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.
So common descent predicts a nested hierarchy if the random sequence generator doesn’t generate random sequences?
So we get this random gene duplication, and then that sequence diverges from the original sequence due to random changes, until magically it’s expressed and found to be useful (by george!) also at random, but that’s not really random sequence generation, and the data isn’t generated at random.
Why doesn’t someone just admit that John is wrong?
Sure it does. It’s what comes of “unguided evolution.” And “unguided evolution” is the only reasonable explanation for the hierarchy.
Well, I do know though that it’s not because “unguided evolution” “predicts” the very hierarchy that we observe.
This thread is definitely a keeper.
Mung actually believes that the only reason genomes aren’t completely uncorrelated is because mutations are guided.
Wow.
How does that follow from anything I’ve said? Please lay that one out in finely-grained detail for me.
LOL. You’re confused again. No, the claim is that it takes very long time for the random mutations to completely erase phylogenetic signal under most biologically realistic conditions.
Whether the very first sequence was created, or generated at random, is actually completely irrelevant to the inference of common descent. The fact that it is faithfully copied over and over again, and occasionally a mistake sneaks in, and that divergence happens as populations split up, is the key factors at work.
No.
No, the data comes from the copying of templates with occasional mutations.
Whether those mutations are random is actually not particularly relevant.
Correct. But a total irrelevancy. The fact that independent phylogenies are significantly congruent with each other is what you expect on common descent.
This doesn’t even make sense at all.
You’re so throughly confused, and you managed to do it to yourself. Whether the mutations that happen are random or not is actually irrelevant. The only criterion for the inference of phylogeny is that it isn’t the same changes happening in parallel over and over again in independent lineages, and that the rate of mutation isn’t so high that the signal is no longer detectable.
The nested hiearchy could have been created with a theistic evolution-type designer behind the scene “guiding” the process of selection, or even making some particular mutation happen here and there. As such, it is at least concievable they aren’t random, yet they’d still yield a nesting hiearchy of life.
LoL. Little man with finger in a dyke?
No.
Do you think that John thinks that Salvador thinks that all organisms are specially created with their genomes randomly generated?
If “randomized data don’t have a hierarchical structure,” and we have before us a hierarchical structure, then it follows that the data is not randomized.
What is wrong with that logic?
Mung:
You’re assuming that if mutations are random, then “the data” must be random. That’s dumb.
Evolution is more than just mutation.
I agree that random mutations does not imply random data. The whole point of inferring phylogenies is to make use of patterns of correlation that come from recency of common ancestry. Only if the common ancestor were very long ago, and each present species had evolved independently from that common ancestor (with no more recent common ancestors of any set of species) would we see random data.
Well, actually, even if it were just mutation, with no natural selection, we would be able to infer phylogenies from the pattern of distribution of the mutant alleles.
keiths:
Mung:
More like “The cat threw up, and someone’s got to clean it up. I guess I will.”
Joe:
Except that Mung seems to be unaware that parents pass genes to their offspring. He thinks that if mutation is random, then every genome should be random:
It’s hard to fathom, I know. But Mung actually believes that.
So you could have this sequence of DNA, totally random, and it gets copied and inherited, and that sequence now becomes your “signal” that you will try to track over time. And this is why you can create hierarchies from “junk” DNA.
So randomized data can have a hierarchical structure. Is that what you’re saying?
It’s far, far, more likely that you are just making stuff up again. 🙂
That’s what I’ll be doing in a few minutes, lol.
It was a direct quote, Mung.
Here’s what you’re missing, Mung.
Let’s say you insert a junk sequence into an E. coli cell. The sequence might be random, but the copies will not be uncorrelated. A daughter E. coli cell will get an accurate copy from its parent, with the occasional error. It’s the combined pattern of similarities and differences that establishes the phylogeny. The fact that the initial sequence is random does not matter, and whether the errors are random does not matter either,
Your statement is obviously incorrect:
On the other hand, if parents didn’t pass copies to their offspring, and if you truly generated each genome randomly, then they would be uncorrelated, and no objective nested hierarchy could be inferred.
Given the historical pattern of inheritance, yes.
Rumraket:
Mung, have you ever read 29+ Evidences? If so, did it baffle you as it did Bill?
It’s been around a while right? Didn’t talkorigins used to be a newsgroup? How long ago was that? I probably read at least some of it. Maybe not all that is currently available:
http://www.talkorigins.org/faqs/comdesc/
But since I accept common descent I don’t get your point. If you have one. What on earth do you think “baffles” me about common descent?
By the way, could you save me some time and point out where Theobald covers unguided evolution vs. guided evolution? Thanks
The claim wasn’t that no objective nested hierarchy could be inferred if each genome was generated randomly.
So it’s all “signal.”
What a relief. So where does “noise” enter the picture?
keiths,
I have read it. Where in this document is the contradictory evidence? This document is about common descent independent of a mechanism.
Why do you think it was necessary to create a document that separated a mechanism out of evolutionary theory?
Rumraket,
So evolving echolocation is easy just like evolving proteins. At what point are you going to start taking a fresh look at your assumptions?
Say it isn’t so Bill. keiths so needs for the mechanism to be unguided that he’s willing to lay his lowly reputation on the line over it.
Help us out here keiths. If mechanism is irrelevant to the evidence, how can the evidence tell us that the mechanism was unguided?
Theobald:
Say it isn’t so boys. Evolutionary theories.
Theobald:
Well ain’t that just a shot to the old nutsack.
But not as easy as evolving an eye! Given the sheer number of times that eyes have independently evolved it is certainly much easier to evolve an eye.
Right Rumraket?
Douglas Theobald:
Descriptive? As opposed to what, prescriptive?
How does a theory that is “a general descriptive theory” entail anything at all?
Mung,
And when pressed about a convergent feature Rum brings out the old mechanism as the explanation.
Given that there is an historical pattern of inheritance, there is an historical pattern of inheritance, yes.
It would appear that Rumraket has not read Theobald. I’m beginning to think that keiths hasn’t read Theobald either.
It’s cute how excited Bill and Mung get when they think they’ve finally found a significant flaw in their opponents’ positions. It almost seems a shame to spoil their fantasy, but I will.
Mung:
Who said mechanism is irrelevant to the evidence? Certainly not Theobald.
What he said is quite different:
colewd,
It wasn’t. He didn’t do it out of necessity, Bill.
Another keeper from Mung:
Derp.
That’s what dazz says when he doesn’t have an argument.
Are you sure he’s not just laughing at you, like I am?
Mung:
keiths:
Did you get an answer, Mung? Or did the Designer do his customary “Mung’s at the door! Everyone be quiet and pretend we’re not home.”
Mung,
I told you already. You don’t understand the very best evidence for it:
Hence my question about whether you had read Theobald.
By the way, do you finally understand why the following statement of yours is wrong?
Allan,
I considered that possibility, and I double- and triple-checked what you wrote. It still looks like a blatant contradiction.
You objected to the exclusion of HGT from ‘common descent’…
…but then you agreed with it:
If you don’t consider HGT to be descent, then why did you object when I excluded it from ‘common descent’?
Right. So again, if you agree that HGT is not descent, why did you object when I excluded it from ‘common descent’?
And how is it not contradictory to both include and exclude HGT as part of ‘common descent’?
(I even considered the possibility that you had some relevant distinction in mind between ‘descent’ and ‘common descent’, but couldn’t come up with a plausible one. Note the word ‘relevant’ there.)
ETA: And in any case, you ruled that out with the following:
Allan,
I’m using ‘common descent’ in the standard way. You are the one urging a broader definition that doesn’t exclude HGT.
Allan:
We’ve never disagreed, as far as I can tell, on the mechanics. The disagreement has always been over the scope of the term ‘common descent’.
I’m not “hung up” on it. I just think it’s a useful distinction, and by all indications, so does the biological community. Why drop a useful distinction, and why redefine a standard term?
The reason you gave is poor:
My response:
Given
a) that your rationale fails, and
b) that the vertical/horizontal distinction is useful, and
c) that the current terminology doesn’t hobble us in describing HGT events interspersed with descent;
what incentive is there for the biological community to redefine ‘common descent’ per your wishes?
Oh, Nick the guy with a PhD in evolutionary biology who couldn’t even answer a basic statistics question, yeah that Nick:
Here was the question I had Barry Arrington pose to Nick:
And predictably Nick folded:
Yeah, that Nick. Hahaha!
Just a stray thought, but this “disagreement” might be why Dawkins wrote a whole book about the survival of genes.
One can get hung up on definitions, but there is a point of view in which descent is about genes (or sequences) rather than about organisms.
This is not incompatible with the notion that sequences come in large packages that usually stick together.
stcordova,
Looking through that thread, it seems Nick Matzke’s cloak fell on Mark Frank who in the most polite way shredded your argument. To me anyway.
We’ve discussed that thread before. Nick was absolutely correct.
As it mutates, yes.
Yes, that too. Both functional and junk DNA.
No because now you’re trying to smuggle that whole explanation you gave into that single word “randomized”. Which is extremely deceptive. And you’re doing that deliberately to mask the iterative copying and make it appear as if a random sequence generator could just generate, say ten sequences, and then those ten sequences would just so happen to yield hiearchical structure.
That’d be extremely, extremely unlikely. Sorry Mung, not falling for your silly rhetorical trick here.
No you haven’t. You’ve tried to read it, and it went okay until you came to that sentence about it being independent of mechanism, which is where you stopped. And you’ve never picked up where you left off. Rather than read the rest of the article, so that you would come to understand why the evidence of common descent is indpendent of mechanism and in what way that is meant, you instead decided you’d found something disagreeable long before you comprehended it, and then came here to start an argument about it instead.
We’ve been over this at least five times as far as I can remember.
There isn’t any contradictory evidence.
Because it really is independent of mechanism. There’s no reason to start blathering about the relative contributions of selection or drift, or multi-level selection, or mutation biases or anything of the sort, because none of that really affects the evidence for common descent.
Rumraket, Alan Fox:
A simple “yes” or “no” would suffice. If not, explain it like you would to college students.
I would say, “yes”, I reject chance as an explanation. Now, why would all disagree with my answer.
What does that even mean? Echolocation evolved regardless of how difficult you think it is.
When you bring something up that merits such an endeavour. You still haven’t.
When are you?
Now onto matter more weighty than Dr. Nick Matzke, PhD Evoutionary biology’s misunderstandings of basic statistics…..
The PHYLIP format (created by our own Joe Felsenstein) is a little hard to use because it is so persnickety — I can’t even put a space in the wrong place without it shooting me down.
I would suppose PHYLIP was the beginning of many good things and since then there have been more forgiving formats and tools.
For sequences of varying length, I want to create radial diagrams like this without having to use the PHYLIP format. Any suggestions?
I don’t know what “chance” even means as an explanation. Please elaborate.
Hmm, that’s unfortunate, because to use Gene searches it’s good to know. For example at the NIH NCBI website:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect
Note the bolded words “chance”.
So you’ve used blast a lot here at TSZ. You don’t know what they mean by “chance” in that FAQ? Is that right? 🙂
and
Let’s try to untangle this. If we start from a random sequence, and then after a few million generations find that (say) 3% of the sites, chosen at random, have changed to other bases, will both of these sequences be random?
Yes, each will be a random sequence.
Will they be two independent random sequences?
No, they will show considerable similarity, because they are not independently derived.
If we look at a region of junk DNA, where the sequence is random, and we look at it in different species, then each sequence would be random, but they are not independent of each other, so there is a signal there which can be used to reconstruct a phylogeny.
And if we look at another region of the genome, one which is also junk DNA, we see different random sequences, and again, the sequences that we see in those same species are not independent of each other. But each looks like a random sequence if considered by itself.
So we can look at the sequences in that second region and infer a phylogeny from them. And then we can see whether the two phylogenies are noticeably similar. That is what Theobald is talking about.
So yes, Mung, even “random” sequences can be used to reconstruct phylogenies. As long as the random sequences in different species are not independent of each other, as they have not diverged so much that the signal of similarity between them is lost. You expressed incredulity, though in typical Mungish fashion you did not actually say that this was not believable.
It works, both in junk DNA and also in non-junk sequences. It is what Theobald is talking about (and he is following the lead of David Penny and Peter Lockhart in their 1982 paper which did similar things but with less data).
And revisiting last year’s winner of a Darwin Award, DNA_Jock speaking of Thermodynamics and Entropy:
What a howler!!!
If you search for “dQ/T is rarely informative” a frequent number one hit for that statement is by DNA_Jock at TSZ. Why is that?
Gee DNA_Jock, why is your claim so unique? Could it be, that you’re the only one who swears by such nonsense.
FWIW,
I and other creationists believe there is some random variation and that phylogenetic tools can be used to trace back MRCAs, especially those of Noah’s Ark and from the original creation.
Nathaniel Jeanson and Rob Carter are the primary researchers on these topics. I visited with Nathaniel this past June at the Lipscomb University conference.