Here is an interesting new lecture on YouTube, by Richard Buggs, who has interacted with people from Peaceful Science before. His topic, which straddles science and Christian faith, would seem to be very relevant to the mission of PS.
I found particularly interesting the first 40 minutes (about trees of life for trees) and the last 4 minutes (about biology and religion in higher education). I’d be interested in hearing reactions to either of those parts.
It seems very superficial. There is of course absolutely no surprise in not having well-resolved phylogenies in species that are still actively hybridizing with each other. And does anyone consider it surprising that different genes support somewhat different trees? He doesn’t talk, when dealing with the “deeper” phylogeny, about how much variance there actually is between the trees given by the various individual genes, and just seems to think that people will suppose that this variance, no matter in what degree, is fatal somehow. But one should expect some disagreement; the fact that he doesn’t elaborate on how difficult these disagreements are to resolve suggests that it’s not really a problem.
I haven’t looked up his Dawkins quotes for context but if I assume they are not out of context, then Dawkins has oversold his case. This sort of thing isn’t unknown for him. But why cite Dawkins? Why not cite someone who actually specializes in phylogenetics? I think that he is probably just trying to appeal to an audience which erroneously imagines Dawkins as a sort of Pope of evolution. Buggs cannot be under that illusion, but he may well know that the audience most sympathetic to his views often is under that illusion.
Is it me, or does Buggs seem to have a bit of an obsession with Dawkins going?
I looked up his J Ball quote, and found it is out of context. Buggs has performed the common trick of quoting a perceived problem, but not the solution offered immediately afterwards.
Buggs quotes this:
"To my mind there is no alternative between abandoning the doctrine of evolution and admitting that the origin of the existing types of flowering plants is enormously more remote than the period as to which we have direct evidence. The difficulty to be got over is the utter absence of such evidence.
Buggs doesn’t quote the next paragraph, which begins:
I shall now endeavour to show you the strong probability that the early development of the chief types of flowering plants took place under conditions such that no record could be preserved for us. I shall first point out that the ancient forms of vegetation belonging to the coal measures and earlier paleozoic formations flourished under physical conditions very different from those now obtaining, while at the same period there were portions of the earth where entirely different conditions prevailed, and where we ought to expect that the evolution of vegetable life would follow a very different course…
But even if it were not taken out of context, it would not assist the ID movement in any way. There is little or no evidence for the evolution of angiosperms. Their origins are still shrouded in mystery. But there is no evidence at all for the design of angiosperms.
I’m sure there are thousands of hours of lectures on phylogeny available online. Could you tell us why we should listen to this one in particular, as opposed to any of the others?
Presumably the fact that he is an Intelligent Design Neo-Creationist is not among these, as that would be just too silly.
In any event, we are very fortunate to have a number of experts on the subject of phylogenetics among the membership of this very group. So, I will wait until one of them confirms that Buggs has a clue about the subject rather than risk wasting time on yet another Discovery propaganda exercise masquerading as science.
Has he? Dawkins says that “… every gene delivers approximately the same tree of life…”
Buggs’s examples show that approximateness, and skip over the fact that if the trees weren’t approximately the same, the outlier technique used to generate them wouldn’t work because there’d be no outliers.
(Buggs is also claiming that John was taking risks inventing ‘signs’ because readers would be able to talk to witnesses of the actual events “if he’s writing very close to the times of the events” - when he wasn’t. He doesn’t even note that ‘John’'s identity is not certain)
It’s all very one-sided with lots of pertinent omissions that render it unconvincing to anyone aware of the omissions. Standard ID fare.
I’ve not heard/read much by Buggs. Now I know not to bother in future.
A bit more info to help guide your decision.
A creationist professor of evolutionary biology in England – Why Evolution Is True
I resist watching long videos, but I think we’ve covered similar material from Buggs before. One might ask Eddie why he finds that lecture interesting.
Hi Eddie
I think his data on plants is consistent with vertebrate data although appear to be more problematic. The problems of inconsistency with the tree get more problematic as you move form sequence comparison to gene/protein comparison to chromosome comparison.
His discussion about the gospel of John and its consistency is also appears true when you compare the Dead Sea scrolls and the modern text of the Torah and the Tanakh. Words do change but the meaning has been preserved in the examples I have seen.
Thanks for posting this.
Just to point out: Bill is massively ignorant regarding every subject he mentions in that post.
One might, and one has. 
One might also have a pretty good idea what the answer is, regardless of whether that answer is volunteered.
I think this would be where that happened:
Richard Buggs: Obsolete Dawkinsian evidence for evolution - Peaceful Science
He says that Dawkins and most others claim that from any gene in an organism you will generate the same phylogenetic tree, i.e., you won’t get clashing trees depending on what gene you pick. But then he says that is empirically false, that you can get a large number of different trees depending on what gene you pick. I claim no expertise, and therefore neither affirm nor deny his statements, but surely it is “interesting” if (a) almost everyone in evolutionary biology does claim that all trees should match, and (b) they don’t. Wouldn’t that be interesting, if true? So that’s why I find it interesting. Does that answer your question?
I also find the last few minutes of the lecture interesting, given that he has spent time in both Britain and the US, and has observed a certain prejudicial treatment toward religious biology students, a treatment that many people here have pretended does not exist.
It would. But it’s not true, and Buggs is smart enough to know that, so then the question is: why does Buggs try to create that impression? There aren’t a lot of possible answers to that question which speak well for him.
Ah, I see
So was he lying when he said that?
Is he just honestly misinformed and ignorant (despite wearing that mortarboard on his head that is supposed to convey the message “I am very smart and what I say is true!”)?
Or are you misquoting him?
I think that about covers all the options.
Fortunately, @John_Harshman and @swamidass have collaborated on a very short and easily digested article that will rectify that problem for you:
Let’s pretend for a moment that it’s true. Just imagine for a moment that most biologists who aren’t phylogeneticists think that it is true that for almost any gene you pick, you get exactly the same tree by phylogenetic analysis. What would be the significance of that? In what way would that matter? What does it imply?
Think about it. In reality it’s more that for almost any gene, the tree you get is usually a bit different. And by “a bit” we are talking a difference comparable to two thermometers disagreeing on the exact temperature in the same room, on the 6th significant figure. Like 21.1041 vs 21.1040 degrees C. But most people think (for whatever reason) that the thermometers agree on the exact temperature.
Now someone named Beetles comes along who is on a personal crusade to inform the public that someone by the name Dawdood once said something factually incorrect about the thermometers. That in fact the thermometers disagree by one part in ten thousand. And it’s a Really Big Problem that Dawdood once said it was an exact match so someone in the public might mistakenly think so. Maybe even other people in biology who aren’t phylogeneticists.
It’s like one of those people who insist that people who say climate change is a “problem for the entire planet” are incorrect and it’s totally misleading, because the planet itself, you know, the basaltic crust and everything below it, won’t suffer from a few degrees increase in global average temperature.
Just by sheer chance, the following paper showed up in my Facebook feed earlier today. It makes an interesting counterpoint to Buggs’ claims regarding the illegitimacy of phylogenetics. I suspect there are many, many similar papers.
Abstract
The Old World flycatchers, robins and chats (Aves, Muscicapidae) are a diverse songbird family with over three hundred species. Despite continuous efforts over the past two decades, there is still no comprehensive and well-resolved species-level phylogeny for Muscicapidae. Here we present a supermatrix phylogeny that includes all 50 currently recognized genera and ca. 92% of all the species, built using data from up to 15 mitochondrial and 13 nuclear loci. In addition to assembling nucleotide sequences available in public databases, we also extracted sequences from the genome assemblies and raw sequencing reads from GenBank and included a few unpublished sequences. Our analyses resolved the phylogenetic position for several previously unsampled taxa, for example, the Grand Comoro Flycatcher Humblotia flavirostris, the Collared Palm Thrush Cichladusa arquata, and the Taiwan Whistling-Thrush Myophonus insularis, etc. We also provide taxonomic recommendations for genera that exhibit paraphyly or polyphyly. Our results suggest that Muscicapidae diverged from Turdidae (thrushes and allies) in the early Miocene, and the most recent common ancestors for the four subfamilies (Muscicapinae, Niltavinae, Cossyphinae and Saxicolinae) all arose around the middle Miocene.
The parallel is poor. He is not talking about trees that are a bit different from each other, but about trees that are, in his view, significantly different from each other. So if anyone disagrees with him they have to look at the data he presents and show that the tree differences he diagrams are not significantly different.
Did you actually watch the first 35 minutes of the presentation where he discusses some of the details? If not, I would suggest you do so before offering another “general” response.
Actually, I was hoping to get a response to the detailed discussion in the video from people who have background in either plant biology or systematics. So I think that @Art and @John_Harshman would be able to comment on the details, and probably also @Joe_Felsenstein.
Again, I neither defend nor reject his claim about conflicting trees. But it does strike me as important if he’s right.
According to your description of the video, Buggs says there should not be any differences between trees according to most evolutionary biologists. Did you just misspeak there, or does he really say that?
Since those three gentlemen all accept the validity of phylogenetics, you seem to be suggesting that they would learn something from this video that the did not know otherwise. Why do you think that is even slightly plausible?
