I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.
Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.
If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.
One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.
That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).
Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.
The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”
So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.
So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.
stcordova,
Fact remains, why clocks?
stcordova,
I don’t; I’m suggesting that the tools are available for you to provide some positive evidence. If you don’t think that’s how science works – you think it only works in the negative – then stop pretending to be a scientist. And give up those hypocritical accusations that anyone else is ‘cherry-picking’.
stcordova,
I’ve read your response again, and it mystifies me. How does the belief of a moon-walking astronaut have any bearing on whether baramins are real, or clocking methodology is artefactual?
I’m not pretending to be a scientist because I don’t claim to be a scientist any longer after I left my job where my formal title was junior scientist in the aerospace industry. I left that job because I got promoted to senior engineer. 🙂
Now I’m in the financial world and do some part time work as a research assistant to a real scientist.
I’m a research assistant in that I gather sequences from databases and read journals and visit the NIH every week. I post some of that here at TSZ. I posted some of that in the nylonase thread. I occasionally point out how the data are at variance with mainstream claims as I did with nylonase.
Anyway, I pointed out the evolutionary clocks on which the Sarcopterygii clade are based don’t agree with the sequence data. If you want to talk science, that is a scientific claim. You can argue for and against. That would be productive.
Arguing over theology and philosophy, that’s mostly pointless as far the question of evolutionary clocks are concerned.
Anyway, here are some things from the Tajima clock test. It can only go two sequences at a time with 1 outgroup. Tajima suggested in principle it can be extended to more than two sequences at a time, but I only have access to the two-sequence version of the Tajima test in MEGA 6.0.
I haven’t double checked the alignments as some of the numbers look funny, but nevertheless here are 3 tests:
Coelecanth and Human:
lungfish and coelacanth which shows coelacanth being speedy Gonzalez fast, but note the bolded lack of divergence:
and Lungfish and human:
Because the Human and Coelcanth move so much faster than the Lunfish, qualitatively speaking the expected triangle might be something like the diagram below, although the JTT matrix suggest something more like a equilateral with human being the slowest.
But the sequences don’t agree with that triangle either, so maybe these molecular clocks are broken too. If so, that is negative evidence against evolution.
That data is all preliminary and it is very small sample size. But I want to nail down the procedures, materials and methods before I move on to another gene.
click link below to see enlarged diagram
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/possible_tajima.png
stcordova,
I’ve seen people – experts in the field – argue with you on this. You have been deaf to their words. Still, I don’t think the Sarcopterygii clade is based on evolutionary clocks in the COX gene. I am prepared to stand corrected, but in any case I don’t have a strong expectation that uncalibrated rates over such an extended period should conform to agreement within any particular error bar. Clocks are notoriously ‘gusty’, hence the need to recalibrate to fossils (something else you don’t believe in dated by something else you don’t believe in, but hey ho).
If you find one method runs twice as fast as another, is that an artefact of the method, or something wrong with the whole notion of clocks? How could you check?
I’ve not been deaf, I’m studying their ideas, especially Joe Felsenstein, whom I and many creationists revere though we have sharp disagreements. As far as experts, I respect them, but there is always room for skepticism even from non- specialists as was demonstrated over the topic of Nylonases that was promoted by experts like Ohno and Ken Miller.
I thought Denton was right about the molecular clocks and so was Fred Hoyle, both complete outsiders, but what they said resonated with me, and neither were creationists, especially Hoyle.
From the Tajima:
Which suggest the Lungfish Coelecanth divergence was long after the Lungfish-Coelecanth-Tetrapod(human) divergence. Ergo, the spirit of the claims of Tetrapodamorpha and Sacropterygii being Tetrapod ancestors is inconsistent with Cox1. We’ll see for other genes.
What is a “created kind”? How do you recognize one? How do you determine if a genealogy is “within Baramin”?
That one’s easy: the Sarcopterygii clade isn’t based on evolutionary clocks. Wherever did you get that notion?
Then you should pay attention to what people are telling you about the difficulties of working with mitochondrial genes at that depth. Look at your printout: “Unique differences in Sequence C 411”; that tells you that Ciona is so far from the other sequences that it’s nearly randomized with respect to them. I doubt your alignment, if you’ve even bothered to look at it. I doubt that your Tajima test can possibly be anything more than noise. In order to work with a mitochondrial protein-coding gene you need a much larger taxon sample if you want to get a decent alignment and a decent phylogenetic analysis, and you have to be very careful about what model you use. Everything you have done so far is useless.
Incidentally, even if your claims about divergence were true, your claim following “ergo” would not be supported. The relationships among tetrapods, coelacanths, and lungfish, as well as their relative divergence times, are not relevant to whether tetrapods are sarcopterygians.
I will also point out that Sarcopterygii and Tetrapodomorpha are not “Tetrapod ancestors”; they are clades to which tetrapods belong. You have consistently been confused about this.
They aren’t based on any evolutionary clocks. Molecular clocks are universally used within species, as they’re pretty close to true at that level, and help a lot. As one gets beyond the species level, molecular clocks gradually get less and less valid. Simply put, as the biology of the species become different, the rate of molecular evolution gets different.
With molecular sequences, with groups hundreds of million years old, basically no one uses molecular clocks.
And of course Sarcopterygii were defined long before molecular data were available. At first they included just the ones that looked like “fish”, but when it became clear that tetrapods were in the clade, they were added. No molecular clocks involved.
Here is an example of a wider-ranging study using numerous mitochondrial genes.This was just to get the divergence times for Coelacanth spp, not to get the clade. The clade is determined by its membership, not by rates of divergence. But, the intent was to cast the net widely, and apply objective criteria.
Joe Felsenstein,
Indeed, I should have been more explicit.
We recognize them about as well as phylogeneticists identify the correct phylogenetic tree, which means we estimate.
There are two kinds of Baramilogists — the Biblical Baraminologists like Todd Wood and Kurt Wise and the Discontinuity Systematicists like Walter ReMine and myself who don’t obsess over specific models and find it loathesome to mix theology with discontinuity studies.
ReMine is credited with co-founding the field of Baraminology with Wise, but then it resulted in two schools of Baraminological thought. I’m in the ReMine camp. So Just clafigying terms. ReMine isn’t a YLC or YEC, but I am, so my criteria are different than his to some extent, so what I say doesn’t represent the other believers in created kinds!
Since I believe the fossil record, and thus probably life is less than 6,000 years old, that is not enough time for a bacterium-like creature to evolve into a giraffe or any other mammal. Hence the bacterial group contains baramin that are not in the mammalian group.
I don’t identify specific kinds, but I think under the assumption of YLC, we can identify the sets of creatures that share sets of shared characters where at least 1 member would be a created kind. Given the assumption of YLC, then differences between human and chimp would be too severe to allow them to evolve from a common ancestor, hence humans are baramin.
Joe asked how I would do taxonomy. I said shared characters. That’s what Linnaeus did, and that’s not too far from the Cladists either and their apomorphies, although I consider these apomorphies to be created.
From wiki:
Well, that’s sort of Linnaen in my book. In the YLC model since there isn’t enough time, I would regard apomorphies as evidence of an individual created kind if it is not also a synapomorphy. Synapomrophies are common designs within groups of created kinds.
I think there is a soft malleable nested hierarchy that can describe biology. The fact that chickens share genes with humans not found in other creatures is an example of why I don’t think an absolute hierarchy can be imposed on all creatures, only an approximate nested taxnomic hierarchy.
As far as what some creationists are interested in, we think humans are a created kind because they are substantially different than primates, and probably mostly for theological reasons many of them believe that.
The interest in Joe Felsenstein’s and other population geneticists work fall in two main areas. The first is mutational load and Muller’s work. This has immediate consequences on the status and health. Because of the mutational load argument, as Graur said, “If ENCODE is correct, evolution is wrong.” So hence I got recruited to report on NIH developments related to ENCODE, 4D Nucleome, and the other “-omes”.
The other area of Joe Felsenstein’s work of interest to creationists is confirming the Table of Nations in Genesis 10. Work on the Kohanim and Abraham modal haplotypes are formal scientific projects. That is of interest to us. On the periphery is Rob Carter and Nathaniel Jeanson’s work on the idea of created heterozygosity.
Jeason has tracked literature on horse breeds. That is interesting in and of itself. In the Bible there are claims of creatures brought in pairs and then some in groups of sevens on the bible. This puts a constraint on the number of common alleles vs. rare variants. This is an interesting bioinformatics question. Jeanson found out even in secular literature, the domesticated breeds from 12,000 years ago (according to historical reconstructions from whatever records) had a lot of heterozygosity that wasn’t evolved over the 12,000 years. Again, there should be a signature of common alleles vs. rare alleles. This are hard technical questions to probe.
At this stage, I’m mostly a clerk doing clerical gathering from gene databases and doing some reporting on the journals and conferences I encounter. So maybe I shouldn’t be the one to take too specific questions on Baramin, but I believe since there wasn’t enough time for life to evolve, many creatures with apomorphies (orphan systems) are created kinds.
Sal:
…those who can spell, and those who can’t.
Allan,
With respect to clocks, we can use an even less esoteric measurement than clocks, but the differences in sequences themselves. How much did one sequence evolve with respect to another over about the same time? We then don’t have to assume constant clocks or whatever, just the final result. The final result are the triangle diagrams I provided.
So the question about the 3 ancestral lines is whether the evidence support them evolving from about the same point in time given the sequence distances. The triangle diagrams, based on evolutionary assumptions, suggest to me the tetrapod line diverged away from Lungfish and Coelcanth’s farther back in time enough to contest the prevailing narrative, at least as far as Cox1 is concerned.
We’ll see what the story is for other genes.
It’s not mentioned in his Wikipedia page. Do you have a reference so I can edit this momentous news in? https://en.wikipedia.org/wiki/Charles_Duke
But given you know none of that actually happened, what really did happen?
Many, but not all? Is that your position?
So it’s possible for creatures to have orphan systems and for them not to have orphan systems regardless of if they were created kinds or not?
That’s soooo useful.
It’s in his book Moon Walker.
Duke visited Campus Crusade for Christ many years ago and gave his testimony. I read the account in the book he autographed.
So type it in. Let’s add it to his Wikipedia page!
Allan, to Sal:
That gets to the heart of the matter, and it explains why this is thread is more about the psychology of fringe beliefs than it is about biology.
I’m sure Joe is thrilled. How is that work going? Who is doing it? When will they be publishing? Where will they be publishing?
You mean that you don’t have evidence for your claims, but you don’t mind because there wouldn’t be in your made-up belief system.
Meaning that there’s no reason to believe your claims. On the other hand, we know that observed designers do not produce pre-divergence homologies while refusing to create homologies in divergent lines, like we find in life.
So we do have evidence against design, none for it.
And some people have seen Bigfoot. Furthermore, one person thinks that aliens stole his wife’s fetus. Am I to believe those claims?
Beyond that, while miracles that one found believable might change some expectations, why would I believe that life was miraculously and ridiculously given the design-constraining patterns of unguided evolution just because I happen to believe miracles can happen?
We’d need evidence of miracles being responsible for life’s characters, not merely evidence for miracles (which we don’t have). We don’t even have any evidence for intelligence being involved in life, and good evidence against that.
Glen Davidson
My initial response is that there has to be a pony in there somewhere.
But no, upon wading through, I find nothing at all that responded to any of my questions, just a mass of irrelevant stream-of-consciousness.
Another interesting bit of psychology.
Sal, now:
Sal, in 2016:
Well sorry to disappoint you. I tried. What I said made good sense to me anyway.
You know that the people in asylums live in internally consistent worlds too, right?
Is that what you said the one time you tried getting your work peer reviewed and got the reviews in? No wonder the aversion to trying again eh?
Glen, to Sal:
That person being William J. Murray. This is too good not to share again:
If so, that’s a big problem.
OMagain:
From the wiki page:
I don’t know if this belongs in a wiki page, but for the benefit of you and the readers:
Yeah but you see John, Sal isn’t here to actually really try to discuss these matters or try to understand anything. Primarily, Sal is active in this thread because he wants to keep up the pretence that a genuine disagreement with two sides of professionals is taking place. To do that, he doesn’t have to make much sense or say much of relevance. He just has to quote a technical article once in a while, put a couple of technical terms in his own words, and show a diagram or graph of some sort once in a while.
To anyone without a clue, this will be enough. That will make it look like Sal is showing how there’s an actual scientific debate going on. Only in the most obvious ways will he admit to having made some sort of mistake as long as it can’t be used directly to show how his young Earth creationism is false.
Case in point was his use of cytochrome c oxidase subunits, rather than cytochrome c. He’ll admit to getting something like that wrong, because the non-truth of creationism doesn’t follow from that. He’ll just pretend to thank you politely and move on back to posting with quotes from papers, use lots of technical terms, and end almost every post with a diagram or graph.
Sal, let’s try that again. Here are my questions, separated for easy reply:
What is a “created kind”?
How do you recognize one?
How do you determine if a genealogy is “within Baramin”?
A creature God created, or the descendants of a creature God created through a miraculous act, like a POOF.
One example I believe was created was the ancestor of Lions, Leopards, Tigers, Panthers. Another example is the ancestor of humans, Adam and Eve.
If it is sufficiently different from other creatures. If it can’t interbreed or hypbridize, that is a start. I might have thought at first a Lion was created kind. I would have been mistaken. Since it can interbreed with tigers, it seems to me then all the creatures that can interbreed with lions or form a ring or connection with tigers through hybridization study then are descendants of the created kind.
For sexually reproducing species, the extant members should be able to interbreed or form a ring at least in principle if they are of the same baramin. Then you can try to infer a genealogy with phylogenetic tools. Otherwise, the phylogenetic tools would be returning errors. Thus if Chimps and Humans are created kinds, the fact their cytochrome-c’s are identical show common design, not common descent.
With bacteria, I don’t know. This is complicated because of HGT. Gene trees are not species trees, especially when talking bacteria. So there are cases, for your question, my answer is “I DON’T KNOW.”
If you feel my methodology is flawed for identifying them, that’s fair game and I don’t mind the criticism. If however you’re trying to say since I can’t identify them, therefore they don’t exist in principle, that is another argument.
No, I don’t say “kinds” don’t exist in principle. I do however say that your inability to identify them is evidence that they don’t exist, because separately created kinds ought to be distinct enough that they could be recognized easily. There is no reason, for example, why they ought to have the same genetic code.
Now, the sole criterion you discussed is hybridization. But you will have to justify that claim. What is your argument that hybridization ought to always happen within created kinds and never happen between created kinds?
Can we agree that “sufficiently different” is a useless term unless you can quantify it?
Yes, just as soon as we can agree that the theory of evolution is a useless term until we can define and quantify what it does.
John Harshman,
And since you are (not) answering questions about evolution, how do we know when the “unfittest” survive?
No I won’t agree to that. But I will say it becomes more useful to the extent it is quantified.
A feature, orphan system, apomorphy, ataopmorphy, whatever you want to call it that can’t evolve in 6,000 years even by prevailing assumptions about the capacity of evolution is sufficiently different to qualify something as created rather than evolved. We could go to more strict criteria like 10 million years, whatever.
