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.
And you’ve not once shown any competence in understanding it.
Glen Davidson
How many times do you have to be told? They degraded into non-functionality, and some likely still exist as pseudogenes.
If you began to read and comprehend competent people, rather than doubling down on denial and incompetent claims by Sal, you might begin to be able to discuss these things in something other than your annoying obtuseness.
Glen Davidson
Why would you expect that? Genes can disappear from lineages analogously to species becoming extinct. If a gene becomes deleterious in a new niche, selection will tend to remove it.
Whole genome sequencing (previously a pipe-dream, recently becoming a cheap production-line process) has supplied a quantity of data outstripping scientists ability to interpret it. Perhaps Sal would like to chip in and explain how he goes about using the on-line comparison services he uses to produce his analyses.
Darn. I didn’t notice it was behind a paywall. Andrew Knoll’s paper is as well. Sorry about that.
I want one of those! 😀
Alan Fox,
You have genes disappearing in one class at 10 times the rate of another. This does not make sense in either guided evolution or evolution by trial and error. You also have fish with 5% more common genes with humans then birds. This is counter to the nested hierarchy claim.
The pattern looks like the result a gene tool box with a designer making choices;
I think you are smart to question Sal’s data because it is devastating to the argument for evolution.
Bill,
Slow down. Show your work.
Tell us:
1) what the prediction is;
2) why you think that common descent makes that prediction;
3) how the evidence falsifies the prediction; and
4) how ‘common design’ predicts the data better than common descent.
Again: show your work. It’s hard for us to replicate your errors. You need to make them explicit by showing the steps in your reasoning.
And just to be clear, “show your work” includes your calculations. Make them explicit.
And we would expect mutations too. Like deletions and duplications. As demonstrated like ten times now.
When you write “fish” and “mammals” and “birds”, what you mean is Zebrafish, Human and Mouse, and Chicken, respectively. Those are not the same things, by a long shot.
Those are not gene losses in birds compared to mammals and fish. The venn diagram does not represent the gene-contents of any clades.
Those 2059 genes not present in chicken, many of them are probably present in birds. And by birds I mean the clade, not a particular taxon.
Are you going to give even a HINT that you will one day come to understand what that diagram shows?
There are also 892 genes present in Human, Mouse and Chicken, but not present in Zebrafish. Many of those could very well still exist in the fish CLADE, yet as we get closer to Zebrafish the number of losses will gradually increase.
Again, gene duplications happen, and so do deletions. They are an observed fact. There isn’t anything going on in that venn diagram that in any way contradicts the nested hiearchy, or realistic rates of gene loss and gain.
Explain how you arrive at this. How do arrive at your calculation of “ten times” and what is ten times what?
You need to explain what “this” is and then you need to explain why “this” is evidence against evolutionary theory.
Glancing at the zebrafish genome paper, I think you mean “homologous”, rather than “common”.
So far, molecular phylogeny has largely confirmed earlier categorisations based only on morphology. Are the authors of the paper worried about their results? Seems not. They write;
They allow the possibility of errors in assigning genes in the chicken listing as well as the probability of lost genes. Note too the gene duplication that occurred in the Zebrafish line.
To you, maybe. The option of an unentailed, immaterial designer is not a persuasive idea to me.
Well, it might be. You seem to have forgotten about eyes and trilobites. If you’d rather we explored Sal’s “devastating” sequence comparison instead, that’s fine.
ETA*
Rumraket,
Why do you think this is true?
Why the massive loss in chickens 2056 and the order of magnitude smaller loss in mice and men? Why greater genetic similarity in Zebra fish then chickens?
This does not explain the order of magnitude difference between chickens and mice/humans.
colewd,
Don’t ask Rumraket to do your work for you.
You made the claims. Support them. Show your work, including the calculations.
You’re badly misinterpreting Sal’s “flower”. Make your reasoning explicit so we can correct your mistakes.
Alan, to Bill:
It’s just as well. The trilobite thing wasn’t going to accomplish anything. It would have been one long exercise in presenting evidence and arguments to Bill, which he would repeatedly deem as unsatisfactory.
The only thing that will satisfy him is Jebus.
Much better to have him attempting — and failing — to defend his conclusions regarding Sal’s “flower”.
No, not 10 times the rate, just 10 times the time. The chicken has been on a lineage separate from mammals for around 300 million years, while the mammals have been separate from each other for somewhere around 60 million, and the lost genes are distributed onto three branches (human lineage, mouse lineage, and combined mammal lineage). Similarly, you can’t compare the single bird to one of the two mammals, because there are three branches relevant to the mammals but only one relevant to the bird, and that explains why there are more genes uniquely shared between zebrafish and chicken than between zebrafish and human. You don’t understand the figure.
Then why do the designer’s choices follow a nested hierarchy so well? And why do the individual gene sequences follow that same hierarchy? I would expect independent insertions of the same gene to have the same sequence. You really haven’t thought this through.
Nobody questions Sal’s data (it’s not his data, but never mind). It’s Sal’s silly misunderstanding of the data that we’re all questioning. And I think your understanding is even poorer than Sal’s.
Alan Fox,
129 Genes move from the zebra fish to the chicken not mouse/human
2059 Genes move from the zebra fish to the mouse/human but not to chickens this is almost 20x so 10x is conservative.
The authors don’t need to be worried because common descent is where all data is force fit in evolution. Their not being worried is a big red flag to me.
This is speculation.
I know but this is making you blind to evidence based on assuming your conclusion or circular reasoning. You caught the terrible cold from Dawkins 🙂
I have an article I will soon post on this.
In Bill’s description, zebrafish are running around promiscuously “moving” their genes to everything with a pulse. They are the sluts of the HGT world.
John Harshman,
The lost genes are present in both the human and mice.
12897 shared genes between humans/mice and zebra fish
10983 shared genes between chickens and zebra fish
Not expected from a nested hierarchy. 17% end up more in the two mammals then the bird.
keiths,
Looks like they are more aroused by hair then feathers 🙂
Alan Fox,
Here is a UD article on the eye. We can assume Trilobites utilize the same biochemistry as a working assumption:
colewd,
Christ, Bill. You’re hopeless.
That makes no sense. Lost genes aren’t present; that’s what “lost” means.
Of course it’s expected from a nested hierarchy. What you are saying is that you expect there to be an exactly clocklike schedule of gene loss. There is no reason for that. Evolutionary rates of all sorts vary. Note also that you should also count the genes shared between human and zebrafish and mouse and zebrafish, since those were lost in chickens, and also consider those shared by mouse, chicken, and zebrafish as lost in humans, since the genes lost in chickens have had an extra 60 million years or so of loss compared to those lost in the mammals.
John Harshman,
Except were not comparing gene loss were comparing gene commonality. The data that zebra fish genes are closer to humans/mice then chicken genes to humans/mice violates the nested hierarchy claim.
The only out is the common ancestor to zebra fish chickens and humans/mice had all the common genes and we are just dealing with loss with an erratic molecular clock. So erratic lost genes can have almost a 20 to 1 variation depending on the branching.
John Harshman,
The genes lost in chickens are present in both humans and mice.
Bill:
It’s frikkin’ hopeless. Bill is simply incapable of grasping the science.
Common descent doesn’t predict which genes will be gained. Common descent doesn’t predict which genes will be lost. Common descent doesn’t predict which genes will be shared. Common descent predicts nothing specific.
Mung:
Derp.
A while back I proposed putting to the test the idea that the nested hierarchy is explained by (common) descent with modification. I’m willing to code an algo that does something like this (simple model of evolution):
1. Define an initial LUCA sequence
2. Mutate it at random for a while and then have it split in two branches
3. Have each branch do (2), and so on
4. At some point stop the program and publish the leaf (extant) sequences
If the tree can be recreated by someone who didn’t run the algo, would our local creos be convinced that the nested hierarchy is explained by evolution?
Cue the reflexive response: But if you code an algorithm, that’s Intelligent Design!
My money is on “but your algo couldn’t evolve an eye”
It has become surprisingly easy now because the governments (US and European) have spent a lot of money on user friendliness and open access. The trick is just getting a couple days training here and there. I was fortunate to get some training at the NIH which serves as hub for a lot of this.
By law gene sequences that were created by federal funds must be made publicly accessible. Obviously the private databases or databases with sensitive patient information is not available.
As far as us not being able to interpret the data, that is correct. The is a lot of data that people haven’t figured out what it means. For example, the nylonase project that Dr. Sanford and I worked on is purely a search of publicly available databases and documents. It’s became readily apparent ideas that have existed for 30-40 were just plain wrong in light of a conceptually simple yet rather tedious database and literature search.
The orphan gene issue and the diagram that Bill Cole and I have talked about is a well-known problem in scientific literature. If you think about it, doing that sort of data synthesis is more of a computational beast than some esoteric exercise.
All you have to do is download human, chimp, zebrafish, chicken, whatever genome lists. Then just do a computational Venn Diagram. The trick is just navigating some of the not-so-well documented procedures for download.
I have to credit Paul Nelson with his work on Orphan Genes. He was so adept at it that evolutionary biologists have published a work he co-authored with Richard Buggs. I extended Paul Nelson’s ideas to the phrase “Orphan Systems” or “Orphan Features.”
https://www.researchgate.net/publication/304039133_Next-generation_apomorphy_the_ubiquity_of_taxonomically_restricted_genes?ev=prf_high
Buggs also created a flower diagram in his specialty and published it in the prestigious scientific journal Nature.
http://www.nature.com/nature/journal/v541/n7636/fig_tab/nature20786_F1.html
*Snicker*
No it doesn’t. Can you explain why you think it does?
Ah, so we are talking about gene loss. Now, it does appear that there has been more gene loss in the chicken (=diapsid) lineage than in the mammal (=synapsid) lineage, and that’s quite an interesting question for further research. But it doesn’t violate any nested hierarchy. It might have something to do with the reduction in size of the dinosaur genome, previously well recognized in the literature.
Do you have a reference or two. I used a few combinations of keywords but didn’t find anything on a Google search.
At the BLAST site?
ETA I see there has been a more recent sequencing of the chicken genome.
Here! I guess this wasn’t used in the zebrafish paper. I wonder if the result would change.
Yesterday I debunked DNA_Jock’s bizarre “You think we’re closet IDers!” claim. I also showed why some comments he proffered as evidence against my argument are actually perfectly compatible with it. Third, I corrected his misconstrual of the main ID argument.
I’ll now move on to some other comments of his. Given his ill-advised flounce, I’ll refer to him in the third person for now. Of course he is welcome to be brave, deflounce, and re-engage the argument at any time. If that happens I’ll resume addressing him directly.
In the meantime, let me point out a confusion of his that may explain the second error I mentioned above.
DNA_Jock wrote:
That’s not right. The problem lies here:
The ONH is compatible with guided evolution, in that the two aren’t mutually exclusive. My position is quite different. I hold that guided evolution doesn’t predict the ONH.
Hence my disagreement with John’s statement…
…and with DNA_Jock’s echo of it:
The interesting thing about Jock’s mistake is that it may explain his earlier error. If he thought I was arguing that the ONH couldn’t be reconciled with guided evolution, then it makes sense that he would look for cases in which guided evolution does produce an ONH, and then present them as a refutation.
Unfortunately for him, they aren’t.
What do you mean by “guided”? Evolution is guided by the niche. If God created the universe, he created the niches. Such guidance produces a nested hierarchy.
Keiths previously:
And this qualification makes what difference, exactly?
Alan,
It maintains a useful and desired distinction, while your suggested usage erases that distinction.
Can your support those assertions?
Useful to whom?
Desired by whom?
What distinction?
And how so?
PS what usage did I suggest?
keiths,
Oh, boy.
keiths,
I was happy to let you have the last word – it makes you so happy, after all – or “flounce”, as you so kindly put it, but your latest re-writing of history was a bit much .
Nowhere did I claim that you claimed that the Four Horsemen (JH, DJ, R, and Z) were IDers, closet or otherwise. That was your addition, your failure at reading comprehension. Re-read the thread.
You responded to JH’s statement by saying “To infer guided evolution from the ONH is as silly as inferring the Rain Fairy from the meteorological evidence” then later stated that you had never claimed that any of the 4H argued we should infer guided evolution. Given the context, yes you did make that claim.
I was merely making fun of your inconsistency. The joke keeps going over your head. Almost as if you were unwilling to admit error.
Moving on.
My apologies for using the phrase “compatible with”; I had forgotten your somewhat esoteric use of this phrase. Try “isn’t compelling evidence against” instead:
As I wrote earlier (ooo-er! quoting yourself is fun!):
Did I bracket your argument correctly?
Would you care to try bracketing my argument?
There you go keiths. Care to return the favor?
1.) What is going to decide the mutation rate?
2.) What will be the basis for branching?
I don’t think this algo of yours will show what you think it will show.
LoL!
First, you debunked a straw man.
Second, you missed the point. Of course guided evolution is compatible with a nested hierarchy.
And last but not least, you misrepresented ID. Go figure.
John Harshman,
Human/mice are closer to chickens then zebra fish.
https://evolution.berkeley.edu/evolibrary/images/evo/sixchars_phylo.gif
I would expect the number of matching common genes to be higher with human/mice and chickens then humans/mice and zebra fish but it is not.
Gene loss is a possible explanation. What you are explaining why the data does not follow what you expect based on your claim of nested hierarchy as a pattern of inheritance. The real issue is the data is not supporting your hypothesis.
What tells us that? Are you willing to accept the genetic evidence for them being closer? The morphologic evidence for them being closer?
https://evolution.berkeley.edu/evolibrary/images/evo/sixchars_phylo.gif
Yes, look at that, the evidence shows the nested hierarchy. Any reason why gene loss has to be in lockstep with that? Do gene duplications and reductions of genomes have an effect on the number of genes that survive?
What about the much closer and much stronger signal of mice and humans? As expected, they share a huge number of genes that zebrafish and chickens lack.
Why are you cherry-picking among the two distant relationships that have relatively few homologous genes? The total difference between 48 and 73, or whatever, isn’t all that much, you know. 25. You’re dealing with numbers that could be affected by a number of factors, or even just randomness.
The real issue is that you cherry-pick data that certainly needn’t have any absolute correlation with the nested hierarchy as shown by genes and morphology. While it’s not certain why we share fewer with chickens than with zebrafish that aren’t shared with the others, the fact is that they’re both rather distant relations, and the numbers happen to be at levels that can be substantially skewed by gene reductions, gene duplications, selection, and just random chance. You’re hanging onto your prejudices by trying to base them on a very thin cherry-picked number, while you ignore the much stronger and far more robust figure of genes shared by mice and humans and not the other two.
It really won’t do for you to ignore the many factors affecting quite small numbers of genes, while you simply ignore what you don’t want to pay attention to, the huge number of homologous genes shared by the two mammals and not by the non-mammals–1602. That is the strong signal, not the few numbers of genes shared with humans by the fish and chicken and not by the other two.
Glen Davidson
Low enough that the common descent signal is not lost
I guess branching after a random number mutations should work.
Why not?
I would note, too, that in the diagram the chicken is depicted as having substantially fewer genes than the zebrafish. I didn’t double-check, but I added up 14,623 genes in the chicken, and 16,806 genes in the zebrafish. That in itself would account for some of the skew that Bill hangs onto desperately, but it also suggests the possibility that the chicken may have lost more genes than the zebrafish did, which would skew the difference even more.
It’s worth noting as well that whatever factors did skew the number of homologous chicken genes shared with humans and not the other two, vs. the number of homologous zebrafish genes shared with humans and not the other two, seems to have affected all of the species on the diagram. The chicken and zebrafish share more genes with each other alone (129) than the chicken shares with humans alone (48) and with the mice alone (43). The mouse has 57 homologous genes with zebrafish alone, and, as noted previously, 43 with chickens alone. There seems to be something that skewed the loss of genes that left zebrafish with more genes homologous with the two mammal species alone than the chicken ended up sharing with the two mammal species alone.
Anyway, by my calculations, 76.7% of zebrafish genes are “shared” with humans, while 80.0% of chicken genes are “shared” with humans. Going by the diagram’s numbers, of course. Certainly those figures accord well with the genetic and morphologic data showing chickens to be more closely related to us than to the zebrafish.
Glen Davidson
That isn’t true. You are demanding an auxiliary and unnecessary hypothesis of clocklike gene loss, which is not connected to the common descent hypothesis. The data don’t support the auxiliary hypothesis, which nobody has advanced, but they do support the main hypothesis of common descent.
LoL.