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.
Erik, to KN:
Erik,
That doesn’t follow at all. Our personal cares need not align with the “cares” of evolution. This should be obvious.
For example, someone chooses to remain childless and uses birth control to that end. Evolution “wants” the person to procreate. The person doesn’t want to procreate.
Philosophical thinking is clearly very difficult for you. Have you thought of taking up another hobby?
Speaking personally, the remarkable patterns of SINE inserts in Cetacea or Rodentia, and the surprising consilience of trees drawn on Intron 7 of Buglate Yabbadoobiase with those drawn on … oh … tRNA-something-or-other, are all the excuse I need to go out a-rapin’ and a-pillagin’.
Biologists are noteworthy for being quite the meanest individuals in the faculty. I think we all know why.
Are you saying that you believe generatio spontanea to be true, or are you saying that you don’t believe in any of the above but are not going to tell us what you believe?
I suggest that when you find a reason to care about truth (and morality in general) you will find it incompatible with evolutionary theory. If you think carefully through what is at stake, you must find something that is either seamlessly compatible with evolutionary theory (and it obviously isn’t) or it must override it, so that evolutionary theory is something negligible in bottom left corner. If evolution is true and we take it seriously, the only option is that truth is a barely defined ephemeral recent epiphenomenon that we should treat with utmost suspicion.
Most people live their lives practically ignoring evolutionary theory and any evident implications of it. As long as this is so, there is humanity worth the name.
So: it’s boiled down to “Common Design is a better explanation for a given pattern because it makes us Behave”?
Allan Miller,
Isn’t it a sort of fact of life that behaving matters? If not, then why is there Moderation Issues and Guano?
Erik,
Sure, behaving matters. But that does not make Common Design a better explanation than, nor even one on equal footing with, Common Descent for a given pattern.
Only for you poor people. Get sufficiently rich or powerful and you can do whatever you feel like.
https://www.washingtonpost.com/news/worldviews/wp/2015/09/24/7-wicked-popes-and-the-terrible-things-they-did/
Available theories are aplenty, but biology as a science is fundamentally in a sorry mess. I’ll leave it to the experts to sort it out. This blog with these people brought me to this conclusion, which is good enough as far as it goes.
Funny you should say that. I always thought that the “design” of male reproductive organs was the most powerful evidence against design. Consider for example the “design”of the penis of Callosobruchus maculatus:
figure
Looks nasty, doesn’t it? It is! It shreds female beetles apart from the inside during copulation. What designer thinks up something like this? I guess the evidence shows that the designer, contrary to popular belief, does not have an inordinate fondness of beetles.
ETA: I seem to be unable to correctly link the image, so added the URL
I don’t think anyone thought the dragonfly and mammalian penis resulted from common ancestry, Sal.
If you are saying that generatio spontanea is a viable scientific theory for biodiversity, then I suggest that the sorry mess is in your understanding of modern biology, not in biology itself.
Modern biology has no understanding of what is viable. They think that the ability to draw the tree speaks for itself, without any regard to the underlying subject matter. And KN says it’s no different from physics, as if physics dealt with matter that just keeps on multiplying itself to no end, instead of having something like the second law of thermodynamics. No understanding at all to be found here.
Erik,
Not really true. Nonetheless, the ability to draw the tree on objective criteria – numerous free online programs are available that will work on user-supplied sequences that were not ‘smuggled in’ – shows that something is going on which needs an explanation in itself. Common Descent provides one viable explanation of this. In fact, ISTM, the only one that flies.
Indeed …
Yes, I get it. You reject common descent, baraminology, ID and special creation. You even mentioned spontaneous generation which is, I hope we can both agree, utterly ridiculous.
What’s left? Nothing! You don’t like the implications of evolutionary theory, but cannot commit to any other position either.
People might be interested in perusing this list of phylogeny programs. Using my uncanny Holmesian powers of deduction, I suspect that it was produced by someone not a million miles from TSZ … [eta – it is an old page for illustration purposes – many of the links fail]
The programs listed represent many, many man hours of effort by many different bioinformatic bit-jockeys. To say nothing of the lengthy undergraduate courses undertaken. All of them unaware, not having talked to Erik or Mung first, that they were wasting their time, and you can in fact ‘draw a tree on anything’. The Universal Phylogenetic Program only needs to find out how many twigs there are, draw a tree with that many twigs, then stick the relevant sequences on the ends.