100,000 years is reasonable based on C14 dates of the fossil record.
You have a talent for saying nothing in a great many words. What you just wrote is so scattered and self-contradictory as to communicate nothing.
I think he’s trying to say that evolution kinda sorta puts a speed limit on certain kinds of developments (or development changes) at some level(s). And because this is the case, IF we can find any examples where this limit is exceeded, we have found The Thumb Of God on the scales.
In a few billion years of trial and error, it produced YOU. Alas, I can’t quantify how many like you there are. Enough to make providing decent educations a real struggle. How much of a struggle? Sorry, can’t quantify that either.
I find it hard to take the science of Sal, or any of the other YECs here, even semi-seriously. Sal has repeatedly tried to argue that natural selection is ineffective (for example, his claims here, refuted by me here). But then, when it comes to how “baramins” differentiated into multiple differently-adapted species in only a few hundred years post-Noah, suddenly mutation can come up with vast numbers of favorable mutations, and natural selection suddenly is incredibly effective and amazingly rapid.
What they really should do is go off and bother geologists, astronomers, and astrophysicists, who are universally against them on the issue of time scales. Once they have convinced, say, half of them of a young earth, they will have put biologists in a hell of a bind. So that should be their priority.
I find it confusing when you conflate mutations with natural selection. Mutations are the creating part, and natural selection is the dying part.
Natural selection can’t create anything, it can only destroy. I think this is one of the ruses of evolution theory, that they constantly mix the two, making it seem as if there is a system, when there is none. Its sort of like how materialists always talk using teleological language. If we want to be accurate (which I acknowledge is not always the evolutionist game plan) Then we should talk about how much variety mutations can create, not natural selection.
Selection is the opposite of creating, it is the destroying part.
Flint, to phoodoo:
That’s the argument IDers should be making against evolution’s effectiveness: “I waited four billion years, and all I got was a phoodoo.”
How did they become different, if their genome / epigenome / transcriptome / epitranscriptome / proteome / epiproteome / etceterome was severely constrained? How could distinguishing characters become introduced in the original design of the original created kind?
Populations produce an excess of offspring, and population density regulation keeps their population sizes limited.
Why am I bringing this in? Because it then implies that lower fitness of one genotype reduces the frequency of that genotype and thereby increases the frequency of other genotypes. It has to since the sum of all genotype frequencies is 1.
So the differences in viability and in fertility between genotypes can bring a rare genotype from a low frequency to a very high one, given many generations. By bringing rare alleles to much higher frequencies, these differences can also bring new genotypes into existence, by genetic recombination. When allele A at one locus, and allele B at another locus are both very rare, there may be no AB chromosomes. But when they each become common, now genetic recombination will produce some AB chromosomes (AB haplotypes) that have never occurred before in that population.
So thanks to the excess of offspring and the limitation of population size, discarding worse genotypes is accompanied by an increase in better genotypes. They’re not separate processes.
Joe Felsenstein,
This complementarity, the simultaneous dilution and concentration at population level, has been explained to phoodoo several dozen times, of course.
True, it’s a PRATT. I seem to recall that the answer is semantic quibbling: that phoodoo knows that, but wants mutation, rather than natural selection, labeled as the creative force bringing about “new information”. In information theory, however, it is quite clear that shifts in frequencies of already-existing signals do change the information content of the message.
Much (not all) the heterozygosity and alleles were created and thus differences were strategically positioned to not cause functional compromise and most of the mutations thereafter are rare variants and slightly damaging.
This leads to two predictions. For humans, there is mutational decay with rare variants. Herozygosity of the major alleles in each lineage for small isolated populations of tetrapods over time results in reduced heterozygosity of that population as mutation is unable to add more variation. It is a testable prediction in principle. Rob Carter and Nathaniel Jeanson have premilimary suspicions this is indeed the case both empirically and theoretically.
For selectively neutral sites, it is.