Huge discordance between gene trees in a new phylogenetic study

_{Denyse O'Leary

February 28, 2020

Genomics, Intelligent Design, Plants}

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A friend alerts us to this Abstract:

Angiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2,3,4,5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species—prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)—and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.
Yang, Y., Sun, P., Lv, L. et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nat. Plants (2020). https://doi.org/10.1038/s41477-020-0594-6

The paper is open access.

From the paper: “Thus, what might account for this deep phylogenetic incongruence between nuclear and plastid genomes? As multiple independent polyploidization events were identified in magnoliids, monocots, Ceratophyllales and eudicots (Fig. 1), allopolyploidization or hybridization is one probable source of genomic discordance.”

“Deep phylogenetic incongruence” sounds like journalspeak for “our current phylogenetic tree is a hot mess.”

Comments

ET, 96: Whatever. It seems to me that you have been making bald assertions and were called on it. So I understand why you would want that to stop. What bald assertions did I make? JVL

Whatever. It seems to me that you have been making bald assertions and were called on it. So I understand why you would want that to stop. ET

@94 JVL
We seem to be arguing/discussing past each other. Seems like a good time to stop.
Can you? Or are you a neuronal 'puppet' with no real agency? Truthfreedom

ET: We seem to be arguing/discussing past each other. Seems like a good time to stop. JVL

The mainstream has thought there would be numerous transitional forms since Darwin. And yet EVERY TIME one is uncovered it is BIG news. When "Lucy" was found it was HUGE news, even though mainstream expected it. JVL said that finding evidence that supported unguided evolution wouldn't be news cuz mainstream expected it. Obviously past cases prove him wrong. And when it comes to falsifying ID- to demonstrate that unguided processes are up to the task. To date no one has been able to do that. That is something that flows from ID's hypothesis, JVL sez:
I think that’s a matter of opinion as there seems to be a lot of people who would disagree with you on that!
That alone proves that JVL doesn't understand how science works. ET

AGAIN, the BEST evidence for macroevolution is presented on talk origins. And yet that evidence is absent a mechanism. If they had the evidence that unguided processes could do it they would have said that. And it pretty much shows that you really don’t know what you are talking about. ET

JVL:
You think I don’t understand the science because I don’t obviously agree with you.
Nope. I say that you don't understand the science because of what you have posted.
I have read quite a lot of both sides.
Doubtful.
It’s particularly bad for ID though since it doesn’t have even close to the same amount of support in mainstream academia.
Nonsense. Unguided evolution doesn't have any evidentiary support. It can't even be tested. That means it is out of the realm of science. You may disagree but you will never support that disagreement. And I am more than OK with that.
What’s going to happen to the ID movement when some of the high profile supporters leave the field of battle?
Nothing. That movement rests on the science and evidence. And neither of those is going away. ET

How about nihilism as the driving force behind science ? I don't think it was what eastern sages had in mind when they prescribed that we should empty our minds. Axel

ET 62: 'IF you think that there is no design then everything we observe is due to unguided processes.'* 'Except for the fact there is no way to test that claim.'' The very nature of empirical science tests it, a priori, and finds it wanting. Surely, science itself is predicated on the immanence of design in the natural world. - hence the emergence of science, as a sort of obsessive preoccupation in christendom. *To me that initially read like a satirical jibe, but of course it's the truth - and more bizarre yet, seemingly one with which ID's infidels feel quite comfortable ! Axel

@78 Mimus
Not sure if it’s more remarkable that Jawa/PavelU’s response to posting under multiple itendities is to create a new one, or that the regulars start arguing with the new fake sock puppet…
Geez Mimus, we are al puppets of our brain chemistry. You know, billions and billions of mindless evolution blah blah blah... Or are you suggesting people can really 'choose' (at least some of) their actions? Can Jawa? Can I? Can you? Truthfreedom

Jawa, 86: I really don’t understand what you’re trying to say with that statement. Please clarify it. Thanks. I think you think I'm evasive and vague because I haven't clearly committed to ID or anti-ID. I suspect, in your mind it's a black-and -white issue: either you are or you ain't. You wanted to play a game with me, taunting me with something I wanted to know by pulling my strings and making me dance to your tune. I haven't really done that and I suspect you're disappointed and losing interest. And I don't think you ever really intended on addressing Mimus's claim. Which, of course, makes you look 'guilty'. Maybe you're NOT posting under more than one username, but why wouldn't you assert that? And if you are posting under more than one username why would you do that? Just to prove how clever you are? To get more attention? JVL

