Blog

This is a page where I pretend I have exciting and important things to say to the world.


9 Oct 2008
Although the online version of the Flora of North America is an excellent resource, particularly because it is freely available to anyone with an internet connection, it unfortunately contains a number of errors. I will beging tracking those errors as I encounter them here.

The main page for the FNA online (http://fna.huh.harvard.edu/, also reachable from http://fna.org) contains a search box that does not function. The search box within the pages for individual treatments, however, functions properly.
Amaranthaceae: The entry for Amaranthus arenicola is missing its distribution map.

7 Oct 2008
After an excellent monsoon season it's starting to dry up here in southern New Mexico. On a couple of recent trips I decided to keep complete lists of plants seen in flower. I used to do this regularly in Indiana but have not done so much in New Mexico, in part because the plant diversity seen on an average hike in New Mexico is often great enough that listing it all can become time-consuming. So without further ado, some plant lists. Plants are flowering (or either flowering or fruiting in the case of grasses & similar plants) unless otherwise noted. Plants photographed for the first time are in bold.

Percha Box, Sierra County, 5 Oct 2008:

Amaranthaceae:
Amaranthus palmeri, Amaranthus powellii, Chenopodium cf. fremontii, Froelichia gracilis, Kraschenninikovia lanata, Salsola tragus.

Asteraceae:
Ambrosia acanthicarpa, Ambrosia monogyra, Artemisia dracunculus, Artemisia ludoviciana, Baccharis salicifolia, Bahia absinthifolia, Brickellia cf. rusbyi, Conyza canadensis, Ericameria laricifolia, Gutierrezia microcephala, Gutierrezia sarothrae, Heliomeris longifolia, Heterosperma pinnatum, Machaeranthera tanacetifolia, Melampodium leucanthum, Parthenium incanum, Parthenium integrifolium, Psilostrophe tagetina, Sanvitalia abertii, Senecio flaccidus, Stephanomeria sp., Thelesperma longipes, Thymophylla acerosa, Trixis californica, Verbesina encelioides, Xanthisma spinulosa, Zinnia grandiflora.

Boraginaceae:
Tiquilia canescens (no fls).

Brassicaceae:
Boechera perennans or porphyrea (plants with neither fls nor frt, not properly identifiable), Sisymbrium irio.

Capparaceae:
Polanisia dodecandra.

Convolvulaceae:
Ipomoea costellata.

Cyperaceae:
Cyperus cf. esculentus, Cyperus squarrosus.

Euphorbiaceae:
Acalypha neomexicana, Chamaesyce albomarginata, Chamaesyce fendleri, Chamaesyce revoluta, Chamaesyce serpyllifolia, Euphorbia bilobata, Tragia ramosa.

Fabaceae:
Dalea brachyphylla, Dalea formosa, Dalea pogonathera, Dalea wrightii, Hoffmannseggia drepanocarpa (no fls but some frt), Melilotus alba.

Lamiaceae:
Hedeoma oblongifolium (no fls).

Loasaceae:
Cevallia sinuata.

Malvaceae:
Anoda cristata (frt only), Sida cf. abutifolia, Sphaeralcea cf. incana.

Nyctaginaceae:
Allionia incarnata, Cyphomeris gypsophiloides.

Oleaceae:
Menodora scabra (frt only).

Onagraceae:
Gaura coccinea, Oenothera caespitosa (no fls).

Poaceae:
Achnatherum eminens, Aristida adscensionis, Aristida purpurea, Bothriochloa sp., Bouteloua curtipendula, Bouteloua eriopoda, Bouteloua hirsuta, Cenchrus sp., Chloris virgata, Dasyochloa pulchella, Enneapogon desvauxii, Eragrostis cf. barrelieri (keys to that sp. and has yellow glandular rings below the nodes, but the inflorescence is more diffuse, larger, etc., than usual for the species), Eragrostis cilianensis, Eragrostis cf. intermedia, Eragrostis pectinacea, Eriochloa acuminata, Leptochloa dubia, Muhlenbergia cf. pauciflora, Muhlenbergia porteri, Panicum cf. bulbosum, Pleuraphis mutica, Scleropogon brevifolius, Setaria leucopila, Sporobolus contractus, Sporobolus cryptandrus, Tridens mutica.

Polygonaceae:
Eriogonum abertianum, Polygonum aviculare.

Pteridaceae:
Argyrochosma limitanea, Astrolepis integerrima, Cheilanthes feei, Cheilanthes eatonii, Notholaena standleyi.

Rosaceae:
Fallugia paradoxa.

Solanaceae:
Chamaesaracha sordida (no fls), Datura wrightii (old withered fls), Nicotiana trigonophylla, Solanum rostratum.

Verbenaceae:
Aloysia wrightii.

Zygophyllaceae:
Tribulus terrestris.

Bar Canyon, Organ Mountains, Doña Ana County, 6 Oct 2008:

Amaranthaceae:
Amaranthus palmeri, Froelichia gracilis, Gomphrena nitida, Guilleminea densa (frt only), Salsola tragus.

Asteraceae:
Acourtia wrightii (frt only), Artemisia ludoviciana, Bahia absinthifolia, Berlandiera lyrata, Brickellia californica, Brickellia laciniata, Ericameria laricifolia, Gutierrezia microcephala, Heliomeris longifolia, Melampodium leucanthum, Parthenium incanum, Parthenium integrifolium, Pectis prostrata (frt only), Sanvitalia abertii, Schkuhria pinnata, Senecio flaccidus, Viguiera dentata, Zinnia grandiflora (few fls left, mostly frt).

Capparaceae:
Polanisia dodecandra.

Convolvulaceae:
Convolvulus equitans, Dichondra brachypoda, Ipomoea costellata, Ipomoea cristulata, Ipomoea pubescens, Ipomoea purpurea.

Euphorbiaceae:
Acalypha neomexicana, Chamaesyce albomarginata (no fls), Chamaesyce dioica, Chamaesyce fendleri, Chamaesyce cf. nutans, Phyllanthus polygonoides, Tragia ramosa.

Fabaceae:
Dalea brachyphylla, Dalea wrightii, Macroptilium gibbosifolium, Phaseolus acutifolius (frt only).

Lamiaceae:
Hedeoma oblogifolium, Salvia subincisa.

Malvaceae:
Sphaeralcea incana.

Nyctaginiaceae:
Allionia incarnata, Boerhavia coccinea, Boerhavia gracillima (one plant), Mirabilis linearis.

Plantaginaceae:
Castilleja integra, Plantago patagonica.

Poaceae:
Aristida adscensionis, Aristida purpurea, Aristida ternipes, Bothriochloa cf. barbinodis, Bouteloua curtipendula, Bouteloua eriopoda, Bouteloua gracilis, Bouteloua hirsuta, Dasyochloa pulchella, Digitaria californica, Enneapogon desvauxii, Eragrostis cf. intermedia, Eragrostis lehmanniana, Leptochloa dubia, Muhlenbergia emersleyi, Muhlenbergia porteri, Muhlenbergia sp. (a small, awnless annual), Setaria leucopila.

Polygalaceae:
Polygala barbeyana (frt only).

Polygonaceae:
Eriogonum wrightii.

Pteridaceae:
Astrolepis cochisensis, Cheilanthes eatonii.

Rosaceae:
Fallugia paradoxa.

Verbenaceae:
Aloysia wrightii, Glandularia bipinnatifida.

18 July 2008
Topozone is dead. Long live Topozone! Er, I mean TopoQuest!

13 July 2008
Continuing with Joko Beck... one of her later chapters in Nothing Special: Living Zen is entitled "The Natural Man":

"Let's take a look at what we might call 'a natural man'. [...] In the Bible a natural man would be Adam before he was expelled from the Garden of Eden--that is, before he became conscious of himself as a separate self. What was that natural man like? What would it be like to be a natural man?

"STUDENT: A natural man would be full of wonder.

"JOKO: That's true, though he wouldn't be aware that he was full of wonder.

"STUDENT: There would be no sense of separation between himself and the world around him.

"JOKO: That's also true. Again, he would have no awareness of his lack of separation."

What does the word "natural" mean here? And how seriously should we take Joko's linking of a natural state of affairs with a purely fictional, imagined state? The situation is complicated by Joko's view that the result of Zen practice is movement towards a natural state. I can think of no particular reason to view self-awareness (or awareness generally) as a product of artifice. Considering our consciousness to be artifical is reasonable if we consider everything about humans (even those aspects of ourselves that we presumably had no hand in creating) to be artificial, but under such a view there can be no such thing as a "natural man". What definitions of the words could cause us to describe our normal states of mind as "artificial" while describing the results of a conscious attempt to change our minds in one direction or another as "natural" without resulting in self-contradiction?

11 July 2008
More thoughts on Joko Beck... within the portion of her message with which I strongly agree, summarized below as "Pay attention to what you're doing," (perhaps "to what's going on" would be better), there is nonetheless the rather large problem of how this is best to be accomplished. The Buddhist approach is of course sitting meditation. The mechanism proposed for this approach is, so far as I can tell (Buddhist writing does not appear, from my very limited experience, to be overly concerned with discussions of mechanism), is that meditation allows us to become conscious of and eventually control or remove those mental activities which tend to separate us from direct experience. This certainly makes a good deal of sense, however it is unclear to me how what the relation of this process to understanding and comprehension is. Awareness without understanding seems as though it would be rather empty. This may of course be the point, but nonetheless we must still live in a world in which there are decisions to be made and actions taken, and we must have an understanding of the situations we find ourselves in so as to make those decisions and take those actions. Further, awareness without understanding strikes me as oxymoronic; what, then would someone be aware *of*? In any case, in Joko's writings there is very little attention given to furthering understanding (or, for that matter, aiding the "functional thinking" that she speaks well of on occasion) and her views thus seem rather lopsided. For instance, Joko correctly points out the damaging effect of false generalizations; but removing generalizations entirely is even more harmful and Joko gives no suggestions for increasing the accuracy or utility of generalizations. So what are we to do? Often, the same mental activities that can separate us from awareness (e.g., making of *false* generalizations) are essential to awareness (e.g., making of *accurate* generalizations). The content makes the difference. We ignore or trivialize the content of our thoughts at our own peril.

27 June 2008
I've now been reading Nothing Special: Living Zen by Joko Beck. This is an interesting book. It has enough of the trappings of ditzy New Age self-help to make me cringe every few pages, but luckily some of the more obnoxious clichés of the genre are ditched in favor of what often appears to be real wisdom. The many portions of Joko's views I agree with in this book generally boil down to an elaboration on the following: "Pay attention to what you're doing." The equally many portions of Joko's views I disagree with are along the lines of: "Once you sit and meditate long enough, you will see X is the case." X may be that judgments are fundamentally invalid and false, that our identity as individuals is an illusion, that the problems we concern ourselves with in daily life are similarly illusory, etc. Maybe she's right. My meditation is sporadic and thoroughly undisciplined at best (to put it another way, sometimes I like to stare off into space for a while), and presumably long, intense meditation would change my views in some form or another, quite possibly towards Joko's views. However, I find all claims that there is a right way (to do just about anything, really) implausible and... irritating. And I find such claims particularly irritating when they are presented in the aggressively nonjudgmental style that is a trademark of so much New Age spirituality and is, alas, quite well developed in Joko's writing. She clearly believes that she knows the right path, and I see no indication she will admit another right path; yet she won't admit that people not on her path are, by her standards, failing. Instead, every few pages like clockwork some phrasing of, "They aren't ready yet, and that's okay," will rear its condescending, passive-aggressive head. I don't mind nonjudgmental thinking (although I feel no need to embrace it myself), but if we're going to have judgment I'd rather have it open and unapologetic. Judgment is OK. What's important is knowing that you're being judgmental, knowing why, and understanding what your judgment means (as an incidental aside, judgment is the prerequisite of forgiveness, of acceptance). Cloaked judgment goes against everything Joko otherwise stands for. But then, self-contradiction doesn't seem to hold much terror in Zen Buddhism.

