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.
The point is not whether common descent caused anything, but whether it happened.
And the statistics that we do was not part of the evolutionary processes, it is done by us later. So asking whether statistics causes anything is, well, silly.
You mean it could have happened without leaving any effects (because non-causes or causally insignificant events leave hardly any traces)? Surely you didn’t mean to say this, because earlier you’ve been all about “the pattern in the data”, so please kindly reformulate.
Also, Harshman has earlier directly stated that common descent is the cause of the pattern in the data. We don’t want an in-house fight, do we?
No. That’s not what was meant. And honestly, how can you even be asking that? It is exactlty because common descent WOULD lead to very specific evidence that this thread exists. That’s the whole point of the thread. To try to motivate those of you who deny common descent to seriously try to understand the evidence for it, and give at the very least an equal if not superior and falsifiable scientific account for it.
There’s a difference between the data itself, and the program used to analyze it.
Sort of like better and better telescopes allow us better and better resolution of different objects.
This says more about you than anything.
Perhaps, and I’m just guessing, that one of the problems here is that none of you have any formal education in the biological sciences? Did you ever learn any basic organic chemistry and molecular biology? Even the basic things I learned to become a lab technician about basic cell and molecular biology significantly helps understanding.
If you really understand the basics of bio and organic chemistry, many other things become much more obvious, and arguments and evidence that in part draw on these basics become all the more compelling if you understand it.
Just to pick an example, Bill Cole seems to think that things like protein-protein or DNA-protein interactions and binding spots are almost impossible to evolve. This is not a viewpoint that can be seriously entertained by anyone who knows the smallest bit about van der Waals forces and intermolecular binding.
Here’s one time I did that thing you’re insinuating can’t be explained, about 2 months ago:
In this post.
I did that again here a few days ago: In this post.
How conveniently forgetful you’ve suddenly become. Is Bill Cole your alter-ego or something?
Btw, that thing about the independence about the data sets. I was never taught that is what “independent” means. As far as I can remember, I have read only a very small piece about it from Theobald’s 29 Evidences for macroevolution-article, and it didn’t go into much detail. (It’s from here. Scroll down to the “criticsisms” section followin the “potential falsification:” section).
Even so, as soon as I read that, it was simply obvious to me that this is the way it was meant, as that is the crucial aspect in which the data sets individual independence is important for the logical validity of the inference of common descent. It had to be how it was meant.
This is the difference between reading for comprehension and reading “scanning for quote-mines”. You don’t understand anything when you just read looking for something you can pick out and disagree with using a naieve interpretation.
colewd,
That isn’t actually the case. It is at least possible for ‘new’ genes to be injected into a line of descent – and it happens, look at HGT. Nonetheless, the evidence is very strong that there is such a line of descent, by looking at the variation that is not of the order of ‘whole new gene’ in extent – ie, the vast bulk.
I would also remind you that, whenever there is a whiff of ‘new gene’ about, Creationists fall upon it like seagulls on a tip, as disproving the entirety of common descent. The have cake/eat cake line of reasoning. But, indeed, as I have mentioned more than once, how does one even notice a ‘new gene’ but for the fact that it stands out in a phylogenetic analysis? You rely on the very thing you try to undermine for your evidence against it.
Rumraket,
But is a very popular trope among the antis, who seem to suck up bits and pieces from the ContraryWeb and go forth, armed with the latest fad, into the far flung corners, seeking out morons like us who are more than happy to get suckered in!
Rumraket,
I don’t know what’s not independent about taking genes that have nothing (as far as one can tell) to do with each other. Of course one could make hay with the parenthesised caveat, but there must be some genetic stretches that are independent in that sense. The promoter of succinyl CoA synthetase is likely to be independent of a ribosomal subunit, or the 4th intron of a gene involved in blood clotting, or a given flank-SINE-flank sequence, to conjure up examples from thin air.
I could think of “independent” things in biology which isn’t.
To pick something extremely obvious, it would be preposterous to compare the tree of a 3′-5′ DNA sequence, with a tree made from it’s 5′-3′ antiparallel strand. These two sequences are obviously not independent, they are each other’s cause. A tree from one can’t “test” a tree from the other.
Perhaps a less obvious example would be to compare a tree using the coding DNA sequence of cytochrome C, with a tree using the amino acid sequence the of cytochrome C protein. Again, these two are not independent, as the DNA sequence is causing the amino acid sequence.
Of course I’d agree that any systematist worth his salt would know to avoid obvious pitfalls like these, it’s just that it is technically possible to end up with data sets for different things which actually aren’t independent, but are systematically linked by a process other than vertical descent.
Mung,
And this is supposed to be a problem for evolution? LoL.
Baby steps. At least he is easing up on understanding Wagner.
Why? I as I understand you, you seem to be basically saying: There’s lots of potential biological function in sequence space – therefore it was probably intelligently designed.
My question then is, Why? How do you get from the observation of the conducive to evolution-qualities of sequence space, to this being an indication of a good design?
Rumraket,
Yes – Creationists typically bet the farm on the exception being the rule. If there is a possibility of non-independence in the data set, all analyses are suspect.
