This was a question posed in my Philosophy of Biology (Phil-Bi)course that I took many moons ago.

Do species exist outside of our own minds, or is the species concept just a concept for us to make sense of the world around us? 

The question is surprisingly hard to answer, especially when you consider that there is no universal definition of species which is acceptable to everyone.

Whereas most people have fairly defined "rules" for what constitutes a species in sexual organisms (and of course these "rules" vary from person to person), I work with bacteria and viruses of bacteria - here the lines of what constitutes a species are very blurred.  For example, the domesticated E. coli I work with in the lab has a genome encoding ~ 4,600 proteins, whereas the E. coli you do not want to find in your spinach has a genome encoding ~ 5,300 proteins - many of the genes for which were acquired by phage-mediated lateral transfer.  Humans and chimpanzees share > 99% DNA sequence homology, and aren't even considered the same genus - we see > 30% DNA sequence divergence in E. coli and call them the same species.  For viruses, the boundaries are even vaguer.... 

 That is pretty amazing.  I did not realize that there was sooo much genetic variation with a given "species" of bacteria.

Are there other species of Escherechia?

There were some that were given species names in the 1960 and 1970s, - I think mostly from cockroaches - before there was a lot of molecular characterization - I think think they have now mostly been adsorbed under the E. coli heading --- although some may have been different enough to constitute their own new groups (I have a nice resource for this in my office, as it is Saturday night - I will wait and give you a follow up...).

Interestingly, the genus Shigella (containing organisms that cause dysentery) is now considered by researchers to be another set of E. coli --- however the name Shigella is being retained for the convenience of clinicians....

One other tidbit - there are numerous species of Bacillus (46 is the number in my head, but that could most certainly be wrong), three of which are of some importance to humans:  B. cereus (which makes for a good joke, and is a cause of food poisoning), B. thuringenesis (named for a sausage, and the source of BT toxin, used as an insecticide), and B. anthracis (causes anthrax).  The genomes of all three have been sequenced, and are virtually identical.  The difference comes from extra-chromosomal DNA that they carry (and could potentially exchange) in the form of plasmids.

Bacteria turn out to be a whole lot different than I learned in school....

Not to run off on a tangent or anything, but do you think that the FBI pinned the blame on the right person concerning the anthrax investigation.  I forget the scientist's name, but I do know that he killed himself. 

It is not a subject that I have deep knowledge of --- it seemed to take forever to tie together - a mystery in itself, and no one seems to be addressing why we have this weaponized anthrax (I honestly doubt he did this by himself with no one noticing) --- at the time it struck me as being a very convenient closing, much like the Ruby assassination of Oswald...  I am not a conspiracy type of person - but I personally think there is more to the story here....

Incipient species was a term that Darwin coined to mean a group of individuals which is on its way to diverging from its parent group to become an actual species.  You really don't hear this term used hardly at all anymore but the relavant point is that subspecies are not necessarily incipient species.  If the barrier which separates the two subspecies is removed then it is very possible that the subspecies may completely merge again.

Fossil species are usually not described at the subspecies level since most differences at this level presumably do not leave fossil traces.  Presumably one subspecies may be markedly larger or smaller than other conspecifics but in practice it is hard to tell whether this difference in size and build is from age, sex, geographical variation (subspecies), or is just another all together species.  Often whether or not the two are even in the same genus may be more of a matter of opinion than anything else.

Does evolution take place at the individual level?  That question is worthy of another thread.

Normally I would say no - in the classic sense evolution is the result of selection on a population of individuals over a series of generations --- after reading Herkeles comment the other day I found myself wondering what I was missing...  and for the life of me I honestly don't know what that statement means....  one can consider for example tumor cells that arise from a collection of mutations and are stringently selected by immune responses - but that is not evolution in the sense that (save for that weird recent instance in australian dogs or dingos or whatever they were) the cell line dies with its host - I guess you could call that extinction.  That is as close as I can come to the idea of "individual" evolution --- but perhaps there is something I am not seeing here....

The "classic definition" of a species, or at least one of its major points is something that we were all probably taught in high school, or perhaps even a biology 100 course.  It goes like this:  a species is a population or group of populations that can only reproduce with themselves.  So good so far, but then we are usually told:  when two species breed they produce what is termed a hybrid--and when hybrids occur they either do not occur naturally very often or they result in sterile offspring (I suppose that they say this so that the very definition of species is not called into question.).  Then they usually give an example or two to support this claim, which in my experience is nearly always the mule (sterile horse and donkey hybrid) or the liger (lion and tiger hybrid, not sure if it is sterile but it would not occur in the wild. 

The problem is that hybrids are RAMPANT in certain clades of animals.  Hybridization in the wild occurs in many species of birds and many species of fish and the hybrids are not typically sterile.  There are even intergenic hybrids in which species of genus 'A' rarely hybridize, and species of genus 'B' rarely hybridize but species from genus 'A' hybridize with species of genus 'B', and this is in the higher animals. 

We have already alluded to the difficulty of determining species in bacteria and viruses.

My tenative conclusion was that species are in fact real but that the higher taxanomic orders are not real.  Now I'm not really sure. 

The D,K,P,C,O,F,G,S,ssp is a valuable tool and seeks to define real relationships but by its very nature all groupings tend to be somewhat subjective.  I do think that the species definition is in need of a revision but I don't know if and when it will occur.

I think that the definition of species as traditionally taught is a useful concept.  I don't think that the grey areas such as mules destroy that definition, because I view horses and donkeys as having a common ancestry as a single species, and that we are observing its gradual speciation into two species. This doesn't destroy the concept of species, but it does destroy the concept of species as a stagnant concept. Also, it shows the limitations upon viewing evolution as only occurring at the gene or individual level.  It is understandable in terms of Gould's punctuated evolution.  This is the level of evolution that is evidenced in the fossil record. 

Mules don't destroy the classical definition of species, they help to define it.  The fact that mules (horse and donkey hybrids) are sterile is given as proof that horses and donkeys are in fact separate species.  They leave you to assume that cross-species hybrids are always sterile--but nothing could be farther from the truth.

Consider the flickers (Colaptes)of north america (north of Mexico).  There were once considered to be 3 species:  the eastern Yellow Shafted Flicker C. auratus, the western Red Shafted Flicker C. cafer and the Gilded Flicker C. chrysoides.  All three of these hybridize in the zones where they overlap and the hybrids are fertile to my knowledge.  The hybrids constitute a certain fairly stable percentage of the population and the hybrid zone is not expanding.  The Red and Yellow shafted ones were recently (perhaps 10 years ago) reclassified as a single species (called the Northern Flicker C. auratus) though C. chrysoides has kept its status as a distinct species.  Should all three be considered the same species?  One argument could be that all three should remain separate species since the hybridization zones comprise a relatively small and stable portion of each's range.  Right now there does not seem to be any stringent rules on classification and it is up to the discretion of the individual ornithologists who tend to be either lumpers or splitters.

I always liked the idea of a species being defined as a gene pool moving through time.