Unrelated rant: Cymbals. Cymbals are the bane of modern popular & rock music. They should simply be taken away from most drummers, to be released on a probationary basis after attendance of a mandatory "safe cymbal" course. No matter how bad everything else going on in a song is, the solution is not to just bang away on those things hoping it drowns it all out. And when there is good stuff going on, for christ's sake lay off for a while. I want to hear that stuff, not a bunch of eight-note bashing. Today's offender: whoever the drummer on Built to Spill's Keep it Like a Secret is. So far, all I can say is that if all the Modest Mouse comparisons are accurate we must hope this is Built to Spill's We Were Dead Before the Ship Even Sank; it has that album's mix of excellent melodies mixed in with a layered approach apparently undertaken on the belief that lots of stuff happening is good, even if half of it is entirely uninteresting and in the way. To put it another way, there's lots of good stuff on Keep it Like a Secret, but most of it can't breathe under the weight of thoroughly uninspired rhythm guitar and those awful cymbals.

5 June 2008
A rather soul-destroying quote from Matthiessen:

"All worldly pursuits have but the one unavoidable and inevitable end, which is sorrow: acquisitions end in dispersion; buildings, in destruction; meetings, in separation; births, in death. Knowing this, one should from the very first renounce acquisition and heaping-up, and building and meeting, and ... set about realizing the Truth. . . . Life is short, and the time of death is uncertain; so apply yourselves to meditation. . . ."

Matthiessen takes this from Lama Milarepa, and we see a basic problem with Buddhism (at least with the form of Buddhism popularized in the United States). Like all religions I know of, it has a carrot and a stick. Christianity has heaven and hell, which are honestly both rather difficult to take seriously; so we can ignore the whole thing and move on. However, Buddhism has a very convincing stick, as seen here. On the other hand, the carrot seems awfully small and awfully far away. Nirvana sounds neither plausible nor appealling. Problems seem unlikely to conveniently disappear if we ignore them; and a life with nothing to strive for sounds... boring, tasteless, soulless. I don't want nirvana for the same reason I don't want a lobotomy. If the only way to avoid failure is to give up trying, I'll stick with failure.

31 May 2008
From Peter Matthiessen's The Snow Leopard, p. 55:

"Somewhere, Einstein remarks that his theory could be readily explained to Indians of the Uto-Aztecan languages, which include the Pueblo and the Hopi. ('The Hopi does not say "the light flashed" but merely "flash", without subject or time element; time cannot move because it is also space. The two are never separated; there are no words or expressions referring to time or space as separate from each other. This is close to the "field" concept of modern physics. Furthermore, there is no temporal future; it is already with us, eventuation or "manifesting". What are in English differences of time are in Hopi differences of validity.')"

Good for the Hopi; but how do they say things like "I'll meet you at my house at 7:00."? Or do they sit around discussing quantum physics all day?

Claims like this (the parenthesied quote is from Benjamin Whorf, so I guess it isn't all Matthiessen's fault) suggesting that certain indigenous languages are ideally suited for expressing fundamental truths by avoiding the "linear" or "analytical" restrictions of European thought & language are always hard for me to take seriously. Surely these are just normal people with daily lives like the rest of us. And yet we are supposed to believe that their language expresses esoteric philosophy while bypassing all the niggling requirements of being able to communicate in the mundane world of houses, times, food, meetings, and the rest? Such a people would have starved to death centuries ago, no matter how enlightened.

So far, association of unfamiliarity with spirituality seems fundamental to Matthiessen's writing. I suspect this underlies most interest in foreign religion and culture throughout the U.S. It thus becomes difficult to disassociate, for instance, Buddhism and escapism--though one might think they should be opposed.

14 May 2008
I've been re-reading Nietzsche's Beyond Good and Evil. One thing that becomes apparent that I had not realized the last time I read Nietzsche (however long ago that was) is that his philosophy has distinctly Wittgensteinian undercurrents. Of course, Nietzsche is known best for his various value judgments and not for the philosophical worldview that underpins them. Those underpinnings are perhaps more interesting but harder to trace since they are not explained as explicitly. The most distinctly Wittgensteinian aspect of the early parts of Beyond Good and Evil is Nietzsche's suggestion that philosophy is limited by language, and that philosophical error often results from mistaking grammar for metaphysics; "we really ought to free ourselves from the misleading significance of words!" But Nietzsche had perhaps not realized that we cannot free ourselves without leaving language behind and becoming mute. Wittgenstein clearly did realize this.

An analogy is perhaps useful here. Imagine language as a bottle into which we pour meaning. Most liquids go in fine, but some will corrode or dissolve the bottle and there are a great many things that simply aren't suitable at all; bricks, for instance, go poorly in bottles. Consequently, what kinds of meanings we convey--and thus the structure of our knowledge and conception of reality--is determined at least in part by language.

Now, there is a problem with that analogy. The analogy suggests that meaning and language are independent, with the former translatable (at least imperfectly) into the latter, whereas properly meaning is subsumed within language. This is the point Wittgenstein often made and that Nietzsche perhaps missed (or at least, I have not yet seen him express it). Perhaps a better analogy is that language is like an Erector Set of knowledge & meaning. Only certain patterns can be constructed. The unconstructable patterns are things that cannot be expressed. Even here we skirt disaster by referring to these unconstructable patterns at all.

12 May 2008
A western kingbird (Tyrannus verticalis) lives in a tree next to my apartment. It sounds like this and calls at night.

18 April 2008
Propagation of two quotes from Annie Dillard's For the Time Being:

Pierre Teilhard de Chardin:
"Purity does not lie in a separation from the universe but in a deeper penetration of it."

Frithjof Shuon:
"It is always man who is absent, not grace."

14 April 2008
Goodbye TopoZone... the formerly free topozone.com has disappeared from the web, with its functionality sunk somewhere into the $50/year functionality of trails.com. This was one of the websites I used most frequently, as it provided free access to USGS topographic maps with easy searching by place name, lat/long, UTM coordinates, etc. Alas, no more. It's a pity USGS can't provide user-friendly online access to its own topographic maps.

8 April 2008
It is wise to remember that any argument, any reasoning, is designed to convince people of a certain background. The premises are never stated in full and they include a wide array of background knowledge without which the argument will fall flat.

An example of this I encountered today, certainly not for the first time, is the role of proof in scientific reasoning. The short version, of course, is that proof has no role in scientific reasoning. As scientists, we do not prove things but can occasionally hope to disprove them. This view, called falsificationism, is for most scientists simply some portion of the foundations that has been there so long it no longer arouses any interest. However, in discussions with non-scientists--particularly with non-scientists who seek to oppose science, like creationists--it causes no end of grief and misinterpretation. Lack of proof is taken to mean uncertainty. "Theory" sounds like speculation. What scientists forget when they try to explain falsificationism and the lack of proof is that they are using arguments designed to convince mathematicians and logicians when talking to people who, for the most part, have background in neither. The proof that science lacks is logical or mathematical proof; science is inductive, not deductive. Were our creationists convinced that we were mathematicians, this would be an appropriate approach to dissuade them. But when non-scientists hear "proof" they are thinking of something more along the judicial lines of "proven beyond a reasonable doubt" than of symbolic logic. In their usage proof is simply strong evidence. So when we say that we do not prove things in science this is a mistake; we do not mean to say that we have no strong evidence, but merely that we are not using the specific form of reasoning entailed in logical or mathematical proof. Most non-scientists have no particular interest in the second point, so why argue it? It merely engenders semantic argument by ignoring the simple fact that meaning is context-dependent.

Related to this is the contingency of all language. It is common for logicians and mathematicians in particular, and to a lesser extent scientists, to want to see structures of language (especially formal languages like those of mathematics) as logically necessary. This view tends to obscure the context-dependence of language and leads to a worldview in which abuses to language are seen as abuses of logic rather than abuses of social norm (as a random example here consider the use of double-negatives; it is merely a normative and contingent fact of mathematics that --1 = +1; it could just as easily be that --1 = -2). This leads also to a great many philosophical errors, wherein some fact about how our language works--some contingent fact about what it is various Europeans mostly concerned with their social lives, farming, hunting, warfare, etc., have wanted to say to each other and how they have chosen to say it--is taken to have metaphysical significance. Descartes provided no critique of our ability to know the external world, but instead some interesting problems in our grammar related to knowledge. Post-modernism is not so new; metaphysicians have long taken reality to be determined by grammar.

5 April 2008
From Ed Abbey:
"Life is already too short to waste on speed."

25 January 2008
More Cormac McCarthy... I read The Orchard Keeper, which includes a new way for Cormac to irritate his readers--weird flashback passages in italics interspersed seemingly at random in the text, usually without any readily intelligible connection to the rest of the narrative. Parts of this book are utterly baffling. I found myself all too frequently reading along and suddenly realizing I hadn't the faintest idea what'd been happening in the last couple of pages. In these passages all the sentences seem innocuous enough but I can't figure out what they add up to. So I have to go back and begin again a little back and hope it makes sense this time. Or just keep going and hope it wasn't anything important.

These disjointed passages stand out in this book particularly because other sections are, unusually for McCarthy, gentle, relaxed, and quite frankly beautiful. In these sections I can start to see him as a truly great writer; but then the spell is broken, jarringly.

I've also begun Cities of the Plain. The protagonists of both The Crossing and All the Pretty Horses are featured prominently. Either I'm getting used to it or his writing has settled down here into something relatively straightforward and intelligible. However, more than halfway in I'm still waiting for a plot.

I also finished Horizontal Yellow. Highly recommended, even if he is wrong about horses. I'll probably re-read it before too long.

16 January 2008
A band I recommend: Sleepytime Gorilla Museum.
Since not many of their lyrics are online (I looked), here are those from a song I particularly like, Cockroach:

O loathsome, crawling thing
be done with your miniscule affairs.
O hungry, creeping speck
I release you from your cares.
Be gone, specks.

Roach!
You live on carrion. That's outrageous.
You're probably contagious.
Blind, crippled, and half-squashed
and yet you carry on.
Your persistence is disgusting.
I could never find myself trusting
a creature that would rather live
in the trash than in the lawn.

Cockroach, your problems are not mine.
I love life, but with you I draw the line.
Not to flaunt my superior design
but next to you I'm practically divine.

Your problems are not mine.
Cockroach, your problems are not mine.

15 January 2008
Geographical errors in Horizontal Yellow: 1) Dan Flores has a picture taken from the east side of the Organ Mountains just south of US 70, and labels it as being on the Jornada del Muerto. However, the Jornada del Muerto lies on the west side of the Organ Mountains, between the San Andres & Oscura Mts. on the east and the Caballo Mts. & Fra Cristobal Range on the west. 2) The cover photo is a view looking south at the Capitan Mountains from the plains southeast of Corona. The back of the book says that this is a view of the Sacramento Mountains. In Flores' defense, however, there is a history of using "Sacramento Mountains" in two alternate and rather different senses, either for the Sacramento Mountains proper, or for the Sacramento Mountains plus all the nearby ranges on its north side (despite the fact that they are very distinct geologically and several of them are not contiguous with the Sacramento Mts. proper). Similarly, one will occasionally see the San Andres Mountains, Organ Mountains, and Oscura Mountains collectively referred to as the "San Andres Mountains". Clearly a better geographical taxonomy is needed in such cases.

Another point on Dan Flores' book, continued from a brief mention yesterday: I don't buy the idea that the arrival of domestic horses in the U.S. was some sort of grand Pleistocene reunion as Flores (and a disheartening number of other authors) suggests. Flores is partially aware of this; he admits that neither the country nor the domestic horse are the same things they were 15,000 years ago, but he suggests that the differences are minor or unimportant--that both are "close enough". I disagree. The southwestern plains of 15,000 years ago had a diverse assemblage of megafaunal herbivores and, more importantly, robust populations of large predators. This is a very different ecology from the depauperate herbivorous mammal fauna and near absence of predators that the domestic horses faced when released into North America. Similarly, the horse has also changed. Just how much in terms of its ecology, I do not know. In terms of temperament and its relation to humans, however, there can be no doubt that the change was profound. The native Equus scotti was not a domesticated animal. It lacked precisely the relationship to humans that causes the great fondness and romanticism with which Dan Flores and many others regard domesticated Equus caballus. In cultural terms the difference between the two could hardly be more profound; we may as well dismiss the differences between coyotes and golden retrievers as irrelevant detail.

In short, the horse Flores has fallen in love with is not American. It is Eurasian. As an advocate of bioregionalism he may as well be singing the praises of Lehmann's lovegrass (Eragrostis lehmanniana; another introduced species that spreads rampantly in parts of the southwest and, like Equus caballus, belongs to a genus with native members).