Yet if one had 5 genes (say) and 2 were not independent, all that means is that one has a 4-gene set. The front and back ends of a single gene are not independent***, so 2 non-independent genes could just be considered one long string.
(*** Though even the front and back of a single gene are to some degree independent. It’s not a simple, dichotomous category. I suspect that it’s utility that counts, not a strict categorisation. Phylogeneticists are not out to prove common descent, but to resolve nodes).
I keep trying to start one, lol.
Which program is the best one? I want to go right to that program.
Or are you saying that in the same way that we pick and choose a telescope that let’s us see what we want to see, we pick and choose a program that lets us see what we want to see. Because that’s funny.
What does this have to do with running a software program to create a phylogenetic tree? Of can the argument for common descent not be made without those programs and the trees they make?
Did you read Joe’s paper?
Do you find it funny because you think the things the telescopes see, don’t actually exist? Because that’s funny.
Perhaps you should see which of your posts I was responding to, and glean a context from that. Could that possibly help shed light on the relevance of my question or do I need to spell it out for you kiddo?
Are you referring to a particular post in this thread where one of Joe’s papers were mentioned? Because I haven’t read all the posts that happened since a few days ago. What does it say, and in what way is it relevant to the independence of different data sets used in phylogenetics?
Are you seriously asking that question because you don’t know, or because you think I don’t?
Mung, we both know you’re not actually an idiot, so don’t try to be one please.
Again the telescope-analogy is apt. There are radiation coming to Earth from distant objects through many different wavelengths in the electromagnetic spectrum, not to mention ways that have nothing to do with electromagnetism at all.
There is radio, microwaves, infrared, visible light, ultraviolets, x-rays and gamma-rays. Then there is neutrino radiation, and there is neutron and proton radiation, other forms of leptons and baryonic matter. Today we are even reading fucking gravitational waves off of distant objects.
All of these types of data require different instruments to detect, and software to analyze and understand.
There are many different types of biological data. And programs go through multiple iterations of bug-fixes, new features get added, they are re-made to run on newer hardware and operating systems. Some of the programs can do almost all of it, some of them can only do smaller things. There are different programs for all these reasons. And none of it has anything to do with a presumed incoherence of evolutionary theory, in the same way the many different ways to detect and analyze data from distant astronomical objects don’t make physical astronomy incoherent.
You’re blathering like an idiot, flailing around in anger trying to find ways to dismiss something you don’t like. It’s pathetic. You’re a grown man, stop acting like a child.
My response.
Yes that’s a nice article, can you state in your own words what it argues and how it relates to this discussion?
Mung,
I think the basic issue is that you’re a simply a contrarian. Whatever ‘it’ is, you’re agin’ it.
Evolution – the science relating to the thing that wanders round the supposed Designed Space, selectively and nonselectively – is ‘incoherent’, you say. Yet, you claim, the space has been designed for this ‘incoherent’ process to stumble around, precisely as described by evolutionary theory, common descent and all. But if you actually had to agree with one of us Godless Hell-bound evilutionists on the subject of evolution …
Mung,
Mung will have immediately recognised that Kirk Durston’s suppositions discussed here a while back contained within them the self-same error that Joe points out in that linked paper. Would that be why Mung was linking it with approval, rather than to make hay with different applications of the term ‘independent’?
Whether god plays Wolfram with existence is fodder for theology.
Rule 30 is just one of a multitude of possible rules. An omniscient being knows all the rules and how they all play out.
I’m all for that!
I am all for reason and logic and what can be shown to be true. Ideology and dogma posing as reason and logic and truth, not so much.
And atheists and evolutionists are about as irrational and dogmatic as they come. Fertile soil indeed. 🙂
I think Mung, mistakenly, brought up that paper because Mung thinks Joe says different data sets used to test whether common descent is true, aren’t actually independent in the way that is important. That’s not what Joe says, but Mung doesn’t know because Mung wasn’t reading for comprehension, Mung was reading looking for quotemines, and found the words “phylogenies”, “independent” and the sentence “thus cannot be regarded for statistical purposes as if drawn independently from the same distribution”.
I think Mung doesn’t actually know what the hell that even says, but Mung thinks it means “genes A and B, or morphological character X and genetic character Y, aren’t actually independent in the relevant way for testing descent”. I think this will be another source of confusion, embarassment and flailing from Mung.
I didn’t say the process was incoherent. I said the theory is incoherent. There are actually a multitude of theories and a multiplicity of explanations and if there is not some principle according to which they all cohere then they are not a coherent whole. They are just a bunch of parts cobbled together. Sort of like organisms themselves.
And I don’t believe evolutionists are Hell-bound. Sorry.
That’s exactly what happened, except for the quote-mining part. 🙂
I was trying to figure out what “independent” meant in the context of constructing phylogenies and why people thought it was so important.
Mung,
But – as we have discussed before – there is not a ‘multitude’ of theories. You think transposition is a different ‘theory of evolution’ from selection, which is a different ‘theory of evolution’ from drift. But, they are simply parts of a whole. You scuttle round trying to foam up the bathwater to make it look like there is some kind of major controversy going on. Much like Erik above, smarmily implying a fight should start between John and Joe on the word ’cause’. Standard Creationist Procedure.
