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.
John Harshman,
There are 30% more substitutions between species in the bird vs croc. How can you claim there is no difference in the pattern? There may be a gene dependent reason but it is clearly worth investigating. One pattern is almost the same and the other has greater difference then between crocs and birds in the myc gene per your paper if the 14% mentioned is accurate.
As far as crocs geographical diversity, you make a good point worth investigating.
stcordova,
This is a good point. Interbreeding is positive evidence for common ancestry.
Before I forget, belated Merry Christmas and Happy New Year, OMagain.
Really, don’t bother.
Certainly, if by “we” you mean creationists. But I do know enough. Why do crocodylians have a nested hierarchy? What’s your hypothesis on that?
I have three other questions. Why is hybridization evidence of common ancestry? Is lack of hybridization evidence against common ancestry, and if so, why? What would you have to know in order to decide whether crocodylians are or are not a single kind?
More evidence that you don’t understand. Phylogeneticists don’t define nested hierarchy in terms of common descent. We explain nested hierarchy in terms of common descent. I’ve told you this many times before, but you either don’t read it or don’t remember.
I’m not sure exactly where you’re getting those numbers. I’m not sure why you think more substitutions makes a different pattern. Aren’t grapefruit and clementines still citrus fruits? I don’t know what you mean by “a gene dependent reason”. The reason for the different distances is that 1) birds have probably been separate for longer than crocodylians and 2) crocodylians probably have a lower overall rate of molecular evolution than birds.
How would you investigate this point, and what would it mean if you found any particular fact?
Why?
That’s a very good question. I bet it goes back to the bible and “baramin” thinking.
Yes you told me, but I don’t agree. I read, I disagreed. I remembered, but I disagreed.
The proof you phylogeneticists are creating nested hierarchies on common descent rather than a straighforward comparison of structure is the way you pair these three skeletons together: lungfish, tuna, pigeon.
Even you admitted you don’t group them according to similarity. So what principle do you group them under? The simple answer is “common descent”, but you’re not wanting to say that because it will belie the circularity of your reasoning which I pointed out and which will be so embarrassing now to admit.
So instead, you talk about anything else, you assert I don’t remember, I don’t read, I don’t understand. Ok, so assume I don’t understand, what criteria then do you use group the creatures together. Rumraket said, “new features”. Huh, new? As in something that was added during common descent? Oops, that’s an implicit assumption of common descent.
No, the answer is that they are grouped according to hierarchical structure in the data. Hierarchical structure can be represented by fit to a tree. Ordering by similarity does not demonstrate hierarchical structure; any data can be ordered by raw similarity. But only hierarchical data can be consistently fit to a single tree.
(Incidentally, I don’t think you know what “belie” means.)
No, it merely refers to differences on a rooted tree. You might suppose that rooting assumes common descent, and perhaps it does. But determination of hierarchical structure doesn’t need a rooted tree, and in fact almost all phylogenetic analyses produce unrooted trees, to which rooting is added later. It’s a consistent fit to an unrooted tree that shows the nested hierarchy in the data. Given that branch lengths on an unrooted tree can vary significantly, ordering by similarity can’t equate to fit to the tree and therefore can’t show nested hierarchy. You could certainly force a tree onto such data, but remember that the nested hierarchy of life is discovered, not imposed.
So, where does the nested hierarchy of the data come from? Do you have an explanation? I do.
It’s a parsimonious explanation for the similarity of crocs.
If you could show the same for a cow mating with a blade of grass and producing viable offspring, then that would suggest a cow and a blade of grass share a common ancestor.
Barring that, you could simple say, “I don’t know.”
If you want to wager on an answer, you can guess or profess faith in an answer. No one certainly “knows” in the formal sense what is true. Ascent to the truth requires faith as a matter of principle because of we lack omniscience.
colewd,
I mentioned TopoIsomerases in my discussion of the RAM embedded in proteins.