Now, the whole situation becomes more interesting when we take into account Flores' rejection of the traditional ideology of wilderness preservation as the pursuit of pre-European pristine America (the reasoning being, briefly, that the America the Europeans arrived in was an anthropogenic and thoroughly inhabited landscape, not a pristine wilderness). Given that rejection, his advocacy of the domestic horse doesn't necessarily require the horse to be native. Nonetheless he consistently describes the return of the horse as the return of a lost native. Another thing that is not clear (yet?) in this book is what sort of new justificatory framework Flores intends to put in place. If we abandon the old wilderness ideology (something with which I agree), what do we put in its place? Or do we view Flores' desire for feral horses as mere personal whim--and let his arguments for conservation and bioregionalism suffer the same fate?

14 January 2008
Other recent books:
1) Child of God by Cormac McCarthy. May as well keep reading him so long as I've started, right? This is one of his earlier books. He didn't use quotation marks then, either. He did, however, use short sentences and short chapters, in marked contrast to his later works. I think if you just stuck all his short sentences together with "and" and took out the chapter breaks, though, you'd get something a lot like the later books. In any case, this charming tale of a necrophiliac hillbilly is not as obviously pretentious as his later works. A good read, if you like that sort of thing.
2) Under the Banner of Heaven by Jon Krakauer. Pretty much what you would expect from Krakauer-does-Mormonism. And, as you would expect, online reviews of it include a contingent of irate Mormons who point out that the homicidal polygamists at the center of this book are not representative of the LDS church. The problem with that criticism, however, is that Krakauer knows these guys aren't anything like typical Mormons and openly says so. What he does suggest here, however, is that although these fundamentalist extremists are so unlike the modern LDS church they aren't quite so different from the early LDS church. Thus there is not too much discussion of modern mainstream Mormonism here. Krakauer's focus on the modern church is limited to how and why it has left most of the extremist views and actions of the early church. What we get in this book is both some sense of how an extremist sect becomes a sober mainstream religion, and how this in turn inspires a fringe of more or less unhinged fundamentalism.
3) Horizontal Yellow by Dan Flores. Only partway through this one. So far I like it quite a bit, although I remain baffled by the horse fetish that takes hold of so many writers about the West.

7 January 2008
A book I read recently that I found not in the least objectionable: Throwim Way Leg by Tim Flannery. I'm a sucker for biological exploration memoirs and this is a good one, even if Flannery does study mammals. In addition to explorations of New Guinea itself there is quite a bit here about its people, who seem an interesting lot. I think I'd like to meet them if it didn't mean dealing with the climate, parasites, &c. of New Guinea. Without being irritated by the book, however, I find myself with little to say.

4 January 2008
So long as this page has turned into a venue for random Cormac McCarthy criticism, here's another noteworthy feature of his writing... his protagonists seem to often encounter people who tell him their life stories at length, with little provocation and little or no response from the protagonist. Sometimes it seems like these must be the moments of meaning that the rest of the books so clearly lack. And yet, while they're generally quite interesting and enjoyable passages, they never quite seem to come together. After reading them I have the feeling of having been moved closer to some deep meaning McCarthy wants to convey, yet still without any clear idea what that deep meaning might be.
A lot of modern television shows (Alias, Lost, Heroes, etc.) seem to use the same sort of technique. Their writers feel that every episode must provide exciting revelations; yet they also realize that nothing can ever be resolved, or there won't be exciting revelations to promise next week. The result, unfortunately, is a continual building of tension that builds towards... nothing. McCarthy's books have something of the same feeling, although not as pronounced and not as obviously manipulative.

3 January 2008
I am now reading another of Cormac McCarthy's books, The Crossing. Since the book begins in Hidalgo County of southwestern New Mexico, an area I have visited several times, I will mention another thing I have found unsettling about all of McCarthy's books I have read so far. When the locations he describes are among those I am familiar with, his descriptions of them are often at odds with my experiences. In this case, McCarthy describes the Animas Valley and Peloncillo Mountains of Hidalgo Co. as being a land of frequent and sometimes heavy snowfall in winter. This simply isn't the case. It is an area of infrequent precipitation in the winter, and this usually not of the frozen variety. In the area where he puts the protagonist's ranch, there are probably a few light snows most winters, with minor accumulation and a quick melt as the sun warms it. Instead, he describes snow several feet deep in the Peloncillo Mountains, a low range that doesn't make it much above 6,500 feet in elevation. This is a pretty severe misjudgement of the climate; his descriptions make the Animas Valley sound like Taos.
Other errors include misidentification of common plants or animals. For instance, on page five McCarthy gives a description of a tree--pale, with bone-like branches and flaking bark--that fits sycamore perfectly. But he says he's describing cottonwood, which looks nothing of the sort and, as the most important and distinctive tree of lower elevations in New Mexico, is a plant any competent observer of the southwest should be well familiar with. He also describes the protagonist stopping at a stand of "blackjack oak" in the vicinity of the Peloncillos, but this species occurs nowhere in the state, coming no closer than central Texas. Oak identification can be a tricky subject, however, and so this error is more understandable.
Similar errors that he has not made (yet?) in the The Crossing but which abound in Blood Meridian and All the Pretty Horses include calling agave "aloe" (a superficially similar genus, yes, but an African one--and again agave is one of the most distinctive and culturally important plants of the area) and some apparent confusion between coyotes and wolves. It often seems that he's talking about coyotes when he mentions wolves, but it's hard to be certain.

Probably it sounds like I'm nit-picking, but location is central to these books. It isn't an afterthought that can be safely ignored here.

Another point before I leave McCarthy alone for the moment--I'm starting to wonder just how many of McCarthy's books begin with a teenage boy leaving home to head into Mexico. So far, I'm at three for three. It's not a bad plot-line, but it's starting to seem redundant.

31 December 2007
I've never thought too highly of "important" literature. "Self-important" or "pretentious" generally strike me as better adjectives. Recently I read "Blood Meridian" by Cormac McCarthy; as important literature goes, this is a very good book. Yet it is pretentious, collapsing under its own weight, written by an author who has clearly spent many hours perfecting his style and worrying at his image. Speech never comes with quotation marks and is rarely attributed. Dialogue is thus hopelessly muddled. Plot and action can barely be discerned under their burden of long, tortured sentences, obscure references, and irrelevant imagery. The characters likewise are indistinct, most of them nearly interchangable. The protagonist is never given a name and barely has an identity at all. Ultimately, there is little left in the book but McCarthy's stylistic oddities and a long series of deaths, most of them violent and senseless.

Yet this book has received so much praise that I may read it again. Perhaps I missed something. I must have missed something, since there barely seemed to be anything there.

On the other hand, I am most of the way through another of Cormac McCarthy's books, "All the Pretty Horses", and find this one much more enjoyable. If we could just get him to drop the endless run-on sentences and start using quotation marks and intelligible attribution of dialogue, we could make a proper piece of good fiction out of it.

12 December 2007
Now I've also read The Mind-Body Problem by Rebecca Goldstein. Overlap with Incompleteness is significant, although the two were written 20 years apart and The Mind-Body Problem is fiction (loosely autobiographical fiction, but fiction) while Incompleteness is (mostly) non-fiction. The impression given by the two books in combination is that Goldstein lives in a very narrow world that she assumes to be the center of the universe; I can't quite decide if this is charming or arrogant. I guess I'll stick with charming for the moment and feel myself slightly superior for knowing that my own worldview is hopelessly provincial, while Goldstein perhaps does not.

In any case, The Mind-Body Problem works very well as an entertaining mix of autobiography and self-exploration, focusing primarily on the role of women in academia (at least, in one particular version of academia--Princeton of the 1960's/1970's) and, conversely, the role of male genius in this world. The book's philosophical pretensions, however, are sometimes irritating. Despite being a professor of philosophy, Goldstein comes across here as a good novelist who dabbles in philosophy, rather than a philosopher who dabbles in fiction. Although I can certainly understand the desire to simplify complicated philosophical issues to some extent, so as to create an engaging novel rather than a dry technical work, Goldstein's attempts at this often seem clumsy. Perhaps non-philosophers won't mind, though.

As an example (the one that I found most irritating, of course) we have a proof of dualism on pages 157-158. My own crude simplification of this proof is: "Since our bodies continue to exist after death but our minds do not, our minds and bodies are fundamentally different things." The argument, as presented, might sound reasonable in context (at least to people without my antipathy towards dualism), however, the same argument would allow us to split off into separate realms any properties of any object that can be lost without the destruction of the object. So instead of dualism, we would end up with a hopeless pluralism... not just mind and body, but color, size, shape, texture, &c., would all live in their own separate realms, connected by God only knows what tenuous strands of metaphysics. After all, the color of an object can change without the object being destroyed, so the color of an object and the object must be very different things inhabiting separate metaphysical realms; and so on for any malleable characteristic you care to think of.

So, the short version is: if you like semi-autobiographical fiction about academia you should like this book. Just don't expect too much from the philosophical bits.

9 December 2007
I recently read Incompleteness: The Proof and Paradox of Kurt Gödel by Rebecca Goldstein. An interesting and well-written book (with minor exceptions; for instance, the prefix "meta" becomes cloying after a few dozen uses), but, Wittgensteinian I am, I'm left wondering what the general importance of Gödel's famous incompleteness theorems is. The narrow importance in mathematics--that Gödel showed Hilbert's program to be unworkable--is fairly clear. (Even this importance, though, is somewhat fishy, since Gödel's theorems rely on Gödel numbering. Roughly speaking, Gödel numbering allows meaning to be ascribed to numbers. Since that meaning is beyond the sort of simple arithmetical system Gödel was targeting, I'm not sure how valid its use is in evaluation of such simple systems.) However, very few who aren't working in academic mathematics have ever heard of Hilbert's program--except, perhaps, in reference to Gödel's theorems--and the alleged import of the incompleteness theorems extends far beyond that narrow, highly specialized sphere.

To provide at least some minimal context, Gödel's incompleteness theorems state that we cannot create a formal mathematical system that is both consistent and complete (i.e., capable of being used to prove all true mathematical statements that can be formulated within it). Hilbert's program entailed the production of a formal mathematical system that is both consistent and complete, so clearly Hilbert & his mathematical followers have a problem. The version of Gödel's incompleteness theorems that has seeped out into the world, however, is the suggestion that exacting mathematics proves any systematization of knowledge to be doomed. Hence post-modernists love Gödel, just as they love Heisenberg (whose Uncertainty Principle is similarly abused), because they think he dooms science, logic, math, etc., to the sort of free-floating, harebrained subjectivity they adore. Much of Rebecca Goldstein's point in Incompleteness is that this interpretation is at odds with that of Gödel himself. Gödel, fide Goldstein, thought his theorems supported a Platonist (rather than, for instance, logical positivist) view of the world, wherein mathematics could rely on objective mathematical truth when formalism alone fails. The result would then be to strengthen mathematics by showing that it is a reflection of objective reality.

Wittgenstein, for his part, described it as a "logische kunststuck", literally a "logical art-piece". From a Wittgensteinian point of view, the Hilbert program was rather silly to start with, founded as it was on the fear of contradiction to which mathematicians are prone. (This fear does have a basis: logically, anything can be proven from a contradiction. Thus, any reasoning that is based on contradiction is fruitless. The fear goes too far, however, when the possibility of contradiction within a formal system is used to discredit the entire system. Like mud, contradiction poses no problems until you step in it--so just walk around.) Gödel simply uses this same fear to undermine the Hilbert program. The whole thing is rather irrelevant and does nothing more, ultimately, than to translate the classic self-referential paradoxes (which, in their various forms, boil down to something like "This sentence is false.") into exceedingly complicated mathematics. The basic fact--that self-reference allows paradox--had by Gödel's time been fairly obvious for several millenia. The translation of this familiar philosophical pothole into formal math is ultimately a demonstration of great skill and ingenuity, but not a surprising or ground-breaking result.

