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 how is this not circular? Because common descent is what you need to prove, not assume. And insofar as you cannot distinguish it from speciation, homologies and what not, then all of these need to be proved separately. Unless circular argument is cool when you personally do it.
Correct, if by “evidence” you mean something else than common descent or speciation.
You probably mean inherited genes as evidence? Sorry, but this is insufficient, because this assumes that reproduction and speciation are the same thing. They are not. Parents yield offspring of the same species, but “common descent” is supposed to demonstrate evolution of different species from one. As distinct from adaptation. What is the evidence for that?
Yup, and another. And then you see differences too. And you say, “Gene loss, also inherited.” It all fits!
What does Common design predict?
Oops. I didn’t mean to make any point. Then I might have to defend it. 😉
Allan Miller,
You chose not to support your claim which was probably wise since it is probably wrong. At this point lets call it a day and move on.
Joe, I notice that whenever you have asked whether members of the genus Zonotrichia are related by common descent, nobody has answered you. And yet this ought to be a no-brainer affirmative even for most creationists. Is TSZ unusual in that only species-fixity creationists are represented here? Is any creationist here willing to agree that these three species (and hey, let’s not forget Harris’s sparrow too) are related by common descent? It would be a start. It would at least begin to help determine where we find common ground and where we part. If that’s even a matter of interest to creationists.
colewd,
Hang on, which claim? You are not the clearest of interlocutors.
I can agree that all dog breeds are the same species. Wolves included.
So what? From this, does UCA follow or at least something like from reptiles to birds? How?
For anyone interested, here’s some literature:
Christian Schlötterer: Genes from scratch – the evolutionary fate of de novo genes. Trends Genet. 2015 Apr; 31(4): 215–219. doi: 10.1016/j.tig.2015.02.007 PMCID: PMC4383367
McLysaght A, Guerzoni D: New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos Trans R Soc Lond B Biol Sci 2015;370(1678): 20140332. 10.1098/rstb.2014.0332
Neme R, Tautz D: Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence. eLife. 2016;5:e09977. 10.7554/eLife.09977
Chen JY, Shen QS, Zhou WZ, et al. : Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet. 2015;11(7):e1005391. 10.1371/journal.pgen.1005391
Ruiz-Orera J, Messeguer X, Subirana JA, et al. : Long non-coding RNAs as a source of new peptides. eLife. 2014;3:e03523. 10.7554/eLife.03523a
Xie C, Zhang YE, Chen JY, et al. : Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet. 2012;8(9):e1002942. 10.1371/journal.pgen.1002942
Bornberg-Bauer E, Albà MM: Dynamics and adaptive benefits of modular protein evolution. Curr Opin Struct Biol. 2013;23(3):459–66. 10.1016/j.sbi.2013.02.012
Andreatta ME, Levine JA, Foy SG, et al. : The Recent De Novo Origin of Protein C-Termini. Genome Biol Evol. 2015;7(6):1686–701. 10.1093/gbe/evv098
Bornberg-Bauer E, Schmitz J, Heberlein M: Emergence of de novo proteins from ‘dark genomic matter’ by ‘grow slow and moult’. Biochem Soc Trans. 2015;43(5):867–73. 10.1042/BST20150089
How do you know they are? Have you tried crossing all dog breeds in existence?
Rumraket has answered most of this already. I would just like to add explicitly (Rumraket implies it) that, as I have previously said, you don’t understand that diagram, and here is yet another way in which you don’t: your definition of “orphan gene” is not what the people who made that diagram were using.
John Harshman,
I brought up the example of Common and Spotted Sandpipers. Erik nearly wet himself because he discovered they occasionally interbreed, and hence could be accepted as commonly descended without undue upset.
These are questions for Harshman and Felsenstein. They are the experts. From experts, it’s fully appropriate to ask how they know what they claim to know.
If something is an empty tautology, it is an empty tautology.
John Harshman,
I would like to see this claim supported by genetic evidence and argument. At this point I have no reason to doubt their ancestral relationship.
I didn’t ask about dog breeds. I asked about Zonotrichia sparrows. And I didn’t ask whether they were the same species. I asked whether they were related by common descent. You have just added another data point for the unwillingness of creationists to answer the question.
So, would you agree that all four species of the genus Zonotrichia are related by common descent, or would you not?
Now of course UCA doesn’t follow, or anything other than that particular group. We’re trying to find out what you think are the limits of common descent. I think the limits are UCA. What about you?
