Dan Kliebenstein

Maybe that is why the idea has always puzzled me, my training from undergrad on was always biochemical genetics with quant. Gave a very different view of systems than developmental genetics.

I feel like there should be some word long lost from the Victorian era.

Even the papers that are only mechanism with no connection to any organismal biology beyond a glancing hand wave in the introduction?

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

The quote, "the question", underlies my difficulties with the article and associated thinking. A good future experiment won't be built around one single question. It will be built to assess innumerable questions including unforeseeables. Where only 30 pages can't dare explain the results.

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 rely heavily on Phylogenes to look at genes of interest and use the phylogeny to assess what part of the Arabidopsis annotation should even be considered transferable.

Have seen too many instances where Blast, even reciprocal pairwise is misleading. And synteny flops.

Is the wording important? For example, a true metabolome from a single organism, tissue, cell, etc. is technically impossible but the word works.

A true pangenome could be biologically impossible as there is always that weird unsampled subpopulation waiting to foul things up.

My favorite example to get students (and others) to really contemplate what stays truly conserved across plants.

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.

From personal experience, duct tape, fortunate last second award and hope. Can make it work for three people for three more years but then research career is over. Shrank lab in half in just the past year. So reports are accurate and we leave the anxiety//stress for 3AM quiet ceiling stares.

Ask a physicist what is interesting in your field and how to do the research?

I kind of wish these protein engineering papers would mention how protein complex interactions are a completely different modeling structure than whole organismal epistatic interactions.

Honestly have no idea if the formation of new tissues relates to general plasticity. It would in body plan measures but less clear in things like gene expression or metabolism. The formed tissues also have aging like in adult flies so it gets quite messy to parse.

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...

final thought. Microenvironment cudgel was used effectively by reviewers to stop this work in plants. A group working on the topic could never get reviewers to say what would be experimental proof it was stochasticity so hit an impasse. The plasticity~stochasticity argument also didn't persuade.

Third, would the corollary to plants more microenvironmentally sensitive be that plants are more environment responsive in general? That might be true in an abiotic context but less likely in the biotic. And flies have social influences on G and GxE not found in plants. So unsure. Leading to the..

Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense Author Summary Systems biology is largely based on the principal that the link between genotype and phenotype is deterministic, and, if we know enough, can be predicted with high accuracy. In contrast...

Second is from our metabolome work and electric grid theory. vmQTL(?) didn't lead to more or less noise but changed where the noise was located in the metabolic network. If one part of the grid is precise, another part of the grid needs slop or it seizes up. journals.plos.org/plosgenetics...

First comes from lovely LacI biophysics work showing that plasticity between conditions requires stochasticity within a condition. A regulatory system needs noise in or it cannot change. So at some level, I'm not sure that I see environmental sensitivity and stochasticity as cleanly distinct.

Microenvironmental sensitivity, now that opens a can of thoughts. Thread follows with my attempt at summarizing my thinking on the topic of microenvironment. Admittedly, it is a tough one that is hard to think of ways to experimentally test either for or against.

I think that difference is largely due to us having homozygous RILs that allowed us to replicate both within and between experiments using a randomized design to directly measure average stochasticity. We did downgrade the data to single sample with direct veQTL map and the signal really plummets.

I wonder if there is a difference between flies and plants in this aspect? We were able to find lots of variance QTLs for expression and metabolism in Arabidopsis without applying a stress. Seemed that the QTL were more about where in the network variance occurred.

Could also be “how do TFs with the same binding site differentiate between genes?”.

Does saying it help clarify anything? Seems to make an implication that may be confusing.

AP

Gai Lan is supposed to be even stronger than Broccoli based on glucosinolates.

Isn’t plant science now too old? Shouldn’t we be plant engineering or synthetic plant biology? I mean what are we if we don’t have the proper modern moniker? It doesn’t matter what we do if the name isn’t in the game,