7 October 2007
How to distinguish Eryngium heterophyllum and Eryngium lemmoni
or
Why I don't like to use the Kearney & Peebles Flora of Arizona


Here is how Kearney & Peebles distinguish these two species:
"3. Plants from a cylindric taproot; lower cauline leaves pinnatifid to bipinnatisect; inflorescence paniculately branched, the heads comate; bracts linear-lanceolate to lanceolate, entire or with 1 or 2 pairs of lateral spines near the middle, commonly yellowish above . . . . . . . 3. E. heterophyllum
3. Plants from a fascicle of fibrous or fleshy roots; lower cauline leaves spinose-serrate; inflorescence successively trifurcate, the heads not comate; bracts broadly lanceolate to oblanceolate, spinose-serrate with 2 or 3 pairs of teeth, silvery-white above . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4. E. Lemmoni"

And here are my observations on the various characters:
"Plants from a cylindric taproot" vs. "plants from a fascicle of fibrous or fleshy roots". This appears to be accurate and, although not necessarily a useful field character, this can be a useful distinction with good herbarium specimens.
"Lower cauline leaves pinnatifid to bipinnatisect" vs. "lower cauline leaves spinose-serrate". This is also essentially accurate, although it could be better worded, for instance by including a more quantifiable distinction rather than descriptive terms that can be somewhat subjective (how deep must the divisions be before the leaf is pinnatifid?).
"Inflorescence paniculately branched" vs. "inflorescence successively trifurcate". This is simply inaccurate. Inflorescences of the two species are quite similar. In both, as we move up the plant we have first several alternately arranged primary inflorescence branches, then a whorl of ca. 3-7 primary branches. Each primary branch of the inflorescence is determinate, and may either terminate in 2-3 heads arising from a single node, or the lateral head(s) may be replaced by secondary branches terminating in groups of 2-3 heads. It seems to be more common for E. heterophyllum to have the terminal groups with only 2 heads, and E. lemmoni to have groups of 3 heads. However, this is by no means a uniformly applicable identifying characteristic, and neither species has an inflorescence that is accurately characterized as "paniculately branched" or as "successively trifurcate", although the primary branches of the inflorescences of either species may (or may not) be "successively trifurcate".
"The heads comate" vs. "the heads not comate". "Comate" is, first, a needlessly obscure term. I do not recall having heard it before, in any context, and although it sounds much like the more commonly used "comose" the meaning is quite different. In any case, a comate head is one in which the bracts of the head are greatly enlarged at the apex of the head and form a leafy projection beyond the flowers. Pineapples are comate. The heads of E. lemmoni are indeed not comate and most heads on most specimens of E. heterophyllum are indeed comate. But some heads on many specimens, and all heads on rare specimens of E. heterophyllum are not comate, or at best indistinctly so. So this is a one-directional character; plants with comate heads must be E. heterophyllum, but plants with non-comate heads could be either species.
"Bracts linear-lanceolate to lanceolate, entire or with 1 or 2 pairs of lateral spines near the middle" vs. "bracts broadly lanceolate to oblanceolate, spinose-serrate with 2 or 3 pairs of teeth". This is accurate, although unfortunately there is overlap in the descriptions.
Bracts "commonly yellowish above" vs. "silvery-white above". I cannot tell if this character is inaccurate, or simply variable and of limited utility. I have only seen E. heterophyllum in the field at two locations (Rucker Canyon in the Chiricahua Mts. and Clanton Draw in the Peloncillo Mts.), but both times the bracts were silvery-white above. No difference in bract coloration is apparent from the herbarium specimens I looked at earlier today, but colors are often unreliable in dried material. Presumably any specimens that did clearly have yellowish bracts could be readily identified but, as with non-comate heads, specimens with silvery-white bracts (which appear to be the overwhelming majority) could be either species.

Although this is the most annoying example I have encountered recently (since this key has resulted in my misidentifying E. heterophyllum as E. lemmoni not once but twice), it is unfortunately not an isolated example. Most keys in the Kearney & Peebles flora are well written and eminently usable. However, a significant minority are not, and while these keys will still usually yield correct identifications if used carefully while comparing specimens of all of the relevant taxa, they often make me feel rather confused and can lead to misidentifications if used incautiously.

3 September 2007
I return this night from the Peloncillo & Chiricahua Mountains. I bring a piece of Agave back, lodged in my arm.

28 August 2007
Got my first rejection letter for a manuscript; specifically, a brief note objecting to poorly supported nomenclatural change in the snake genera Pantherophis & Pituophis by Burbrink & Lawson.

Reviews are anonymous, but of course it's hard to resist guessing who the reviewers are based on their comments. One review appears to be from Burbrink; he very nearly says so and it is clear enough from the views expressed. It is, predictably, uniformly negative and includes, in addition to a couple of minor but correct points, many that appear to result from nothing more than a negative reaction to criticism. For instance, I am told that I do not have a clear grasp of why phylogenetic hypotheses generated by Bayesian inference should be preferred over those generated by maximum likelihood. This is true--I don't have any idea. The reason I don't have a clear grasp of this, however, is related to one of my criticisms of Burbrink & Lawson--they prefer a BI tree but do not give any clear explanation of their reasons for doing so, nor cite any author that provides such an explanation. So I am criticized for not understanding a point that the authors did not make. So it goes.

The author of the other review is less obvious. In initially suspected it might be David Hillis, but have now learned that this is not the case. Most of the comments from this reviewer are relatively minor criticisms, although he did notice a significant omission on my part. Many comments relate to PhyloCode, and some of these are interesting. Some background explanation is necessary:
Several phylogenies have recently been published for the tribe Lampropeltini, which includes the genera Pantherophis and Pituophis among others. The status of the genus Pantherophis varies between these phylogenies. Depending on the phylogeny, the genus may be either: 1) monophyletic; 2) unresolved; 3) paraphyletic with respect to Pituophis; or 4) paraphyletic with respect to the genera Arizona, Bogertophis, Cemophora, Lampropeltis, Pituophis, and Stilosoma. Burbrink & Lawson suggested that, based on topology "3", Pantherophis and Pituophis should be synonymized, with no discussion of the alternate topologies (despite the fact that "4" was produced by one of their own analyses).
I objected to this, on fairly obvious grounds. My second reviewer suggests that under PhyloCode the situation would be unproblematic. PhyloCode is a system in which taxa are explicitly clade names, rather than being defined based on content; a taxon in PhyloCode is something like "all members of the smallest clade including species X, Y, & Z". So definitions of taxa never change on different trees; but content often does change. With appropriate definitions of the relevant taxa in the present situation, content of Pituophis could remain unchanged, but content of Pantherophis would change radically on different trees. I don't see, however, how this removes the problem. Instead of having different content-based definitions of generic names, we would have constant clade-based definitions with varying content. The result is the same: differing content of taxa. And in fact the amount of variation increases. Under traditional Linnean nomenclature, we have two alternatives: a) we either stick with previous usage & have two separate genera, Pantherophis and Pituophis, or b) we accept Burbrink's proposal & Pituophis now includes species formerly included in Pantherophis. Under PhyloCode, we have four possibilities corresponding with the four published topologies, either: 1) Pantherophis includes only those species previously assigned to the genus; 2) content of Pantherophis is undefined; 3) Pantherophis includes previous members of the genus as well as members of Pituophis; 4) Pantherophis includes previous members of the genus as well as members of Arizona, Bogertophis, Cemophora, Lampropeltis, Pituophis, and Stilosoma. Furthermore, conventions for stating which alternative is being used by an author are simple and well-known under the traditional Linnean system. "Pituophis sensu Utiger et al. (2002)" would indicate alternative "a", and "Pantherophis sensu Burbrink & Lawson (2007)" would indicated alternative "b". But what do we do when using PhyloCode? There is no established convention. I suppose something like "Pantherophis, according to the cladogram of Burbrink & Lawson (2007), figure 2" would work, but this presupposes more knowledge on the part of the author. To know what "Pantherophis sensu Burbrink & Lawson (2007)" refers to, I need to know which taxa Burbrink & Lawson included in the genus. To know what "Pantherophis, according to the cladogram of Burbrink & Lawson (2007), figure 2" I have to know both what the PhyloCode definition of "Pantherophis" is and what topology is shown by the figure referred to. Keeping track of PhyloCode definitions should be easier than the corresponding Linnean requirement; under PhyloCode, there would be one published definition per taxon name, whereas in traditional Linnean taxonomy there may be several. Having to know published topologies, however, will often be much more difficult than keeping track of taxonomic proposals in Linnean nomenclature. There are often many more published cladograms than there are published taxonomic proposals; in this case, there are at least 8 published cladograms relevant to delineation of supraspecific taxa within tribe Lampropeltini.
PhyloCode certainly produces different problems than does traditional Linnean nomenclature. However, I can see no indication that it produces fewer problems, and can certainly see cases in which it produces more of them.

27 August 2007
Back from a couple days in the field. Hiking up steep mountains at night is very odd, I've discovered. I went most of the way up Mt. Riley Friday night. On steep slopes on the east side, I found myself on a 45-degree slope unable to see top or bottom of the mountain. Kind of an odd mix of claustrophobia and vertigo. Worth doing once; maybe again.

24 August 2007
Following up from yesterday, here's another paper from the Crews lab that contradicts their preferred hypothesis of progesterone induction of pseudocopulatory behavior:

B.G. Dias & D. Crews, 2006. "Serotonergic modulation of male-like pseudocopulatory behavior in the parthenogenetic whiptail lizard, Cnemidophorus uniparens." Hormones and Behavior 50: 401-409.

This one does at least have a minimal discussion of the anomaly:
"The absence of male-like pseudocopulatory behavior by OVX+P animals [lizards with implanted progesterone] might be due to the need for a decrease in levels of estrogen to accompany an increase in progesterone levels (as observed in naturally cycling animals), a hormonal profile not achieved by implanting animals in the OVX+P group with only progesterone."
Since the lizards in question had their ovaries removed and thus are producing no endogenous estrogen, it seems that they would indeed have a "decrease in levels of estrogen", but I'll readily admit my ignorance of most of the physiology involved. The main point remains: we now have two papers showing no induction of pseudocopulation by progesterone, and one showing it. So the effect is, if nothing else, not repeatable. Another point of interest is that in this, and the other Crews lab papers on experimental manipulation of pseudocopulatory behavior I have read, the authors find it necessary to induce pseudocopulatory behavior by implanting testosterone in order to study it. This is presumably because intact lizards do not exhibit the behavior often enough to study, and naturally-occurring hormones do not induce this behavior reliably. So Crews lab experimental design & data do not seem to support the Crews lab contention that this is a common, natural behavior. This also has the further effect that most of the advantages of using a parthenogenetic lizard to study the evolution of sexual behavior are nullified. It's not exactly clear what the behavior of androgenized females has do with evolution of behaviors in natural populations.

23 August 2007
Further thoughts on pseudocopulation in Aspidoscelis.

The story David Crews likes to tell about the role of hormones is something like this (e.g., in his 1987 Scientific American article):
Crews coincidentally observed pseudocopulation in captive A. uniparens, and wondered what was going on. He first thought that perhaps A. uniparens had elevated testosterone levels that produced male-like copulatory behavior in this all-female species. Research down this line was only partially fruitful. It turns out that exogenous testosterone can produce male-like sexual behavior, but there is no detectable testosterone being produced by these lizards. So he figures it must be some sort of unusual activity of a typical female hormone. Male-like behavior turns out to be limited to post-ovulatory females with high levels of progesterone, and further experiments show that in both female A. uniparens and the majority of male A. inornata, one of the parental species of the hybrid A. uniparens, progesterone can elicit male-like sexual behavior. So now we know the hormonal basis of pseudocopulation: male-like sexual behavior is produced in these lizards by progesterone, a hormone typical of the female reproductive cycle.

As I mentioned, he was telling basically this story back in 1987, and though the Crews lab has continued to do research on pseudocopulation in Aspidoscelis for the last 20 years, this part of the story hasn't really changed. Now here's the interesting part. In 2003, Sakata, Woolley, Gupta, & Crews published a paper entitled "Differential effects of testosterone and progesterone on the activation and retention of courtship behavior in sexual and parthenogenetic whiptail lizards." This isn't a particularly good paper (for instance, readers are challenged to understand what, exactly, is going on in Figure 2, to comprehend why the length of behavioral trials for expression of male-like sexual behavior varies, apparently at random, among experiments, or to explain the absence of any experimental control in Experiments 3 & 4), but it does have one rather intriguing result. Sakata et al. find no elicitation of male-like sexual behavior in A. uniparens by progesterone. Their Experiment 2, which looks at the difference in percent of ovariectomized individuals of A. uniparens exhibiting male-like sexual behavior after implantation of testosterone, progesterone, or cholesterol (this experiment does have a control), shows that progesterone produces results statistically indistinguishable from those of cholesterol. Now, you would think this would change the story, right? Nope. In their conclusion, Sakata et al. simply cite previous work as having shown that "both testosterone (T) and progesterone (P) can activate courtship behavior" (p. 528), and do not even discuss the fact that their present study found no such activation.