What genetic evidence and argument would support the claim? I’ve given you genetic evidence and argument for paleognath birds, and you rejected that. Why would you be prepared to accept anything similar for sparrows?
It doesn’t. But even if it did explain that particular difference, you’re still not answering the question. Why IS there ANY difference between two species of bacteria, and between plants and squid? Why do all mammals not use an identical cytochrome c? Why is the one from yeast different from the one from jellyfish?
Why is the phylogenetic tree you get from cytochrome C highly significantly congruent with the phylogenetic tree you get from comparative morphology? Or some other basic metabolic enzyme?
These are the facts you are supposed to try to explain
I somehow have the impression that you have already been doing that — demanding more when you are unsatisfied with the explanation given.
I didn’t make any mistake, you just misread me. At no point do I infer they are homologous because they perform a similar role.
I inform Sal (for the second time in about a month) that those that are homologous, also perform similar roles. He has let himself be confused by the naming of the individual proteins.
You’re not getting away with this one Erik. You said you were fine accepting that all dogs belong to the same species. Why are you fine with that?
That’s not a question for John or Joe, they can’t answer why you are fine with accepting all dogs belong to the same species. So why are you fine with that, Erik?
Why? Why can you agree with that? What is it that makes it reasonable to you, to agree with that?
John Harshman,
If the DNA differences were within the range of what we could expect from species we know share common ancestors like people or dogs. The small amount of paleognath sequence comparison I looked at was much wider than same species variation.
I’m fine with it for the sake of the argument, because John Harshman complained that “creationists” here do not agree enough for there to be common ground. Now I want to see what possible common ground he can offer based on this agreement.
Apparently none,
Yadda yadda. Still not happy.
If you had evidence, you would not need to ask for agreement in the first place.
Neil Rickert,
Do you have evidence the claim has ever been explained?
Erik,
Because a tautology is not a circular argument. It’s definitional. You will find that many definitions are tautologous. I was emphasising that common descent as a concept is definitional, not empirical.
If we have a process of genetic copying, it is a potential mechanism for sequence identity that we cannot simply rule out by fiat.
That makes no sense.
No it doesn’t. It assumes that reproduction continues through the process of speciation – a process of divergence.
No it isn’t. The pattern of genetic identities is evidence that speciation has occurred, not a demonstration of it.
Why do you keep bringing adaptation into it? It has nothing to do with the issue.
Well, yes. Of course it fits. One would not expect a theory to be composed of parts that don’t fit. As I said earlier, the pattern of similarities and differences is what counts, not one or the other alone. A change can be both ‘similarity’ and ‘difference’ – it is a difference outside the group that shares it; a commonality inside. Both roles are informative of relationship.
If the loss of a particular gene is congruent with many other genetic changes also restricted to the same taxonomic groups, even approximately, it would take a particular kind of individual to view the mutual support of these separate genes as an invention of circular reasoning.
Whatever one happens to see, as far as I can tell. Any pattern, all patterns, no pattern.
Well, UCA does not follow. This is what I have been saying. Finally there’s something we agree on. Is this the common ground you were looking for?
Oh, but in reality you don’t. Is that what you’re saying?
Allan Miller,
This is how you support a claim?
Last I heard, “baraminologists” were using conventional methods of phylogenetic inference within “baramins”.
See the Methods section of the Wikipedia page on “Baraminology” and the links from there.
colewd,
You reckon that the differences among metazoans can be accounted for by differential ‘requirements’ for apoptosis. I would suggest that the person who needs to support a claim is actually you, here. The role in apoptosis relates to binding of cardiolipin, and the chemistry of that bound complex – a very low-level function, and one that can’t be varied without at least potentially interfering with the vital function of electron transport. Neutral variation is more probable than functional variation.
I don’t see a reason for different amino acids in rabbits and wombats, and greater differences in crocodiles.
So, one way in which that claim ought to be capable of evaluation is in looking for a constraint or relaxation in animals that is not present in groups without the apoptosis role.
That is, I suggested a way to test your claim, and this is the thanks I get.
Sure we have a process of genetic copying. But having species that breed different species is a whole different claim, up and above genetics. Different animal species don’t have quite the same genes, do they? You make it all about genes, but it’s really all about species. Genes do not replicate themselves. Species do, via genes, and they replicate specifically themselves, not some other species. A species breeding some other species is a completely different claim that requires different evidence.
If genes are a specific attribute of a species like any other part of the organism is a specific attribute of the species, then they are insufficient evidence for common descent.
If Common design predicts whatever pattern one happens to see, and we happen to agree on the pattern, then Common design should be at least as good as Common descent. So why do you think descent is better? What makes it better?
Allan Miller,
What do you mean that apoptosis is a low level function? There are north of 200 genes involved in this process. It appears you don’t want to really go into this. Lets table for now.
How do you know people and dogs share common ancestors? And you have just shown that you will never accept evidence for common descent of two species. That’s extreme even for a creationist. Why do you adopt that criterion?
No. Though I’m glad you have finally noticed that what you claim to have been saying is not something that anyone disagrees with. No, the common ground I’m looking for is the part you snipped, about how far down the tree you think common descent goes. That’s why I’ve been trying to get you (or any creationist) to tell me whether those sparrows are related by common descent. What do you say?
colewd,
The number of genes involved is absolutely no indicator of the extent to which one would expect species-specific variation. It is a basic ‘housekeeping’ function, like intron splicing, metabolism, etc etc etc. All of these are complex, but at the level of the cell, not the multicellular organism. Apoptosis is a slightly special case because it has a role in development. But still, I doubt very much that variations in cytochrome c across animal species are in any way related to apoptosis.
I’ll go into it as much as you like – you seem unwilling to support your claim in this regard. Your claim being that the variation amongst animals is due to the role in apoptosis.
Yes. But it seems that you were not satisfied with the explanations given.
Yes, because you still won’t answer what ought to be a very simple yes/no question. Why?
Erik,
Maybe it is, maybe it isn’t. You seem unwilling to entertain, even for the sake of discussion, the possibility that two species are different purely because they diverged from a common ancestor. Their genetic commonalities – sequential commonalities, even down to the order of genes on the chromosomes in closely ‘related’ species ‘ – is a data point in favour of that scenario. You reject it out of hand.
Because it does not predict just any old any pattern; it predicts this pattern
So, an evolutionist is someone who simply accepts this argument out of hand? Thanks for being clear and straightforward for once.
Erik,
Hmmm… I’m sure there’s a formal logical expression for the fallacy you commit there. ‘Talking shite’ would be my approximation.
Look, you are apparently here to make converts, but I am here to learn from experts. I cannot make any assumptions about “how far down the tree” as long as we are not clear about what the tree represents and how you came to that conclusion.
Trees can represent many things. What’s the evidence that this particular tree represents common descent? “Nested hierarchies” or homologies or such are not the evidence. They are the same tree under a different name.
Yes, but also intelligence would reasonably be expected to do certain things differently, like making rigid bird wings out of single bones rather than out of ancestrally articulated bones. Even stupid designers wouldn’t simply make things more complicated in ways that appear to derive from the past, and by no means is the Designer said to be a stupid being (nor could be).
For similar reasons, languages typically have illogical holdovers from the past.
Not that the reasons why life’s patterns fit well with common descent and poorly with common design hasn’t been explained to Erik repeatedly. He just reiterates the same dull questions regardless, indicating poor uptake.
Glen Davidson
Well, you are the one talking shite if you say I reject your argument out of hand. I have my reasons, I have laid out the reasons, and you have no answer. That’s about it.
Erik,
You haven’t given a reason for rejecting the case that accumulated divergence can lead to incapacity to interbreed. You’ve just chosen that as your somewhat arbitrary cutoff, and set up an impossible experiment – you want to see the moment of partition.
In fact, why should we suppose that organisms that can interbreed are commonly descended? Doesn’t work for Adam and Eve.
If we can find some common ground where everybody agrees we should find the same pattern, we might actually be able to establish that phylogenetic inference is a valid approach, and move on to more interesting issues.
Allan Miller,
The paper I cited supports that cytochrome c binding (for apoptosis) is different in different animals. Different sequences are required.
colewd,
That different sequences exist is not evidence that different sequences are required. One could simply say the same about the electron transport function; you’ve added nothing by talking of apoptosis.
Which reminds me. You accept common descent, right? Don’t you accept phylogenetics as a valid methodology or weren’t you speaking for yourself?
John Harshman,
We can positively identify people and dogs that share common ancestors. This creates a comparative standard we can count on.
So, hands up who thinks reproductive incompatibility cannot evolve?
Erik,
Chortle. “Common design predicts”? Don’t make me laugh. Fortunetellers “predict” things in the same way. When “common design” predicts something on some basis other then it following the words “common design predicts” wake me up.