JVL @84: “ You want me to take a stance that you can argue with so you’re disappointed that I’ve avoided that.” I really don’t understand what you’re trying to say with that statement. Please clarify it. Thanks. jawa

ET, 81: LoL! JVL is trying to baldly assert that which he has no right to. ET, 82: You’re not really discussing anything. You are just saying there is a disagreement. But you don’t seem to understand the science and the evidence. You think I don't understand the science because I don't obviously agree with you. Maybe you should just read the literature that IDists have written. Then do the same for the evolutionists. And wonder why Richard Dawkins had to use a telic process in order to demonstrate his concept of cumulative selection. Then wonder why all papers on the evolution of something are almost 100% speculation. Or why the long term evolutionary experiment has FAILed to produce new genes, new proteins or new protein complexes. I have read quite a lot of both sides. And I see both sides being completely entrenched and increasingly antagonistic to each other. That trench warfare isn't helping either side. It's particularly bad for ID though since it doesn't have even close to the same amount of support in mainstream academia. What's going to happen to the ID movement when some of the high profile supporters leave the field of battle? JVL

<bJawa, 79: If you can’t take the heat of the discussion, then maybe quitting is the best thing to do. Your responses to some of the questions seem so vague that sometimes I get the impression that you are dodging the questions. Basically your answers sometimes raise more questions. It seems like a never-ending story. I can point to specific cases for illustration. However, i could keep asking until you can produce comprehensive answers. You want me to take a stance that you can argue with so you're disappointed that I've avoided that. JVL

Mimus, 78: Not sure if it’s more remarkable that Jawa/PavelU’s response to posting under multiple itendities is to create a new one, or that the regulars start arguing with the new fake sock puppet… Which user names do you think are actually the same person and why would someone do that/ JVL

JVL:
I’m just discussing the disagreement and wondering if there is a possible resolution.
There is. Tell those in the unguided camp to put up or shut up. Tell them to address the evidence and science or get out of the way.
Is it not possible to discuss the discussion and not be assumed to be on one side or the other?
You're not really discussing anything. You are just saying there is a disagreement. But you don't seem to understand the science and the evidence. Maybe you should just read the literature that IDists have written. Then do the same for the evolutionists. And wonder why Richard Dawkins had to use a telic process in order to demonstrate his concept of cumulative selection. Then wonder why all papers on the evolution of something are almost 100% speculation. Or why the long term evolutionary experiment has FAILed to produce new genes, new proteins or new protein complexes. ET

LoL! JVL is trying to baldly assert that which he has no right to. ET

Jawa
If you can’t take the heat of the discussion, then maybe quitting is the best thing to do.
With respect, JVL is trying to have a discussion with ET. One is being honest, civil and logical. The other is ET. Ed George

JVL @77: “Maybe I should just quit.” If you can’t take the heat of the discussion, then maybe quitting is the best thing to do. Your responses to some of the questions seem so vague that sometimes I get the impression that you are dodging the questions. Basically your answers sometimes raise more questions. It seems like a never-ending story. I can point to specific cases for illustration. However, i could keep asking until you can produce comprehensive answers. But at this point I have to logout so that another avatar can login. :) jawa

Not sure if it's more remarkable that Jawa/PavelU's response to posting under multiple itendities is to create a new one, or that the regulars start arguing with the new fake sock puppet... In any case, doesn't say a whole lot of good stuff about the vitality of this site or the ID movement... Mimus

ET, 75: Except they won’t tell you. We have to. It hasn't been hidden. It just hasn't been promoted by the non-design crowd. Duh. But you have baldly asserted more than that. I don't think so. Look, the BEST evidence for macroevolution is presented on talk origins. And yet that evidence is absent a mechanism. If they had the evidence that unguided processes could do it they would have said that. And it pretty much shows that you really don’t know what you are talking about. Sigh. I'm not making an argument. I'm just discussing the disagreement and wondering if there is a possible resolution. Is it not possible to discuss the discussion and not be assumed to be on one side or the other? I understand your feeling of being discriminated against but is that a reason to label someone who is trying to understand the situation? Maybe I should just quit. JVL

Asauber, 74: “But others disagree” is not an argument. It’s a deflection that could be made about anything and everything if you don’t like something. Nothing is beyond dispute, I guess. It’s a variant of the Argument Sketch, not an argument. Correct. I'm not making an argument. I am just discussing a situation and wondering if there is a resolution. JVL

JVL:
It hasn’t been buried in that it is still accessible and easy to find.
Except they won't tell you. We have to.
Again, there are dissenting views.
I know. I am getting at the reason for it.
There is a disagreement.
Duh. But you have baldly asserted more than that. And yes, people disagree for personal reasons. Look, the BEST evidence for macroevolution is presented on talk origins. And yet that evidence is absent a mechanism. If they had the evidence that unguided processes could do it they would have said that. And it pretty much shows that you really don't know what you are talking about. ET

JVL, "But others disagree" is not an argument. It's a deflection that could be made about anything and everything if you don't like something. Nothing is beyond dispute, I guess. It's a variant of the Argument Sketch, not an argument. Andrew asauber

ET, 70: And you are very wrong. It would definitely be Nobel worthy and very big news. Okay. You don’t speak for any scientist. You definitely don’t speak for the majority. Scientists know better than to assume what has to be demonstrated. But they are very vocal when their assumptions are shown to be true. I can only give my impressions, which might be incorrect. Clearly it has. No one has taken it on to show that unguided processes can indeed come up with 3 or more cumulative effect mutations. No one wants to. No one cares. It hasn't been buried in that it is still accessible and easy to find. The only thing that is clear is that people will deny the science and evidence. Again, there are dissenting views. You haven’t pointed out anything. You have just made unsupported assertions. There is a disagreement. Nature can produce what the laws of nature allow. And there isn’t anything in those laws that allows for nature to produce coding systems from the ground up, literally. People can disagree with that. But they do so for personal reasons only. I hear you. But others disagree. That is just the case. JVL

Truthfreedom, 69: So if I told you ‘you’ are an ‘illusion’: what would you think? I would think you were wrong. JVL

JVL:
Again, I am just pointing out the gulf.
Again, I am just pointing out the facts. And we know what the crux of the matter is. ET

JVL:
I was trying to explain why demonstrating unguided processes are capable would not be big news.
And you are very wrong. It would definitely be Nobel worthy and very big news.
It’s because that’s been the assumption of the majority of scientists so there would be no need to celebrate it.
You don't speak for any scientist. You definitely don't speak for the majority. Scientists know better than to assume what has to be demonstrated. But they are very vocal when their assumptions are shown to be true.
It’s not been buried, clearly.
Clearly it has. No one has taken it on to show that unguided processes can indeed come up with 3 or more cumulative effect mutations. No one wants to. No one cares.
Again, there is a dispute, that is clear.
The only thing that is clear is that people will deny the science and evidence.
I’m merely pointing out that a lot of scientists do not accept the design inference.
You haven't pointed out anything. You have just made unsupported assertions. Nature can produce what the laws of nature allow. And there isn't anything in those laws that allows for nature to produce coding systems from the ground up, literally. People can disagree with that. But they do so for personal reasons only. ET

@68 JVL
Sure feels like I am. Descarte and all that.
So if I told you 'you' are an 'illusion': what would you think? Truthfreedom

Truthfreedom, 67: But you surely can make inferences. Are you a consciouss being or are you not? Sure feels like I am. Descarte and all that. JVL

@66 JVL
I’m not here to be converted or to convert.
But you surely can make inferences. Are you a consciouss being or are you not? Truthfreedom

Truthfreedom, 65: The materialist side can not account for consciousness. Since you (we all) are a consciouss being(s), just make the inference. There is a disagreement, a real gulf. I'm just noting the situation and what I think the core difference is. I'm not here to be converted or to convert. I am not your adversary. But there seems to be a real us-vs-them attitude which seems to mean that every commenter is judged and relegated into one camp or the other. If no one accepts any kind of middle ground then should we give up finding a resolution? JVL

@60 JVL
One side is right and one side is wrong.
- The materialist side can not account for consciousness. Since you (we all) are a consciouss being(s), just make the inference. Truthfreedom

ET, 62: Except for the fact there is no way to test that claim. Again, I am just pointing out the gulf. And what I think the crux of the matter is. JVL

ET, 61: No, really because thinking and demonstrating are two very different things. Einstein didn’t get his glory until after the 1919 solar eclipse in which his equation was demonstrated to be true. I was trying to explain why demonstrating unguided processes are capable would not be big news. It's because that's been the assumption of the majority of scientists so there would be no need to celebrate it. I don’t believe you I could be wrong. It's my impression. They want it buried and forgotten. The paper was great when evos thought it refuted something Behe said. Now they realize it puts the nails in unguided evolution’s coffin. It's not been buried, clearly. I just think it's implications have been interpreted differently. And there isn’t any dispute. Just people in denial who have nothing better to offer. Huge difference. Again, there is a dispute, that is clear. And it's also clearly not going to go away anytime soon. You are denying the design inference. You are denying how science works. I'm merely pointing out that a lot of scientists do not accept the design inference. I'm just observing. JVL

JVL:
IF you think that there is no design then everything we observe is due to unguided processes.
Except for the fact there is no way to test that claim. ET

JVL:
Not really because that’s what the mainstream has thought for quite a while.
No, really because thinking and demonstrating are two very different things. Einstein didn't get his glory until after the 1919 solar eclipse in which his equation was demonstrated to be true.
Most working biologists (and scientists in general) think there is no design in biological evolution.
I don't believe you
I haven’t specifically looked for comments on that paper but it’s clear if it was considered a major game changer then there would be a lot of comments and upheaval.
They want it buried and forgotten. The paper was great when evos thought it refuted something Behe said. Now they realize it puts the nails in unguided evolution's coffin. And there isn't any dispute. Just people in denial who have nothing better to offer. Huge difference. You are denying the design inference. You are denying how science works. ET

Truthfreedom, 58: There is a mind behind all of ‘reality’ or there is not. One side has to win. One side is right and one side is wrong. Whether or not one will win is something we're going to have to wait for. Unless there's a third way . . . I'm not sure what that would be but I like to keep an open mind. JVL

ET, 56, : I don’t carte. I know they don’t have anything to refute what I say. Fine! I'm not trying to convince anyone. There is only a dispute because of personal biases. We have the science, they do not. They can disagree with that but reality is against them. You may be right. I'm only pointing out there is disagreement. And that it's unlikely to be resolved anytime soon. And, I THINK (personal opinion), it revolves around the acceptance or non-acceptance of the design inference. IF you think that design is obvious and ubiquitous then the constant and unending assumption it doesn't exist sounds like madness. IF you think that there is no design then everything we observe is due to unguided processes. I don't have an answer. JVL

@54 JVL
And it is okay to have disagreements;
There is a mind behind all of 'reality' or there is not. One side has to win. Truthfreedom

ET, 55: Yes, it is because they haven’t. If they had it would have been big news. Not really because that's what the mainstream has thought for quite a while. Good for them. We are still waiting for their testable hypotheses. Okay. They who? Why isn’t in peer-review? Why can’t you link to it? Why hasn’t anyone refuted that paper? What do you want me to say? Most working biologists (and scientists in general) think there is no design in biological evolution. So all the research published would be considered in support of that view. I haven't specifically looked for comments on that paper but it's clear if it was considered a major game changer then there would be a lot of comments and upheaval. I am not going to budge because then facts and science support me. And all you have is your continued bluffing and denial. I'm not bluffing or denying anything. I am merely pointing out that there is a dispute. I am trying really hard to acknowledge that and be respectful. JVL

JVL:
Again, other disagree with your interpretations of the implications of that paper.
I don't carte. I know they don't have anything to refute what I say. There is only a dispute because of personal biases. We have the science, they do not. They can disagree with that but reality is against them. ET

JVL:
It’s not BS that they think they have.
Yes, it is because they haven't. If they had it would have been big news.
Again, there are a lot of people who disagree...
Good for them. We are still waiting for their testable hypotheses.
They think they have...
They who? Why isn't in peer-review? Why can't you link to it? Why hasn't anyone refuted that paper? I am not going to budge because then facts and science support me. And all you have is your continued bluffing and denial. ET

