Reviving Office Hours

Shoot. I would.


Curtis, I appreciate the compliment, but the bottom line is that I would be happy to host “office hours” focused on John Polkinghorne. For example, we might perhaps
start with comments and questions on this:
and then move on to consider this:
and perhaps also this:

I don’t know how “votes” are tallied for this notion, but I will wait to hear from Joshua whether this is an attractive option.



That’s another good idea - office hours based on the work of another prominent figure. I like it!


Very attractive.

I’d also like to host office hours on Arthur Compton, a WUSTL figure and Nobel Laureate you’ve written at least three articles about. Any chance we can do him first?

When would work for you @TedDavis?

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@NLENTS, who would you pull in first?

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I’d have to think about it. I know a philosopher who does work on personhood in the age of AI. That sounds cool, no?


@T.j_Runyon @NLENTS - Crocodile phylogeny would be a very good context for discussing the mathematical basis for building trees/nested hierarchies. Not going into all the details of the math (which I know to be highly technical), but more in the sense of its use of an algorithm to select the most probable tree, the null hypothesis (no tree) is excluded by statistical significance testing, etc.

A lot of folks think that it’s all an exercise in choosing to “see” a tree based on nothing more than a pre-existing bias in the realm of biology. Seeing how it really works with crocodiles would be quite instructive.

I’m sure there are many other aspects of evolutionary biology that could be illuminated by the study of crocodile phylogeny. So I would be on-board for such an office hour.


Operational question here… must it be done in real-time? Some of these things are nice if they go slowly over a long period such that people can read, digest, etc.


African or European?? :slight_smile:

If we get tired of croc phylogeny (which I would also be interested in hearing about), I would love to get somebody here to talk about the ongoing controversy regarding whether ctenophores or sponges are the sister group to all other animals.

I haven’t followed the debate much recently, but near as I can tell there are various research groups that are all generating high-quality data and using the latest phylogenomic techniques, but they get very different answers to which lineage is the sister to all other metazoans.

Unfortunately, I don’t know any of the researchers involved in this debate personally (other than Casey Dunn, who I’ve met but he certainly wouldn’t remember me). Anybody have some connections they could reach out to on this?


Right off the bat I’m interested to know who is the earliest known member of Eusuchia. So I think you hosting one of phylogenetics using crocs as an example would be very beneficial.

That was exactly my reasoning, too. :slight_smile:


I’m surprised, but then I direct you to Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003; 52:386-402. You can easily find it on Researchgate.


So I have confirmed an office hours with @TedDavis for August 12-13. Does anyone want to host one of the other ones suggested here?

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What about Josh Denny? I’d be really interested to learn more about All of Us, especially privacy concerns, the role of AI, and the future of tailored therapies.

I would be happy to host one approaching phylogenetics by looking at the example of the croc paper I cited above.

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@Jordan I think it’s gonna be hard to get josh to agree.

@John_Harshman can you write a brief summary to prep everyone and decide on when you’d like to do it?

I will admit I don’t know quite what this “office hours” thing entails. The brief summary would be the paper itself. I would hope that people might read it and ask about any bits they don’t understand. We could start with the abstract:

“The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design and then sequenced an 1,100-base pair fragment that includes both coding and noncoding regions and informative indels for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agreed on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa and together are the sister group of Crocodylidae. Kishino–Hasegawa tests rejected the morphological tree in favor of the molecular tree. We excluded long-branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny,we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions and investigated the effects of different coding schemes for two obvious morphological similarities of the two gharials.”

So here is a thread setup for you to engage with people: John Haarshman: The Phylogeny of Crocodiles.