Against the naming of fungi (2013) | Hacker News Reader

Against the naming of fungi (2013)

sciencedirect.com

48 pointstosh13 comments

Pretty interesting. The reasoning is basically because people like to categorize fungi based on their morphology, which varies wildly depending on conditions and life stage:

> The morphology of a colony growing on a leaf or an agar surface is a snapshot of an organism at a particular stage of development. The organization of mycelia and the shapes and sizes of spores are modified by temperature, water and nutrient availability, acidity, and other environmental variables (Slepecky & Starmer 2009). This means that mycologists employ a lot of subjectivity in determining which features of phenotype are the ones that segregate species.

> For 250 years mycologists have tried to reconcile fungal diversity with the Linnean fantasy of a divine order throughout nature that included unambiguous species. This effort has failed and today's taxonomy rests on an unstable philosophical foundation.

Wow, I knew there were similar problems for prokaryotes (esp. w/ horizontal gene transfer), but didn't know it extended to fungi and never quite thought about it that way.

It extends far further than that. There are cases of interspecies breeding in mammals (A + B = C). What species are the offspring (C + C = C?)? What if such offspring continue to breed? Sometimes, the offspring are not sterile! Do they become a new species. What if, over a few generations, you get a healthy mix of (CCBA + ACBC = ????)?

See https://en.wikipedia.org/wiki/Polar_bear#Taxonomy_and_evolut...

The idea of categorizing things is a convenience that our minds and our society employ to keep things simple. It works in a large number of circumstances. However, it is important to realize that these categories are not 100% rigid and that situations arise that are not simple to categorize. The result is sometimes broadening the definition of a particular category, creating a new category, or ignoring the uncomfortable situation. In reality, it is important to acknowledge that reality does not answer to our whims and needs to categorize things and just accept that clear lines can't always be drawn.

Then there's also species with distinct morphological populations within the se habitat.

http://www.zoology.ubc.ca/~schluter/stickleback/stickleback_...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353498/

We attended a meeting of the Seattle Mycological Society this past summer and our novice ears perked up at the discussions around names. You would hear speakers attempt to use the scientific name and set off debate, but use the common name to achieve understanding, and then would proceed to use some descriptive term in the event that it was sub-species or variation. So, while perhaps scientifically frustrating in its lack of rigor, using those common names plus descriptors certainly fixed it for everyone apart from the practicing professional mycologists.

Who has enough influence in the field of mycology to drive a shift from "Latin binomials" to "digital codes"?

I would argue against this idea because:

1. The mapping from Latin binomial to digital code is not a difficult problem if there is a universally used, standardized database of fungi.

2. Human mind does not think in digital code. The name exists for human understanding not for machine.

3. Latin is a dead language that does not evolve. The meaning of a word in any living language (e.g., English) would potentially change over time.

Rather, I think the real problem is that Latin should be revived in the biology curriculum. One does not even need to learn verb conjugation to know what species names mean because only nouns and adjectives are in the binomials.

As far as I understand, most Latin used in naming of species isn't Latin at all.

Classical Greek in Latinized spelling, I would add. Still, the noun/adjective declensions are Latin.

That has already happened. The NCBI maintains a taxonomy tree: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=...

In this case human the identifier of human is 9606, all kinds of stuff about the human can be queried through this ID. All fungi are classified somewhere under the node 4751. (Even though this website looks awful, its one of the better and most useful resources of the NCBI.)

However this whole taxonomy business is a pretty difficult issue. According to the article, fungal research is (was?) wasting time on morphology. However, even though taxonomic classification through phylogeny is probably a massive improvement, it doesn't solve all issues. In this framework a species is usually defined by some sequence identity cutoff of ultra conserved proteins in the genome. This works probably pretty well for for most eukaryots, however becomes somewhat of an odd measure for bacteria, where two of the same bacteria can have a very low sequence identity of highly conserved proteins. Then you also have another issue, that once you want to classify a new organism, you might only find contaminated, miss classified or in any other way bad entries in the reference databases. Morphology as a sanity check probably makes sense.

Its a big field with a lot of different trade-offs trying to be united under one umbrella. There are no silver bullets.

You don't have to run faster than a #2175, you only have to run faster than the other #3306 to avoid being eaten...

I vote UUIDs instead.

Use feature detection instead.

You don't need to know what it is called. All you need to know is that it is big, brown, has four legs, big teeth, is gnarling, and is staring at you like you look at a freshly-made butter croissant.

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