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.
If you like, you may call them POOFamorphies. It won’t change a thing; tetrapods share a few of them with lungfish/coelacanths that are not shared with other “fish”.
Regardless whether you prefer common descent or common design, that remains a remarkable fact.
So they pick two hundred and fifty one genes shared between 22 species, all of them found in the cell nucleus – “CHERRY PICKING”.
And you picked (by accident because you thought it was cytochrome c) the 1-subunit of cytochrome c oxidase, which is found in mitochondria instead of in the nucleus, with about half as many species. But somehow it’s them who are cherry picking?
It would not even be possible for you to fit the textbook definition of psychological projection any better.
colewd,
And yet you feel able to argue for Common Design as a viable alternative to this thing that you don’t know what ‘it’ is?
If two individuals or sequences, or groups of the same, share genetic ancestry, they are said to be ‘commonly descended’. I know, science can be tough to grasp sometimes …
Bill has moved on to yet another phase it seems. So far he:
1) maintained that common design is a better explanation for the nested hierarchy then common descent
2) questioned that the nested hierarchy exists.
3) asked for the definition of a nested hierarchy.
And now, he is asking for the definition of common descent. Really, he is like Benjamin Button sometimes.
Mung,
What? That makes no sense. If two entities share common ancestry, that is a node on the tree. Their shared characteristics delimit a subset of the broader set in which they nest. That’s a nested hierarchy, at the level of a single node.
Mung,
I’m not the one thinking the evidence weak, so I don’t know what ‘weak evidence for common descent’, as a general thing, would look like. I only know what the evidence there is looks like, not some hypothetical in which present evidence is absent and there is something else instead.
I think the evidence is strong because genetic identity is only known to be produced by template based nucleic acid replication. This logic is (to repeat something of a mantra) sufficient to legally establish paternity, forensic association, and even, taxonomically, to infer common origin in species pairs such as Spotted and Common Sandpipers, or Nile and Saltwater Crocodiles – at least, among some Creationists with a passing acquaintance with the natural world.
So, if that logic is accepted at all, as we follow broader and broader taxonomic groupings we find that percent identity goes down progressively, but does not disappear at a discontinuity. In the absence of this discontinuity, I think the logic continues to hold throughout the series. There is no obvious point at which common descent stops being the explanation for genetic commonality, and ‘Common Design’ takes over.
You need to be a bit more precise on what you think of as ‘extensive’, as a threshold below which you think the inference breaks down. I think if there is – say – 40% identity, that is actually a huge amount, needing explanation, and takes us a looooong way down the taxonomic hierarchy.
Of course we can. Why would you even need to ask? It does, however, introduce a complication that need be of no concern when looking at species patterns.
Here is a useful basic introduction to homology search. In it, the following bold statement is made:
People that think this kind of ‘pairwise’ analysis breaks down at some taxonomic remove could helpfully point to the place, in a cladogram of their choosing***, where they think that inference breaks down.
*** (Note that this has nothing to do with the nested hierarchy as such, which is a layer of support superimposed upon this kind of quite naive inter-branch comparison).
Wow, this concept sounds about as useful as the one about fitness.
So, to be clear, you now have a problem the concept of two individuals sharing an ancestor?
Corneel,
Where did I ask for a definition of common descent?
Is the definition of them sharing ancestry that they are commonly descended? Or is the definition that they are commonly descended that they share ancestry?
Survival of the fittest. Undoubtedly!
Allan Miller,
I used universal common descent as a working assumption. I now see your definition falls a hair short of that one 🙂
How much of the tree of life falls into this category? I see below you and Mung are debating a line of demarkation for descent and design. Do you think you could establish descent with an expected DNA sequence variation of 1%?
colewd,
You always stick the implicit word ‘universal’ in front, both in reading and in writing. If I don’t see a word, however, I don’t address it. Do you think that universal common descent is something significantly distinct from common descent as defined? Would it be legitimate to say that the issue is Universal Common Descent vs Universal Common Design? What is the Universal Common Design?
Two random sequences would be expected to align at 25% of positions. It is possible (see the reference above) to statistically assess the likelihood of two non-homologous sequences aligning by chance. Below this threshold, you could not establish common descent, though you cannot rule it out either, because ongoing divergence must eventually result in that 25% figure, even in sequences that really do commonly descend.
As to what is a ‘reasonable’ threshold – take your pick. But you would have to wonder why the alignment is statistically significant, if you chose one that was too high.
Rumraket,
Hilarious. If a definition is simple, it’s useless, in phoodoo world.
How, at this late date, is it still possible for you to misunderstand so completely. Yes, it’s the pattern. No, it isn’t just the overall similarity. Please read entire posts instead of just little snippets you can distort to fit your purposes.
No. I’ll agree that the name sounds like common descent, but it doesn’t have to be defined that way. It can be defined purely in terms of general vs. restricted distribution, purely topologically. In fact trees are built without the need to define character states as either derived or primitive, because the analysis is unrooted. The root, and thus character polarity, is imposed, generally by outgroup.
Intuition is a poor guide to any science. What is this, the Force? “Trust your feelings, Luke”? I prefer to rely on rational thought.
Mung,
Lifted from your citation. Universal Common Descent is a “working assumption” according to UC Berkeley.
What a monster assumption. My fine alma mater has balls 🙂
You’re fooling yourself there, since you believe in sudden, recent creation. That means you have to ignore most of physics, especially anything to do with nuclear decay. I’ll ignore the rest of the insults.
I’m getting tired of you not reading my posts, just searching them for quote-mines. Is that really the sort of thing a good Christian ought to do? I’ve explained two ways to analyze data containing orphan genes, and yet you still come up with this irrelevant crap.
Now by “orphan genes” I mean genes with no detectable homologs in some groups; incidentally, I doubt that there are many within animals, so there’s in fact a third way to analyze what you are calling by the name: since they’re almost entirely part of gene families, you can analyze the families, with genes branching by duplication events to produce parallel trees from different variants.
So now three ways, all of which you will just ignore to make your quote-mined points.
Allan Miller,
I think universal common descent is implied by some and not by others. You can see below that UC Berkeley uses it as a working assumption for evolution. We all know that common descent occurs the question is how much of life’s diversity does is represent. Common design is not universal as we know at least in species diversity is created by descent because we observe it.
The challenge is that you need to take the whole genome into account and see if known processes like genetic recombination and mutation are likely to account for the change. Along with sequence differences there are epigenetic changes that Sal has brought up and alternative splicing differences that have been discussed in several recent papers.
I do think that close study of in species variation is a good benchmark as the evidence of descent is strongest here.
colewd,
I don’t think obsessing over ‘universal’ adds anything of value. Most Creationists are arguing near the twig-tips, not the roots. The purpose of my endeavour is to try and get someone – anyone! – to focus on the rationale for inference of Common Descent in a clade where it is non-controversial, then to navigate outwards to try and pinpoint where they think the one (Descent) shades into the other (Design) – a boundary invisible to phylogeneticists and to BLAST searches.
Extraordinarily hard, this task!
Allan Miller,
I think you are spot on where this discussion should go.
Allan Miller,
But we have the best and brightest driving it. 🙂
It’s here.
.
I was reading that as if you were asking for a clear definition of common descent. Others read it like that as well. At 4700 comments in, this looks a bit tardy.
Corneel,
Fair enough. It was a comment not a question. Very early in the discussion I asked for a definition of a nested hierarchy as you pointed out and had no luck getting an answer. After thousands of posts I started to understand the concept.
Then stop participating for your own sanity. I really don’t mean you any harm. You’re one of the most decent guys here at TSZ, but I think your on the wrong side of truth.
You’re so convinced you are right you don’t even see you are using circular reasoning. The circular reasoning is embedded in your training and practice which is ubiquitous in your field. This circular reasoning leads to cherry picking and distortion of logic.
Let’s go back to your insistence I don’t understand. The definition of derived character:
From wiki on synapomorphy:
https://en.wikipedia.org/wiki/Synapomorphy
Now you’re expert enough that if you don’t like that wiki entry, you can try to set the wikipedians straight with your own edit, but it seems to me, a lot of your colleagues would not want you to try to remove the premise of common descent from the definition of derived character.
Remember the last time this was attempted:
https://en.wikipedia.org/wiki/Transformed_cladistics
There you go. You pretend like I didn’t even cite and mention this stuff earlier in the discussion. That’s because in your own mind you want to convince yourself I don’t understand, am not familiar with literature. The alternative of course is that the problem is not with me, it’s with the belief system you’ve adopted.
I feel for you John, you’ve invested so much of your life to a theory that is at best speculative. A mind like yours might have done wonderful in another field of biology like anatomy and physiology….instead you’ve invested it in a theory built on circuitous reasoning and cherry picking and equivocation…
About 2200 comments into a thread is “very early”? mmmokay. I answered your question by the way.
How soon they forget.
Haha, yes that would be the other option I guess.
colewd,
What my detractors here have been trying to pin on me is that I don’t understand. I don’t comprehend, blah blah blah…..same old playbook for the last decade….
They insist I use their definition of nested hierarchy based on the ASSUMPTION of common descent, not the nested hierarchy that is based purely on structural and functional considerations.
Notice how they reacted when I asked a simple question about the similarity of 3 creatures: Lungfish, Tuna, Pigeon. Which of the 3 possible pairs of creatures are more similar in skeletal structure:
1. Lungfish and Tuna
2. Lungfighs and Pigeon
3. Tuna and Pigeon
The answer is of course Lungfigh (Sarcopterigiian) and Tuna (Actinopterygiian) are the most similar.
But this would so violate their implicit claim that we (mammals, birds, amphibians — tetrapods) are more similar to Lungfish(Sarcopterygiian) than Tuna (Actinopterygiian) are to Lungfish (Sarcopterygiian). This is the claim implicit in this graph:
https://en.wikipedia.org/wiki/Actinopterygii#Classification
In contrast, a gene tree which I created with the Cox1 gene accords better with the idea Tuna and Lungfish are more similar than Lungfish and Pigeons. Now pigeon isn’t there in my graph, but many tetrapod sisters of the pigeon are there.
It is a DIFFERENT nested hierarchy. They keep arguing there is only one nested hierarchy. Not true. Depending on the gene or sets of genes that are picked,one gets a different tree.
The question is which tree is most representative. Well, if one believes in Common Design, the question is one of conceptual utility, not that there is a right or wrong answer. But if one argues there is common descent, then there can be one and only one tree. But when the data gives multiple conflicting trees… that is evidence against common descent. But they don’t want to hear any of it. They would rather put the focus on me than actually defend the case from the data.
Click to enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2017/10/nj_differnces_circled2-111-1.png
Yes, try to reason with Sal, or leave that off and save your sanity.
Too true.
Glen Davidson
Of course you didn’t get an understanding of the nested hierarchy from IDists/creationists. The only alternative would be to learn from the science side, and you received copious references and links to such sources (Theobald, anyone?).
That’s the problem with “learning” primarily from the pseudoscientists, though.
Glen Davidson
Corneel,
Thanks for jogging my memory. Well, I stand corrected less then half way through and you did not provide a definition as I see now.
stcordova,
As evidence of Cornels response to my request for a definition the tactic appears to create confusion so they can continue to make the claim that no one else understands the inference.
At this point I am skeptical that you don’t understand 🙂
Since one of my comments to glen davidson was guanoed here:
I’ll repeat the question with the offending phrase replaced with sarcasm:
Same old shit, same nastiness.
Decent people respond to what the person has written, rather than demanding that one comply with nonsense.
Glen Davidson
stcordova,
The claim that the pattern we see is the result of inheritance is a big claim and I think the data you provided puts into question the matching of phylogenetic and morphological trees which are an important part of their claim.
I agree with Allan Miller that the right tactic is to go back to nesting where we know ancestors are related and look at the data. We should look at least at sequence comparison, epigenetic marking comparison and alternative splicing comparison to see if a claim of a transition is reasonable among species that we don’t currently know share an ancestor.