Now, I anticipate the question will be “why do there have to be so many?”.
Erik,
Two comments:
1. Irony is dead.
2. I’m reminded of the White Knight’s song A-sitting on a Gate.
But wait, haven’t you been telling the experts they’re all a bunch of idiots who have no idea what they’re doing? How can you leave it to them, when you’re so much smarter and know so much more? Please, we beg you, tell us your ideas so we at least have something to work with in cleaning up our mess. We obviously can’t do it on our own.
Oh, I care about truth and morality. But I am not finding any incompatibility.
It is recent, in the sense that “true” is a property of linguistic expression, and language is relatively recent.
Epiphenomenon? No, of course not.
That’s as bright as asking, what subatomic particles does evolutionary theory predict? Are you so dense that you can’t understand the point about inference? Do you understand epistemology at all?
Moving away from your inability to deal with what is analogous, and your focus on what is not analogous in playing your little word games, the fact is that cosmologists, geologist, and astronomers infer past “evolution” of phenomena all of the time based on effects that are rather specific to certain causes. Has anyone observed the causes of a star turning into a red giant, or is it a matter of effects that point back toward causes, not, of course, being interested in made-up causes like “creation” or “design” that lack any kind specific indications that could show that they happened?
And who has ever determined that “nothing comes from nothing”? How would that be possible to do? There’s far less evidence specifically pointing to that than specifically points to evolution by reproductive descent, although I’m sure that doesn’t matter to you.
The principles of inference of cause from effect are analogous. Messed up again, you did. It goes back to your blank and false statement that evolutionary theory gets causation from correlation unlike other branches of science, when of course that’s standard practice. Hume covered that quite well.
Yeah, if he’d fashioned the strawman you’re attacking.
Glen Davidson
He’s also said that he was here to learn from the experts.
Consistency is the hobgoblin of little Eriks.
Glen Davidson
I am still stuck on this.
So in reconstructing a phylogeny, Erik wants us to use, not the abstractions, but the actual organisms? We make a diagram and tie actual animals to the tops of the lineages? So not DNA sequences but individual animals?
Thing is, it’s hard to do with elephants (for example) because they are very heavy and hard to move. Not to mention whales.
Says Mayr, “…transspecific evolution is nothing but an extrapolation and magnification of the events that take place within populations and species…”
This answers my question to the point. Nothing about abstract correlations that may or may not look like a tree, but directly about the supposed/proposed causes that might give rise to such. If you did biology, instead of statistics, you would have been able to come up with this too, and perhaps even helpfully elaborate it further.
Allan Miller,
I came across this yesterday and was interested in your thoughts since we discussed whether cytochrome c supports common descent or common design hypothesis. Looks like apoptosis is mission critical for embryo development. Apaf1 is what cytochrome c binds to for apoptosis triggering.
colewd,
I do think you are missing the points I make:
1) Your ‘apoptosis function’ is restricted to multicellular organisms.
2) Basically, a cell either dies or it doesn’t. Apoptosis does not appear to have the need for fine grained, species specific variation in the binding of cardiolipin or Apaf1.
3) Adding a function to a gene does not change the probable phylogenetic information in that gene’s variation, unless that variation can be shown – not just assumed – to have a variable role in relation to your added function for the various isoforms.
4) Whatever you do for cytochrome c, you have to do again for several thousand genes before you can realistically dismantle common descent.
5) And, having done so, you still have to explain why the pattern has all the expectations of common descent.
Erik,
There are good things inside this theory like antibiotic resistance and population genetics, and you are absolutely right here but they are stuck because Darwin’s grand claim of universal common descent has not been followed by a cause mechanism that is compatible with how cells are driven by DNA blueprints.
Even worse these DNA chemical blueprints live inside a sequence with almost an infinite number ways to arrange that sequence.
How would you recommend they get unstuck?
colewd,
Fortunately, new organisms are not assembled by random pick from almost-infinite sequence space.
Start waving Bibles around?
Erik,
Is it your experience that biologists are dismissive of evolutionary theory?
Allan Miller,
I think this is an unsupported claim. I would not expect convergent evolution and think its emergence contradicts the pattern.
