New Lecture on Trees of Life, Science, and Christianity

Conversation Side Conversation
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This is unclear. The antecedent of “one’s” in “one’s own lab” is not given. Does “one” refer to some researcher or faculty member? Or does it refer to the student? If the latter, are you saying there are places where undergrads are given their own labs to research in? That would be odd, considering that most schools have to carefully budget lab space; it’s hard to imagine any administration assigning a room to some sophomore or even senior, so that he could practice the art of research, when there would be stiff competition for limited lab space among professors, post-docs, and graduate students.

In short, you’re not being clear. Maybe the other molecular biologists here will know what you mean, but the general layman won’t. Who are these undergrads, what year-level are they at, where are these labs, who’s paying for the lab equipment and lab time, and are these undergrads working alone or under supervision, etc.? And do they pick their own topics of research, or are they assigned something by a faculty member? You’re offering a very muddy picture.

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NO. Do you not realize that top-tier institutions bring in prospective students for interviews? Why do you keep fabricating?

Not undergrad lab supervisors.

Minor.

The much longer letter from the professor in whose lab the student worked. Not some “volunteer” thing, but actually doing science, something you clearly don’t understand.

NO. You’re obsessed with this bizarre notion of “volunteering.” It’s usually more work for the undergrad’s colleagues in the lab. They are being educated, something that goes right over your head.

NO. There’s that set theory problem again. I’m telling you what is MOST important, not the ONLY thing. Are you really incapable of comprehending the difference between them?

Lots. Let’s see if you are capable of figuring out where that was. PubMed is free, remember?

NO, and we never called it “volunteer lab work.” First you were obsessed with falsely describing this as a job, now as volunteering. Try reading this slowly: the student is getting far more from this transaction than the professor.

To you, obviously, primarily because you can’t grasp how science education works in top-tier institutions. You also keep inserting complete fabrications of motives and rewards.

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No.

What an idiotic demand. There has to be a dozen quotes, and they have to be from “leading phylogeneticists at Harward, Cambridge etc.” - as if those are necessarily institutions where leading work in phylogenetics occurs - saying something oddly specific.

Look, I’m going to have to explain something very basic about science to you that you appear not to understand. It’s the results that count, not who says them or where they work, or the impact factor of the journal where it is published. So here’s what you need to know:

When two independently determined trees mismatch by some branches, they are called “incongruent”. In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al. 1984; Penny et al. 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al. 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see “Statistics of Incongruent Phylogenetic Trees”.

The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

“Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106.” (Penny and Hendy 1986, p. 414)

Turns out my analogy to thermometers that disagree by as little as one part in ten thousand was quite good.

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Your answers don’t add up to anything. They’re just individual shots at individual statements and questions of mine. You give no exposition. You don’t explain anything. I’m still almost completely in the dark regarding the scenario you are describing about this student who supposedly gets lab experience while still an undergrad.

Start right at the beginning with an example, a real-life or even fictional example. Say, for example, there is an undergrad student at Smalltown U. named “Jimmy.” At some point in his four-year program, according to you, “Jimmy” starts doing lab research. Tell us how it comes about. Does Jimmy walk up to some prof at the institution, and say, “Professor X, I’d like to work in a lab to get the taste of real research?” Or does Professor X walk up to Jimmy and say, “Jimmy, you seem quite bright and may have the makings of a scientist; how’d you like to get some real lab experience?” And at what year-level is Jimmy when this first discussion takes place? Where is the lab located? On the university campus, or in some privately-owned pharmaceutical company, or where? And who is going to be in this lab with Jimmy? The professor who spotted his brightness? Other undergrads? A graduate student? A post-doc? Or is Jimmy all by himself, like a little kid with his first chemistry set? Who decides what the research program will be? Jimmy? Or someone else? Who pays for the lab? The university? If the research requires $10,000 worth of chemicals, does Jimmy just ask for them, and the school coughs up? And who is monitoring Jimmy to make sure his research is useful, and that he’s not just playing around with his chemicals for his own amusement? Does Jimmy have to write up this research? For whom? A post-doc? A prof? An outside industry? Or does some prof or post-doc write it up for him?

You are making general claims about what happens, without explaining with any concrete example (whether actual or fictionalized) of what you’re talking about. You’re not helping your reading audience. There are hundreds of people who drop in on this site and read these posts. Most of them are not research scientists and most of them have not done graduate research in any life science or any science at all. Many of them have not even a bachelor’s degree in any laboratory science. (E.g., their degrees may be in computer programming or history or law or something else.) And many of them are from other countries, where the science education system, both grad and undergrad, differs in some ways from the American system you know. You don’t seem to be making any effort at all to communicate to this range of readers here. Maybe if you worried less about uttering demolishing point-by-point put-downs aimed at me, and more about carefully describing an aspect of American undergrad science education, you’d produce posts that were educational instead of polemical.

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Building a portfolio of experience has become pretty important; above and beyond the transcript some sort of curriculum vitae is expected. To get an idea, just google images for “undergraduate poster competition”, and you can view hundreds of results for undergrad research. Much of it is impressively specialized. These poster presentations have become common add-ons with discipline conferences and university events, and offer the opportunity for undergrads to showcase and converse about their work to anyone who stops by. Students keep these files of course, and these may be valuable for later discussions.

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To buttress points already made that you continue to ignore, it is interesting that Buggs has nowhere in the talk actually stated or shown what evolutionary theory predicts(to predict something he’d have to model it, and to model it he’d have to set parameters and justify them), and for that reason obviously he has not done an actual comparison between theory and observation.

How can you persist in misrepresenting Buggs lecture like this?

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No misrepresentation, because I never said he was correct in what he was asserting. But he is clearly asserting that the conflicting trees contradict what would be expected from theory. And as I already said, I fully expected everybody here would say he was wrong. There are never any surprises on this site. Not only can I predict in advance that any book, article, or lecture by an ID proponent will be declared to be not just wrong in some respects, but riddled with error all through; I can also predict that even if I simply present a video or book title and say, “This looks interesting,” I will be understood by everyone to be defending the work, and will be attacked for doing so. Talk about conditioned reflexes!

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I’m not clear on where in the video he asserts this. Can you give some time stamps?

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Dictionary definitions are based on common usage. They are updated to follow changes in common usage. But perhaps you think lexicographers decide what a word should mean and then insist everyone else follow their lead.

[citation needed]

Added: Note that the original article was about graduate students, not undergraduates. What Eddie and his fellow undergrads did is not definitive.

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Interesting! Reminds me of “Science Fair” competitions that some high schools used to send students to. And I can certainly imagine that some keen undergrad student might want to present something at such exhibits, and I can also imagine that if they did, they would put it on their c.v.s and that some graduate schools would be impressed by the initiative. I’m not questioning that these events take place now, and they might have even taken place back in the 1970s, which is the only period I commented on. But I’m still unclear how, if the research required the use of university chemistry or biology or physics lab facilities, undergrads could get the use of them. To take physics for example, at one school I knew well, they had a particle accelerator, and profs, post docs and grad students were all competing for precious time on it, and administrators had to carefully apportion access. It’s hard to imagine that they would reduce a grad student’s or post-doc’s accelerator time so some sophomore could spent time bombarding nuclei for a glorified science fair project. I certainly never heard of it happening.

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I’m puzzled. Surely you saw the diagram he gives, where he shows a whole cloud of conflicting trees derived from different genes in a particular plant species? And surely his commentary indicates that he regards this as in conflict with what theory predicts, because (according to him) theory predicts that the trees from different genes should all be the same, or close to the same? Again, he might be wrong in characterizing “what theory predicts,” and therefore the conflicting trees may not damage the theory at all. I’m passing no judgment on that. But I thought it was obvious what his line of argument was.

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A petty attempt to catch me out, as usual. Context should have told you that I was not talking about the definition of “colleague” but about who uses it. Yes, the dictionary captures the current sense of “colleague”, but dictionaries don’t specify in what subcultures the word “colleague” is more or less common. My point was that it is less common in some subcultures than others. Undergrads use the word much less often than professors or grad students. Factory workers and store clerks use it less often than members of medical or law associations. Faizal was accusing me of being ignorant of the dictionary definition, but I was perfectly aware of it; it just was not relevant to my claim. But then, Faizal, like you, makes a career here of trying to catch me out on what he thinks are slips of language. You, Faizal, and Mercer should all get together for a wine and cheese party and practice catching each other out on pedantic points. I’m sure you’d all have a great time keeping score and declaring the winner of the day. You could make the losers pay for the wine and cheese.

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This probably happens because most[1] ID proponents are, in your own words, “amateurs and dilettantes, writing about subjects in which they have zero academic training.”

You say you don’t trust Wikipedia for this reason, yet you seem perennially horrified that others demonstrate that ID proponents similar lack of expertise leads them to make frequent and egregious errors.

The amusing thing is that Wikipedia is fully aware that the vast majority of its editors are not experts in the fields they are writing about, and so sets policies and guidelines to compensate for this – most notably WP:NOR and WP:V. The result is, for articles that are subject to a reasonably high level of scrutiny, a reasonably good level of quality (obscure articles are often of much lower quality however).

(The alternative, an online encyclopedia written solely “by invited or approved expert authors” has already been tried – it’s called Scholarpedia – but as the relatively tiny number of articles it has (1,804) demonstrates, the model doesn’t scale nearly so well.)

ID has no such checks and balances in place, which results in the mix of lies, half-truths, and misrepresented and cherry-picked data we all know and love – or in your own words, “riddled with error all through”.

  1. Buggs himself would seem to be a potential exception to this in that he may have sufficient expertise such that he should know better. ↩︎

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:rofl:

:rofl::rofl:

Eddie wants “quotations” from “phylogeneticists”. He doesn’t want citations to published papers, and he doesn’t want data. He has no interest in looking for himself. He is asking for an argument by authority.

@Eddie, this is the “Peaceful Science” board, not the Peaceful Spoonfeed-me-with-quotes board.

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Interesting fact: “Spoonfeed” is the longest English word which has its letters in reverse alphabetical order.

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Very good. Then you should have no problem finding at least one single example of the term being used in the sense that you claim it is used by the man in the street. For instance (hypothetical example): “In undergrad, my lab partners and I dreamed of the day when we would be grad students or maybe even professors, and could finally refer to each other as ‘Colleague’”.

I look forward to what you find.

That’s nice. I don’t care what entirely arbitrary and self-serving rules you want to make up to avoid admitting the gaffe you have committed here. Your implicit accusation against @John_Harshman of dishonesty and/or incompetence, however, is duly noted.

I would I like you to clarify: Are you saying only that you, personally, do not know whether the observed divergences from a tree pattern are within the range predicted by common descent? Or are you saying that this is a scientific question whose answer, at the moment, is not known to anyone?

I personally would not consider a person who uses the opportunity of an inaugural lecture to spread lies about his colleagues and his own supposed area of expertise to be one to inspire trust. But that’s just me.

So I’m not the only one who has noticed this. That is reassuring.

You actually said he asserted that most evolutionary biologists believe there should be no conflicting trees whatsoever.

Do you still claim that is what he said?

If so, do believe his claim is correct?

Yes, that is rather important, isn’t it?

So it is very odd that you not only seem uninterested in taking the steps that would allow you to answer it yourself, but that you have dismissed or ignored the answers given to you right here in this very discussion by qualified experts in the field.

Why ever would that be?

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Pretty much all of the research presented comes out of the student’s position with a lab and is done at the initiative and under the direction of senior leadership. In Canadian research universities, there are an array of scholarship and agency programs to make this happen.

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It should be noted that in this lecture Buggs is doing nothing more than regurgitating an old ID trope that was debunked as long as 14 years ago:

Do Different Genes Mean Different Phylogenetic Trees? | National Center for Science Education (ncse.ngo)

As I said, I have had the pleasure of attending a number of these lectures over the years. I cannot recall a single one in which the speaker spent 40 minutes speaking, not about his own research, but promoting an erroneous claim that had been made in a 15 year old high school textbook.

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I couldn’t find anywhere where he says what the theory predicts, nor how what he observes is in conflict with that. No. What he actually says is something along the lines that Richard Dawkins says the gene trees should be “the same”, which he interprets to mean Dawkins says they should be identical, and then goes on at length about how gene trees in various plant clades aren’t identical in the sense he took Dawkins to imply.

It’s just very odd because as a scientist one would think Richard Buggs would be aware of things like uncertainty and statistics, and if he’d read Penny and Hendy 1982 which he himself refers to, he should also be aware that trees that have numerous incongruent branchescan still have a degree of similarity that is highly statistically significant. Particularly considering how the different trees they evaluate in that paper have incongruencies and yet are still found to be highly similar.

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No, just highlighting that you don’t know what you’re talking about.

Really?

Here’s the context:

You were talking about the definition of ‘colleague’, and contrasting the dictionary definition with common usage. You were not, at that point, talking about who uses the word.

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