Since common descent only attempts to explain the nested hierarchy it is very limited as an explanation for the diversity of life even if it turns out to be true.
colewd,
As you were discussing computer systems, it may be fair to say there is no single absolute way of conceptualizing a classification system. There is no problem with that. We can classify genres of music, but there not need be and single way absolute way to classify music.
However, certain groupings make more intuitive sense based on structure. For example classical music would naturally be a distinct genre than speed metal. The same could be said of movies.
The problem for common descent is that evolutionists claim there is one and only one hierarchy, and that all data point to one-and-only one evolutionary pathway. But this falls apart with Horizontal gene transfer, convergence, and mechanistically infeasible pathways.
The reason I keep harping on the comparison of the Lungfish and Pigeon is that it highlights the infeasibility of common descent without some statistical miracle.
In the process of trying to group things naturally by overall similarity vs. cherry picked similarity, the feathered wings, the toes, the claws, the avian lung, the avian thermoregulation, etc. etc. vs. the absence of these characters in the lungfish become brutally apparent. But as John Harshman said, common descent doesn’t explain the origin of these characters!
So common descent doesn’t account for the branching patterns of diversity when the patterns of diversity involve the punctuated POOF-like presence of characters in one group that are absent in another. At best, and this would be a stretch, common descent might account for the similarities, but even then it needs POOFS to make that happen.
The problem is however, if a fish can’t evolve claws and feathered wings, then a fish didn’t evolve into a bird, and common descent is falsified. Therefore the similarities are because of common design, not common descent.
stcordova,
I agree here especially with convergent evolution. Mung’s little tune still rings in my head.
Look at how many times eyes have evolved so you see how easy it is to evolve an eye.
I have no problem trying to reconstruct a phylogenetic nesting WITHIN a species. For example, where individuals can interbreed this is totally fine as in the cases highlighted here regarding DNA:
stcordova,
Exactly. If as a working assumption both common design and common descent are true the science is to try and find the real lines of demarkation.
I asked this question of Glen Davidson, one of the leading champions of evolutionary theory and determined foe of creationism:
Glen could say, “1”, “2”, “3”, or “I don’t know,” or “I’m undecided”. Instead he responds with such gentle words fit for all the children reading:
Ah, but Glen, this is a simple question about comparative anatomy. Surely you’d like to enlighten the readers of your opinion. You don’t ever seem to hold back how you feel. How do you feel about those lungfish, tunas, and pigeons. C’mon glen, no need to clam up now. You got to help Rumraket out, because he suddenly clammed up on that same simple question.
C’mon, in the spirit of Christmas, won’t you even venture to offer an opinion. You’ve hardly withheld an opinion before, but now that a trivial question comes up, you clam up. Why? 🙂
And? What does that have to do with anything?
Actually I very much doubt it would take only 12 generations to get “carbage trees”. Even at that distance there’s still going to be some signal left. It would be trivial to test.
But even if that was correct, it doesn’t matter. There was still convergence of independent phylogenies despite these confounding factors. If it had been more realistic genome sizes and mutation rates, there would have been an even stronger convergence between individual trees. Because the factors that erase phylogenetic signal (reversal and homoplasy) are much lower in real biology.
That means you should find it EVEN MORE CONVINGINC when my example STILL showed convergence of independent phylogenies.
And none of that matters, because that constrains sequence towards function, it doesn’t constrain sequence towards branching orders of phylogenetic trees.
Do you understand what that means Bill?
I have addressed all the versions of common design you have been able to dream up.
Then I would have to question your sanity, or intelligence, or both. What the hell does “convergence of c mos gates” even mean?
What does that mean? Try to explain yourself.
Then do it. Show it.
Then do it.
Then do it.
Do the work. I did.
What does that even mean? “Nest the mac laptop”? “simulate common design as they are built by the same company”? What the fuck does any of that even mean? You just type random, barely related words.
So you reject the notion of biblical kinds as common ancestors of the various “baramins”, and you think all species on Earth had to have been on the Ark.
Not physically possible.
It’s not the proper question, which is why you’re asking it.
Same vicious nonsense from the person too rude to respond to what I wrote.
Glen Davidson
Yes. He is counting on the thread reaching at least 22,000 comments.
Let me repeat the answer: They aren’t grouped merely by how superficially similar they look. Clades are defined by characters exclusive to the group.
And why would a phylogenetic tree constructed by alignment of 251 nuclear genes corroborate the morphological tree?
Hardly. It explains the convoluted development of organisms, like the otherwise strange case of rigid wingbones being fused out of several separate bones during early development, bones that used to become articulated in terrestrial dinosaurs. It’s not the whole story, but it does explain why development doesn’t begin with a more rational choice.
It helps to explain the progression of life, including transitionals, like the poor flyer Archaeopteryx, and why such transitionals tend to be mosaics of the new and the old.
It’s a major part of the explanation for vestigial organs, like the teeth of young baleen whales that fall out without being used, or the vertebrae of our coccyx.
Common descent explains why life doesn’t get to use better organs from separate lineages, so that we don’t get bird lungs, and birds don’t get mammalian auditory ossicles.
Pseudogenes for yolk proteins in placental mammals are explained substantially by common descent, much like other pseudogenes.
Many of these are related to nested hierarchies (not the progression of life, to be sure), but the point is that the nested hierarchy is a kind of abstraction built out of many facts that are explained (at least in part) by common descent. To take the abstraction as the sole thing being explained (which would still be one more thing than common design does), when in fact it is involved in explaining nearly everything in biology, is certainly a major reductionist error.
Glen Davidson
When you’re going to lie about other people it usually helps if they’re not present to call your bullshit. I already answered your ignorant question here.
“I think you’re confused. I it is not that they are supposed to be “more similar” in their shared characters, it is the presence of certain characters that yield particular groups. So when chickens are grouped with lobe finned fish in sarcopterygii by the method of cladistics, it is because they share at least one particular character not present in actinopterygii. Whether the shape of their skulls and spine are more similar between the lungfish and the tuna is irrelevant, as they are essentially a character shared by all three species, e.g. they are vertebrates.”
“It’s not based on the degree of similarity of shared characters you gimp. Hiearchies are defined by characters exclusive to a particular group. You can find a snake and a worm superficially similar with their long slim bodies, but the snake is a vertebrate and the worm is not.
Carl Linnaeus didn’t group snakes and worms together Sal. Why?”
LOL. Well done quoting an article that says this:
“Because creationists lack scientific research to support such theories as a young earth … a world-wide flood … or separate ancestry for humans and apes, their common tactic is to attack evolution by hunting out debate or dissent among evolutionary biologists. … I learned that one should think carefully about candour in argument (in publications, lectures, or correspondence) in case one was furnishing creationist campaigners with ammunition in the form of ‘quotable quotes’, often taken out of context.”[3]
Gotta admit he’s got you nailed there.
We also learn that Patterson (the transformed cladistics popularizer) said this:
“[i]n terms of mechanism … the neutral theory of molecular evolution is a scientific theory; it can be put into law-like form: changes in DNA that are less likely to be subject to natural selection occur more rapidly. This law is tested every time homologous DNA sequences are compared. … But neutral theory assumes (or includes) [the] truth of the general theory – common ancestry or Darwin’s ‘descent with modification’ – and ‘misprints’ shared between species, like the pseudogenes or reversed Alu sequences, are (to me) incontrovertible evidence of common descent” (p 119).
Since you’re all about argument from authority this should cause you to think.
I believe you.
Tuna and lungfish have gills exclusive of birds, they have a similar skeletal structure exclusive of birds. What’s your problem? Lungfish have a lung, but that isn’t an avian lung. So even by your terms, you can’t seem to answer the simple question. Which pair among the three have the most overall similarity based on YOUR criteria.
1. lungfish and tuna
2. lungfish and pigeons
3. tuna and pigeons
Use YOUR criteria and explain to the readers and me how you arrive at an answer. You keep saying I don’t understand. Ok, so let’s go through a small character list and see your methodology.
Surely you’re not going to buy what other people say rather than exploring the question yourself with own inquiring mind. If you bought what other people said, you’d still be believing Ohno’s claim about Nylonase NylB.
C’mon Rumraket, this shouldn’t be that hard a question to answer. Use YOUR criteria, and see what you come up with.