This is a 2-minute video of how TopoIsomerase cuts and then repair DNA in order to unknot (uncoil) DNA. Without TopoIsomerase, it would not be possible to replicate DNA in the manner that is replicated (outside of Rolling Circle replication).
How it cuts and repairs shows what powerful molecular machine it is. How it knows when and where to cut and repair DNA is still an unanswered question. Obviously it must be regulated. I provide this 2-minute video for your amusement and wonder at the works God has made:
You group them according to homologies, which Owen worked out before he accepted evolution. Earlier, homology was a mystery, but certainly seemed to group organisms in non-arbitrary ways, while analogies grouped organisms in ways that ultimately did seem arbitrary, despite the attempt to match up certain similarities.
To be sure, taxonomy did continue to rely on analogy as well as homology for some time after Owen had worked out the difference between the two. With cladistics, though, homology rules, notably with synapomorphy. I suppose I do think that by now common descent is assumed, but then why wouldn’t it be? It’s strongly indicated by the nested hierarchy(ies), as well as by fossil succession.
Glen Davidson
What do you mean by that? What’s a parsimonious explanation for the similarity of crocs?
Again, why?
I don’t know what?
That has a name: epistemic nihilism. Not pretty.
Nothing in that post made any sense whatsoever. I can’t even tell what you were trying to say.
Awh c’mon, I actually like you. I don’t say such nice things to DNA_Jock or Entropy or Glen Davidson or (gag) Gregory.
Speaking of other people I like. Merry Christmas and Happy New Year dazz and newton and Richard Hughes.
colewd,
Why? Why can’t interbreeding individuals be separately created, if any degree of identity can?
All the interbreeding capacity indicates is that the genetic identity between two haploid genomes is sufficiently high to permit successful F1 meiosis.
It’s not uniform in practice, but one can idealise it. Suppose there were a threshold identity, X%, permitting interbreeding. The actual percent identity varies by y. If genomes were X+y% identical, you would declare them commonly descended. If X-y% identical, you would say they were not. I don’t see the rationale here – especially if y is imagined to become infinitesimal. It is clear that the general trend of ongoing evolution must be to move in the direction of X-y%, from X+y%, if genomes are free to diverge. So, if you find two species with significant identity that nonetheless cannot interbreed, it must at least be possible that they evolved to that state from an interfertile state.
Allan Miller,
How did you get this question out of the statement I made?
Allan Miller,
I would say that interbreeding is evidence they are commonly descended. One piece of evidence. If I witnessed both births that would nail it 🙂
Happy New Year, Allan.
colewd,
You regard interbreeding as positive evidence for common descent, and hence sufficient to prefer it over separate creation at that particular degree of relatedness, so far as I can ascertain. I don’t see why.
colewd,
You seem to have simply ignored the argument I presented in the blockquote. Happy New Year anyway!
Allan Miller,
The first part is right. I had not thought through preference over separate creation. I would say that if interbreeding is possible then the probability of common descent goes up.
This is not really my thinking at this point as I don’t see it as this black and white however I do think your argument has merit as a way to discuss potential lines of demarkation.
Where clear lines of demarkation start to form in my mind is large sequence variation, large alternative splicing variation and large change in chromosome structure.
An example is the chimp to man change where in order to claim common descent without Devine intervention you would have to figure out how the chromosomes could fuse through a reproductive process and then get fixed in a population. Not trivial.
colewd,
Yep, you want to leap from the argument looking at infinitesimal distinctions to the gross. But do you accept the possibility that a non-interbreeding pair of populations can arise by evolution, by pushing the amount of residual genetic identity between separated populations below my hypothetical interbreeding threshold X?
Allan Miller,
I have no reason to doubt this is possible but the devil is in the detail 🙂
Again, why?
Happy Holidays
Right, and this fusion becomes THE REASON the new ape reproduces, through thousands upon thousands of new generations. The people aren’t being selected for their good teeth, or climbing ability or strength, they are being selected for this one and only one reason at the beginning. Because if that wasn’t the case, and nature were selecting for other traits instead, it of course would die out rather quickly.
