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Really fascinating workshop happening rn on prokaryotic taxonomy. Most people find taxonomy boring, but there's currently a massive shift happening. As an outsider and panelist in this workshop, I'm going to do a thread on the situation.
BACKGROUND: the current Code of taxonomy requires that in order to actually name a bacterial species, you need to deposit a culture of it in two culture collections. Obviously, this is a very high bar just to name something.
But ALSO, it means that ANY bacterial species that cannot be cultured on its own can not get a real name!
That means that every pathogen, every symbiont, every prokaryote that we know from sequence data that we don't know how to culture, is given a "candidatus" name.
At this point we KNOW that biology is waaaaay more complicated that just thinking every organisms lives on its own and we can put it in a bottle. SO, we are actively deciding that we can not name the complexity of prokaryotic life.
This is strictly a human issue. We make the rules, nature doesn't gaf. People have decided that the bar for naming something is that it can be placed in culture by itself.
So people can just fix it right? You don't know taxonomist.
We had a workshop in 2019 to figure out how we fix this. Came up with a plan that was forward looking and used DNA sequences, which is literally what the field is using for phylogeny, which is the backbone of modern taxonomy.
This alternative was published in 2020 https://www.nature.com/articles/s41564-020-0733-x
But the Plan A introduced here was voted down by the establishment. So now we have a Civil War
Two options were presented with how to move forward, fixing the current code or making a new one that will "run in parallel" (read: in direct competition) with the current system.
Here's the thing: People who are pushing the science forward want to be able to deal with the massive backlog of pseudonamed species without a huge barrier. Are they going to fight the system that refuses to acknowledge them or move to the new system?
It is inevitable that the more inclusive system will supplant the current system. There will be some people who hang on to the traditional system, but a more flexible system that allows more people to participate and to actually name what is out there will prevail.
The refusal to officially name things that can't be independently cultured is a massive barrier that is made for no reason other than Rules, and is a barrier to describing the natural world.
So at this moment, we're seeing a major shift. The people and institutions that want to hold the line, and those who want to move to a modern system that allows for incorporating the known diversity in the world.
And this seems like an easy fix, but it's not. It's a massive shift that is seeing major resistance.
So how do we move forward? How do we balance the need to deal with the firehose of DNA data that has revealed the breadth of diversity, while maintaining some structure that allows some structure that is viable?
Every system of nomenclature is rooted in deep history and is inherently backwards looking. We do not have the person power to characterize biological diversity at a real scale. Taxonomic expertise has declined over time and the field is heavily skewed towards senior scientists.
It's critical that we embrace technology to solve this problem. I don't personally think that we should move towards full automation, but we need to balance data generation and nomenclature.
Forcing taxonomy to adhere to rules meant for 1921 and not 2021 is placing unnecessary barriers to progress.
There has to be a re-evaluation of the rules that takes into account new technologies and the current system is woefully behind in a way that is inhibiting progress internationally.
Is the proposed Plan B perfect? Probably not, but it's a critical step forward and the resistance to naming diversity we can observe in many ways, but can't submit as a clean culture, is mind boggling to those of us who haven't " grown up" with these restrictions.
So I hope that those interested in prokaryotic taxonomy (which apparently includes me now) begin to see the new system being proposed as a breath of fresh air that will not cause chaos, but instead match taxonomy more closely to biology.
Ok, so there's a lot of interest in this thread. I will try and reply to everyone as I can. Ironically I'm talking phylogenetics in lecture this morning!
