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,
It does not put science in doubt because most of science can be explained within our space time. The theory of gravity can explain a cause called space time curvature all which exists in the natural world.
There is a point where the explanation may cross the boundary of explanations on our side of space time. Candidates include the origin of life, the origin of matter, the origin of gravity etc. This does not stop of us from understanding properties of these things and creating predictive models.
Common descent is an explanation that Darwin used to compete with special creation as an inference to explain the diversity of life. Natural selection was the driving mechanism in his explanation.
If now you add divine change as a possible cause there are other non detailed ways to explain the pattern of the nested hierarchy that don’t stumble into obstacles such as Sal’s flower. You set up this debate with common design as an alternative. If common design is true then it most likely occurred out side of space time so our ability to explain it is certainly limited, however we can still collect evidence that certain new life forms were an outside space time construction.
Right, unless you think made-up causes are legitimate.
Unless God’s doing it all. You can’t get away from the fact that if you get to make up causes in one area you can do it anywhere at all.
How do you know that?
Oh, you decided that. Conveniently fits with your religion, too. What a coincidence.
Oh, so why aren’t you predicting design strategies and scenarios, rather than trying to set up a false dilemma?
No, it was an actual explanation, which special creation was not. Darwin’s particular viewpoint on the matter (which I’m not sure about, but who cares?) hardly matters.
Yes, it was an actual cause, not one conjured up by Biblicists.
Nothing is problematic about “Sal’s flower,” although you’ll claim there is using a variety of ignorant attacks. And you can “explain” anything, including murders, by “divine change” if you’re at all consistent. But you’re not.
An alternative to what? Some other bullshit? It’s certainly no alternative to the one explanation with evidence that unavoidably produces the pattern. Even if it were a real cause with evidence, it wouldn’t be considered by anyone with scientific standards as a reasonable alternative to the cause that entails the results seen. Because it doesn’t entail those results.
Your ability to locate anything out of space-time is utterly non-existent. It would be no different if you said it’s located in fairyworld.
Glen Davidson
A professional phylogeneticist knows better than to use bad data to build a tree. In this particular case, an inadequate taxon sample of a highly divergent mitochondrial gene should not be expected to produce valid results. Nor is it necessary for me to do a new analysis with nuclear genes; been done. A quick search should find you many examples.
You misunderstand Sal’s flower, but then again so does he. What are these other “non detailed ways”? And did you add “non detailed” just so you could avoid the need for evidence?
John Harshman,
None of us understands Sal’s flower including you. All of us can create a story that explains it but we are probably wrong. You are discounting outside space time explanations for the flower but including them in your explanation of common descent.
If you eventually realize the circular reasoning going on inside evolutionary biology I will be very impressed.
I added non detail because of the difficulty of an outside space time detailed explanation. That does not stop us from collecting evidence that points to an outside space time solution.
colewd,
Outside space time explanations. What about hobology, sutinacity and the influence of mingulous sontans? There’s a lot to cover before we get to outside spacetime explanations.
Wouldn’t any evidence point to a non specific explanation?
colewd,
One thing I’d like to see you and Sal do is generate a more fine grained version of ‘the flower’. It is highly restricted in terms of its taxonomic sampling. My prediction is that the gross count differences between any two species on that diagram would subdivide into progressively smaller and smaller bins as your taxonomic sampling grew richer. The differences would progressively diminish towards the assumed twigs. How can I have this expectation? Well, I didn’t go outside spacetime, if that’s what you’re thinking.
And no, the burden of proof isn’t on me.
That is what’s called projection. I do understand Sal’s flower. It isn’t difficult. No “outside space time explanations” are necessary or desired.
What circular reasoning?
So you have no explanation whatsoever, and disguise that with a buzzphrase.
John Harshman,
Have you ever considered that you might be wrong???
On the other hand ..
John Harshman,
It is not difficult to tell a story. Validating your story is another matter.
Your claim about Sal’s flower. A claim about gene loss and gain without feasibility study. Gene loss and gain is the explanation based on the assumption of common descent just like the claim of multiple losses of flight in birds.
John Harshman,
A buzz phrase like common descent.
Allan Miller,
I know, its really scary out there. 🙂
colewd,
Bill, I had such high hopes for you once, but now you’re reduced to catchphrases. I have pointed out just how well Sal’s flower fits a nested hierarchy. It’s evidence for common descent. What is your alternative explanation?
And the claim about multiple losses of flight, when you have never even read the paper or looked at the evidence, is just insulting.
Well here is a Christmas Fudge. I learned how to fudge data like a professional phylogeneticist toward a foregone conclusion. This is the tree using Bone Morphogenetic proteins with Shark’s as an outgroup. It tells the story evolutionists want to hear. It’s amazing how you can build all sorts of different looking trees by cherry picking data.