That’s a pretty tall tale.
I find evolutionists don’t like to try to imagine these first events and their progression. They just say, well, it happened somehow.
In real life, identifying the “first events” is effectively impossible. We might notice, for example, that within a breeding population some subgroups tend to breed with one another statistically more than with members of other subgroups. We might speculate that this breeding population might be undergoing sympatric speciation for some reason. But there is no “first event.” After some perhaps many thousands more generations, this might result in complete breeding isolation. Species branchings are gradual processes that sometimes do NOT run to completion.
My understanding is that for small differences in breeding among subgroups, perhaps even the breeding organisms can’t tell the difference. It would be tough to identify why they might be getting “selected apart.” It might even be that whatever physical differences eventually emerge might or might not suit the slightly changed subgroup to any particular niche. The branch either fails to complete, or the new species itself fails.
phoodoo:
phoodoo,
I’m not sure it would help, but have you ever considered taking a course on the basics of evolutionary biology?
Just a reminder of the rules:
So claiming fellow members lack intelligence is against the site rules (and as about as helpful as telling short people they need to be taller). There is no rule against a charge of a specific instance of ignorance, since that is rectifiable with a little study.
Why, are you hoping to hire someone to teach you?
Perhaps; regardless, finding populations that cannot interbreed is not, because of the possible progression I outlined, a good reason to doubt that their genetic identities are due to their common ancestry.
Nor does finding populations that can interbreed itself indicate common ancestry, rather than the extent of inter-population heterozygosity, ie the extent of their % alignment. Interbreeding has an effect on gene flow, and hence on maintaining a population around a ‘mean’ of overall divergence, but it is not a reasonable boundary at which the inference of common descent is robust on one side, circularly speculative on the other.
A mutation, like a chromosome fusion, might be fixed in a population by mere drift. It could also be the case that the mutations giving early humans an advantage, co-existed in individuals with the fused chromosome, making it a “carry-over,” or maybe the fusion is behind some phenotypic advantage. We don’t know. But there’s plenty of reasonable possibilities. It’s not as if inconsequential fused chromosomes never happen.
Which makes me wonder why on earth would you propose it.
Of course we like to imagine these first events and their progression. It’s creationists who are never happy if we do, or if we don’t. If we do, then we’re making up “just-so stories.” If we don’t, we’re guilty of not imagining.
Either way, just imagining won’t tell us what happened. Imagining potential scenarios is helpful for designing strategies to figure out if any of what we have thought might be the case. If no strategy comes to mind, then we have to wait for more data, maybe better technologies, and much more thinking.
Obviously, since we see it, it happened somehow. What’s so wrong about it?
Alan,
TSZ functions much more smoothly in the absence of your (and Neil’s) goofy moderation decisions.
Don’t spoil it.
Keep reasonably to Lizzie’s rules and you’ll be fine.
Alan,
Lay off the moderation and you’ll be fine. It’s when you start guanoing that things get fucked up.
TSZ functions much more smoothly in the absence of your (and Neil’s) goofy moderation decisions.
keiths,
And please discuss moderation issues in the appropriate thread. You should be aware of these rules by now.
Moved a comment to guano.Please discuss moderation issues in the appropriate thread.
And another. Moderation issues, moderation issues thread.
By the way Happy New year everyone. Especially as 2018 promises change for our US members!!!
Alan:
Will 2018 be the year you finally follow through and resign, as you said you would? That would be something to look forward to.
John Harshman and others have criticized my YLC claims by saying the anomalies I cite are minor. I sharply disagree.
One of the most famous Paleontologists/Evoltuionary biologists in history was Stephen J. Gould. It is well-known fact, albeit mostly forgotten, he had a YEC PhD student who was an undegrad student also of Paleontologist David Raup (the best of the best), by the name of Kurt Wise.
