasonably inferred to be due to Common Descent. Aren’t they?
Convergent evolution was discussed in the Origin of Species? Really?
Darwin predicted it? Do tell.
phoodoo,
Yes. Why are you so helpless? I easily found a relevant excerpt, from Chapter Six of the Origin:
Maybe you should read it one day?
you guys just gave phoodoo the ultimate reason to reject convergent evolution : that it was Darwin’s idea
Until what? There is not even a single example of this anywhere in the diversity of life. I think you’re confused again.
You have egg on your face.
Yes. That’s still the case. Evolving the same eye by the same pathway by the same mutations in parallel in independent lineages have not happen even once in the history of life.
No, that’s simplistic. Eyes have evolved multiple times, and there has certainly been convergence in structures and functions. But is has not happened to any significant degree in genetic pathway.
This is demonstrably just some fantasy you’ve been taught to believe by maliciously designed creationist propaganda.
And it isn’t.
You should when you make claims. I like how you’re here basically complaining that people ask you to back up your claims with evidence. I get that you’re not used to critical analysis of claims in sunday school.
Yes this is often the response because you IDcreationists make objections that are so inane they don’t even have problematic entailments for evolutionary biology.
Which raises the question why creationists keep being surprised by it? It’s like you can’t even read. Latest case in point, you haven’t read, or simply don’t remember having read The Origin of Species.
Thanks for confirming that all the responses you get are all totally valid.
Why would it be? This is just like the “even if it were so what?” one you made above. Same response.
Who even says that?
And they demonstrably did, every time they claim to have done so.
The responses you get should cause you to change your mind, they’re all valid and sound. But you won’t, because of your intense religiously based cognitive biases.
keiths,
Yea, he calls it a difficulty, and nowhere is he saying it was predicted. He is saying how do we explain it.
Subtlety is such a struggle for you.
Anyway, with the Convergence balloon busy flubbling away the last of its air as it bounces off the walls, would phoodoo care to answer the question I, Ancient Mariner-like, ask of each who passeth … where does Common Descent cease, as a reasonable inference from sequence commonality? Which is the approximate taxonomic level at which sequence commonality ceases to have been reasonably inherited from a common ancestor, and instead has somehow been injected as a matrix for a ‘TRG’? Is it the species, the genus, the family, the order … ?
phoodoo:
Even the obvious is lost on you. You asked:
I answered your question…
…and provided you with a Darwin quote.
The fact that you look like an ass is your own doing.
And then he does exactly that.
Why would it need to be explained if it was predicted?
And the explanation he gives:
Natural selection must have done it!
There are mechanistic barriers to changing proteins in various species, especially the higher eukaryotes. So even without the philosophical ideas I put in, you have mechanical issues. Since you seem to forget the functional constraints, here they are again:
Genomic
Transcriptomic
Proteomic
But one could also say
Genome/Epigenomic
Transcriptomic/Epitranscriptomic
Proteomic/Epiproteomic
Perhaps to emphasize the point, although “epiproteomic” isn’t well used in the literature, but for our purposes it is the post-translational modifications.
So what are the genomic/epigenomic limitations. Did you forget about the enhancers sitting on exons where one gene is regulated by molecular machines sitting on the exons of another gene???? And in passing one should note some gene structure are preserved, the exons are mostly preserved, but the introns are very different.
The reason the genomic sequences, exons included, can serve as scaffolds is made possible by molecular machines docking there. This is done because of the binding sites on them. I showed from ENCODE 2015 Wesley Pike’s presentation of the Vitamin D receptor, for example. The binding sites can be direct or indirect. That is, not only can the binding site directly draw a molecular machine, but also the pattern of histone modifications created by other machines that have written, read, and erased the histone modifications at that site. I showed one example with the PolyComb repression complex using a trans chromosomal regulatory lnc/RNC known as HOTAIR. Another powerful example is FIRRE. One cis-regulatory lncRNA is XIST. This stuff is influenced by sequence. So before you’re to quick to think the exons are free to mutate so easily, consider that.
Then there is the transcriptomic/epitranscriptomic level. We are only beginning to understand post-transcriptional modifications to RNA (aka the epitranscriptome), but we do know microRNA regulation happens, the miRNA motifs are deeply conserved on the genome, so this constrains what happens on the exons. Then there are A-to-I edited regions that include the exons on the edited dsRNA loops. We don’t know exactly what they do. But in addition to that, because there are epitranscriptomic post-translation chemical modifications on the RNA (the count is already over 100 confirmed classes) these involve again binding site constraints! So the genome which makes the transcriptome may not be as easy to mutate without causing functional constraint as you believe.
Then there are the post-translation modifications on proteins. Not only is there base function, like catalytic activity on enzymes, there are phosphorylation, acetylation, methylation, and whatever other “-ation” events that require specific binding sites. This in addition to the fact about half of higher eukaryotic proteins are glycoconjugated.
These are all sorts of issues that appear in cell-type specific and developmental stage specific and cell phase specific contexts.
Did you even bother to address the differing aspartic acid positions for glycoconjugation in the species specific Rhodopsins? How did those evolve randomly without making the creature blind so that you get the nested species hierarchy?
What is unbelievable is you guys just gloss over these mechanistic issues like they don’t even exist! So, yeah there is plenty there to tell you macro evolution has some major hurdles, instead you just cherry pick the data that seems to favor your viewpoint and don’t even acknowledge the rather substantial issues I raised.
And worse, the list I just provided doesn’t even broach the orphan system, and what Change Laura Tan calls TREGs (Taxonomically Restricted Essential Genes).
The data are not deluding you, if you examine it impartially, it is your own willingness to ignore data you find disagreeable. That is the spirit of strong delusion God has sent you, it’s not the actual data that is deceptive if you examine all of it. You can believe the pencil is bent or not, the data will actually tell you if you’re willing to examine it. Don’t blame God if you want to believe the pencil is twisted. The same goes for doctrine Universal Common Ancestry. You’re looking at everything through the wrong lens, so to speak. Have a change of heart and maybe you’ll see things more clearly.
With respect to fish-tetrpod evolution, the debate over what outgroup to use to create the phylogeny seems like straining at gnats.
https://www.readbyqxmd.com/read/27026053/resolving-the-phylogenetic-position-of-coelacanth-the-closest-relative-is-not-always-the-most-appropriate-outgroup
The Tetrapods would nicely “nest” withing the Sacropterygii if the sequence divergence pattern were something like:
That would be a credible nesting pattern to say tetrapods evolved from Sarcopterygii fishlike creatures.
Instead we have something approximate (given that they have 98-99% coverage):
So the net result is having to strain at outgroups to say whether the Coelecanth is closer to humans or the Lungfish is closer to humans! This seems like a rather minor point in the scheme of things, but maybe not quite as bad as wondering if we are closer relatives to a oak tree or a blade of grass.
The actual cytochrome-C pattern, vs. one that would be more convincing to me of common descent echos my complaint in the OP, if there is common descent, mammals descend from other mammals, not Sarcopteryian fish! This would be the pattern that would be persuasive that we descended from Sacropterygiian Fish:
but instead it is, for Cythochrome-C,
And the phylogenetic software also drove home the point. I defended the point I made in the OP regarding the Sarcopterygiian fish.
Axel Meyer said, “Evolutionarily speaking we are Sarcopterygian fish”, but Sal Cordova says, “Truthfully speaking we at NOT Sacropterygian fish. We are mammals. Fish are fish, they are not mammals, and mammals are mammals, they are not fish.”
stcordova,
I read your whole post, but you seem to have forgotten to address my concern.
If you deny that the objective (or “phylogenetic” whatever) nested hierarchy exists, then you don’t need to defend “common design”. Nor does it make sense to argue that God created one.
So does it exist yes or no?
A structural and molecular taxonomic hierarchy exists. That is objective. The problem is that except for trival cases, there is not one unequivocal phylogenetic tree out of the buzzillion possible phylogenetic trees that arrive at the taxonomic tree.
The trees I generated with phylogenetic software look pretty much like the creationist Linnaen trees that have been accepted for years. Notice the fish and mammalian clades are distinct! We are not fish, unless one uses a very strained interpretation of the tree, like say fusing lungfish and tetrapods into the Rhipidistia clade. I cited scientific papers that object to that force fit of data.
The Phylogenetic Nested Hiearchy does not exist, however the Taxnomic Nested Hierachy exists, it is real, and it can be constructed without the assumption of common descent.
And now for a very subtle problem which I alluded to regarding the lack of sufficient sequence divergence between closely related groups. It was this claim that got John Harshman up in arms over coalescence theory. I predictied these silly anomalies would pop up, and in the course of this discussion, I found evidence confirming my prediction. I will comment on this shortly.
That is nothing short of moronic. Mammals had to evolve from something that isn’t a mammal, obviously. So at some point as you go back in time, the mammal clade will converge on the last universal mammalian ancestor. This species in turn must have evolved from non-mammalian ancestors.
There isn’t a conflict between speaking “evolutionarily” and speaking truthfully. They are the same thing. You seem to confuse the colloquial or typological definitions of fish, with cladistic definitions. There are also monophyletic and paraphyletic definitions.
At bottom this is really just an argument about semantics and you’re basically just saying “to me a fish is an organism with gills that live all it’s life in water”, and with this colloquial meaning of fish in mind, you want to make it seem as if it is preposterous to group mammals with fish. But when mammals are grouped within fish (and thus ARE fish, cladistically speaking), that doesn’t make them “organisms with gills that live all it’s life in water”.
Wikipedia actually makes perfect sense of this relationship, including the fact that there are different naming conventions. https://en.wikipedia.org/wiki/Fish:
“Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. They form a sister group to the tunicates, together forming the olfactores. Included in this definition are the living hagfish, lampreys, and cartilaginous and bony fish as well as various extinct related groups. Tetrapods emerged within lobe-finned fishes, so cladistically they are fish as well. However, traditionally fish are rendered paraphyletic by excluding the tetrapods (i.e., the amphibians, reptiles, birds and mammals which all descended from within the same ancestry). Because in this manner the term “fish” is defined negatively as a paraphyletic group, it is not considered a formal taxonomic grouping in systematic biology. The traditional term pisces (also ichthyes) is considered a typological, but not a phylogenetic classification.“
My bolds.
Sal, some times you’re going to have to come to terms with the fact that in the technical literature, some words used have a slightly altered meaning compared to every day speak.
Saying mammals (and all other tetrapods) are Sacopterygians is to speak truthfully. But it is a CLADISTIC or PHYLOGENETIC, not a TYPOLOGICAL category.
You grossly mistake the meaning of “sarcopterygian”, what the controversy (if any) is, and what the main difference is between your cytochrome c tree and that of other folks. Your original claim was that “fish” were a group and mammals (and presumably other tetrapods, though you didn’t say) were separate from that group. Any differences in relationships among the three living sarcopterygian groups, tetrapods, lungfish, and coelacanths, are irrelevant to whether those three groups form a clade. In other words, the relevant species in your cytochrome c phylogeny is the tuna, the only non-sarcopterygian bony fish in the tree. According to all published phylogenies, the tuna is outside Sarcopterygii, and you put it in the middle. Your tree has a “fish” clade, or at least can be rooted so as to put even the shark into that group. That’s the problem with it. But I don’t think even you know what you mean by “fish”, and you seem unaware of the central issue.
So what’s the explanation for its existence? And what makes you say that the phylogenetic nested hierarchy a) doesn’t exist and b) differs from the taxonomic nested hierarchy?
stcordova,
Talking of cherry-picking … why would you base your entire analysis on cytochrome c?
You confuse distances with cladistic relationships. Your claims are only valid if there is a perfect molecular clock. None of the methods you have used so far makes such an assumption. Ask your teacher.
stcordova,
If you knew what you were doing, you’d actually find that amazing. You can pick a low-level molecule, whose job is to shuffle electrons (yeah, yeah, and have some role in apoptosis) and recover the Linnaean tree, using a method that has no merit.
stcordova,
As for the rest of your post; Instead of accusing us of cherry-picking, consider why there is substantial variation within species for every category of functional constraints that you mention. Just to pick one example from your Gish-Gallop: differences in glycosylation are the basis for the AB0 blood type polymorphism we observe in humans. There are thousands and thousands of similar polymorphism in every conceivable organism. How does that square with your exquisitely fine-tuned designs?
If we can agree that the latter is arbitrary, then we are done. Neither common descent nor common design are required to explain a subjective construct.
You can start a new thread on the
watchmakerorphan featuresI refer the reader to this diagram of the supposed phylogeny of Coelecanths, Lungfish, and Tetrapods (from tetrapodomorphans):
https://en.wikipedia.org/wiki/Sarcopterygii#Phylogeny
I’ve already stated not every scientist agrees with the Rhipidistia clade. I could just as well be a Tetrapodamorpha-Lungfish-Coelecanth clade, or a Tetrapodamorpha- (Lunfish-Coelecanth) clade. I’m sure someone can come up with some fancy sounding Latin name to make illusions seem like reality, but that is not essential to the point being made.
The point is We have approximately 3 lines of descent:
Since they diverged supposedly about the same time, we need not strain over whether Rhipdistia is real or not. So what pattern of sequence divergence would we approximately expect given molecular clocks and that the lines are reproductively isolated therefore it limits application of coalescence theory to explain pattern anomalies. The divergence should look something like this give or take a percent here or there:
But it doesn’t!!!!! It looks like, for Cytochrome-C anyway:
Did the Coelacanth and Lungfish lines CONSPIRE to simultaneously evolve so slowly??????????? You think I’m making this anomaly up? You might think so, but then I found this:
https://www.smithsonianmag.com/science-nature/dna-sequencing-reveals-that-coelacanths-werent-the-missing-link-between-sea-and-land-25025860/
BALDERDASH! That “evolving” slowly is an artifact of the phylogenetic tree chosen and the wrong interpretation of the fossil record and the assumption of macro evolution, not that it is evolving slowly.
What is really really bad, and what the article didn’t point out is that the Lungfish and Coelecanth distances suggest both creatures simultaneously adopted slow molecular clocks for no good reason!
I saw the same blasted anomaly with Cycads trees. I suspect it exists in the aaRS genes of bacteria. Heck practically huge families of genes within species. One just has to be willing to see it. And need I remind the reader, here is paleontologica” confirmation of this anomaly:
https://academic.oup.com/mbe/article/19/9/1637/996854/The-Paradox-of-the-Ancient-Bacterium-Which
I’ve just laid out data points demonstrating the standard phylogenies are rife with anomalies. I contend the anomalies are indication the standard phylogenies are wrong.
Nope. You got it totally backward. This is real:
Rhipidistian is not real, it is an illusion.
Taxonomic hierarchies are real, as matter of principle, 99.99999% of possible phylogenetic hierarchies are not real, maybe even 100.00% of them. The 99.999999% figure is derivable from this essay I linked to earlier:
https://academic.oup.com/sysbio/article-abstract/27/1/27/1626689?redirectedFrom=PDF
This has been comprehensively debunked on this very site. And you’re Gish galloping about complete irrelevancies again.
Freaking too funny. You guys bash colewd over the head with cytochrome-c and now that the favor is returned and I bash your arguments with cytochrome-c, you complain I’m using cytochrome-c.
Did you notice the Smithsonian article suggests the anomalies are geneome wide? How the heck did all the lungfish AND coelecanth genes conspire this way?
stcordova,
Sal, you’re being incoherent again. Please be extra careful to make whatever point you are trying to make clearly, explaining your reasoning and evidence step by step. Otherwise you just come off as Captain Queeg. (I’m thinking of his “It all began with the strawberries” meltdown.)
So why do you assume a molecular clock? Why do you assume that the fishies are oddly slow rather than that the mammals are oddly fast?
It’s not an essay; it’s a scientific paper. And you appear to have no idea what it means. Yes, the number of possible trees increases very rapidly with the number of taxa. But it turns out to be fairly easy, using modern phylogenetic methods, to find the correct needle out of that haystack when the data are good. You claim to have respect for Joe Felsenstein, yet here you quote-mine him shamelessly. Get yourself some shame.
In fact you have laid out no such data points. That you think you have just shows how little you know, despite being in a course, about phylogenetics.
It appears (did appear) without the assumption of common descent.
It leads open minds to the idea that it comes from common descent.
Glen Davidson
Then I have no idea what you are talking about. Pehaps you can clarify by answering John’s questions:
What is the explanation for the existence of the “taxonomic” hierarchy? How does it differ from the “phylogenetic”hierarchy? And what makes you say that the phylogenetic nested hierarchy does not exist?
It happened in the Lenski eksperiment. The molecular clock changes in independent lineages in parallel, and descendants inherit the clockrate. It is an observational fact that this happens. Nothing has to “conspire” for this to happen.
And here you’re confusing determining the exact branching order using a single gene, with determining whether there is common descent of the species in question
What we explained to Bill Cole, and to you, using cytochrome c, is the extremely high level of congruence between independent phylogenies (in that case, as Theobald showed, cytochrome c phylogenies compared to morphology). This is evidence of common descent, the consilience of independent phylogenies.
What you’re talking about is resolving how the tree really looks. As in, what is more closely related to what?
The fact that it can be difficult to resolve the exact interrelationships among certain groups does nothing to take away from the evidence that the species included in the analysis are virtually certainly all commonly descended. Mung also seems to have confused these two different points several times.
We can make an analogy here to human family relationships to clarify the point. It might be very difficult to determine the exact relationships among ten different descendants of Ghengis Khan, but much more easy to demonstrate that all ten of them really are descendants of Ghengis Khan. Is person 1 more closely related to person 2 or to person 3? Ambiguities in the data can make it hard to determine, especially if they all “branched” closely in time. But that fact does not cast doubt on them being closely related.
See. Even Salvador accepts common decent.
Now if someone would kindly ask him why he accepts common descent in these three specific cases but not others.
Sal is rather famous, even among fellow IDcreationists, for not ever experiencing that particular emotion. Anybody remember that whole “quisling” quote from Barry Arrington?
If you only know one thing, do what you know.
Speaking “evolutionarily” is just another way of saying “story-telling.” So what does it mean to be speaking truthfully when telling a story? Does the story of Snow White and the Seven Dwarfs speak truthfully”?
It’s a true story though. Some stories really are true. And it is in this case.
99.9999…% possible ones don’t as a matter of principle.
Refer to this paper and connect the dots:
https://academic.oup.com/sysbio/article-abstract/27/1/27/1626689?redirectedFrom=PDF
So, your belief in the phylogenetic tree rests on that hypothetical .0000……01% of the population of hypothetical trees. So what is the necessary condition for that tree to be real? Common descent. But common descent is the premise you are wishing to prove, soooo, without recourse to circular reasoning phylogeny is not formally provable.
However taxonomic relationships, such as the fact we are more morphologically similar to chimps than to blades of grass.. That is real.
Don’t you see you are conflating concepts in desperate attempt to justify phylogeny. Taxonomy and phylogeny may correlate, but they are not the same thing.
Preach it brother, preach it.
Well, he brings plenty of shame onto himself.
Glen Davidson
Sarcopteryian fish is redundant.
http://www.newworldencyclopedia.org/entry/Sarcopterygii
I don’t know. Are they? Does similarity mean shared ancestry?
What does that even mean given a hypothesis of universal common descent, where even dissimilar DNA sequences share a common ancestor?
Not necessary to preach when there is evidence. Though I have to admit it is rather ironic that you’re basically conceding that asserting a conclusion with no supporting evidence or argument constitutes preaching.
So natural selection is like human inventors.
He was confused by Darwin’s use of analogy instead of just being woodenly literal.
Typological categories are real, cladistic and phylogenetic categories are illusory, at least most anyway, as a matter of principle. Can we say Rhipidistia?
The easiest way is claim divine inspiration and divine mystery
Care to expand? Does this follow from some design principle?