I had to do a lot of tossing out of data. For example, I couldn’t even get a lungfish BMP! Tuna BMP? Sturgeon BMP? Forget it. When I put it what pathetic little homologues were available from these creatures, it gave absurd results. Maybe I should post them so you can see the effect it has on the phylogenetic “reconstruction.”
There you go, a Sarcopterygiian clade that puts tetrapods inside it. Screw the fact it doesn’t agree with the other gene tree I built. Just cherry pick the tree you like with the most fudge.
Click for larger image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/11/bmp_fudge.png
Are you truly confusing phylogeneticists of fudging data? Where is your evidence for such a thing? I know you have no shame, but don’t you have just a little prudence?
In what way is this “cherry picking”? Did you choose the sequences purposely to achieve that result?
Or perhaps you could go with the tree supported by the bulk of the data, or by the best data. Didn’t I tell you that nuclear genes should work better for this purpose than mitochondrial genes? There’s a reason.
John Harshman,
John, I have read the paper multiple times and looked at the DNA sequences and the sequences in the supplemental data set. The data has many differences in the sequences between birds that are claimed to share a common ancestor. This is in the best case troubling for a conclusion of shared ancestry. Multiple loss of flight is based on the assumption of common descent which is not well established in the paper.
I understand that it is standard procedure in evolutionary biology to assume common descent as a working hypothesis and you were doing nothing out of the ordinary in making the conclusions you did. The critique is coming from an outsider who is questioning the basic assumption. This discussion is about questioning the basic assumption of common descent and exploring common design as a competing hypothesis.
You mean the non detail competing explanation, how does one go about that?
newton,
Neither explanation is detailed.
Only one is actually an explanation. And yes, it’s because it does explain the details of patterns of fossil succession and of heredity.
So no, you don’t get to equate your non-explanation that doesn’t manage to match our “pathetic level of detail” with something that is based on facts, details.
Glen Davidson
There is also multiple loss of genes! That is the explanation of the “flower diagram”. The more accurate term is the PAN-GENOME diagram.
There is a problem. If one explains the pan-genome diagrams as the result of gene loss, then one implicitly invokes a poof from where all other genomes commonly descend and slowly lose genes. Poof doesn’t exactly agree with an evolutionary theory of adding new genes over time.
FWIW, here is one description of Pan-Genomes for bacteria.
https://en.wikipedia.org/wiki/Pan-genome
If for example, one looks at the pan genome of E. Coli it resembles another diagram I posted earlier. But there is a problem if one is invoking evolution of new genes as an explanation. Many of the genes that are only in some strains of E. Coli are not necessarily new, but appear in other bacteria. So the pattern could be explained a lot in terms of gene loss, and in fact experiments have strongly indicated this. But suppose some strains have truly unique genes. Well this is also a problem since Orphan Genes don’t have credible ancestors. Common descent doesn’t do a good job of explaining things without ancestors!
Which ever way one interprets pan-genome diagrams, common descent seems like it will encounter problems. Common design by miraculous special creation seems more agreeable to me. Nothing John Harshman has said rescues common descent. He ignores glaring problems. As I’ve pointed out, once one is committed to common descent, there is no difficulty or data point disagreeable enough to overturn that commitment. So even if a miracle was a cause, that epistemological commitment will preclude seeing the truth.
One reason people believe in common descent is the nested hierarchical patterns in individual gene trees (not just species trees). But the hierarchical patterns between genes don’t give the same tree. I showed it with the contrast between Cox1 and BMP. The BMP one was particularly bad because I took out a lot of offending datapoints. Maybe I should have left them in so that it would leave an even more absurd looking phylogeny where Tuna and Lungfish were even more extreme outgroups than the non-vertebrate Ciona!
So not only might we have loss of flight, but loss of genes, and mangling of genes that give absurd conflicted nested hierarchies.
As much as I respect the math that Joe Felsenstein and colleagues have put together, the uncertainties of phylogenetic reconstructions don’t give a lot of satisfaction for someone who likes more tidy answers like me.
I see. So E. coli B REL606, E. coli ATCC 8739, E. coli B171 and E. coli APEC O1 and all the dozens of other strains are specially created kinds. Did I understand that correctly?
Nope. That’s wasn’t the point, and I have no opinion on whether the strains were created or evolved.
But if they came from a common ancestor, the Pan-Genome shows gene loss not gene gain (except for HGT). Experiments and observation suggest gene loss is a major reason for the structure of such pan genomes. But as I pointed out, the fact the genes in some strains are unique to that strain but also conserved in other bacteria, implies that if that gene is not there from HGT, it is because all the other strains have lost that gene!
Given the tendency for losing genes of nominal functional value, why then would it be expected new genes would evolve such that there is a net gene gain? That’s a problem for common descent as an explanation for the complexity of designs.
If genes are so easily disposed of, then how will TRGs and orphan systems evolve. To paraphrase Koonin, “Reductive Evolution is the Dominant Mode of Evolution.”
https://www.ncbi.nlm.nih.gov/pubmed/23801028
“Punctuated by episodes f complexification?” As in POOF!
You seem to be spending a large amount of time critiquing the nonexistent details of evolutionary theory. Sal draws diagrams with them. There is no appeal to forces beyond space and time creating them.
For instance:”John, I have read the paper multiple times and looked at the DNA sequences and the sequences in the supplemental data set. The data has many differences in the sequences between birds that are claimed to share a common ancestor. ”
Sounds like details and you having an issue with them , anything comparable in design?
How can you have such strong opinions about evolution and none about design?
I am trying hard to understand. I thought you didn’t believe genes can be lost from complex molecular networks, because they are IC. You have told us repeatedly that they do not even tolerate that many changes to their components (the genome, epigenome, transcriptome, epitranscriptome, proteome, epiproteome, etc). Yet these simple prokaryotes seem to have tolerated the loss of hundreds of genes.
Or perhaps all this variation was “frontloaded” in some ancestral cell like with the lions/ tigers thing we previously discussed? But then we should be able to trace the phylogeny by the pattern of gene losses and you have effectively accepted limited common descent, right?
Yeah, no detail in common descent.
http://www.onezoom.org/life.html/
I’m afraid you understand nothing. Common descent may be a working hypothesis, but the data test that hypothesis. Common design isn’t a hypothesis unless you can tell me how to distinguish common design from common descent. Differences in sequences are expected from common descent. If there were no differences, we could not build a tree. The differences we see between species are exactly the same sort of differences that are observed within species, just more of them. Common descent is very well established in that paper, and in fact we went to a great deal of trouble in the paper to rule out other possibilities.
But if you would like to point out alternatives we didn’t consider, or any other serious weaknesses of the arguments, please do so.
Thanks for trying so hard to understand.
There is a difference between functional compromise and survivability and selective advantage. Someone can lose organs and survive…. In fact parasites that LOSE genes often have immediate selective reproductive advantage. But they are functionally compromised in that they traded short term reproductive advantage for possible disadvantage in another environment. So there again, real selection in the wild destroys function rather than create it.
Function is not the same a selective advantage. It may or may not be correlated with immediate survivability. The Peackock’s tail is functional, but it may well be a survival disadvantage for the entire population of Peacocks/Peafowls. This problem wasn’t lost upon Darwin.
So take the example of blind cave fish or blind Gammus Minus. The eye might not tolerate too many genetic losses, but in a dark environment where there is metabolic cost to maintaining and eye, losing an eye could be reproductively advantageous. It doesn’t mean however there wasn’t functional compromise in the process of gaining reproductive advantage!
The problem for evolution, like the Peacock’s tail, is one of extravagant Rube Goldberg complex function that is sometimes a liability for survival. The error most evolutionists make is equating reproductive fitness with functional complexity. Big mistake.
Look at a house of cards. It is evidently designed. It has no reproductive advantage. But its design can be easily compromised. There are lots of designs in biology that seem to transcend or defy survival advantage. The iconic example of functional complexity that is a survival liability for the species (not for the individual) is the Peacock’s tail (which made Darwin sick because it told Darwin he was wrong):
Corneel,
Here is a compilation of Bird behavioral rituals that often coincide with their anatomical features. Like the Peacock’s tail, personally, I find evolution of such extravagance not believable. The one at 4:24 in video was really compelling:
Your first parenthetical statement contradicts your first sentence. Of course a peacock’s tail confers a survival (meaning reproductive) advantage. It doesn’t matter whether it’s a liability for the species as long as it’s an advantage for the individual. While that may have made Darwin sick, he did discover sexual selection. Why do you discount it?
Also, what’s god doing creating species liabilities? Doesn’t that argue against intelligent design?
My pleasure
So you accept adaptation by natural selection but only in regressive evolution. Correct?
Darwin already saw that the increased mating success of a peacock’s tail would generate a competitive advantage. But I take your point that complexity is not necessarily evidence of that.
But there remains the point that dozens of genes were apparantly lost from complex biological systems once environmental conditions allowed it. Yet you simultaneously maintain that the interconnectedness of extant molecular networks are intolerant of mutation. In my view, these two statements are incompatible.
Yeah, I saw those. Really cool.