Wise gives the YEC perspective in the following 45 minute video and explains the problem of bio purturbation. You see, one might complain that I’m illiterate, but one can’t complain Kurt Wise is illiterate. After all he was Gould’s PhD student at Harvard and Lewontin’s graduate research assistant.
The relevant part is 9 minutes in.
https://www.youtube.com/watch?v=FWUwkeLT5YQ&t=587s
How is this relevant to common descent and common design? There simply wasn’t enough time for common descent to evolve the variety of forms on the planet. Ergo, the patterns of similarity are the result of common design via miraculous special creation, not random mutation acting on commonly descended creatures over millions of years.
I’ve tried to argue against common descent using the Old Fossil Record paradigm, and my claims sort of have traction there, but that all may be un-needed work if indeed the fossil record is young, just as I pointed out in the OP.
Allan Miller,
Do you think the probability of common ancestry is the same whether two populations can interbreed of not?
Of course you do. You have to, because if they’re minor you have no case, and you have to have a case because you know you’re right. Not the way science works. Have you considered the major anomalies in a young-earth position?
Of course you’re illiterate. For one thing, it’s “bioturbation”. Wise isn’t illiterate, just so committed to his cause that he ignores all contrary evidence. For example, Wise thinks the K/T boundary is the end of the flood, and yet those laminated sediments he thinks should only happen during a global flood appear in rocks of all ages, including all parts of the Cenozoic. Go figure.
How, then, do you account for the sequence of taxa in the fossil record and the nested hierarchy of life, which fit each other quite well? How do you account for radiometric dating, magnetic reversal correlations, historical patterns of plate tectonic events, metamorphic rocks (particularly blueschists exposed at the surface), terrestrial sediments, and biogeographic (and paleobiogeographic) patterns, just off the top of my head?
No, they don’t, except in your fertile inner life.
Yes, of course. The evidence of common ancestry is not ability to interbreed. After all, that ability is primitive and can be lost in separated populations over time. Conversely, why do you think separately created populations should not be capable of interbreeding?
There are rabbits on top of the Applachian mountains burrowing in pre-Cambrian rock. The sequence is a sequence by cherry picking out anomalies. I pointed one anomaly where bacteria were in 200 million year old amber that had identical DNA to modern bacteria. The layers are often horizontally laid out, and some are on top of each other in the wrong order. That’s hardly a sequence over time.
You ad hoc rationalized away an anomaly like you did the Faint Young Sun Paradox and C14 and unracemized amino acids and DNAs. These aren’t minor anomalies. You keep insisting you explained it to me and I don’t understand. But me not accepting flimsy explanations is not the same as me not understanding, it could be just as well you have a flimsy explanation, just like your explanation of spliceosomal introns or how about the many introns we share with plants like A. Thaliana than animals like nematodes and fruitflies. How do new spliceosomal introns get created and what’s the explanation for those patterns.
Well, that’s your best card to play, that Sal is “illiterate”. Ok, so explain the burrowing anomaly that Wise points out. Do you have an explanation? I’m all ears. The case of YEC doesn’t rest on me, but on the facts.
You’re criticism of WIse saying the flood ends at the Cenezoic doesn’t refute the problem he pointed out with bioturbation.
I’m not sure what you’re trying to say there. Are these living rabbits? I doubt they can burrow in rock. Are these the fabled Precambrian rabbits? Please cite something to clarify and support this claim.
Nobody believes the Permian bacterium story. Rocks in the wrong order always show evidence of overturning or faulting to explain them. You can’t get rid of the time sequence that way. Those aren’t even anomalies, much less major ones.
I’d say they are. You are the one cherry-picking here. You ignore the bulk of the data to concentrate on your little stories. The data fit together to make a coherent picture, but your supposed anomalies are all over the map. You can’t even settle on a date for creation or for the flood. And your anomalies are only anomalies because they contrast with the coherent picture coming from the bulk of the data.