I think this is becoming harder to support given its integration with embryo development. It has to turn on at the right time which is coordinated with another biological process. More irreducible complexity and evidence supporting design.
colewd,
The support for the claim that common descent predicts a nested hierarchy is that a nested hierachy is indeed what one gets from a process of serial copying with errors and bifurcation. I’ve done it in a computer, and with a photocopier. You can track pathogens and pathogenicity using this assumption. I don’t know why you deny it.
You seemed very shy of defending this position on the ‘Convergence’ thread I started for that specific purpose. Care to do so now, in that thread? There is negligible convergence at the molecular level, beyond stochastic variation during divergence. (Yes, I know about echolocation).
The fact that the developmental pathway as a whole necessarily varies with different organisms in no way supports your contention that this variation is due to the different isoforms of cytochrome c. At a low level, ultimately a cell either dies or doesn’t. You seem to be suggesting that the entirety of an organism’s form rests upon the isoform of cytochrome c it possesses.
All species are always evolving. It’s hard to tell who or what is just along for the ride.
LoL. No, evolution doesn’t “want” the person to procreate.
Thank you.Yet more evidence that modern evolutionary theory is incoherent.
If the data is so fantastically congruent, why the need for so many programs?
Alastair Reynolds did a series of sci fi book on elephants in space. I think there was also something very much like a whale in space in the series.
Allan Miller,
For echolocation, an eye, a circulatory system, a central nervous system that take north of a 100k nucleotides to build your claim requires there to be almost as many arrangements that build these sequences then that don’t. I think the claim is absurd and you don’t. I honestly don’t know where we go from here.
Convergent evolution claims multiple occurrences. This is a real strength of the design argument, explaining the origin of sequences that build complex functions like echolocation.
Right. That would be phylogenies in search of independent data sets.
Phylogenies and the Comparative Method (PDF)
Those were the good old days, eh Joe?
Willful Ignorance: The Mismeasure of Uncertainty
None of that follows. There’s no reason at all why our care for truth and goodness is undermined by evolutionary theory being true.
It’s true that most people live their lives in ignorance of evolutionary theory, but there’s no reason why their lives would be worse off if they were accept it..
This line of reasoning is even more ludicrous and sophistic than Plantinga’s EAAN.
Mung,
No it wouldn’t. You know there’s a diffference between an argument and just saying stuff, don’t you?
Mung,
Gah, right on cue. Like I never anticipated that one:
I could write your stuff for you.
So why should there be a perfect, simple, universal program ‘if evolution were true’? Do you know what the different variant programs are actually doing?
colewd,
No, it doesn’t. That is a ridiculous claim. Eyes don’t get assembled from random space either. I honestly can’t see what process you think takes place in nature that picks extensive random strings from sequence space and cobbles them together.
So, do you think that dragonflies and mammals both being possessed of dicks is a problem for evolutionary theory? What makes us think that they are, respectively, dragonflies and mammals?
Mung,
Yet another substance free quote from a book, by someone, about something.
Far be it from me to disappoint!
I’m more interested in why they are doing what they are doing.
There aren’t just a multiplicity of programs, there’s a multiplicity of categories of programs. Makes one wonder if there are any unifying principles at all involved.
I bet I have a book (or two) on phylogenetics around here somewhere…
Maybe John or Joe will start a thread and explain why we need so many different programs to do the same thing.
Absolutely. I am a studious follower of keiths.
Mung,
They aren’t doing the same thing. But equally, if all it’s about is ‘you can build a tree on anything’, why is there not just one program, doing that? Do you think the programmers are all mad, or stupid, or something?
If they are anything like me I would go with mad. Definitely mad.
https://en.wikipedia.org/wiki/What_Mad_Pursuit
Without explanation as it is now, you should better not have pressed Reply. I can put the exact same level of substance right back at you:
There is no reason at all why anyone should accept evolutionary theory. Truth and caring would be unaffected if the theory vanished off the face of the earth this instant.
Mung:
Allan:
Though for verisimilitude you’d need to drink a lot or bash yourself in the head periodically with a brick.
Allan Miller,
I think the claim that any of the sequences can form in nature is completely without support. Ok how about the light sensitive spot story. Where did the sequences from a light sensitive spot come from? Where did the additional sequences from that improves this to real vision. We don’t have any explanation that is short of wild speculation except for design.