18 August 2007
Some thoughts on pseudocopulation in Aspidoscelis...

David Crews & associates have studied pseudocopulation between females of parthenogenetic Aspidoscelis in captivity for several decades now, and have argued throughout that it is an important factor in the reproduction of wild populations. This view was criticized extensively early in the studies of Crew et al., but little criticism has been published in the last two decades. I've been skeptical for a few years, though, and it doesn't seem to me that the criticisms have ever been satisfactorily answered. My present discussion is spurred by a 2003 article by Miriam Solomon, "The Whiptail Lizard Reconsidered", since it includes many of the salient misconceptions and omissions.

The central question in attempts to understand pseudocopulation in parthenogenetic Aspidoscelis has been whether this behavior is primarily an artifact of captivity, or occurs frequently in the wild. M. Solomon discusses this on p. 321:
"Reproductively inactive lizards do not pseudocopulate (so, it isn't just artifactual behavior created by the stress of captivity, nor is it behavior unrelated to reproductive physiology) (Moore, Whittier, Billy and Crews 1985 and Moore, Whittier and Crews 1985)."
The first conclusion here is erroneous, the second accurate. Condition-sensitivity does not imply that a behavior is not an artifact of unusual conditions. It may only mean that it is a relatively complicated artifact, sensitive to variation within unusual conditions rather than only to the unusual conditions themselves. Another mistaken assumption here (repeated later on the page as well) is that increased stress is the only unusual aspect of captivity. However, unusual captive behaviors need only be caused by an aspect of the captive conditions that differs from those experienced by animals in the wild; increased stress is hardly the only such factor available and in fact greatly increased density of captive populations, not increased stress, has been the most commonly mentioned unusual aspect of captivity suggested by critics (e.g., Cuellar in the 1993 book "Biology of Whiptail lizards (genus Cnemidophorus)". M. Solomon's discussion of this question continues on p. 322:
"There is one paper, however, that addresses a lingering worry, referred to by Collins and Pinch as "the most salient piece of negative evidence" (p. 116): why has pseudocopulation not been observed in the field? As late as 1989 (Paulissen and Walker) there is puzzlement about this. Well, now the important observations have been done. Crews's 1991 paper with Young reports the first documented observation of pseudocopulation (by an observer not involved in the debate), and also reports a new study giving indirect evidence of pseudocopulation in the field from measurement of bite marks (this was a much better study than the first such study). McCoid and Hensley (1991), Eioer (1993), Paulissen (1995) (the same Paulissen who in 1989 doubted that pseudocopulation occurs in the field) and Bezy and Enderson (2002) have reported pseudocopulation in nature in a number of parthenogenetic lizards including C. uniparens."
Yes, pseudocopulation has been observed in the wild; however, the published reports are either indirect or of the "man bites dog" variety. For instance, the report of Bezy & Enderson (2002) is noteworthy and publishable only because it is such a rarely observed phenomenon; while such reports do help establish that pseudocopulation occurs in the wild, by their very nature they also suggest that it cannot be common. Indirect evidence is somewhat uncertain; published reports from indirect evidence have not uniformly suggested that pseudocopulation is a common occurrence, and since parthenogenetic species typically co-occur with sexual species, it is necessary to distinguish whether bite marks come from pseudocopulation with other females, or from copulation with males of co-occurring sexuals; both are known to occur at unknown frequency in the wild. Observational studies in semi-natural conditions (large outdoor exclosures, rather than the small indoor aquaria of Crews et al.) are another important source of information not mentioned by Solomon. Beth Leuck conducted several such studies, and never observed pseudocopulation among parthenogens. She did, however, observe a number of copulations between sexuals in the same studies. Unobserved pseudocopulations may, of course, have occurred; but they must have either been far less common than copulation between individuals of sexual species, or for some reason much more difficult to observe. On the whole, it seems to me that we know pseudocopulation does occur in wild populations, but that it appears to be much less common than sexual copulation and that claims that it is frequent enough to physiologically replace sexual copulation in parthenogens remain unfounded.
One of the implications of this is interesting, but has rarely been explored. Parthenogens like those in Aspidoscelis are of great interest in studies of the evolution of sex. The central question in that field is, roughly: Since asexual taxa can, all else equal, out-reproduce sexuals by a factor of two, why don't asexual taxa replace sexuals? If parthenogenetic Aspidoscelis are physiologically entrenched by their sexual history, and cannot realize the potential two-fold reproductive advantage because of hormonal reliance on copulatory behavior that occurs too infrequently in the wild to effectively replace sexual behavior in gonochoristic species, this provides an answer. However, it may be over-looked in part because it is not the kind of answer researchers are generally looking for; it is a suggestion that all else cannot be equal, and thus undermines search for a general explanation.
Another facet of the question that is generally overlooked is that pseudocopulation may not be a characteristic of parthenogens, but one of whiptails generally. Crews & Moore (1993, in "Biology of Whiptail Lizards (genus Cnemidophorus")) mention, briefly and without further discussion, that pseudocopulation is also observed when females of sexual species are housed together in captivity. This important observation has not been followed up, that I am aware of; this is odd, since it fundamentally changes any picture of the importance of pseudocopulation in whiptails. It renders the suggestion that pseudocopulation is something new that happens in parthenogens to allow them to accommodate the absence of males, which seems implicit in most of the work of Crews et al. and in interpretations of their work, untenable. Instead, perhaps parthenogens in Aspidoscelis can arise only because pseudocopulation already occurs in the genus; but they cannot displace sexuals because pseudocopulation doesn't happen often enough.

19 July 2007
Yes, it's been a long time since I wrote anything here.

Now, there's nothing some scientists like better than pointing out the gaping flaws in the work of others. I happen to be one of those scientists, and, with that in mind, here are my thoughts on a recent paper by E.B. Rosenblum: Convergent Evolution and Divergent Selection: Lizards at the White Sands Ecotone. First, a brief summary, taken from portions of the abstract:
"Three lizard species [Aspidoscelis inornata, Holbrookia maculata, and Sceloporus undulatus], distributed along a dramatic environmental gradient in substrate color, display convergent adaptation of blanched coloration on the gypsum dunes of White Sands National Monument." ... "I find species differences in degree of background matching and in genetic connectivity of populations across the ecotone. Differences among species in phenotypic response to selection scale precisely to levels of genetic isolation. Species with higher levels of gene flow across the ecotone exhibit less dramatic responses to selection. Results also reveal a strong signal of ecologically mediated divergence for White Sands lizards. For all species, phenotypic variation is better explained by habitat similarity than genetic similarity. Convergent evolution of blanched coloration at White Sands clearly reflects the action of strong divergent selection; however, adaptive response appears to be modulated by gene flow and demographic history and can be predicted by divergence-with-gene-flow models."

The problems in this study show the importance of basic biology & knowledge of ecology. First off, this is based on mitochondrial DNA and the results show higher gene flow between sample sites for the teiid Aspidoscelis inornata than the two phrynosomatid species, Holbrookia inornata and Sceloporus undulatus. Mitochondrial DNA is, however, a biased marker; since it shows only matrilineal relationships, it will consistently underestimate gene-flow in species with male-biased dispersal. Not a terribly good choice, then, but perhaps defensible because it is far easier to work with than any of the alternatives; however, the deficiencies need to be addressed and they aren't. Most lizards, including phrynosomatids, do have male-biased dispersal; but teiid lizards don't. So we would expect that, even under similar patterns of overall gene flow, phrynosomatids should show more geographic structure than teiids because of differences in sex-biased dispersal.

Second, differences in microhabitat use & behavior, although mentioned, are given short shrift. From the paper:
"A previous study comparing activity patterns between H. maculata and S. undulatus at White Sands found that H. maculata spent more time in open areas and was less closely associated with vegetation than S. undulatus (Hager 2001a)." ... "Therefore, it is plausible that H. maculata is more visible to predators and that selection pressure for substrate matching is higher in this species."
This is an important point. If we want to look at background matching, we need to measure the backgrounds relevant for the lizards. A lizard that spends a lot of its time under bushes needs to be cryptic under bushes, not merely on open sand; even if it matches its background just as well as a lizard spending most of its time on open sand, it will be darker and more strongly patterned. And, guess what, the species that spends most of its time on sand, Holbrookia maculata, is indeed lighter and less-patterned than the other two, and so the observed results fit perfectly with expectations based on what we know of the ecology of these lizards. Moreover, ordering of taxa in order of brightness is the same on White Sands and off: Holbrookia maculata is always brightest, Aspidoscelis inornata is always darkest, and Sceloporus undulatus is always intermediate--a good indication that something more than different facility in matching White Sands substrates is going on. But an important role for microhabitat use and behavior is rejected for, so far as I can tell, no particularly good reason.

A third, and related, problem is poor knowledge of White Sands:
"Second, intermediately colored S. undulatus [and A. inornata!] could be locally adapted to the intermediate substrate color at the margin of the dune field. However, in contrast to the large expanse of pure gypsum habitat, the band of intermediately colored ecotonal substrate is extremely narrow, often only meters wide. Given the likelihood of gene flow across the ecotone in this species and the restricted area of the ecotone, natural selection would need to be implausibly strong to provide an adaptive explanation for maintenance of intermediate color morphs."
I've spent some time wandering White Sands. The basic situation is this: there's a large active dune field with very white sand and small, slightly darker interdunal areas; to the west of this area there are flat, crusty, white, alkali flats; to the north, east, and south, the dunes get progressively smaller, narrower, more vegetated, and slightly darker in color while the interdunes get much larger and significantly darker. These large interdunes toward the edge of the dune area are a major portion of the White Sands area, and are intermediate in color between the active dune field and the soil of the surrounding flats of Tularosa Basin. The "extremely narrow" ecotone is exactly what you see along the road at White Sands National Monument in the area of the Big Dunes Trail, one of E.B. Rosenblum's collection sites, but it is not at all an accurate representation of the situation otherwise. Importantly, Aspidoscelis inornata is very abundant in these large interdunal areas, whereas Holbrookia maculata is not (I haven't seen enough Sceloporus undulatus, OTOH, to have any idea of their distribution). This comes back to the point above: what background is relevant to the lizards? This is determined by behavior and abundance across habitat types and cannot be estimated by simply choosing a half-dozen sites, treating them as monoliths, and seeing how well the lizards at each site match open soil or sand.

And then we have another problem: phenotypic plasticity. We don't know whether or not color differences between White Sands and other populations of these lizards are heritable, and we do know that most lizards, including phrynosomatids, have some level of plasticity in coloration. For instance, a 1958 study by R.E. Bundy & J. Neess suggests that the major factor in background matching by the phrynosomatid Phrynosoma modesta is plasticity.

And now we're down to nit-picking. There are more than three lizards with light-colored populations on White Sands, but the "other two" are never mentioned: Phrynosoma cornuta and Uta stansburiana. I wouldn't bother mentioning this, except that E.B. Rosenblum says: "In this study, I ask how the complete lizard fauna at White Sands has responded to natural selection across a common ecotone." No, this study examines how 3/5 of the lizard fauna at White Sands responds to selection.

In conclusion:
1. The genetic markers used do not provide a neutral estimate of gene flow, and this bias, although fundamental in interpretation of the results, is ignored.
2. Alternative explanations that fit the data at least as well as the preferred hypothesis, that gene flow limits crypsis, are rejected either without good cause or due to poor knowledge of the area.

4 January 2007
Thoughts on sex-ratio in ants:
The usual explanation of sex-ratios in ants goes something like this: In a monogyne colony with a singly-mated queen, queens are equally related to both male and female alates and thus should favor a balanced sex ratio, while workers have a relatedness of .75 to female alates and .25 to males and should therefore favor a female-biased sex-ratio of about 3:1. If queens mate multiply this relatedness asymmetry is reduced (because relatedness to male alates, which carry only the queen's genes through parthenogenesis, stays constant while relatedness to female alates, which now may be half-sibs rather than full-sibs, decreases) and the tendency for workers to favor female-biased reproduction should likewise diminish. If there are multiple singly-mated queens, the relatedness asymmetry remains constant but average relatedness to either male or female alates drops, presumably reducing indirect fitness effects for workers of a female-biased sex ratio. Based on this, in monogyne singly-mated colonies a sex ratio approaching 3:1 is taken to indicate worker control of reproduction, a sex ratio approaching 1:1 is taken to indicate queen control, intermediate values are interpreted as the result of conflict and partial control by each group, selective killing of male larvae by workers is interpreted as a manifestation of parent-offspring conflict between the queen and workers, and so on and so forth.