I don’t recall ever explaining spliceosomal introns to you. I don’t know all that much about how they arise or go away. It could be that I have a flimsy explanation for the things I have explained to you, but I don’t think so. You on the other hand have no explanation at all. Why is there a nested hierarchy of life? Why, your cherry-picking to the contrary, is there a clear fossil sequence, and why does it match that hierarchy so well?
No, that’s by no means my best card. But I can’t help it when you parade your deep knowledge in ways that suggest your ignorance.
Again, Wise’s explanation isn’t self-consistent. As for an explanation, I think he’s exaggerating the universality of deep, ubiquitous bioturbation for effect. What he describes happens to the depth he describes in some places, I suppose, but certainly not all. And no, we don’t expect laminated sediments from a global flood. Of course, there isn’t actually any model of that flood; it’s just whatever you need it to be at the moment, with no attempt at consistency.
Yes it does. If the sort of bioturbation he describes is universal except in deposits from the Flood, there should be no layered sediments after the Flood. Or before it. That’s his point: layers are a sign of the Flood. His story is not self-consistent.
Then all the more reason you should not be claiming it’s a fact that they evolved, you should say, “I don’t know” which you did, but you should also say, “I believe despite the lack of an explanation of how” — which you haven’t done because maybe, you’ll show everyone you’re no different from me. You believe in something you have no explanation for. That’s ok, but it’s something you don’t want to admit, lest you sound like a creationist.
It doesn’t have to happen at great depth. A geological strata a kilometer in depth taking 100 milliion years to form accumulates at an average of 10 MICRONS a year. The burrowing doesn’t have to be very deep at all.
There will be a lot of creationists at ICC2018, and I don’t know if Wise will have time for me given how huge the conference is, but I can pass your objection on to him and others there if they’re willing to take my questions.
Even aside from the flood, that’s evidence the fossil layer was laid down quickly and the creatures suffocated. That’s evidence against slow burial over time independent of Wise’s other beliefs.
Wise is a paleontologist trained by Raup and Gould. It’s sounds to me he found something that’s legitimate.
What do you mean by “they evolved”? I haven’t been talking here about mutation at all, just common descent. You can use presence and absence of particular introns as phylogenetic markers; that’s about all that’s relevant here.
You really think that sediments accumulate at a constant rate? Do you know anything at all about geology?
I have little faith in your ability to state my objections coherently and correctly, but go for it.
What you call “slow burial over time” is something that generally happens only in very restricted environments: deep ocean, some lakes. Deposition, in general, is episodic. You know even less about geology than you do about biology, so it’s hard to discuss these things with you.
Credentialism again? Hey, I was trained by Raup too. And what seems to you is irrelevant, given your ignorance of the subject, and depends entirely on your desire to have support for YEC.
Is there a “true” sequence you can point to where the anomalies have not been removed?
What is the ratio of anomalies to non-anomalous elements of the sequence?
Why is there any pattern at all given what you think happened:
1. Hydrodynamic sorting through water velocity and specific density of the fossil.
2. Ecological zonation, habitat, etc., e.g., deep sea, shallow sea, shoreline area, coastal plain, swamp, highland, forest, etc.
3. Biogeographical separation, e.g., organisms separated by mountain ranges, lakes, oceans, etc.
4. Mobility, intelligence, and differential escape factors.
5. Chance.
6. Preservation bias, e.g., small or large population, hard or soft parts, aerial forms such as birds, etc.
7. Tectonically Associated Biological Provinces (TABS). This is a new and exciting possibility opened up by John Woodmorappe
http://www.creationmoments.com/content/difficulties-geologic-column
Seems to me surprising we observe sequences of fossils at all given it was all mixed up in a big sandy bowl for a month all at once.
This is something John Harshman hasn’t refuted. It’s a 32 minute video show experiments and direct observations of quick stratification.
If the fossil record is young, the patterns of similarity are due to common design, not common descent because there is not enough time for evolution: