On the thread entitled “Species Kinds”, commenter phoodoo asks:
What’s the definition of a species?
A simple question but hard to answer. Talking of populations of interbreeding individuals immediately creates problems when looking at asexual organisms, especially the prokaryotes: bacteria and archaea. How to delineate a species temporally is also problematic. Allan Miller links to an excellent basic resource on defining a species and the Wikipedia entry does not shy away from the difficulties.
In case phoodoo thought his question was being ignored, I thought I’d open this thread to allow discussion without derailing the thread on “kinds”.
I think FMM might have suffered a short-circuit somewhere.
I really hope, for your sake, that you’re physically attractive.
How do you define “essence”?
John Harshman,
Here is the key problem to solve: determining that they are related by decent. If you have build a tree where the nodes have been determined to be the result of decent then your argument is not circular. How you determine is critical. Since there is no known mechanism that you can generalize like in the case of gravity, where you can observe and test the mechanism, each node should be supported by the accepted method of determining that speciation has occurred.
I think common decent is very hard to verify and I believe its use in the creationists work on baramins is also problematic.
.
I note that you have completely abandoned the claim that any of this is circular, which is what my response was actually about. Your idea seems more circular to me, in its form of a Catch-22: before you can use a phylogenetic tree to show that species are related by common descent, you first must show that they are related by common descent. Do you see how crazy that is?
I’m not sure what you would mean by “determining that speciation has occurred”. What sort of evidence would you require, exactly? My claim is that our ability to produce a consistent tree is good evidence that speciation occurred. Why isn’t it?
As for mechanisms, I don’t see the relevance, but we do know quite a bit about how speciation happens. But I think you may mean something different by “speciation” than scientists do. It refers to the evolution of reproductive isolation between populations. Nothing about cats giving birth to dogs.
If I can accomplish anything at all with you, I hope at a very minimum to get you to start spelling “descent” correctly. Can you do that?
Robin,
Hi Robin
I am familiar with this paper. I agree that there is evidence supporting common decent but there is also contrary evidence.
I believe the problem with the analysis is the assumption that the evolutionary mechanism is stochastic. In addition we are discussing only a few proteins that need to be explained. In the theoretical UCA there are tens of thousands of proteins that that need to be evolved de novo. Stochastic processes cannot build the largest of these proteins IMHO and I am very skeptical that probabilistic processes can even build the smallest.
John Harshman,
Where do you get that idea from? For all I know there are only about 1300 protein folds. And why should UCA need all of them?
Or any of them?
Bloody hell. I have RL to deal with for a couple of days and everyone piles in with better answers than I could manage.
So unfair!
colewd,
You are making the common mistake that LUCA was the only organism around at the time, and had no ancestors or evolutionary history.
Such as?
You are mistaking the UCA for the first cell or first life. Not the case. It’s just the most recent common ancestor of all life that survives today. There would presumably have been an extensive history of life before that point, just as there was an extensive history of dinosaurs and birds before the common ancestor of living birds.
It also doesn’t make any sense to demand explanations for every single protein in LUCA to substantiate common descent.
RNA world?
John Harshman,
How does a phylogenetic tree show that creatures are related by descent? It shows that creatures are related by the criteria you established but unless you have established descent then all the tree is showing is relationships you have observed.
Descent is a very special claim. Without a change mechanism it is extremely difficult to establish broadly.
The tree is a vehicle to organize information logically and show relationships that you have established. It is organizing evidence. It is not in itself evidence for what you are claiming specifically happened at every branch. If you use the tree as evidence for common descent, without establishing common descent occurred, then circular reasoning can become an issue.
I understand your comment regarding the definition of species. I learned the definition from you.
Why do you say that? Leading ID figures such as Michael Behe don’t query common descent. It’s only YE Creationists that reject it for religious reasons.
Well, I have no idea. I believe Larry Moran favors metabolism first but as a layman I don’t have an opinion, I just read the experts with interest. My point was that one doesn’t need to know how LUCA came to be to know that UCD is well supported by evidence
Allan Miller,
What do think LUCA is? Is It a single eukaryotic cell? Are you saying the life has multiple origins?
You seem to believe that the tree was built arbitrarily, that the data was used to “force” a tree under the assumption of common descent. That’s not the case. The data shows there is a nested tree. And the only logical explanation for a nested tree is common descent
Laymen are allowed to have opinions. 🙂
I’m persuaded by RNA world thanks to Upright Biped (a commenter at UD and previously here). His “biosemiosis” argument is sunk by considering earliest organisms as based on RNA which fills the dual role of gene storage and enzymatic activity.
colewd,
The most recent ancestor of all surviving lineages
Hardly. It is the ancestor of all living organisms. But yes, I think all lines ultimately coalesce upon a single cell. Just not eukaryotic.
No. It could have, but that is a separate question to LUCA, who is likely to have lived hundreds of millions of years after any origin(s). The evidence is that there is only one MRCA for all extant life, though there is no reason there could not have been more. There’s just no evidence there were.
This calls for a thread! Highly speculative but fascinating topic. A quick google search seems to suggest that’s an already controversial topic here, so maybe I’ll just keep looking up info on that
Alan Fox,
Not me, then? 🙁
Alan Fox,
I don’t agree at all that this is a religious debate. Here is my discussion with Michael Behe. Move to 1:23 into the video. for the the common descent discussion https://youtu.be/hIy7BhVgPCs
Do you know, looking in again, I was thinking of adding your contribution as an edit but I see you beat me to it. You won’t believe me now!
My bad!
It doesn’t have to be. But my impression is that YECs like Sal have no reason to argue about “flood” geology, other than a literal reading of the Old Testament?
ETA superfluous other
I tried watching, colewd, but you mention a paper you have written. Is it available publicly. I prefer written material to video.
Alan Fox,
I have not written a paper on common decent. I am really trying to learn the subject. The video shows Behe’s real position. He sees problems with explaining the differences but chooses not to engage because he thinks it is a secondary discussion.
Alan Fox,
Heh heh!
This is how science works: if hypothesis A predicts observation X and hypothesis B does not, and we observe X, we prefer hypothesis A to hypothesis B. Common descent predicts that character data will have nested hierarchical structure. Nothing else predicts that. Therefore we prefer common descent based on the data. Get enough data and a strong enough, consistent signal in those data, and I’d say we have “established” descent. It’s up to you to present an alternative that explains the data as well or better. Hey, I’ll even take nearly as well. Good luck.
What’s very special about it? And why is a mechanism necessary? Anyway, we do have such mechanisms. Have you, by the way, changed yourself from demanding a mechanism of speciation to demanding a mechanism of “change”, whatever you mean by that?
Back to that again? You’re just repeating a claim you haven’t justified and which I believe I have shown to be incoherent. You’re the one asking for circularity: I can’t use the tree as evidence for common descent until I prove common decent.
Then I don’t understand what you’re trying to say. We know quite a bit about how speciation works. If that’s what you need in order to say that common descent can happen, we have that already.
Alan,
See this comment on the Ark Encounter thread.
https://www.sciencedaily.com/releases/2016/07/160719214826.htm
Except you have missed out some parts!
I really can’t be bothered to go an dig up your prior comments on this, but if you insist on this behaviour then I will!
The simple fact is that while you may claim that a species is ‘a particular group of things or people that belong together or have some shared quality’ is it not also the case that you say that when humans have difficulty separating out one species from another that god does not have that difficulty? That to god each species occupies a single intersection and each intersection contains a single species. And that’s true even if we can’t ourselves separate out one species from another? And as god created each species directly they are obviously separate, even if we can’t tell.
You do know people have memories right? And I noticed you did not deny you’d said those things, you just did not respond to my question. So there is some moral being in there somewhere, deep down….
Oh, so colewd is Bill Cole. I had a few interchanges with him at Larry Moran’s blog (Sandwalk). I should have noticed it’s him since he was using the same arguments about lack of mechanisms there. Of course he ignored all the explanations about molecular clocks and everything else and he’ll just keep repeating the same debunked mantras no matter what. But then again that’s what all creos do
John Harshman,
If hypothesis A and B are weak for different reasons then I think your science is weak. The what else could it be hypothesis. Common descent is a leap of logic without sold empirical footing. My argument is we don’t have a clue how diversity occurred.
The common decent claim and putting organisms into a tree like organization are different things. Your tree could be based on similar colors or it could be based on the weight of the animals. None of these are evidence for common descent. The evidence that establishes the branches as representing common descent is critical. John, I know you understand this based on a prior comment when you were trying to defend common descent as not being circular.
Now, if you can get evidence that common descent occurred on one branch, how would you then argue that the theory is universally valid?
@ colewd
I had another go viewing the video. Behe (using a trick pool shot analogy) seems to be championing the kind of Deism that, were I predisposed to requiring religious explanations, I might consider as at least not in conflict with observed reality. An omniscient, omnipotent, omnipresent god creates a universe with all its properties but then can only intervene in accordance with those properties.
colewd,
The obervation that genetic commonality indicates relationship is well established. It is hardly a massive leap in the dark. Do you reject it at all taxonomic levels? How do you decide where the boundary is?
Divergence between separated gene pools, iteratively. What’s so hard about that?
colewd,
It is very easy to defend against that accusation, when the case that is is circular has not even been made, merely asserted. If the best you can do is ‘it is’, a simple ‘it isn’t’ is all that is needed to refute.
What an utterly stupid thing to say… again. The tree is built using molecular data, precisely because the mechanism by which it flows from one generation to the other is well known. Actually other sources of data, like morphological, embryological data, etc… can be used and were used prior to the discovery of the genome and the trees built with those were astonishingly similar. The consilience is overwhelmingly conclusive whether you like it or not.
colewd,
The difference being that, in biology, multiple character states converge on the same tree. Each gene cross-references the other(s). This is an aspect you have yet to grasp; it has been said before.
And remember Carl Linnaeus built his branching tree just on comparative anatomy. Today we have molecular phylogeny and, blow-me-down, it matches!
And how is that working out for you?
What would you expect to see if common descent was true?
Allan, to colewd:
Theobald covers this in depth. Will you ever summon the courage to read him, colewd?
“But it’s not evidence!”
What else can they say? If the evidence didn’t fall into the tree pattern, then that would be evidence against evolution, and they’d be thrilled to say so.
Since it does, all that can be claimed is that it isn’t evidence for evolution. We’re simply not dealing with people who use the evidence to find the results, but people who have the “results” and accept only the evidence that fits those results.
Glen Davidson
You may think my science is weak, but that’s how all science works, so you are in essence claiming that all science is weak. The empirical footing of common descent is in fact the evidence we have that makes no sense without that hypothesis: the fossil record, our ability to make phylogenetic trees, biogeographic patterns, etc. The way to show that evidence to be weak is to present an alternative explanation for all of it that works nearly as well, preferably better. You have no such. Yes, we can only test theories that we have thought of. I don’t see that as a problem.
I ask again what evidence you have against common descent. So far it’s just “I personally can’t imagine how it works.”
The first sentence is true. The common descent claim follows from our ability to put organisms into a treelike organization. A hypothesis and its consequences or predictions are indeed not the same thing. But no, my tree couldn’t be based on similar colors or weights. Any tree from such things could not survive any tests of consistent support or replication using different data. In those cases, the tree would be imposed on the data, not emerge from the data as is the case with phylogenetic trees. You don’t understand the nature of the evidence, so it’s no wonder you don’t recognize it as evidence.
It isn’t clear to me what you’re trying to ask about there. That the existence of a clade, say Muscidae, is not evidence for universal common descent? Sure. So?
Alan Fox,
What Behe is saying is that his argument is for design as an inference. The pool shot was just a speculation that the whole of information could have been front loaded. He never claims that he believes this. Later in the conversation he says that he does not think we are ready to speculate the “how” of the design until we get substantially more new information.
What does any of that have to do with common descent?
John Harshman,
All science strength or weakness depends on the strength or weakness of the evidence.
Darwin came to a conclusion about UCD but now we have lots of additional evidence. Some supports the hypothesis and some is very problematic.
It is true that I do not understand the criteria determining that 2 species share a common ancestor.
colewd:
And:
And:
colewd,
Please have the common decency to spell “common descent” correctly!