ughaibu wrote:

Rumraket wrote:

ughaibu wrote:You're mistaken, UCA accepts distinct origins.

Ahh yes, with the caveat that it went through a single species bottleneck.

Theobald doesn't state the requirement for a "single species bottleneck", not even under his vague definition of species. Perhaps you should ask him to specify what does and what doesn't come under "a broad version of the Biological Species Concept", you maybe be talking about the same thing, you may be not.

I quoted a piece of the paper that directly contradicts what you say here.

Rumraket wrote:

ughaibu wrote:Theobald doesn't state the requirement for a "single species bottleneck", not even under his vague definition of species.

I quoted a piece of the paper that directly contradicts what you say here.

Rubbish.

Rumraket wrote:

Theobald 2010 wrote:UCA requires a ‘bottleneck’ in evolution in which descendants of only one of the independent origins have survived exclusively until the present (and the rest have become extinct), or, multiple populations with independent, separate origins convergently gained the ability to exchange essential genetic material (in effect, to become one species).

In the first scenario there is no bottleneck of only one species, in the second there is an eccentric definition of species. Bearing in mind earlier posts in which horizontal transfer appears to have been considered to be inconsistent with a UCA conjecture, please state your position on this; is the occurrence of HGT sufficient to qualify organisms as members of the same species?

ughaibu wrote:

Rumraket wrote:

ughaibu wrote:Theobald doesn't state the requirement for a "single species bottleneck", not even under his vague definition of species.

I quoted a piece of the paper that directly contradicts what you say here.

Rubbish.

Really?

ughaibu wrote:

Rumraket wrote:

Theobald 2010 wrote:UCA requires a ‘bottleneck’ in evolution in which descendants of only one of the independent origins have survived exclusively until the present (and the rest have become extinct), or, multiple populations with independent, separate origins convergently gained the ability to exchange essential genetic material (in effect, to become one species).

In the first scenario there is no bottleneck of only one species

Then what the fuck does "UCA requires a ‘bottleneck’ in evolution in which descendants of only one of the independent origins" parse into in your world?

ughaibu wrote:, in the second there is an eccentric definition of species.

Again, the way I understand that section is that Theobald implies that HGT happened to such an extend that in effect, a single species emerged. The fact that gene flow can happen through HGT, is not what made it a 'single species', but the end result of the extend to which it happened did.

ughaibu wrote:Bearing in mind earlier posts in which horizontal transfer appears to have been considered to be inconsistent with a UCA conjecture, please state your position on this; is the occurrence of HGT sufficient to qualify organisms as members of the same species?

This seems to be nothing but an attempt to highlight that no species concept is perfect and that nature doesn't sit in our nice little definitional boxes.

Rumraket wrote:The fact that gene flow can happen through HGT, is not what made it a 'single species', but the end result of the extend to which it happened did.

ughaibu wrote:please state your position on this; is the occurrence of HGT sufficient to qualify organisms as members of the same species?

Again, I suggest that you sort it out with Theobald, because you appear to mean different things and I'm not your go-between.

Edited to request.

ughaibu wrote:

Rumraket wrote:

ughaibu wrote:please state your position on this; is the occurrence of HGT sufficient to qualify organisms as members of the same species?

The fact that gene flow can happen through HGT, is not what made it a 'single species', but the end result of the extend to which it happened did.

Again, I suggest that you sort it out with Theobald, because you appear to mean different things and I'm not your go-between.

You've misquoted me here because I appear to be answering a different part of your post than I did.

Rumraket wrote:

ughaibu wrote:

Rumraket wrote:The fact that gene flow can happen through HGT, is not what made it a 'single species', but the end result of the extend to which it happened did.

Again, I suggest that you sort it out with Theobald, because you appear to mean different things and I'm not your go-between.

You've misquoted me here because I appear to be answering a different part of your post than I did.

Sure, but this was nearer to an answer than what you wrote after you quoted my question was. If you like, I'll edit the post and reverse the positions, do you want me to?

ughaibu wrote:

Rumraket wrote:

ughaibu wrote:Again, I suggest that you sort it out with Theobald, because you appear to mean different things and I'm not your go-between.

You've misquoted me here because I appear to be answering a different part of your post than I did.

Sure, but this was nearer to an answer than what you wrote after you quoted my question was. If you like, I'll edit the post and reverse the positions, do you want me to?

Not that it's overly important in this context specifically, I just think it's common courtesy.

I do take your point that under a broad biological species definition for example, HGT can potentially make all of extant life become one big population of the same species, since there's a potential for gene flow between all individuals. On the other hand I wouldn't nessecarily interpret that kind of gene flow as being equivalent to that which happens during mitosis or meiosis(there's a reason it's called horizontal, after all). Of course, in the world of microoganisms, everything becomes... muddled?

ughaibu wrote:

dtheobald wrote:I'm using UCA in the modern sense, complete with its genetic implications, in the way that Crick and Dobzhansky used it after the DNA and genetic code revolution.

Which seems to be a set of ad hoc redefinitions by which UCA is pretty much established as a trivial truth, at least, any question of interest concerning the question of "UCA or not?" appears to be removed.

It's hard to argue against the subjective impression that something is "trivial" --- you can think that if you want. But it is not an obvious fact of our world that all life now on the earth is genetically related. It takes a good bit of argument and rather exceptional evidence to demonstrate it. It was not accepted by Darwin, nor was it generally accepted by the biological community until about 1970. And today there are serious biologists who question it (e.g., Mike Syvanen, Carl Woese, Ford Doolittle, Craig Venter). It is of course possible, as Darwin suggested, that there were seven or so original common ancestors from which modern life is derived. Furthermore, Darwin never used the phrase "universal common ancestry", so there is not even the possibility of a redefinition, as you claim. I will venture that the reason you think the modern definition is "unintuitive", to you, is because you are unfamiliar with the background knowledge of the biologists who are my intended audience. You seem more of a philosopher sort, no?

ughaibu wrote:
The opening post of this thread makes little sense if it's a question about your notion of a UCA, Darwin's "all the organic beings which have ever lived on this earth have descended from some one primordial form" is a more reasonable interpretation. Anyway, the UCA supporters can quibble with your directly about these matters, now that you're here.

I'd be surprised if Mononoke agrees with you. From the posts I've seen most everybody here understands the concept pretty well.

ughaibu wrote:
Establishing UCA as a pretty much trivial truth means that your argument and analysis were redundant, but it does not support your contention that "by accounting for the trade-off between data prediction and simplicity, model selection theory provides methods for identifying the candidate hypothesis that is closest to reality". Neither do your non-specific remarks about Bayes factors, Cox axioms and a "rational person".

Of course UCA doesn't support that claim, as should be obvious, since that is a general claim about model selection theory. The Cox axioms do, however, provide a strong justification.

dtheobald wrote:

ughaibu wrote:Which seems to be a set of ad hoc redefinitions by which UCA is pretty much established as a trivial truth, at least, any question of interest concerning the question of "UCA or not?" appears to be removed.

It's hard to argue against the subjective impression that something is "trivial" --- you can think that if you want.

"Trivial" wasn't used in a subjective sense.

dtheobald wrote:Darwin never used the phrase "universal common ancestry", so there is not even the possibility of a redefinition, as you claim.

All the terms, universal, common and ancestor, have conventional meanings, so of course redefinition is possible.

ughaibu wrote:

dtheobald wrote:

ughaibu wrote:Which seems to be a set of ad hoc redefinitions by which UCA is pretty much established as a trivial truth, at least, any question of interest concerning the question of "UCA or not?" appears to be removed.

It's hard to argue against the subjective impression that something is "trivial" --- you can think that if you want.

"Trivial" wasn't used in a subjective sense.

The only objective sense of "trivial" of which I am aware is mathematical: all variable parameters in a functional equation equal null.

ughaibu wrote:

dtheobald wrote:Darwin never used the phrase "universal common ancestry", so there is not even the possibility of a redefinition, as you claim.

All the terms, universal, common and ancestor, have conventional meanings, so of course redefinition is possible.

The only "conventional" meanings in science are the conventionally used scientific ones --- c.f., "force".

dtheobald wrote:

ughaibu wrote:universal, common and ancestor, have conventional meanings

The only "conventional" meanings in science are the conventionally used scientific ones --- c.f., "force".

Okay, and as the majority of this site's membership aren't biologists and are thus outside your intended readership, they are unlikely to intuitively interpret terms to their correctly assigned technical meanings. And as you have still not stated completely and precisely, what position it is that you're defending, at least some members are probably citing your article, in support of their position, without knowing whether or not they actually agree with you. (I'm assuming that the supporters of UCA have some clear idea of what they support, and dont simply support the words, whatever they might mean.)
You have stated that "the proposition that all extant life is genetically related" is exactly what you mean by UCA, and you give some further considerations, followed by stating that:

dtheobald wrote:You may find it "broad", but it is just a restatement of the traditional idea of universal common ancestry

As it stands, your definition allows for UCA to include distinct origins, horizontal transfer and not to require a single species bottleneck, at least, you didn't object when I suggested this. Horizontal gene transfer has been characterised as reception of genetic material from an organism which is not an ancestor, so I suspect that some members will be surprised to find that a common ancestor model can depend on HGT, certainly I was. Further, the lack of a requirement for a single species bottleneck and the restriction to known extant life, compromise conventional meanings of "common" and "universal", respectively. In short, it appears that your technical definitions allow for a UCA model in which, given any two examples of extant life, there needn't be any organism which both, once lived and stood in an ancestral relationship with both the extant organisms.
As your UCA model requires none of its conditions, non-technically understood, it reduces to the notion that all known extant life is genetically related, but this statement is trivial; one can examine known extant life and define a relationship across the genetic material. This means that UCA can be true by definition, and is, consequently, uninteresting.
So, for the sake of those who support UCA and cite your article, please make a statement about the following things:
1) does UCA preclude HGT
2) what exactly is "a broad version of the Biological Species Concept"
3) do the various relevant dissenting biologists agree with your answers to 1 and 2?

ughaibu wrote:

dtheobald wrote:

ughaibu wrote:universal, common and ancestor, have conventional meanings

The only "conventional" meanings in science are the conventionally used scientific ones --- c.f., "force".

Okay, and as the majority of this site's membership aren't biologists and are thus outside your intended readership, they are unlikely to intuitively interpret terms to their correctly assigned technical meanings. And as you have still not stated completely and precisely, what position it is that you're defending, at least some members are probably citing your article, in support of their position, without knowing whether or not they actually agree with you. (I'm assuming that the supporters of UCA have some clear idea of what they support, and dont simply support the words, whatever they might mean.)

I have to say, whatever someone who isn't a biologist thinks he understands universal common ancestry to mean isn't an issue for anything other than said person's education. If people are arguing for a specific position, it's their job to research exactly what that position is before they open their mouth in support of/against it. If they (random layment who accept evolution) "disagree" with what is understood by universal common descent, then random laymen have an obligation to update their understanding to correspond with that which is accepted by professionals biologists, not the other way around.

Average Joe on the street doesn't get to define what a Black Hole or a parsec is either.

Rumraket wrote:whatever someone who isn't a biologist thinks he understands universal common ancestry to mean isn't an issue for anything other than said person's education. If people are arguing for a specific position, it's their job to research exactly what that position is before they open their mouth in support of/against it.

Fair enough.
1) do you have a position on the UCA question?
2) if so, what is that position?
3) does UCA preclude HGT?
4) what exactly is "a broad version of the Biological Species Concept"?
5) do the relevant dissenting biologists hold with this definition of "species"?
6) do they agree with your answer to 3?

ughaibu wrote:

Rumraket wrote:whatever someone who isn't a biologist thinks he understands universal common ancestry to mean isn't an issue for anything other than said person's education. If people are arguing for a specific position, it's their job to research exactly what that position is before they open their mouth in support of/against it.

Fair enough.
1) do you have a position on the UCA question?
2) if so, what is that position?

1. Yes.
2. The evidence collected testifies to it's factual validity. In other words, it's true.

ughaibu wrote:3) does UCA preclude HGT?

Unless I don't understand what "preclude" means, no.
pre·clude (pr-kld)
tr.v. pre·clud·ed, pre·clud·ing, pre·cludes

1. To make impossible, as by action taken in advance; prevent. See Synonyms at prevent.
2. To exclude or prevent (someone) from a given condition or activity: Modesty precludes me from accepting the honor.

So, you're asking "Does Universal Common Ancestry exclude/prevent/make impossible by action taken in advance, Horizontal Gene Transfer?" ?
My answer would then be 'Obviously not, Weird question by the way'.

ughaibu wrote:4) what exactly is "a broad version of the Biological Species Concept"?

Since I'm not a biologists, I can only relay that I undestand it to be that sexually reproducing individuals belong to the same species if they can interbreed. In regards to species of bacteria, this definition:

James T. Stanley wrote:Bacteriologists have not yet adopted a concept for a species. Bacterial and archaeal species are defined on the basis of phenotypic properties and whole-genome DNA-DNA hybridization. Each species must have unique phenotypic properties and exhibit more than 70% DNA hybridization among strains. This combination of phenotype and genotype, sometimes referred to as the polyphasic species definition, was a breakthrough in bacterial taxonomy and has served microbiologists very well by stabilizing the field and bringing uniformity to classifying species of Bacteria and Archaea.

ughaibu wrote:5) do the relevant dissenting biologists hold with this definition of "species"?

How does one determine who are "relevant" among "dissenting biologists", and who are "dissenting biologists"? Are their supposed dissent in relation to the definition of "species" important to what is understood by 'universal common descent' in this specific context?

ughaibu wrote:6) do they agree with your answer to 3?

I can't answer 6 without knowing the answer to 5 and I don't see how 5 relates to 1-4 before I know the answer to my last question in my answer to 5.

Rumraket wrote:2. The evidence collected testifies to it's factual validity. In other words, it's true.

This statement is nonsense, frankly.
But in any case, thanks for answering.

ughaibu wrote:

Rumraket wrote:2. The evidence collected testifies to it's factual validity. In other words, it's true.

This statement is nonsense, frankly.
But in any case, thanks for answering.

In what way? Are you going to sophistrysize me now?

Rumraket wrote:

ughaibu wrote:

Rumraket wrote:2. The evidence collected testifies to it's factual validity. In other words, it's true.

This statement is nonsense, frankly.

In what way?

After posting, it occurred to my that by "it's true", you may have meant 'I believe it'. In which case, your statement would have been okay. However, if you're claiming that UCA is true, as an historical fact, then you have exceeded your warrant. Also, if you're saying that evidence testifying to the factual validity, of UCA, can establish it as true, this too is unsupportable.
By the way, "factual validity" is a peculiar construction, I take it you mean the state of being a fact, or something similar, by this.

ughaibu wrote:

Rumraket wrote:

ughaibu wrote:This statement is nonsense, frankly.

In what way?

After posting, it occurred to my that by "it's true", you may have meant 'I believe it'. In which case, your statement would have been okay. However, if you're claiming that UCA is true, as an historical fact, then you have exceeded your warrant. Also, if you're saying that evidence testifying to the factual validity, of UCA, can establish it as true, this too is unsupportable.
By the way, "factual validity" is a peculiar construction, I take it you mean the state of being a fact, or something similar, by this.

Yes, if you're simply calling for some more rigorous use of language in describing what my position is, it would be:

I believe it to be true on the basis that the collected evidence seems to imply it.

And no, I can't be bothered digging much deeper into an exposition of why it "seems to imply it", other than to state that it rests partially on the observed process of inheritance and the results thereof.

Rumraket wrote:if you're simply calling for some more rigorous use of language in describing what my position is, it would be:
I believe it to be true on the basis that the collected evidence seems to imply it.

So your answer to 2 is that you're a realist about UCA.

ughaibu wrote:

Rumraket wrote:if you're simply calling for some more rigorous use of language in describing what my position is, it would be:
I believe it to be true on the basis that the collected evidence seems to imply it.

So your answer to 2 is that you're a realist about UCA.

This is probably not a surprise to you but I'm not much of a philosopher, so i'm not sure what is understood by being a realist.