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.
Creationist: “Note all those gaps in our knowledge, you have no explanation for this or that and you never will because you can’t pretend you can even begin to grasp God’s creative powers”
(Minutes later)
Creationist: “Look, I have a proof of God based on the Principle of Sufficient Reason, and you can’t reject it cause if it was false there would be tons of unexplainable stuff”
m’key
Moved a post to guano.
I address that here.
Mung,
The claim was yours – that 3 (or 4) differences indicates separate origin. As in not commonly descended at any remove, as far as I can make out from subsequent discussion. You’ve since said you’re neutral on the matter – you don’t know what it indicates either way.
Obviously, take away 4 you’re left with 60, which is a pretty high proportion. There are only so many possible causes of the pattern; common descent is certainly in the race and worth a punt.
Separate origin of what? Separate origin from what?
What motivated the endosymbiotic theory for the origin of eukaryotes if not separate origins of various components of eukaryotes?
Common ancestry and the nested hierarchy is a theory of vertical descent with modification. The eukaryotes, if the symbiotic theory is to be believed, did not have their origins in vertical descent with modification.
There is a reason for the book title Acquiring Genomes.
The components of the eukaryotic cell had separate origins. I thought, based on previous discussions, that you accepted this. I thought I was saying something non-controversial. Silly me.
So take this cell that is not a eukaryote yet. How did it evolve by vertical descent with modification into a eukaryote?
The theory is that it acquired genetic material, genetic material that was acquired rather than inherited. Why is this theory accepted and do the codon differences in mitochondria have anything to do with its acceptance. That was my question.
So far, crickets.
And here we are, 1855 comments in, and no creationist, including Sal in the OP, has attempted to address the subject in the title. I think that at this point it’s possible to venture the hypothesis that it’s because they can’t. There is no explanation for nested hierarchy — the bulk of the evidence for common descent — other than common descent.
LoL.
John Harshman,
Miller and Rumraket reported that Whale evolution is not a problem for a nested hierarchy. The idea that an enormous sea going creature shares a common ancestor with a land dwelling mammal. This leads me to think the a nested hierarchy is just a human arrangement of historical data. What are your thoughts?
The best explanation for the evidence for common descent is common descent.
My thoughts are that, after all this time, you still have no idea what the nested hierarchy of life is or what the evidence for it looks like. No wonder you can’t address it.
So, is it your contention that whales are not mammals? That they were created separately from land-dwelling mammals? That all the features they share with other mammals (and specifically with hippos and other artiodactyls) are just “a human arrangement of historical data”?
Mung,
You’re the one who said it. Don’t you know?
Well, yes, some time has been spent trying to establish whether you mean that they had a common ancestor, or that they didn’t. It’s an obvious and trivial aspect of endosymbiosis that the components were separate. But the question here is whether these components themselves had a common ancestor.
No, but the two components had separate histories back to a common ancestor. That, at least, is where the evidence points.
Well, as I noted in a later comment, if all you meant was that they came from 2 different, but ultimately coalescent, lineages, I had no argument with this. But you appear to have been saying that they did not share common ancestry at all. If you’re not saying this, fine.
Not entirely fair. I answered a question I thought you were asking, and in that response I alluded to the genetic codes of the components.
I will try, though you don’t appear to accept my efforts with good grace.
Here are 3 codes:
_________1_________2_________3_________4_________5_________6
1234567890123456789012345678901234567890123456789012345678901234
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
The first is the ‘standard’ (eukaryote nuclear) code, the second vertebrate mitochondrial, and the third the bacterial, archaeal and plant plastid code.
Now, since the third code applies to both components of the endosymbiotic event, we can see that the code actually can’t figure very strongly in endosymbiosis theory. On the evidence, at the moment of endosymbiosis, the two components, archaeon and bacterium, may well have had the same code (can’t be known for sure). One could say that the 3rd code should be called ‘standard’. The first and second are strictly derivatives of this – respectively, the eukaryote nucleus and the vertebrate mitochondrion. But, with typical species chauvinism, we’re the ‘standard’. [eta – 1 and 3 are the same codon-per-codon. They differ in initiation codons, not shown].
Plant plastids, however, remain with the bacterial code intact, consistent with a more recent origin from cyanobacteria, with no subsequent modification.
A factor to bear in mind here is genome size. It is far easier to amend the code in a small genome than a large one, due to an increased likelihood of minimal codon usage reducing the constraint on that triplet. Plastid genomes are several times the size of mitochondrial ones.
My thoughts? That the nested hierarchy of the data positively screams in your face. One has to work hard to deny it.
McGowen MR, Gatesy J, Wildman DE. Molecular evolution tracks macroevolutionary transitions in Cetacea. Trends Ecol Evol. 2014 Jun;29(6):336-46. doi: 10.1016/j.tree.2014.04.001
John Harshman,
Whales have unique features of which the origin is hard to explain like echo location, their size and their location in the ocean. You say they share a common ancestor with perhaps hippos yet could you be wrong? If your are wrong then the nested hierarchy that we see is wrong. This is ok as a tentative human construct.
Common descent is a claim about a process. The process starts with reproduction and ends with a different animal type. A nested hierarchy appears only to be a humans interpretation of how to arrange the data and does not address the process of how a new animal type is formed.
colewd,
I’m sure you’ve been given links to the SINE data on whales. I wish you’d read them.
Molecular phylogenetics says yes. And hippos are are really well adapted to their mostly aquatic lifestyle. Mothers even give birth under water. It’s not a huge leap to a fully aquatic lifestyle.
And then thinking humans realize that the obvious interpretation of the nested hierarchy requires explanation, and note that common descent explains it as does nothing else.
Others just try to find excuses to ignore it.
Glen Davidson
No, I couldn’t be wrong, or at least I’m as close to “couldn’t be wrong” as science can get. But since you’re unwilling to look at the data and apparently incapable of understanding any analyses, there’s no way I can support that certainty for you. But it’s very far from tentative. I notice, by the way, that you ignored all my questions.
You mistake the process. Common descent is nothing more than reproduction plus branching. You still misunderstand it as having something to do with the origin of characteristics. Common descent doesn’t address the process of how a new animal type is formed; that isn’t what it’s about at all. The fact that you and all your first cousins are descended from your grandfather does nothing to explain why your cousin Fred has 100 particular mutations. And you don’t need to know the causes of those mutations to know that Fred is your cousin.
Alan Fox,
Can you support this claim? Do hippo’s have echo location? If convergent evolution is real why not an alternative tree with fish as an ancestor? The nested hierarchy appears to be just a human construct of the data which is almost certainly flawed.
Convergent evolution is strong evidence against common descent and for common design.
Is it possible to ignore all the data, all the arguments, this much without realizing it? Is it possible at this late date that Bill is anything other than a conscious troll? I ask this seriously.
colewd,
And therefore what can we say about common design in general then, from knowing that?
For example, we can say that if convergent evolution is designed then it appears to happen over very long time scales. Therefore the designer causing it is something outside our experience.
Perhaps you could rank aliens, time travelling humans, Jesus Christ superstar and de lard in order of what seems most likely to you? Of course, feel free to add your own choice.
Also now that we have identified convergent evolution as designed, what is the next step that we should take in order to progress science and expand our knowledge?
John Harshman,
We agree that common descent is describing a process. In the case of Fred we have a external way to validate. In the case of the whale and the hippo we don’t. You are making a claim about a process. How do you validate that the process you are claiming actually occurred?
Design on the other hand is not a process but a project which has to be planned and executed.
Yes. Here’s one paper. There’s more. Much more.
OMagain,
Convergent evolution is a name for features evolving separately in lineages. This is not what we would expect from the data if the process of common descent actually explains the origin of new animal forms.
Scientific research is about priorities. Priorities are generally set by probability of a successful outcome, the social/economic impact of that outcome, and the resources required for that outcome.
As usual you ignore almost everything in my response. Why?
What external way is there to validate that Fred is your cousin? As for common descent, we can see all stages of divergence in nature, from none, through separate species, and beyond. Where is the point at which you claim these stages don’t grade into each other? (There is none). We know how reproduction works. We know a good deal about how speciation works. But we really don’t need any of that. Common descent is the only explanation for nested hierarchy. Nobody has ever come up with another, including the over 1500 comments in this thread. That’s all the validation necessary.
But if you wanted external validation, wouldn’t fossils do that?
Meanwhile here’s where we stand on whether whales are descended from land mammals:
Science:
SINEs
DNA sequences
Anatomy
Physiology
Fossils
Bill:
They look kinda like fish
Checkmate, evolutionists!
Alan Fox,
That site really should try to keep the citation connected to the paper itself. That was Mol Biol Evol. 1997 May;14(5):537-43.
John Harshman,
The nested hierarchy is a human arrangement of the data. As Alan’s paper cited paper stated it is highly tentative.
If the arrangement of the data is uncertain can the nested hierarchy be certain? Does the data really fit into a nested hierarchy that will not change?
We can arrange the data in this tree therefor the data is the result of reproduction from a single tree or a few trees? How do you establish the line of demarkation?
Looking at Alan’s paper there were 15 to 20% differences some of the DNA sequences of animals that are nested in the tree. Any comments?
John Harshman,
You agreed previously that you could not support this claim.
Yes John, it is possible. Think Glenn Morton. I never really get any troll-ish vibes from Bill. I think he’s absolutely genuine. He doesn’t get it and he really does think he has the upper hand in this argument.
One of the biggest recurring themes in these discussions is that most of the time, the people we argue with simply don’t try to understand. They don’t read for comprehension, they seek things to oppose. This makes all the difference in the world.