Okay. So just to make sure, you are now aware that Joe’s paper is not about testing whether common descent is true, but testing particular hypotheses about correlations between phenotypes among closely related species, or phenotypes and the environments the species in question live in, right?
Alright, you got me there, but …
When we say that common descent results in a pattern of similarities in aligned DNA sequences, we mean that the evolutionary forces in those lineages result in that pattern. Generally, the changes are unrelated to the speciation events that resulted in the tree. They are happening for the usual reasons DNA sequences change.
When there is a speciation, the resulting species continue to change and as a result diverge from each other. When a new lineage arises. it does so from one of the lineages existing at that time. Which one it arises from affects what pattern of similarities we will see. If two lineages, A and B, exist 5 million years ago, and continue changing, then when another lineage C arises, it matters whether it is a speciation of A or a speciation of B. That affects what patterns we see that let us infer that the tree is ((A,C),B) or (A,(B,C)). The process of change in C is not necessarily different, but the starting point is.
Our interest is in figuring out what the tree is (because that gives us insight into what to expect in lots of other regions of the DNA, and lots of other characters).
So common descent can be inferred, when the processes of change in each lineage are different, with only their starting points affected by the tree.
Yes. 🙂
And you are now aware that I didn’t quote-mine the paper, right?
Interesting that Mung brought up my 1985 comparative methods paper.
It shows how one can use a phylogeny, inferred from other data, to see whether two characters (say, brain weight and body weight) are evolving independently of each other. In that case one has enough evidence from other regions of the genome to infer the tree. For that one does need regions that whose evolutionary changes can be regarded as independent of the evolutionare changes in these characters.
When we infer the phylogeny (the pattern of common ancestry) we don’t need to use traits whose changes are absolutely independent, but just independent enough that as we take more traits we accumulate information about the phylogeny. For us to be misled about the phylogeny the whole set of traits (or all the DNA sequences we used) would have to have fairly tightly correlated changes.
An argument that holds that we are being misled by nonindependence when we infer phylogeny has to assume implausibly strong correlations between everything and everything else.
Mung,
He said, dogmatically.
Mung,
I sometimes wonder if you’re confusing ‘coherent’ with ‘cohesive’.
Given that there is a version of ID that’s ‘occasional-tinkering’, and another that’s ‘creating the searchable space’ – even before we get onto the ones that are indistinguishable from Genesis-Creationism – can we conclude that ID is incoherent?
cohesive: cohering or tending to cohere; well-integrated; unified
I don’t see enough of a difference to matter.
ETA:
Did you mean incohesive?
Mung,
If you say so. Makes me wonder why there are two words, but hey, you’re the expert. So …
Take your pick. Whichever word you think applies to evolution. Does it apply to ID? If not why not?
Allan Miller,
One of the advantages of the limitation of the ID argument is that it keeps it coherent.
“God did it” is coherent.
A good deal of ID blather fails to be exactly consistent or reasonable, but at its most basic ID is too simple-minded to be particularly non-cohesive, or whatever you wish to call it.
Glen Davidson
“You see,” a typical creationist or ID advocate will say, “we accept that evolution occurs, because things are always changing. But we …”
(Choose one)
1. Don’t think that there is evidence for speciation
2. Don’t think there is convincing evidence for common descent
3. Don’t think there is convincing evidence for universal common descent
4. Don’t think there is evidence for common descent of chimpanzees and humans
5. Don’t think that there is evidence for origin of really novel major groups by ordinary evolutionary processes
6. Don’t think that there is evidence for origin of really really novel major groups by ordinary evolutionary processes
7. Don’t think you have explained the Origin Of Life
8. Don’t think you have explained the origin of the universe
9. Are pretty sure that the Nazis were following Darwin’s orders
1. Disagree
2. Disagree
3. Agree
4. Disagree
5. Depends
6. Depends
7. Agree
8. Agree
9. Nazis and other Evilutionists.
Still waiting for Erik or colewd to explain why they reject a hypothesis — common descent — that fits the evidence stunningly well, while embracing another — design — that doesn’t fit at all, since it makes no predictions.
A comment I made five years ago(!) to gpuccio:
keiths,
I think you conflate common descent with a natural origin of mutations. The first does not depend on the second. The nested hierarchy is evidence for common descent but not for a natural origin of mutations. However, the evidence from which we infer that hierarchy does provide evidence for a natural origin of mutations too. But they aren’t the same thing.
John,
I disagree.
Our ability to infer an objective nested hierarchy points not merely to common descent, but to unguided common descent, in which variation is incremental and inheritance is primarily vertical.
Guided common descent permits large variations within a single generation and large amounts of horizontal transfer. Under those circumstances, we would not expect to be able to infer a single, objective hierarchy, even though one exists. The IDer’s only recourse is to assume that the Designer is an evolution mimic, either by inclination or by limitation. I have yet to meet an IDer who can justify that assumption.
Here’s how I put it to Flint: