The annual rodent patrol service in exchange for nesting platform payment is back. We are still having discussions on snakes.

Thoughts on this theoretical. Create an artificial standard with no evidential support and is technically impossible to exclude a large body of work that directly implicates the novelty of a related body of work.

So jazzed for my colleague @gittacoaker.bsky.social for being elected as an AAAS Fellow! She's an outstanding scientist, leader, mentor, and colleague

The baby is trying to be an equine influencer with his photo shoots.

My major conclusion from plant pangenomes papers is that there is a ton of gene loss at all levels of the phylogenies. This leads to the smaller conclusion that proving horizontal gene transfer versus unusual gene retention in the face of massive losses will be a major problem.

What if a super successful fungal plant pathogen has little evidence of structural variation, horizontal gene transfer or their ilk? It’s just a nice Mendelian meiosis and inheritance, etc. does that make it the odd one?

In random asides to ignore: The GO term glucosinolate (terpene, etc) is a generic grouping that does not group by mechanism, regulation or function. It mainly groups by a chemical moiety within a diverse set of compounds. So better to not make mechanistic, regulatory or functional ideas from it.

What if our assumption that regulatory networks are highly conserved is wrong? And every accession, individual, subspecies, etc does things very differently using the same tools?

By studying how a switch on the wall works, how much do we learn about how a light bulb creates light? In todays issue of random thoughts while cleaning horse stalls.

Things are so weird that I am seeing the same people that once said “glucosinolates are so limited that nothing about them has any generalizable insight and shouldn’t be funded”, now say “glucosinolates are so well studied we should use the info to train AI to predict other systems”.

Anyone else think it is possible for a paper to be too mechanistic?

Anyone know of the word for things like fitness, flowering, growth, quantitative disease resistance, etc. that are actually not singular things but instead grouping terms that encompass diverse mechanisms and phenomena, misleading that they are a singular entity?

We really need to come up with a way to better name genes across species. Using the Arabidopsis name, e.g. MYC2, in something like Cymbidium is basically never true as there are so few true 1:1 orthologues across plants.

Check out our new preprint by @octaviarmn.bsky.social and @liobarueger.bsky.social in collaboration with @meikeburow.bsky.social - we investigate the spatial effect of glucosinolates on root microbiomes in Arabidopsis and Camelina! www.biorxiv.org/cgi/content/... lots of cool stuff!

Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥 www.biorxiv.org/content/10.6...

Did you know that most knockouts in Arabidopsis actually do have phenotypes and aren't some redundancy situation? All you have to do is measure in multiple tissues in multiple environments and then the phenotypes show up. Redundancy was an assumption never tested.

Any inklings if ChatGPT is being used by prospective students to assess which faculty are best at a given university? Wondering if integrated scientists are punished by ChatGPT algorithms as those algorithms likely direct focus to specialists in defined field rather than generalists across fields.

Happy valentines a couple of days early.

A sure sign someone doesn’t do integrative research; never having had to adjust the wording, structure or style of a manuscript independent of the journal style.

If you at the cloning of QTLs since the early 90s, we have always known structural variants were important for phenotypic variation. The pangenomes are confirmation rather than origination of the idea.

In the age of internet searching, etc. What is the point of a ScienCV or any biosketch for a grant proposal?

Question for the #PlantPathology community. What is your favorite work showing how a pathogen detects the plant and responds? e.g. does Pseudomonas sense host/non-host and adjust?, Xanthamonas?, Blumeria?, etc?. Trying to build up a literature base independent of google.

🌱From Trends in Plant Science: Evolution-informed pest management pinpoints PUB21 as a key switch for citrus HLB resistance, with AI-designed peptides boosting immunity and killing the pathogen. (Daniel J. Kliebenstein) ▶️ www.cell.com/trends/plant... #PlantScience #PlantPathology

Question for the #PlantPathology community. What is your favorite work showing how a pathogen detects the plant and responds? e.g. does Pseudomonas sense host/non-host and adjust?, Xanthamonas?, Blumeria?, etc?. Trying to build up a literature base independent of google.

New paper with @smishra677.bsky.social! How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process. 1/ www.biorxiv.org/content/10.6...

One last Christmas puppy evening!

The brothers are finally together albeit with a bit of fog.

Predicting epistasis across proteins by structural logic by the amazing Michelle Tang et al www.pnas.org/doi/10.1073/...

Ever wondered if diverse plant species respond similarly when infected by the same exact pathogen? Infect different asterids and rosids with the same Botrytis genotypes and teh short answer, quite differently. www.biorxiv.org/content/10.6... @annajomu.bsky.social @ccaseys.bsky.social (1/3)

The combined ideas of shifting to a fixed monetary supply via crypto and increasing population seems to have nothing to do with abating inflation. Instead it is a giant hedge to shift all inflation costs onto the havenots and the next generation. And fix wealth in few hands forever.

How much do you think pathogens "measure" their host to plan their attack? Do they simply say "likely host, attack." and then hope it works. Or do they say "Host X, attack with chess Plan X". And if they "measure" how do they "measure"?

Bruce Hammock was a scientific legend, brilliant and kind. He was always happy to talk and collaborate without ego. Like many others, I will miss him. 💔

On NLR evolution, any thoughts about a potential for something equivalent to the MHC locus in plants? A meta-stable syntenic position across the viridiplantae that constantly spits out such completely new NLRs that we haven't realized it exists because no NLR orthology?

An interesting and rarely juxtaposed dichotomy of theories/assumptions/thoughts(?) on plant specialized metabolites. 1) specialized metabolites are costly to produce and at loggerheads with growth. 2) specialized metabolites are largely discarded and not catabolized/recycled. Thoughts? #secmet

Someone wants their Christmas peppermint.

#ASPBPlantCellTuesday #ICYMI

#ASPBPlantCellTuesday #ICYMI

Bummed to see corn plants drawn so clearly wrong. The tassel does not magically turn into an ear on the top of the plant. Not a great look for a plant journal.

Interesting how I keep seeing papers say that QTL mapping of enzyme variation to metabolite to insect herbivory and tritrophic interactions hasn't been done before. #secmet

What if generalist pathogens aren't brute killers but poly-specialist perfectionists, optimizing to each host.

Settled for a long winters nap.

What are everyone's favorite papers showing that individual plant TFs function to coordinate primary and specialized metabolism? Rather than solely regulating a specialized metabolite. #secmet

An atmospheric holidays.

Every time a scientist says "my area of expertise takes years of training but I can learn the rest from a book" a chatGPT agent gets its wings. Every single gd time.

Reupping this perennial #MPMI question, has an apoplastic Superoxide dismutase been cloned and proven to take RBOHD O2-• into H2O2? Or are all the models still assuming?

Every time a scientist says "my area of expertise takes years of training but I can learn the rest from a book" a chatGPT agent gets its wings. Every single gd time.

Maybe the best way to really affect the companies suggesting genetics to design your kid .. Pass legislation making those companies legally and financially responsible for any and all known and unknown pleiotropies and epistatic interactions. Nothing better than unknown and unlimited liability.

An interesting aspect of transcriptomics on plant-pathogen interactions. The data exists to say that plant hormones don't have synergistic or antagonistic interactions, instead it is a property of the output gene. For example, there are lots of genes in the datasets showing SA-JA synergism. #MPMI

Elli Cryan, coadvised by @spicybotrytis.bsky.social and I, giving her exit seminar next week! Zoom link in the alt text

Interesting phenomena in pop and evo genetics, when you have loci or even sequences associated with a trait, that is considered generalizable information. Once you know the actual function of these genes their perceived generalizability inherently decreases. Even if the only change is knowing fnxn.