This explanatory framework is interesting because there is both a fair amount of empirical support for it and some errors in its formulation. One conspicuous absence is the role males may play. Because males are produced parthenogenetically from unfertilized haploid eggs, when a male mates with a queen he will have a relatedness of 0 to any males the colony later produces, and males that could impart genes causing a female-biased sex ratio would have increased fitness as a result; the ideal sex-ratio for males, from the point of view of relatedness in the next generation alone, would be 1:0 (the ideal proportion of males increases from 0 if future generations are taken into account). Furthermore, although queens are equally related to both male and female offspring, the haplodiploid reproductive system of ants means that, all else equal, male offspring, which give rise only to females, will produce only half as many "grandchildren" for a queen as will females, which produce both male and female offspring. So, although an account of the queen's direct, single-generation fitness alone would suggest she should favor a 1:1 sex ratio, when reproduction of the next generation is included the favored sex ratio becomes 2:1. If all this is correct, both males, queens, and workers should all favor a female-biased sex-ratio, although to differing degrees and with substantial variance associated with changes in reproductive structure of colonies.

Now, how to interpret variation in sex-ratio, killing of male larvae by workers, dependence of said killing on the number of mates a queen has had, and all those other phenomena ...?

2 January 2007
Further thoughts on polygyne ants... in Solenopsis invicta the switch to a polygyne colony system has been linked to a single gene (Krieger & Ross, 2002; Science 295(5553): 328-332); this is interesting but not really very informative evolutionarily, beyond establishing that there is a genetic component to the social system. In Linepithema humile, the switch to a polygyne colony system has been attributed to a genetic bottleneck (if all individuals in a population are very closely related, all members of the population may treat each other as kin; Tsutsui et al., 2000; P.N.A.S. 97(11): 5948-5953), to increased costs of competition in the denser populations of the introduced range, and thus selection against uncommon recognition alleles (Giraud et al., 2002; P.N.A.S. 99(9): 6075-6079), or to a combination of a bottleneck and selection against uncommon recognition alleles (Tsutsui et al., 2003; P.N.A.S. 100(3): 1078-1083). However, the last-cited paper undermines any argument for selection against uncommon recognition alleles since it shows that nestmate recognition is learned in Linepithema humile, and that currently existing "supercolonies" of L. humile are being maintained by learned broad recognition in spite of diversity at recognition alleles. The same paper also shows competitive superiority of monogyne colony workers against those of polygyne colonies, which further confuses the situation; competitive superiority of polygyne colonies, however, could still occur if in their introduced range these colonies can overwhelm monogynes through sheer numbers, a possibility supported by the higher nest density and abundance of polygynes compared to monogynes. These results from Tsutsui et al. (2003) furthermore argue against a genetic bottleneck alone causing current unicoloniality, unless the present genetic diversity arose after the recent formation of a unicolonial social structure, which seems unlikely. Another cause of unicoloniality that has been suggested in other ants is nest site limitation: if ant densities are high, good nest sites may all be occupied and queens may have no choice but to attempt to enter existing nests, giving rise to polygyne nests if they are successful.

29 December 2006
I recently read E.O. Wilson's autobiography, "Naturalist". Excellent book. It's also gotten me on an ant kick again. Dangerous. Today's exciting phenomenon of note: a polygynous form (having multiple queens per colony) of the Argentine fire ant (Solenopsis invicta; a.k.a. "imported red fire ant", a name concocted for political correctness) in the U.S. occur at 10-30 times the density of monygynous (one queen per colony) forms, and forms interconnected "supercolonies" without explicit colonial territories. This is odd. According to kin selection theory, one of the reasons you get cooperation in social hymenoptera is that the haplodiploid sex determination system of the hymenoptera produces the rather unusual effect that, if the sex-ratio of reproductives is female-biased, workers are more related to the queen's offspring than they would be to their own. But in a polygynous colony, any given worker may have a relatedness of 0 to the offspring of a particular queen. All else equal, polygyne colonies should be on thin ice; relatedness no longer favors cooperation. But instead, polygyne colonies in this species show greater cooperation, with cooperation extending from the within-colony level to the between-colony level.

Even more interesting, this is not an isolated phenomenon, but a repeated pattern in highly-invasive ants.

28 December 2006
Possible answers to previous questions...
1: Yes; some obvious potential venues of cooperation include population synchronicity (e.g. masting in oaks), fertilization of ovules with non-self pollen rather than selfing, nutrient transfer to conspecifics through mycorrhizae (to the extent that this is under a plant's control, which may be very limited).

Cooperation is a somewhat limited word, though, and traditional preoccupation with altruism may obscure the evolutionary important phenomena. What are of interest to me are any processes that promote success above the individual level, whether they promote success at the individual level or not...

2: No; the limitation is that any genes acting at higher levels must pass through the gateways of lower-level selection first, and since success at these lower levels is so much more direct, obvious, and measurable, higher level selection of all kinds tends to be ignored.

26 December 2006
Question of the day:
Can plants cooperate?

Second question of the day:
Is there any inherent reason that kin selection shouldn't apply above the population or species level?

19 September 2006
More bits of Stebbins; p. 262:

"Hybridization between well-established and well-adapted species in a stable environment will have no significant outcome or will be detrimental to the species populations. But if the crossing occurs under rapidly changing conditions or in a region which offers new habitats to the segregating offspring, many of these segregates may survive and contribute to a greater or lesser degree to the evolutionary progress of the group concerned."

p. 270:

"There is little doubt, therefore, that the majority of the examples of hybridization and introgression which can be foud in plant populations at the present time are asociate with the disturbance of old habitats and the opening up of new ones through human activity.

15 September 2006
Disturbing quote from this article: "If we're not willing to use it [non-lethal weaponry] here against our fellow citizens, then we should not be willing to use it in a wartime situation," said Wynne. [Air Force Secretary Michael Wynne]

I find weapons that are non-lethal but incapacitating very disturbing. They make abuse of power easier to justify--after all, you're not killing anyone--but to think that using nonlethal force is inherently unobjectionable is absurd. And arguing that American civilians--or any unconsenting civilians--are appropriate guinea pigs for weaponry of any kind is downright evil. If we need test subjects--start with Michael Wynne. If he's not willing to use it on himself, he shouldn't be willing to use it on any of the rest of us.

Now more Stebbins quotes; pp. 189-190:

"The common ground of agreement between these definitions may be expressed as follows. In sexually reproducing organisms, a species is a system consisting of one or more genetically, morphologically, and physiologicall different kinds of organisms which possess an essential continuity maintained y the similarity of genes or the more or less free interchange of genes between its members. Species are separated from each other by gaps of genetic discontinuity in morphological and physiological characteristics which are maintained by the abscence or rarity of gene interchange between members of different species. The above sentences are not to be construed as this authors definition of a species, since several different species definitions are possible within the framework of their meaning."

But--isn't it precisely the problem of existing species concepts that they try to limit us to a single axis for discerning species, rather than admitting of several different axes, as Stebbins' sentences above do? Why not embrace such a broad and inclusive definition--merely because it could be subdivided?

p. 202:

"The second alternative [the first was multiple species concepts] would be to recognize that at any given moment in the evolutionary time sale, reproductive isolation is important in keeping distinct only those populations which are sympatric or which overlap in their distributions."

In other words... Mayr's Biological Species Concept is applicable only to sympatric or overlapping populations. This criticism has been hemmed and hawwed over for five decades now, but has never been addressed in a coherent fashion. And it is precisely a multidimensional species concept that will allow us to overcome this problem, as well as those that plague the other species concepts. Why, after all, would we expect groups in multi-dimensional space to always be identifiable along a single axis, like that of reproductive isolation?

11 September 2006
Unrelated thoughts... first, the legacy of September 11th, 2001:

Two wars won militarily in years past, still being lost in every other way imaginable. One a war of revenge, the other... god knows what.

How many thousands killed for this? Or millions--we don't know. How many Arabs equal one American? How many eyes for one eye?

How many enemies made? We learned this lesson, between World War I and World War II. Enemies conquered and then rebuilt become allies. Enemies conquered and left to fester become new and greater threats. When did we forget?

The legacy is death and distraction. Force misapplied and evil still afoot.


And the other topic, Pluto's planethood. There was a letter to the editor in our student newspaper announcing a march for Pluto, in opposition to its demotion, for the honor and memory of Clyde Tombaugh, Pluto's discoverer. But science is not merely a popularity contest; if it were, the accomplishments of scientists like Tombaugh would not be particularly important, but merely historical fads. And Tombaugh's accomplishments were not semantic; they cannot be erased merely by changing a word. Those supporting the march forget, or never knew, these facts.

6 September 2006
Another quote from Stebbins, p. 34:
"All [Dobzhansky, Mayr, & Huxley] agree that species must consist of systems of populations that are separated from each other by complete or at least sharp discontinuities in the variation pattern, and that these discontinuities must have a genetic basis."

This remains essentially the case with modern disagreements on species concepts. The disagreements are not in what species are, but in what is the best axis on which to look for discontinuities.

And Stebbins, p. 35:
"In fact, it is likely that most families in which the genera are well-defined have suffered the extinction of many species, and further that most boundaries between neighboring genera represent gaps left by species which have perished."

The importance of extinction in observed patterns remains often overlooked and misunderstood. In most cases monophyletic taxa, for instance, were previously paraphyletic groups in which sufficient lineages have subsequently become extinct.

Stebbins continues:
"If this fact is kept in mind, then the search for natural boundaries to genera has some meaning to the evolutionist and is not entirely a matter of convenience."

5 September 2006
I keep forgetting to write anything here. Went many places over the summer, now I'm continuing to botanize in the semester, not taking any classes but running the lab for Plant Taxonomy. Recently read several books by Annie Dillard: Pilgrim at Tinker Creek, The Living, For the Time Being, and Teaching a Stone to Talk. All highly recommenended, especially P.a.T.C. and F.t.T.B. I also read a biography of Marcus E. Jones, an early western botanist, by Lee Lenz. Poorly written but worth reading. I just started Stebbins' Variation and Evolution in Plants. Very interesting so far; here's a quote from the first page:

"The hierarchy of categories is a multidimensional pattern of variation in nature, and the gaps or discontinuities give reality to the various categories."

I think (and hope) he means taxa by "categories". This seems to be his usage elsewhere. There are several other interesting quotes in the first few dozen pages that I may put up later.

12 May 2006
End of semester. I prepare to become less productive.

I read "The Foundations of Arithmetic" by Gottlob Frege. I guess I know what numbers are now. I thought I knew earlier. More interestingly, Frege thought he knew earlier; he often uses a rather odd form of argument that puzzles me. The basic form is, in trying to discover the essence of an entity you create some sort of conceptual construct and then compare the properties of the construct with the properties of the entity. You create a conceptualization from which our uses of the entity can arise; but this ignores the basic problem. Either the entity is some pre-existing thing, and its uses arise from it; or the entity is a conceptualization to begin with and it is its uses. We are left with either a mirage or a duplicate.

Perhaps a new conceptualization creates new uses; but then it cannot be judged by its similarity to the old concept.

In specific reference to Frege's explanation of what numbers are, he has either explained the already-known, or created a new concept different from that of number. He searches for depth where there is no depth; 2+2=4 is an explanation, not something in need of explanation.

18 April 2006
I recently read Wittgenstein's "Zettel". Quotes of interest (to me, perhaps others):

p. 70: '"Heap of sand" is a concept without sharp boundaries--but why isn't one with sharp boundaries used instead of it?--is the reason to be found in the nature of the heaps?'

p. 77: 'There are for example degrees of pleasure, but it is stupid to speak of a measurement of pleasure. It is true that in certain cases a measurable phenomenon occupies the place previously occupied by a non-measurable one. Then the word designating this place changes its meaning, and its old meaning becomes more or less obsolete. We are soothed by the fact that the one concept is the more exact, and do not notice that here in each particular case a different relation between the "exact" and the "inexact" concept is in question: it is the old mistake of not testing particular cases.'

p. 123: 'There might be a use of signs made, such that they become useless (perhaps they are abolished) as soon as the bearer has ceased to exist.
'In this language-game the name has the object on a string, so to speak; and if the object ceases to exist, the name, which has done its work in conjunction with the object, can be thrown away.'

