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solipsist comments on Open thread, Dec. 8 - Dec. 15, 2014 - Less Wrong Discussion
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Off the top of my head, "A collection of organisms which can interbreed with each other and produce fertile offspring", for sexual organisms, and "what humans decide is a species" for asexual organisms. Would an expert be able to do better? The word seems too old and the concept to vague to have a tight definition.
"Species" is not a clean concept in a world with viruses, clines, and ring species.
More precisely, "species" is a map marker made by someone who likes discrete, mostly tree-like maps (legacy of Aristotle?)
"Species" is one rung on the phylogenetic ladder. Whether a given edge case should be classified as a species or as a subspecies can be debated, but in practical terms it is useful to have a tree-like map, because it allows you to assess the phylogenetic distance between two groups.
Also, compared to the range from class to genus, "species" is relatively clear-cut.
That works as long as a virus doesn't transfer genes from one species to the next and thus invalidates the tree structure.
It depends on your goal. What a lot of non-biologists don't realize is that the ladder keeps going after species down through subspecies and beyond. In terms of bacteria, which do undergo horizontal gene transfer, we generally refer to them by their strain in addition to their species. The strain tells you where you got the culture, and, in lab settings, what it's used for. CAMP Staphylococcus aureus is used for the CAMP test, for example -- because you know where the strain comes from, you can be reasonably confident that it will behave like other bacteria of that strain. If you have a different strain of Staphylococcus aureus, you expect that it would probably also work for this test, but by the time you get as far away as Staphylococcus epidermidis, it's quite unlikely that you could use it successfully for the CAMP test.
In theory, you could do a DNA extraction and see if your organism has the right genes to do what you want. In practice, it's usually cheaper and easier to use a strain that you know has the right characteristics -- even among bacteria with 20 minute generation times, genetic drift is still pretty slow, and what little selective pressure there is is pushing for the strain to keep its useful properties (i.e. we throw away bad cultures).
The phylogenetic tree model is used because it makes useful predictions about the world, not because it represents the way the world actually is.
Yes. I'm not denying that such models do have use. But on the other hand people outside of biology do often consider them to represent the world as it actually is.
I think we're in agreement here.
Only if you define the tree genetically and not via ancestorship. Trying to go from one approach to the other is bound to be messy.
In the age of DNA sequencing all the good maps are done based on genetic data.