ET, 52: Trichromatic vison requires more than two specific mutations. And it relates to the primate lineage. That means there isn’t enough time in the universe for unguided processes to produce trichromatic vision. Again, other disagree with your interpretations of the implications of that paper. I'm not saying you're wrong, I'm saying other people say you're wrong. You can disagree with the facts but that will just expose your personal bias and your denial of the science. Me pointing out there is a dispute is just stating a fact. And it is okay to have disagreements; sometimes that's how progress is made because both sides work to figure out the truth. JVL

ET, 49: That is total BS. I KNOW they haven’t. And I also know that you will never find anything showing that they have. It's not BS that they think they have. You disagree. We're not resolving the issue and I don't think we can. 50: And I know the people who disagree with the design inference don’t have a scientific alternative. Again, there are a lot of people who disagree and we are not going to be able to resolve the issue. Except that is not how science works. Again, the two sides are not going to agree. Then have them demonstrate why I am wrong. No one has been able to do that yet. They think they have, you think they haven't. We're not getting anywhere which why I think it's not sensible to argue here. They can’t even simulate their claims on a computer. They have nothing but their denial of the design inference Okay. 51: Intelligent Design has the scientific methodology to test its claims. Unguided evolution doesn’t even have that. That alone tells us everything. I've got nothing else to say. You're not going to budge and those who think the design inference is incorrect are not going to budge. It would be nice to find some middle ground but I don't think it's going to happen. JVL

Consistent with recent experimental observations for Drosophila, we find that a few million years is sufficient, but for humans with a much smaller effective population size, this type of change would take >100 million years.
Trichromatic vison requires more than two specific mutations. And it relates to the primate lineage. That means there isn't enough time in the universe for unguided processes to produce trichromatic vision. You can disagree with the facts but that will just expose your personal bias and your denial of the science. ET

Intelligent Design has the scientific methodology to test its claims. Unguided evolution doesn't even have that. That alone tells us everything. ET

JVL:
I know that there are a lot of people who disagree with the design inference.
And I know the people who disagree with the design inference don't have a scientific alternative.
Again, if a researcher is convinced there is no design then they would think their work supports unguided processes.
Except that is not how science works.
Well, clearly there are a lot of scientists who disagree with your reading of the implications of that paper.
Then have them demonstrate why I am wrong. No one has been able to do that yet. They can't even simulate their claims on a computer. They have nothing but their denial of the design inference ET

JVL:
They think they have, you think they haven’t.
That is total BS. I KNOW they haven't. And I also know that you will never find anything showing that they have. ET

ET, 46: And yet they cannot demonstrate such a thing. So they lose. They think they have, you think they haven't. I'm not sure it's worth arguing about if it just comes down to accepting the design inference, i.e. there's not much else to say about it. JVL

ET, 44: The only people who disagree with that clearly do not understand how science works. Sir Isaac Newton laid it all out in Principia. It is a fact that the way to refute any given design inference is to slice off the designer requirement with Occam’s razor. And to do that you just have to demonstrate tat nature can do it with any intelligent agency involvement. That is how it works with forensics. That is also how it works with archaeology. So I will stick to reality. You can have your disagreements because they are meaningless. I know that there are a lot of people who disagree with the design inference. And if there is no design then everything we observe is down to unguided processes and therefore it has been demonstrated. I know you disagree but I don't see a way to resolve the issue. hen they should publish it in peer-review. Until then it is meaningless. Again, if a researcher is convinced there is no design then they would think their work supports unguided processes. There is a peer-reviewed paper titled “Waiting for TWO Mutations” which totally refutes Dawkins’ idea of cumulative selection. For example, it all but proves that trichromatic vision is out of the reach of unguided processes. Well, clearly there are a lot of scientists who disagree with your reading of the implications of that paper. I don't know what else to say; there are two sides which seem unable to compromise. JVL

JVL:
Anyway, I think there are intelligent people that think that unguided processes have been discerned to be up to the task.
And yet they cannot demonstrate such a thing. So they lose. ET

Kairosfocus, 43: opinions are of no account. Were there an actual demonstration, there would be Nobel prizes. There are not, that speaks. I'm not sure what Nobel category they'd be in . . . hmm . . . Anyway, I think there are intelligent people that think that unguided processes have been discerned to be up to the task. Likewise, I think there are intelligent people who think they haven't. I'm saying it's a matter of opinion because it seems the nicest way to discuss the situation. You may find some data compelling, I may not. I may think certain results make the issue indisputable, you might think they're rubbish. There doesn't seem to be a way to resolve that situation but it doesn't mean we shouldn't be nice to each other. By the way, do you know why the ability to edit posts for 20 minutes after they are first submitted has disappeared? It's not just me, others have the same issue. JVL

JVL:
I think that’s a matter of opinion as there seems to be a lot of people who would disagree with you on that!
The only people who disagree with that clearly do not understand how science works. Sir Isaac Newton laid it all out in Principia. It is a fact that the way to refute any given design inference is to slice off the designer requirement with Occam's razor. And to do that you just have to demonstrate tat nature can do it with any intelligent agency involvement. That is how it works with forensics. That is also how it works with archaeology. So I will stick to reality. You can have your disagreements because they are meaningless.
I think some scientists believe they have tested it.
Then they should publish it in peer-review. Until then it is meaningless. There is a peer-reviewed paper titled "Waiting for TWO Mutations" which totally refutes Dawkins' idea of cumulative selection. For example, it all but proves that trichromatic vision is out of the reach of unguided processes. ET

JVL, opinions are of no account. Were there an actual demonstration, there would be Nobel prizes. There are not, that speaks. KF kairosfocus

Et, 41: The way to refute it is to demonstrate that unguided processes are up to the task. To date no one has been able to do that. I think that's a matter of opinion as there seems to be a lot of people who would disagree with you on that! First there needs to be a way to test the claims of unguided processes. No one knows how to do that. So that would be a problem. And opinions don’t matter. What can be tested does. Yup. I think some scientists believe they have tested it. I see you disagree which is fine. JVL

JVL:
It depends on whether or not the design inference is correct doesn’t it?
The way to refute it is to demonstrate that unguided processes are up to the task. To date no one has been able to do that.
If it’s a mix then some work needs to be done to distinguish between what is and what is not designed.
First there needs to be a way to test the claims of unguided processes. No one knows how to do that. So that would be a problem. And opinions don't matter. What can be tested does. ET

ET, 39: What is the evidence for unguided processes with respect to biology? Hopefully it’s something other than genetic diseases and deformities. It depends on whether or not the design inference is correct doesn't it? If there is no design then it's all down to unguided processes. If it's all design then there is zero evidence for unguided processes. If it's a mix then some work needs to be done to distinguish between what is and what is not designed. Any one person's opinion doesn't really matter does it? We're still looking at the real data aren't we? JVL

JVL:
I disagree with him about the evidence for unguided evolution processes and the ‘obvious’-ness of things being designed.
What is the evidence for unguided processes with respect to biology? Hopefully it's something other than genetic diseases and deformities. ET

Jawa, 35: What specifically you disagree with in Martin_r comments about the Unbelievable Dr Cronin vs Dr Tour debate? I disagree with him about the evidence for unguided evolution processes and the 'obvious'-ness of things being designed. 36: Do you like science? Specifically biology? Yes. Do you like GPuccio’s scientific contributions to this forum? I haven't read any recently so I'll not offer an opinion. Do you agree with gpuccio’s latest OPs and commentaries about protein functional information jumps? I haven't read them so I have no opinion. Jawa, 37: My comment @30 was related to @25 and @12 which are not related to you. You chose to get involved. I will ignore such comments from now on. JVL

My comment @30 was related to @25 and @12 which are not related to you. You chose to get involved. jawa

JVL, Do you like science? Specifically biology? Do you like GPuccio’s scientific contributions to this forum? Do you agree with gpuccio’s latest OPs and commentaries about protein functional information jumps? jawa

JVL, What specifically you disagree with in Martin_r comments about the Unbelievable Dr Cronin vs Dr Tour debate? jawa

Jawa, 30: JVL, Please, see again my comment @25. Thanks. I responded in 26 which you acknowledged in 27 31: Do you agree with everything that Martin_r wrote in the new thread about the Unbelievable discussion between Dr Cronin and Dr Tour ? Do you mind if we move this discussion there too? Thanks. No, I do not agree with everything martin_r wrote. But he's pretty adamant and I'm not sure it would be productive to discuss his position with him. I'll think about participating in that thread. 33: Do you remember that your first comment in this thread @13 directed at me was an off-topic curiosity question explicitly associated with Mimus? Well, then you should understand my comment @30. ???? then why was it addressed to me? You said , @16 if I answered your questions you'd answer mine. How many more questions do you want me to answer? JVL

JVL, Do you remember that your first comment in this thread @13 directed at me was an off-topic curiosity question explicitly associated with Mimus? Well, then you should understand my comment @30. :) jawa

JVL @29: Always. :) jawa

JVL, Do you agree with everything that Martin_r wrote in the new thread about the Unbelievable discussion between Dr Cronin and Dr Tour ? Do you mind if we move this discussion there too? Thanks. jawa

JVL, Please, see again my comment @25. Thanks. jawa

Jawa: Still busy? JVL

Jawa, 27: As you stated it correctly, that wasn’t directed at you. I would encourage anyone who is interested in the topic to check out the previous episode. The podcast was published on November 22nd and is available through iTunes. A couple of weeks earlier was a really fascinating episode called Is It Rational to Be Christian wherein the host, Justin Brierly, debated an atheist and explained why he's a Christian. Really, really good. It changed the way I thought about some issues. I also have to step away from my computer. Will try to come back later. It's Sunday, stuff to do!! JVL

JVL, As you stated it correctly, that wasn’t directed at you. I also have to step away from my computer. Will try to come back later. jawa

Jawa, 25: I’m still waiting for a response to my comment posted @12. That wasn't directed at me but I'm happy to answer it: Regardless of who posted it, wouldn’t you be interested in watching a very recent discussion on OOL between two leading-edge scientists that may have important things to say about that controversial topic? Why not? Because you’re not interested in serious scientific discussions? Another reason? Yup, that's why I listened to it. I am a subscriber to Unbelievable. Just to let you know, I've got to get on with some things so may not respond quickly but I will continute to respond unless I tell you otherwise. JVL

I’m still waiting for a response to my comment posted @12. jawa

Jawa, 23: I’m not done with my “on topic” questions yet. Your off-topic curiosity must wait patiently until the on-topic questions are responded satisfactorily. Deal? If a question isn’t answered satisfactorily then it automatically may provoke additional questions. Agree? Do I have a choice? Aside from abandoning my question. Go ahead, ask. (I think you meant 'responded TO satisfactorily' by the way.) JVL

JVL, I’m not done with my “on topic” questions yet. Your off-topic curiosity must wait patiently until the on-topic questions are answered satisfactorily. Deal? If a question isn’t answered satisfactorily then it automatically may provoke additional questions. Agree? jawa

Jawa: 21: Wrong observation. The comment posted by PavelU @2 is more on topic in this discussion than your off topic question. OOL is much more related to the current OP than your curiosity. Alright. Anyway, I answered your questions. JVL

JVL @19: Wrong observation. The comment posted by PavelU @2 is more on topic in this discussion than your off topic question. OOL is much more related to the current OP than your curiosity. jawa

Jawa, 17: Wrong assumption. I changed my question before I saw your post. Don’t assume things so lightly. Be careful next time. Alright. Jawa: 18: How would you summarize what happened in that discussion between Dr Cronin and Dr Tour? Back to that then anyway . . . It was a complicated conversation. I would summarise it as an origin of life researchers trying to indicate a possibly productive area of research countered by a skeptic who wanted to be sure no one was promising more that what was possible. But that's very, very general. There was a lot of to-and-fro and, in some ways, the conversation was disappointing in that Dr Cronin and Dr Tour sometimes seemed more interested in speaking against each other's position rather than discussing the science. Just my opinion. JVL

Jawa, 16: I’ll answer your “off topic” question after you respond my questions which are more related to the topic of the current OP.If you’re really interested in my ”off topic” answer, you’ll prove it by responding my “on topic” questions. Deal? Not sure why you're trying to 'police' the discussion, your motivations seem a bit odd. Especially since you were the one that introduced the video into the conversation. So you can change the topic but when someone actually answers that question you change the issue? The abstract seems to suggest that two species genomes were fully sequenced and it may have highlighted some disparities between existing gene trees. But, as the last line of the abstract says:
Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.
So it seems more work should be done to clarify the situation. Which makes sense. JVL

JVL @16: How would you summarize what happened in that discussion between Dr Cronin and Dr Tour? jawa

JVL @15: “ Ah, I see you’ve changed your comment @14 since I posted my reply. I’m not sure why you did that.” Wrong assumption. I changed my question before I saw your post. Don’t assume things so lightly. Be careful next time. jawa

JVL, I’ll answer your “off topic” question @13 after you respond my questions which are more related to the topic of the current OP. If you’re really interested in my ”off topic” answer, you’ll prove it by responding my “on topic” questions. Deal? jawa

Jawa, 14: Did you watch the video PavelU posted @2? That video comes from the Unbelievable radio programme broadcast in the UK and available as an audio podcast. I listened to it yesterday as a matter of fact. It was considered part 2 of a conversation with Lee Cronin, part 1 having been broadcast last Autumn. (Justin, Lee and Jim all make reference to the previous episode.) I highly recommend the programme, not every week is fascinating but many are. So, just out of curiosity, is what Mimus is saying correct: are you posting at UD with more than one user name? Should I assume your dodging the question is a tacit 'yes'? Ah, I see you've changed your comment @14 since I posted my reply. I'm not sure why you did that. JVL

JVL, Do you have any comment on the current OP? jawa

Jawa Just out of curiosity, is what Mimus is saying correct: are you posting at UD with more than one user name? JVL

Mimus, Regardless of who posted it, wouldn’t you be interested in watching a very recent discussion on OOL between two leading-edge scientists that may have important things to say about that controversial topic? Why not? Because you’re not interested in serious scientific discussions? Another reason? jawa

To be honest, posting as multiple personalities and having fake discussions and even arguments between them is a type of lying. It makes it impossible to have a good faith conversation with you. I also think it points to a less then healthy connection to this website and topic, which I do not want to enable. Mimus

Mimus, Regardless of who posted it, wouldn't you be interested in watching a very recent discussion on OOL between two leading-edge scientists that may have important things to say about that controversial topic? Why not? Because you're not interested in serious scientific discussions? Another reason? Why do you encourage others to ignore my posts? What is it that you dislike about them? BTW, remember that anonymous visitors are reading what you're writing here. jawa

No,I didn't watch the video you posted under pavelU. I ignore all of your posts, and encourage others to do the same. Mimus

Mimus, Did you watch the video PavelU posted @2? Contrary to what PavelU claims, the video shows how Dr Lee Cronin embarrassed himself mumbling all kinds of nonsense when Dr James Tour asked him very serious questions. Dr Cronin's promised breakthrough that would reveal a chemical path to OOL got discredited from the start of their discussion. At some point I felt sorry for Dr Cronin. jawa

Just a reminder that pavelU is a sock puppet account run by the person who posts as jawa (and olv and a bunch more). I guess this is his idea of a credulous evolution supporter... Mimus

PavelU @2: Did you watch that video? Did you understand their discussion? Apparently you didn’t. jawa

Mung:
It’s encouraging to see that we are finally accepting the evidence for common descent.
That all depends on what you mean by "common descent". ET

@PavelU please, the person who explained (according to your wild imagination) in 2015 the OOL, surely has a name. (People usually have names in the real world). Which one is that? No one in the scientific community knows him! Let me kindly remind you that science fiction and science are not the same. Harry Potter is not part of the methodological sciences . :) Truthfreedom

It's encouraging to see that we are finally accepting the evidence for common descent. Mung

Attention ID proponents: Here's Dr Lee Cronin's OOL explanation that could win the Evo2.0 $10M prize soon PavelU

"Deep phylogenetic incongruence” sounds like journalspeak for “our current phylogenetic tree is a hot mess.” You may want it to sound like that, but it's not the case. "Deep" means close to the root of a tree, but huge or profound. If you read the paper, this of about one node in the tree, and they show that discordance between gene trees should occur if the species tree they estimate is correct. Mimus

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