[HN Gopher] What is a species, anyway?
___________________________________________________________________
What is a species, anyway?
Author : slow_typist
Score : 25 points
Date : 2024-02-19 18:59 UTC (4 hours ago)
(HTM) web link (www.nytimes.com)
(TXT) w3m dump (www.nytimes.com)
| johnea wrote:
| Basically any group of organisms that have sex with each other...
| hef19898 wrote:
| And produce fertile offspring.
| kjkjadksj wrote:
| Some humans would fail to meet that definition
| camdenlock wrote:
| ... and produce viable offspring. An important distinction,
| because without viable offspring, genetic transmission halts.
| gnatman wrote:
| Y'all should read the article. It goes into more depth than
| these two comments! For example, two species can have sex,
| AND produce viable offspring, but NOT produce fertile
| offspring. Like a donkey and horse producing a typically
| infertile mule. Horses and donkeys are not the same species.
| onychomys wrote:
| And sometimes you can have two things that everybody agrees
| are different species but which happily hybridize (with
| fertile offspring) all the time!
|
| https://www.princeton.edu/news/2020/05/07/gene-flow-
| between-...
| eviks wrote:
| Viable=fertile here
| InitialLastName wrote:
| Some mules are fertile:
| http://news.bbc.co.uk/2/hi/science/nature/2290491.stm
| d35007 wrote:
| The article tries to explain why your answer doesn't tell the
| whole story. Did you read it?
| dang wrote:
| " _Please don 't comment on whether someone read an article.
| "Did you even read the article? It mentions that" can be
| shortened to "The article mentions that."_"
|
| https://news.ycombinator.com/newsguidelines.html
|
| (your first sentence is good though!)
| d35007 wrote:
| Got it, thanks boss.
| mcapodici wrote:
| Except - https://en.wikipedia.org/wiki/Asexual_reproduction
| bjornsing wrote:
| And also some individuals within a so called ring species:
| https://en.m.wikipedia.org/wiki/Ring_species
| antod wrote:
| Thank you. Saved me posting it as a counter example.
| Basically nature will nearly always be able to defeat human
| efforts at putting things in neat boxes.
| kjkjadksj wrote:
| Thats certainly a valid way to do it. It really doesn't matter
| how you define species as long as you say how you've done the
| defining. Its just a human word like wall or chair. That being
| said depending on your research question, certain definitions
| of species might be better suited than others. For example if
| you just consider reproductive compatibility, then certain
| human couples with fertility issues would be considered
| different species because certain genetic incompatibilities
| mean they are unable to produce viable offspring.
| a_gnostic wrote:
| *Any group of organisms that can have sex to make viable
| offspring. (So bacteria don't have species?) Doesn't change the
| fact that there are 49 million kangaroos in Australia and 3.5
| million people in Uruguay which means if the kangaroos were to
| invade Uruguay each person will have to fight 14 kangaroos.
| mobilejdral wrote:
| There is the long standing joke around the Geeks and Jocks. The
| don't usually have sex with each other. Genetically they have
| even diverged with genetic attributes that you typically find
| in one and not the other. They are even more successful at
| having grandchildren if they mate their "own type" due to to
| certain genetic combinations that both parents will give to the
| kids. Are they two species?
| ciconia wrote:
| https://archive.ph/YkgOw
| neonate wrote:
| http://web.archive.org/web/20240219150630/https://www.nytime...
| slibhb wrote:
| Biologists discovering philosophy. See
| https://en.wikipedia.org/wiki/Lumpers_and_splitters and
| https://en.wikipedia.org/wiki/Universal_(metaphysics)
| onychomys wrote:
| The problem goes back to at least 1859 and was really codified
| by Ernst Myer in 1942, it's not exactly something we're just
| now discovering.
| slibhb wrote:
| I wasn't saying it's a new discovery. My first link mentions
| Darwin who wrote about in the 19th century.
|
| It is a discovery for people who are taught that the
| distinctions between species are very clear and then learn
| otherwise.
| jolt42 wrote:
| I've assumed for a long time that the number of species is way
| over-inflated, just because it sounds cooler to discover a
| "species" rather than some variation within a species.
| MostlyStable wrote:
| There is always going to be difficulty in trying to put
| categorical labels on continuous distributions.
|
| I've long wondered whether abandoning the concept of "species" in
| favor of some continuous measure of genetic relatedness would
| work.
|
| From a practical, everyday standpoint, it would obviously be
| unworkable. We created the idea of species because in day-to-day
| life it's incredibly useful and only breaks down in some pretty
| niche edge cases (again: from the perspective of a lay person,
| those edge cases are both more common and more important to the
| scientists working with them). But as far as scientists, and
| particularly phylogenists and evolutionary biologists/ecologists
| go, it seems like we might save, if nothing else, a ton of effort
| that currently goes into trying to fit the round peg of nature
| into the square hole of our categorical system.
|
| That being said, phylogeny is at best only tangentially related
| to my own expertise so I'm sure there would be difficulties that
| I haven't though of.
| kjkjadksj wrote:
| Most people use genetic relatedness when constructing
| phylogenies today. People in the field understand species
| labels are just discrete terms. Some fields like metagenomics
| don't even consider the species much and group things by genus
| or some higher level instead because of the difficulty of
| defining this stuff. Not to mentioned most of what you sample
| using metagenomics is going to be a population pool (think
| someone extracting dna out of soil or stool, there's billions
| of organisms you are sampling potentially in that one sample).
| You start to think less of "do i have this organism and what
| does this mean" and more "what gene sequences am I detecting
| out of this pool and what does this mean for the resulting
| proteins being released in the environment and what that does"
| ak217 wrote:
| Yep - metagenomics/phylogenomics practitioners have learned
| the hard way that trying to focus on species definitions gets
| you nowhere (if you think defining a species in multicellular
| sexually reproducing eukaryotes is hard, wait till you see
| what bacteria do - it's basically a free-for-all; and on top
| of that, short read metagenetic DNA sequencing gives you a
| soup of DNA that is very hard to precisely partition by
| source).
|
| I consider the focus on species and speciation to be a
| science social phenomenon more than anything else, a lot of
| it attributable to the prestige of being the one to
| "discover" the species (a.k.a. describe it in a way that
| sticks).
|
| The flipside is that the science of phylogenomics is
| incredibly fruitful, in that as we collect more complete
| information about genomes and their diversity and patterns of
| conservation, we are able to better understand life in all of
| its forms. It's also very data intensive and computationally
| complex - some of the most sophisticated data compression,
| suffix tree construction, hashing, and clustering algorithms
| are used in this field.
|
| An unsung group of heroes in the face of this insane
| complexity is the scientists at NCBI whose job it is to
| organize all of the taxonomic and reference genetic/genomic
| sequence information (they are the ones who build the
| GenBank, RefSeq, and NCBI Taxonomy databases). Their work is
| as close as it comes to the source of truth on this. While
| the GenBank FTP server is easily overwhelmed by modern
| workloads trying to ingest this data, AWS and GCP provide
| high throughput mirrors (https://aws.amazon.com/opendata/,
| s3://ncbi-blast-databases, gs://blast-db).
| vrosas wrote:
| Humans have an inherent need to label, categorized and
| segregate things into discrete buckets that I find fascinating.
| zmgsabst wrote:
| Because it's highly effective.
|
| You just slap a topology on things and you get an effective
| type theory that gets mostly good results which allow you to
| elide most of the complexity. This in turn allows you to
| reason about more complex things at a loss of fidelity --
| what we call abstraction.
|
| If you think being able to recognize a forest rather than be
| overwhelmed by the number of leaves on trees is useful, then
| you understand why humans do that.
| bryik wrote:
| A couple years ago I worked on an internal tool for the
| regulatory division of an agriculture company that involved
| mapping endangered species boundaries. The Environmental
| Protection Agency requires the company review potential impact of
| a proposed herbicide on endangered species inhabiting areas where
| the herbicide might be used (or drift).
|
| The question of "what is a species" made me go a bit insane. I
| really wanted a unique identifier for each "species", but kept
| running into edge cases like species that changed scientific
| names (so you'd need name + date to resolve it). Occasionally
| people would refer to species by common name, but a common name
| can resolve to dozens of different scientific names. I don't
| think people realize how difficult and awkward it is to build
| software that deals with ambiguous entities.
|
| This is a tangent, but the US Fish and Wildlife service has a
| cool tool for exploring endangered species [0]. I had a few
| issues with the data, but was overall impressed with how easy it
| was to access and how deep it goes (there are gigabytes of
| shapefiles representing endangered species boundaries offered in
| zip files). Preble's meadow jumping mouse [1] had a range so
| complex that its shapefile was 250 MB, the complete set of
| shapefiles covering all species' ranges was 2.5 GB--this single
| species of mouse took up 10% of this! For comparison, the Topeka
| Shiner's range shapefile was only 147 KB.
|
| [0] - https://ecos.fws.gov/ecp/report/adhoc-
| creator?catalogId=spec...
|
| [1] - https://ecos.fws.gov/ecp/species/4090
| cynicalpeace wrote:
| Many of these categorization issues can be resolved with a simple
| "I know it when I see it" test, made famous by the Supreme Court
| case Jacobellis v. Ohio
___________________________________________________________________
(page generated 2024-02-19 23:00 UTC)