They are however the result of sexual selection. Are you familiar with sexual selection theory, like Ronald Fisher’s runaway selection or Zahavi’s handicap principle?
But sexual selection makes no sense if its just for the sake of preferred sexual selection.
The whole point of sexual selection is that the reason they are being selected is for because the trait holds a better survival advantage.
If the only survival advantage is that its sexually selected, then even you have to admit that is pretty circular.
We’d better take this discussion to the “fitness” thread, or give it it’s own OP.
I will just note here that the sexually selected trait confers, if anything, a survival disadvantage. The fitness advantage lies in the securing of
multiple matingsincreased mating success in male-male competition for females.ETA: corrected phrasing
Yes we should move the discussion of fitness to it’s appropriate thread.
We should move the discussion of moving discussions to its appropriate thread.
I responded in the fitness thread to your post about sexual selection.
Male-male competition, female choice, female-female competition, male choice. All of the above are considered sexual selection.
And the peacock’s tail is a result of female choice, NOT direct male-male competition. You are right.
At least something we can agree on for a change.
Yes. It is selection between individuals (females selecting males), but hardly anyone seems to see that species that exercise such selection have a disadvantage as a group! This isn’t exactly what group selection theory predicts, but one can consider the physical evidence that it is disadvantageous to the group to have such elaborate mating rituals that favor metabolically costly phenotypes like the Peacock’s tail.
One might argue, “why didn’t females wise up and chose more metabolically efficient males?”
Bird species are going extinct at an alarming rate, whereas creatures that don’t have such complexity and mating and reproduction rituals (like bacteria) are persisting. Birds like the birds are paradise are wonders to behold because of the extravagance they have that goes so far beyond mere survival, and it appears such extravagance is a liability to the species.
I learned of Darwin becoming sick when he looked at the Peacock’s tail when I watched the PBS series on evolution many years ago. That’s when I learned of his sexual selection theory. The series pointed out that prior to Darwin, such extravagances in nature were believe to be designs to make man wonder at his creator. I think that is the correct explanation, not sexual selection, because sexual selection between individual seems to not agree with the favoring of an entire species.
Here again, “selective advantage” is equivocated. Yes it is “selectively advantageous” between individual male traits, it’s not selectively advantageous for the group as a whole. One thing that really bothered me about population genetic models is that theory predicts “fitness is ever increasing” between individuals, right up until the point the entire species is wiped out!
Wiens, Salthe, maybe a few others have pointed out this sort of problem in one way or another regarding population genetic models. Wiens in particular argues this is the mechanism of extinction after environmental disturbances whereby ever increasing fitness at the individual level for short term makes the entire population at risk of extinction in the long term. Short term gain for the individuals, long term loss for the group.
John Harshman,
Sure, but I saw 30% DNA sequence difference in species that you had directly sharing a ancestor based on the additional data you pointed me to. At what point do we say that common descent is a questionable hypothesis given it requires the extraordinary claim that birds lost flight multiple times.
In this case common design could include the possibility that the bird was separately created in its current location. Depending on your assumptions this is a much simpler explanation.
Like under the assumption that magical fairies exist.
Glen Davidson
I am.
It doesn’t need any detail. It’s only meant to explain the nested hierarchy, that’s all.
Assumes facts not in evidence.
You have forgotten to present your support for this claim. Doubtless an oversight.
Why would this be a problem? And what species are you talking about here?
Why is that an extraordinary claim? Are you aware that there have been over 700 losses of fight within the family Rallidae alone, and many more in other families? If you reject common descent, what else can explain the pattern in the data?
What assumptions could possibly make that explanation simpler? How would it account for the sequence data?
A couple of problems: first, group selection is much weaker than individual selection and would generally not be expected to have a strong effect on the course of evolution. Second, there are reasons to suppose that costly ornaments might be advantageous to the population, as under the handicap theory they are signals of superior genetics and thus aid females in choosing the best mates. (This works only if the ornament is less costly to high-quality males than to low-quality males.)
I’d like to see your data on the rate of bacterial extinctions compared to the rate of bird extinctions. I think you’re just making this up.
Maybe, maybe not. If it is, though, doesn’t that argue against a benevolent creator. Of course your creator may care nothing for species and be willing to cause excess death and suffering just so he can have pretty colors.
Why is that a reason to reject sexual selection? It seems that you are attaching a moral dimension to evolutionary processes, one that comes from your preferences rather than nature.
I assume that Wiens is John Wiens and Salthe is Stan Salthe, but what publications of theirs are you citing here? It’s customary to give full references in cases like this.
John Harshman,
An out of space time design or a special creation. This better accounts for a 30% sequence deviation and the birds location.