And a random thought: math in biology exists to assure uniform analysis and representation of data. Statistics &c. are notational conventions. New methods that are not accompanied by decision rules governing their application are not progress, but undermine the purpose of all mathematical methods. When multiple methods already exist without a means of deciding among them, we have a severe problem. Standardized decision among methods is more important than the question of whether one method or the other is in some sense more accurate.

11 April 2006
Rain!
<insert appropriately joyful exclamatory verse here>

25 March 2006
I took a trip through southeastern New Mexico and then down to Big Bend from the 19th to the 23rd. Those areas have gotten a bit more rain than we have here in Las Cruces, but I guess their rains were too little, too late--not much of anything in flower, and it's pretty crispy out there. This made the supposed goal of the trip, collecting Boechera, somewhat superfluous (though I did still find a few) and so I was forced to entertain myself with merely hiking and photography instead. The things I do for botany...

I've got most of the landscape type images online now. First I went to Wind Mountain, then to Sitting Bull Falls in the Guadalupe Mountains. In between those, I got hailed on whilst trying to sleep in my Tercel. Disrupted the peace of my slumber somewhat. Anyways, I then headed down to Big Bend National Park, visiting the Lost Mine Trail, the Window Trail in Chisos Basin, the South Rim of the Chisos, and finally The Chimneys with adjacent Red Ass Spring. Where I've visited places before, the new and old pictures are mixed together so as to confuse you.

14 March 2006
I gave a talk yesterday resulting from my various species-related cogitations. You could watch the powerpoint file and try to imagine my rather erudite and witty commentary, if so inclined.

8 March 2006
It's National Procrastination Week. I ought to celebrate!

Well, I'll do that next week...

7 March 2006
An addendum to my earlier inchoate mutterings about math in science:
Part of the question is whether math has an explanatory role in and of itself. I think this depends in large part on the audience and is part of the divide between biologists who advocate mathematical primacy and the rest of us. To be blunt, for most biologists math is not explanatory; when you add an equation into a discussion you increases the number of things that need to be explained. Instead, math is primarily a tool allowing uniform and explicit comparison of different sets of data, hence the focus on p-values and so forth. However, those biologists who are highly mathematically competent appear to think that an equation is an explanation, rather than something to be explained. As a result they become rather unintelligible to those not sharing their particular proclivities. This of course does not incline us to become more comfortable with math, but heightens the sense of mathematics as an alien and baffling world.

As a recent example... suppose you're trying to look at how variation in selective pressures influences the ability of genetic variation to persist in a population. This variation can come in two basic forms: spatial variation and temporal variation. In a simple case, we might have two genotypes in a population and two environments that members of a population are exposed to. One genotype gives its bearer greater fitness in one environment, the other genotype gives greater fitness in the other. Those two separate environments might be co-occurring microhabitats (sites closer to or further from a body of water, for instance), or the result of variation between years (years with more or less rain).
If you're a mathematical biologist trying to explain whether temporal or spatial variation is more likely to promote polymorphism, you demonstrate that the set of equations describing spatial variation in selection gives the overall fitness of each genotype as a geometric mean, whereas the set of equations describing temporal variation in selection gives the overall fitness of each genotype as a harmonic mean. Then you conclude that spatial variation is more likely to promote polymorphism.
The number of people to whom that will be an explanation (even with the various equations and so forth inserted, as I have neither the time nor the inclination to do) is quite small and, as it would happen, a non-mathematical explanation is possible and actually rather simple. When there is spatial variation in fitness, if the two genotypes are randomly assorted each one will end up having some representatives in the environment it does well in. When there is temporal variation, the environment is going to be universally bad for one of the two genotypes in any given year. As a result, either of the genotypes is much more likely to get wiped out by a bad year than by a bad microhabitat, and spatial variation in selection is more likely to let both genotypes persist.
This sort of explanation is not only more immediately comprehensible, but makes it more obvious what kinds of preconditions are being assumed and how they might be violated. (For instance, I can figure out how organisms might avoid a temporarily bad environment and upset this reasoning; I can't think the situation through in terms of organisms differing in ways that yield geometric rather than harmonic mean fitnesses!) However, if you read a population genetics textbook, you're likely to see only the mathematical explanation. The way I figure it, if you want to only explain the biology itself, there's no reason to offer anything more than the plain-language explanation. If you want to explain both the biology and how to treat that biology in a more precise mathematical framework, both explanations should be provided along with brief exposition of the relationship between the two.

5 March 2006
Spring hasn't exactly sprung, but I think it's done about as much springing as it intends to. I was on the west side of A Mountain yesterday & saw six species flowering: Baileya multiradiata, Thymophylla pentachaeta, Dimorphocarpa wislizenii, Nerisyrenia camporum, Physaria gordoni (or maybe fendleri; they look rather too similar), and Streptanthus carinatus. Wandering around Las Cruces today, I also saw some Sphaeralcea, Phacelia integrifolia, a couple clumps of Eschscholzia, some kind of Erigeron, & a lone Rafinesquia. Not quite last year's display, but at least we're getting some stuff blooming out there.

20 February 2006
I just got tickets to fly to Indiana in May. Disturbing as the idea is, I miss the place. I've also been reading more Wittgenstein recently, and trying to figure out what the purpose of math is; I suppose I'm supposed to just take the importance of math on faith and dutifully study it, but even if I take it as given that math is important I still need to figure out why. What purpose, exactly, does it serve? In what situations do I need math, and in what situations is the math superfluous or even obfuscatory?

As it is, there seem in biology to be two groups: A) those who always assume that a mathematical explanations is not only helpful but necessary and B), those who don't understand the mathematical explanations given by those in group A and view math as just a set of equations that you have to plug things into every now and then. Neither group has analyzed the situation in any coherent fashion. Those in group A generally can't explain what exactly the math is doing for them, simply insisting that it is necessary. Those in group B just wish they didn't have to bother with the whole thing. My tendency is to fall into group B.

So I'm reading Wittgenstein's "Remarks on the Foundations of Mathematics" and thinking things over. My impression so far is that a cogent criticism of the group A position is possible, and that the current group A position is in part an obfuscatory force that has created the group B position. There are people who don't understand the purpose of mathematical explanations because those who do understand those explanations both haven't been able to coherently explain their purpose and have inflated their scope far beyond reality... instead of a useful tool, math in biology has become a priesthood. I hope at some point to get a criticism of the group A position worked out at least in its general outlines, right now I have a rather disjunct set of ideas.

30 January 2006
I submitted a letter to the editor for the journal Taxon, which they'll be publishing. Not a hugely significant publication (letters to the editor aren't peer-reviewed, for instance), but my first publication in a scientific journal nonetheless. It briefly discusses an argument for the inclusion of paraphyletic (including an ancestral form and some but not all of its descendants; as opposed to monophyletic groups, which include an ancestor and all of its descendants) taxa in classification. I won't go into it in detail here, but might put up a citation once it's out into the world.

I've also been spending some time thinking about the concept that species are individuals. Often this is phrased as "individuals in the philosophical sense" or "individuals in the logical sense"; a problem should be obvious: definitions of "individual" will vary between philosophers and between logicians, and none of the various possibilities is generally known within the biological community as a whole (or, for that matter, in any community other than the philosophical or logical community), and so we've got a phrase whose referent is both ambiguous and largely unknown to the audience of interest.
Furthermore, it's not at all clear that there is any sort of native interpretation for "individual" in this context. Application of the word, then, is solely by analogy. Given that the analogy is, as mentioned, to an unknown concept, this isn't very helpful. Consider trying to describe the town of Lordsburg, New Mexico, to a New Yorker by saying it's like the nearby town of Deming but smaller and without the Florida Mts. nearby. At this point, unless you have found the exceedingly rare New Yorker familiar with New Mexican towns, you now have to explain what Deming is like in order to have accomplished anything by the comparison of Lordsburg with it. So why not just explain Lordsburg in the first place?
Why explain by analogy to an unknown, if direct explanation is possible?

More explicitly, one of the things people have hoped to accomplish by calling species individuals is to convey that they are historical entities, with distinct beginnings and ends and perhaps some modifications in between. This is opposed to earlier conceptions of species as classes; categories are (in some sense) timeless, unchanging, etc. So then we wonder: is it obvious to the average biologist that, by calling a species an individual, we mean that it is a historical entity of some kind? The answer seems to be "no", since authors wishing to make this point feel it necessary to spell things out and say something like, "Species are individuals; and by "individual" I mean a historical entity." Then... is invoking the "individual" concept necessary to make this point? Again, no--we can either explain directly, by describing characteristics of species (an originating speciation event, eventual extinction) which establish historicity, or we can even come up with temporally-limited classes (e.g., "a species is a class of organisms having members after time x and before some future time y). Either of these is a viable alternative to the individual-based argument, though the latter is not a particularly elegant or intuitive way of doing things. Well, then... surely we at least have made some progress by establishing that species are historical entities, even if the individual-based argument is not the only one, or even necessarily the best one, right? Again, I don't really think so... the "species are individuals" concept first came up in the 1970's, by which time it would have been very hard to find a taxonomist who wasn't aware of basic evolutionary events like speciation and extinction; we already knew species had temporal limits, so calling species individuals in order to establish those temporal limits seems rather like a clarification desperately in search of a confusion.

More generally, there are no intrinsic limits to the conditions that could be set on the membership of a class. Any claim about species that could be accomplished by describing them as individuals could be accomplished by describing them as classes. It might be more difficult, but this is just a pragmatic argument and the "species are individuals" proponents think they are making an ontological argument.

21 January 2006
Most interesting website I've come across this month:
NOA A: Precipitation and Temperature
Through this you can get maps of the US showing things like: precipitation, including absolute and percent deviation from normal, for everything from the last week to the last year; similar maps for temperature; and changes in temperature and precipitation over the last four decades.

I also just re-read Ed Abbey's "Desert Solitaire" and read "Wittgenstein's Poker" by Edmonds & Eidinow (about heated disagreement between Wittgenstein & Popper; though there's a reason Wittgenstein is in the title). Both highly recommended. Here're a few quotes of particular interest to me at the moment from "Desert Solitaire":

page xi of the introduction:
"For my own part I am pleased enough with surfaces--in fact they alone seem to me to be of much importance. Such things for example as the grasp of a child's hand in your own, the flavor of an apple, the embrace of friend or lover, the silk of a girl's thigh, the sunlight on rock and leaves, the feel of music, the bark of a tree, the abrasion of granite and sand, the plunge of clear water into a pool, the face of the wind--what else is there? What else do we need?"

page 30 & 31:
"I've had this tree under surveillance ever since my arrival at Arches, hoping to learn something from it, to discover the significance in its form, to make a connection through its life with whatever falls beyond. Have failed. The essence of the juniper continues to elude me unless, as I presently suspect, its surface is also the essence."

from page 273:
"Where is the heart of the desert? I used to think that somewhere in the American Southwest, impossible to say exactly where, all of these wonders which intrigue the spirit would converge upon a climax--and resolution. Perhaps in the vicinity of Weaver's Needle in the Superstition Range; in the Funeral Mountains above Death Valley; in the Smoke Creek Desert of Nevada; among the astonishing monoliths of Monument Valley; in the depths of Grand Canyon; somewhere along the White Rim under Grandview Point; in the heart of the Land of Standing Rocks. Not so. I am convinced now that the desert has no heart, that it presents a riddle which has no answer, and that the riddle itself is an illusion created by some limitation or exaggeration of the displaced human consciousness.
"This at least is what I tell myself when I fix my attention on what is rational, sensible and realistic, believing that I have overcome at last that gallant infirmity of the soul called romance--that illness, that disease, the isidious malignancy which must be chopped out of the heart once and for all, ground up, cook, burnt to ashes... consumed. [...] In answer to the original question, then, I find myself in the end returning to the beginning, and can only say, as I said in the first place: There is something about the desert..."

There are parallels in Wittgenstein. The last sentence of the "Tractatus Logico-Philosophicus" is:
"Whereof one cannot speak, thereof one must be silent."