It is possible to read words without spending a single conscious thought thinking about what they mean. That’s probably how Bill reads. He scans through the text, probably speaks in an internal voice in his head the words he read without thinking about them, and just “picks up on” certain key-words that make him think of topics for rebuttal.
I should have noticed the paper was published in 1997. Here’s another paper by the same author from 2011.
colewd,
Things that were tentative in 1997 are not necessarily still tentative.
Have a look at this paper. Note that this is not about the evolution of the whales from land mammals at all, but about the use of SINE data to resolve clades within the cetaceans. Try and understand the methodology – what SINEs are, why they are considered a reliable marker, how they correlate with other forms of molecular data, without the barrier of your incredulity regarding land-to-sea transition.
I mean really, really give it a try.
These people don’t spend years and dollars on this stuff simply because they are blinkered ideologically-motivated thickoes. Other reasons are available.
Are you sure I said that? Where?
No, you misunderstand the paper. As usual, you just cherry-pick little bits that you think you can use and ignore everything else. Scientific papers are, by tradition, modest in their claims (unlike the press releases that often accompany them). The nested hierarchy in those data is real, not a human construct. What was tentative at the time (though I’m sure strictly pro forma in Gatesy’s opinion, even then) has since been confirmed many times by orders of magnitude more molecular data and by new fossil discoveries. This paper even comes before the near-simultaneous discoveries by Gingrich and Thewissen of whale astragali.
That was a question for you. I say there is no line of demarcation, because there is in fact a single tree. Now if you’re asking how we can tell whether there’s one tree or separate trees, it’s by phylogenetic analysis. Strong support for a tree tells you that it’s real.
Sure. Differences accumulate over time. The longer the time, the more differences. Why would that be a problem?
Alan Fox,
That could be misleading though. Whales evolved 50 million years ago, hippos about 15, and both from (probably) fully terrestrial ancestors.
Allan Miller,
OK, but looking at the cladogram posted by Rumraket, there is some suggestion the common ancestor already had some adaptations toward a semi-aquatic lifestyle.
Yeah, but that’s based only on the extant species. Note the “reduced hair”: not something you will get from a fossil. And there are no anthracotheres or entelodonts in that figure.
My thoughts? That the evidence of design positively screams in your face. One has to work hard to deny it.
Thank you for your opinion.
Because it’s mostly nonsense.
I have an ark for sale.
Mung,
I think you’d need to be a little more specific.
Mung,
One careful owner.
Allan Miller,
From my beloved alma mater 🙂 The hierarchy becomes nested through the use of extinct animals.
They so back up your claim that hippos are 15 million years old and whales 50 million years old.
How do we do a DNA comparison of extinct animals with extant animals to support the nested hierarchy claim?
So the paper you cited on sines as a phylogenetic sorting tool only shows animals with their own tree branch.
Why don’t you know the first thing about nested hierarchies and how they’re determined?
Do South Pacific languages require ancient writings to determine that they fit into nested hierarchies (if they do)? Of course not, one only has to determine that one diverged from another one earlier than than a later one to be able to diagram the nested hierarchy. Changes in grammar, or certain lost or gained words could be used to determine how long ago languages diverged, in relation to one or more other related languages.
Plus, nested hierarchies were determined well before DNA was even understood to be the chemical of inheritance. Early nested hierarchies were largely determined according to morphology, which is also how fossils generally are determined to fit into phylogenetic relationships.
You need to learn the basics of biology, especially evolution. Merely objecting with your ignorant presuppositions is pretty useless, especially as you tend to ignore (likely in part because you don’t understand) responses made to you.
Glen Davidson
Glen, to colewd:
Bill is demonstrating the Jebus Effect for us.
Rumraket:
It’s the Jebus Effect in action.
Rumraket:
Mung:
Mung, too, is afflicted by the Jebus Effect.
Allan, to colewd:
He can’t risk it. The more he learns, the more ridiculous creationism appears. So he fights hard to remain ignorant.
It’s the Jebus Effect.
I take it the Jebus Effect is what we used to call Morton’s Demon?
And yet you have no better explanation ,it has to sting a bit
colewd,
So what you are saying is there is absolutely nothing we can do to expand our knowledge past the “fact” that convergent evolution was designed.
You can’t even come out and say that yes, this rules out XYZ but supports ABC. You just give a Trump-like “yeah, whatever research is priority will be our priority for research” nothing burger.
Mung,
If the evidence of design positively screams in your face, it appears to be screaming “stop here, this is sufficient”.
If the evidence of design is really there you’ll be able to meet the challenge I’ve set colewd. What does that evidence allow us to rule out regarding the designer of the design? For one, we can say that the designer must live a very long time. For another we can say that designer appears to be constrained in a very similar way to how evolution would be constrained, if evolution were real.
Stop sitting on the fence for once.