Generic hostility: state of play (Part 7)
A few last thoughts (for now) before I sack out:
As usual when things get talked out, we're converging in some areas and sticking to our guns in others. I think the main battlegrounds now are these: (1) as an ardent rank-free phylogenetic taxonomist, Randy objects to me talking about genera as ranks, and (2) he objects to me talking about this method being used to identify genera when it's been tested on so few things.
If I've left anything out or mischaracterized his views, I'm sure he'll let me know. :-) Watch this space.
To which I respond:
(1) Look, bitches, I learned my phylogenetics at Brent Mishler's knee. It's not that I don't get the arguments for rank-free taxonomy. I love 'em, in fact. But I also find genera damn useful in my day-to-day work. Taxonomy is just a model, and models are judged on utility. I'm a nominalist (as opposed to an essentialist), so I'm happy to use genera as useful mental constructs without believing that they Really Exist As Ranks In The Tree Of Life. That's the main reason I was (and am) so excited by the MALDI-MS stuff--IF there was a method that picked out genera (i.e., monophyletic groups of the same phylogenetic depth that we usually associate with genera) based on objective criteria, that would be something; it would be a little bit of evidence that maybe genera (i.e., ifyouknowwhatImeanandIthinkyoudo) are a little bit real, that there is something special about that particular phylogenetic depth, that we're not just whistling Dixie. Please don't let the length of that sentence disguise the fact that it's dangling from a very big IF.
(2) On the other point, the alleged prematurity of touting this method as a genus-catcher when it's so new and so little-tested: I didn't publish it in Nature, or chisel it into the face of a mountain. I didn't even have it here on the blog to begin with. It was in a damn e-mail, and if a man can't let his enthusiams run away with his good sense in e-mail, then we are living in a cold, dead world indeed.
Also, another labmate, Katie Brakora, sent this in response to my flame attack, and has graciously given me permission to post it.
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Subject: Re:
---------------------------------
To which I replied:
---------------------------------
Hi Katie,
I like your "just another tool in the kit" stance. All I intended to convey was, "Hey, this is cool," but obviously what came across (to some) was "Hey, stop yer grinnin' and drop yer linen, I've got the universal panacea bottled and ready for sale over here!"
And no need to apologize for parentheses, semicolons, em-dashes, ellipses, italics, ALL CAPS, excessive quotations, and especially long lists set off by commas; all of these are useful--nay, indispensable--tools of the adroit writer. Indeed, if I had my way every one of my sentences would consist of two clauses joined by a semicolon; that's just how I roll.
Cheers,
Matt
------------------------------
Finally, really, whether the winds of fate brought you here right after this was posted or six months hence, if you have something to contribute, please do e-mail me or post a comment. I will get back to you.
As usual when things get talked out, we're converging in some areas and sticking to our guns in others. I think the main battlegrounds now are these: (1) as an ardent rank-free phylogenetic taxonomist, Randy objects to me talking about genera as ranks, and (2) he objects to me talking about this method being used to identify genera when it's been tested on so few things.
If I've left anything out or mischaracterized his views, I'm sure he'll let me know. :-) Watch this space.
To which I respond:
(1) Look, bitches, I learned my phylogenetics at Brent Mishler's knee. It's not that I don't get the arguments for rank-free taxonomy. I love 'em, in fact. But I also find genera damn useful in my day-to-day work. Taxonomy is just a model, and models are judged on utility. I'm a nominalist (as opposed to an essentialist), so I'm happy to use genera as useful mental constructs without believing that they Really Exist As Ranks In The Tree Of Life. That's the main reason I was (and am) so excited by the MALDI-MS stuff--IF there was a method that picked out genera (i.e., monophyletic groups of the same phylogenetic depth that we usually associate with genera) based on objective criteria, that would be something; it would be a little bit of evidence that maybe genera (i.e., ifyouknowwhatImeanandIthinkyoudo) are a little bit real, that there is something special about that particular phylogenetic depth, that we're not just whistling Dixie. Please don't let the length of that sentence disguise the fact that it's dangling from a very big IF.
(2) On the other point, the alleged prematurity of touting this method as a genus-catcher when it's so new and so little-tested: I didn't publish it in Nature, or chisel it into the face of a mountain. I didn't even have it here on the blog to begin with. It was in a damn e-mail, and if a man can't let his enthusiams run away with his good sense in e-mail, then we are living in a cold, dead world indeed.
Also, another labmate, Katie Brakora, sent this in response to my flame attack, and has graciously given me permission to post it.
-----------------------------------
Subject: Re:
Eggggscellent. Standing ovation, from the far corner.
Seems this new method's main (and significant) contribution (if only to vertebrates, which are implicitly important to, approximately, 6.5 billion people on earth - or did we hit 7 billion the other day?) is adding (a small corner of) the molecular dimension to those "entities" of the distant past which are only known from morphological characters, and, if you're lucky, histological ones. As molecular characters, they are subject to the same problems and considerations as those from the living, including problems of evolutionary rates, long branch attraction, etc, ad nauseum. So the fuck what. We can work with this.
As for genera, if we define them monophyletically (a reasonable goal, in my book, when combined with ecological labels as an alternative method of grouping "stuff"), then presumably we're smart enough not to rely on a single criterion for membership. Context, people. It's another tool in the bag, weapon in an increasingly fine arsenal. Only time will tell if it's as useful as the 1911 Colt .45. It's our job to find out.
Yes, shoot me for my use of parentheses. They are among the finest of non-word literary inventions, second perhaps only to the even more emphatic (-) thingy.
Katie
---------------------------------
To which I replied:
---------------------------------
Hi Katie,
I like your "just another tool in the kit" stance. All I intended to convey was, "Hey, this is cool," but obviously what came across (to some) was "Hey, stop yer grinnin' and drop yer linen, I've got the universal panacea bottled and ready for sale over here!"
And no need to apologize for parentheses, semicolons, em-dashes, ellipses, italics, ALL CAPS, excessive quotations, and especially long lists set off by commas; all of these are useful--nay, indispensable--tools of the adroit writer. Indeed, if I had my way every one of my sentences would consist of two clauses joined by a semicolon; that's just how I roll.
Cheers,
Matt
------------------------------
Finally, really, whether the winds of fate brought you here right after this was posted or six months hence, if you have something to contribute, please do e-mail me or post a comment. I will get back to you.
posted by Dr. Vector at 12:24 AM
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