& the most interesting section of "Wittgenstein's Poker", to me, is the following from page 158:
"The theory that meaningful statements have either to be analytic (where truth or falsity can be assessed by examining the meaning of the words or symbols employed--"all triangles have three sides") or open to observation became known as "logical positivism," and many logical positivists [i.e., the Vienna Circle] took the Tractatus as their Bible. [ ... ] The total accuracy of the Vienna Circle's interpretation of the Tractatus is another matter. Wittgenstein had parceled up propositions into those which can be said and those about which we must remain silent. Scientific propositions fell into the former category, ethical propositions into the latter. But what many in the Circle misunderstood was that Wittgenstein did not believe that the unsayable should be condemned as nonsense. On the contrary, the things we could not talk about were those that really mattered. Wittgenstein had spelt out the point of the Tractatus in a letter to a prominent avant-garde editor: 'The book's point is an ethical one... My work consists of two parts: the one present here plus all that I have not written. And it is precisely this second part that is the important one.'"

The logical positivist interpretation had been mine, as well, but this view seems much better... I think I need to read & re-read some more Wittgenstein.

20 January 2006
Further comments on Jared Diamond's "Collapse":
In reference to blaming businesses for pollution and so forth--it is a duty of the public to hold businesses accountable for unethical, immoral behavior in which the public is harmed for private profit. Removing companies from the potential for blame in their pursuit for profit above all else erodes the ability of the public to fulfill this duty. As much as blame is an imperfect and often ugly concept, it remains a necessary part of the process.

This is part of a larger problem; while Diamond is correct that part of being able to adapt to new situations, culturally, is the ability to jettison cultural values that are no longer functional and now hinder progress, he neglects the other half of this, that we must also create new cultural values or, better yet, coopt old values to perform new functions in our society. He seems to see cultural values as primarily a hindrance, whereas they are also a tool of progress. Taking this into account means we need new kinds of ethics and morality to allow us to evaluate new possibilities and prohibit harmful practices that weren't previously important, not the rejection of parts of current morality that aid us in establishing accountability for new harmful practices.
Ideally we would react in a purely rational fashion rather than relying on emotionally-charged and often inaccurate moral constructs but, realistically, this will not happen at a societal level.

Regarding TV pundits:
A couple weeks ago, a Republican spokesperson rejected current Democratic resistance to (or at least lack of enthusiasm for) Bush's (via FBI) investigation of the spying leaks as represeting "selective outrage" compared to the previous strong advocacy of investigaion of leaks involving Wilson's wife's identity as a CIA operative. Rhetorically this is a good move. It has enough truth to be convincing and awkward to refute, but enough falsity to be useful for deception.

The ideal response in terms of brevity and comprehensibility (and thus ability to convince) would be to point out that it is not the Democrats but both parties that have switched sides in the two cases; the Republicans can't attack the Democrats without atacking themselves. The downside is that, likewise, the Democrats leave no room for attacking the Republicans, and the whole thing is made to look like just another partisan squabble.

The better response, in terms of accuracy and cogency but too long and complicated for a sound byte, is that the Wilson leak appeared to represent a violation of law and erosion of natoinal security by the administration in order to bully a political opponent. And, likewise, the administration spying we learned about through the recent leak also represents an abuse of power for political gain. In both cases, Democrats are objecting to presidential abuse of power; there is no inconsistency, it's just the role of intelligence leaks in the two cases that changed. In the Wilson case, an investigation of the leak would serve to expose and potentially react appropriately to an abuse of power. In the spying leak, an investigation of the leak would serve a diversionary purpose, obscuring the abuse of power and decreasing the possibility of a correct response. But in both cases the goal of these Democrats was the same, holding the administration accountable for illegal or immoral behavior. This is one of the duties of congress, and congressmen cannot be faulted for attempting to fulfill it.

23 December 2005
You know what's a threat to national security? A president we can't trust with the power to defend our country.

Impeach.

And keep on impeaching until we find a real American in this administration. Someone, anyone, interested in leading the country rather than duping it, trashing it, and milking it for cash.

18 December 2005
Highly recommended reading:
What You Can't Say

The gist is: there are moral fashions as well as clothing fashions, and they restrict not just what we can say but what we think. He then goes on to discuss various ways in which those moral fashions and their influence can be discovered. Of those, one is particularly ironic--that arbitrary moral fashion is probably at work when we find something unspeakable that most other human societies have found perfectly acceptable. The irony is that this suggests we can avoid the effects of society-level conformity by embracing species-level conformity. However, the most interesting way of identifying the effects of moral fashion that he suggests is that whenever a statement, act, etc., is denigrated through labelling rather than by demonstrating it to be incorrect or harmful, odds are moral fashion rather than reasoning is at work. When a good argument can be presented, it is always more compelling than labelling; hence labelling is a fall-back in the absence of compelling argument.
My favorite example of this is the word "intolerant", because it is an ironic example. When someone accuses you of being intolerant, what they mean, of course, is that they are unwilling to tolerate your (intolerant) viewpoint. Maybe they have good reasons for doing so, but those reasons are not demonstrated by the label "intolerant", which is given simply as a proof of hypocrisy. The problem, of course, is that a great many things people say and do are intolerant and some of those should be rejected for that very reason. When, for example, the intolerance is based on moral fashion rather than reasoning. And round and round we go... the invalidity of the labelling argument is hidden by the fact that it often arrives at the correct result.
Another problem is that, when moral fashion happens to be yielding correct answers, the labelling argument is typically much quicker and effective than direct rebuttal. It's hard not to use it. Would you rather spend weeks digging up and analyzing studies on the comparative abilities of men and women in management situations in order to try to justify an equal-opportunity policy, or just reject the alternative as sexist? The situation is further complicated by the fact that, in practice, shorter arguments are more convincing than long arguments.
This is one of the many cases where using invalid argumentation is a rational, productive approach. It requires the expenditure of less time and energy, and the results are more convincing. But, then, how do you reject the cases where using invalid argumentation is deceptive, counter-productive, irrational?

Another essay linked from www.paulgraham.com:
A Civic Duty to Annoy
I agree with the sentiments, but after reading a few similar essays linked from the "What You Can't Say" article, I find myself trying to come up with arguments in favor of conformism...

14 December 2005:
I went to the Pyramid Mountains, south of Lordsburg in Hidalgo Co., NM, with Jeanne Tenorio on Sunday. Nice little mountains, mostly reddish/tan rhyolite but with various bits of other stuff in there, too. I was hoping there might be some good ferns, but things were pretty dry and all I saw were Pellaea truncata and Cheilanthes lindheimeri. My main reason for going was simply that I hadn't been and, despite having driven by them several times on I-10, hadn't even noticed them. Turns out there's not just a whole lot to notice. A good place for aimless wandering nonetheless, and with excellent views of the Peloncillo and Dos Cabezas Mts. to the west.

I'm now reading "Collapse: How Societies Choose to Fail or Succeed" by Jared Diamond. So far an excellent book. He espouses a viewpoint I've seen before and disagree with, though. He suggests that, since the purpose of a business is to make money, we can't really blame them for doing so in the most efficient manner possible, even when that happens to involve poisoning land, water, and people. There are a few ways to respond to this:
1. If we can't blame the businesses for doing their best to make money, since that's their job--well, they can't blame us for wanting to blame them for their actions, either, since that's part of our job. Diamond does mention that holding them accountable is part of our job, but still seems to want to reject the idea that the businesses can be blamed for screwing things up for the rest of us. While blame probably isn't the most useful concept in this context, trying to separate blame from accountability and rejecting the applicability of blame comes awfully close to rejecting accountability, too. For those thinking moral culpability isn't applicable, it's probably best to just not talk about moral culpability rather than attempting a one-sided rejection of moral culpability for businesses. If talking about moral culpability isn't helpful in the situation, then neither is any attempt to reject moral culpability, either.
2. The purpose of a business is to make money, true. But this doesn't mean that it is in the best interests--even from a purely financial perspective--for a business to try to avoid being accountable for damages it causes. For instance, there's an ASARCO copper smelter in El Paso. It was closed earlier because low copper prices made it a losing venture. Now copper prices are higher, and ASARCO wants to reopen, but they are facing strong opposition because of earlier pollution problems and an unwillingness on ASARCO's part to either redress past pollution wrongs or to take measures to prevent further pollution. Trying to avoid accountability is now keeping ASARCO out of business in El Paso.
3. The "we're just doing our job" defense has been tried before. The Nuremberg War Trials come to mind. While the crimes involved are totally dissimilar in kind and scope, the arguments are not--a crime is a crime is a crime whether it's part of your job or not. If making money hand-over-fist by mining requires a business to destroy other people's livelihoods, lands, and health then it's not acceptable. That it might be part of a business accomplishing its goals just doesn't matter.

26 November 2005:
I'm a binge-reader, I think. Recent books:
Centennial, James Michener
Rising from the Plains, John McPhee
Encounters with the Archdruid, John McPhee
Guns, Germs, and Steel, Jared Diamond
Blood Brook, Ted Levin
The Flight of the Iguana: A Sidelong View of Science and Nature, David Quammen
And I'm about halfway through The Boilerplate Rhino: Nature in the Eye of the Beholder, also by David Quammen.

Brief thoughts on a couple of those:
Centennial was one I didn't have too high hopes for starting off, since the front cover announces the book as the basis of some sort of "spectacular" televised series, and the only other thing I know about Michener is that "South Pacific" was also based on one of his works. So I expected populist drivel, to be perfectly blunt. But I read it anyways, and the short version is: it'd be an excellent book if you tore out the first 200 pages or so. Don't worry--that still leaves you with about 800 pages of reading. That first section consists primarily of narratives of the hopes and desires of non-sentient animals and confused accounts of evolutionary history; the first can't be done well, the second just isn't done well by Michener. The rest, though, is a brief history of the United States as it relates to Colorado, and is very well done, especially in its surprising honesty. Though I wouldn't've expected it in any TV-ready book, he doesn't shy away from discussing the many unpleasant and unflattering aspects of American history. The view you come out with is one of the West having been made by believable, understandable human beings who made their share of mistakes, rather than the sort of sanitized, glorified cowboyism that usually infects accounts of the American West.

Blood Brook was interesting for similar reasons. Large portions of it are the sort of intimate observations of wildlife that usually end up off in Bambi-land, but instead Levin maintains an unusual degree of equanimity and, when you least expect it, is suddenly discussing--with equal equanimity--things like eating pileated woodpeckers, cleaning rattlesnake skins for mounting, and so forth. He demonstrates by example a pragmatic approach to nature that sees us as part of nature without anthropomorphizing nature or hiding its unpleasant aspects and, moreover, without hiding or denying our unpleasant aspects.

24 November 2005:
Random thoughts:
There's no good word for the people who were in North America before Europeans arrived. "Indian" is hopelessly inaccurate, though perhaps useful in demonstrating European ignorance. "American Indian" is self-contradictory, though it does at least avoid some confusion. "Native American" I object to simply because I was born here and am just as native as anyone else, yet I'm not a "Native American". Sure, some people's ancestors were here a lot longer than mine, but I've never been able to take the idea that ancestry determines a person's identity seriously. Culture is far more relevant in identity; and while Indians have had cultures here for much longer, and cultures much more intimately associated with the area than any culture from Europe, there are still problems with calling Indians "Native Americans" in a cultural sense of nativity--the pre-European cultures of North America are, for the most part, nonexistent. And North America's changed a lot, too, so cultures that were American would no longer fit. The simplest solution would be to use whatever word they had for themselves--but Indians never had a collective word for themselves. Which brings up another point: the Indians were never a cohesive group, something which referring to them by a single name obscures.

We are dependent on cars because we create cities that are unlivable without them. This is the purpose of a zoning board.
The incomprehensible corollary: those furthest from the city depend most on cars.

On a related note, from the point of view of botanizing, hiking, etc., cars are a mixed blessing. With them, we can go far to experience new places. Because of them, we have to go far to experience much worthwhile.

I come across a quote from William Blake, in "The Marriage of Heaven and Hell" today:
`One law for the Lion and the Ox is Oppression.'
By this standard, modern public schooling is often oppressive; and I agree. Unfortunately, further exploration of the concept leads into disquieting areas. The basic problem is: who can we trust to determine who the lions and oxen are? and who decides what is appropriate for each?
Is our choice between oppressive uniformity and oppressive prejudice?

20 November 200