Ampliatio and the Arbitrary Animal Preserve

The little blobs of orange in the image above (click the image to to enlarge a bit) are monarch butterflies, which winter in great number in the trees of Natural Bridges State Beach in Santa Cruz. Natural Bridges contains the only dedicated butterfly preserve in California.

In recent memory there were "bridges" at Natural Bridges, archways carved in the little promontory of mudstone rising on the south side of the lagoon where Moore Creek seeps into the Pacific. The larger of the two arches, in accordance with the long-term geology of the situation, collapsed one year in a particularly forceful storm. A single smaller bridge remains, visible as a shadowy semicircle above the waterline on the rock. The plural of "Natural Bridges" is earned by ampliatio, as discussed previously.

Lake Lexington, November 2007

Lake Lexington is a reservoir in the Santa Cruz Mountains above Los Gatos, California. It's part of the Santa Clara Valley's water system. They've drained it to do some work.

You can see the brown interdicting mound of the dam in the distance. Normally the water would reach about halfway up the dam, and lap the ankles of the eucalytpus on the surrounding shores.

Fire-tested Argument

Then you call on the name of your god, and I will call on the name of the LORD: and the god that answers by fire—he is God."
[…]
Then the fire of the LORD fell, and burned up the sacrifice, the wood, the stones, and the soil, and also licked up the water in the trench. When the people saw this, they fell prostrate and cried, "The LORD, –he is God, The LORD, –he is God!"

Then Elijah commanded them them, "Seize the prophets of Baal. Don't let anyone get away!" They seized them, and Elijah had them brought down to the Kishon Valley and slaughtered there.

You can raise all the intellectual challenges you want about faith and the origins of the universe, but at the end of the day, you have to worship the god who can set you on fire.

We like to think Elijah stood in front of the howling column of heavenly fire, straightened his robes, turned to the crowd and said, "Thus, my opponent's argument falls." Then, he finished the debate in the way that all debates should be finished: by having the losers slaughtered.

— David Wong, The 9 Most Badass Bible Verses, via Scott McLemee's Quick Study

Long ago in rhetoric the "Shut up about that" rule was concieved as an alternative method for effectively striking specific people and groups of people and what they might have to say from the list of those who could continue to argue the given point. Every formal argument has such a rule. Slaughtering the losers does directly ensure that their argument will go unheard in every case, and the "Shut up about that" rule in rhetoric cannot hope to be as utterly terminal as that, however much it hopes to achieve the same end, the silencing. As the volume of nattering coming from those under the injunction of the "Shut up about that" rule reaches its critical peak, the probability of their ending in the Kishon Valley increases as well, sad to say.

The Great American Novel vs. The Death of the Novel, a progress report

Time seems to be running out for the appearance of that hopeful monster, the Great American Novel, which was a project first bruited about in the early decades of the twentieth century and never taken to heart more tenaciously than by Norman Mailer, who died recently without quite realizing his own ambitions in this regard.

I'm sure Mailer was aware that The Executioner's Song is a magnificent book, and that his own high regard for it would be shared unfailingly down the ages by those who read it. And yet in the end he felt he hadn't created the thing, the Great American Novel that every novel writer of his generation had been led to believe was out there to be had.

Well, it was always more of a goal than a destination, The Great American Novel, and it doesn't even come up much anymore, really, even in the context of some wistful plan to throw down everything and devote oneself to art. People would most likely opt for music or acting these days if it came to that. The people who make novels have their own good reasons for writing them, but I don't think many novel writers nowadays are solely motivated by a desire to make that singularly great American one that once seemed possible in the back of the mind of many, and on the tip of the lip of Mailer for most of his career.

Mailer literalized the hunt for the Great American Novel as an agon for writers with their dedicated talents jostling for its prize, competitors for the thing that just might be had, might be made by dint of the superior effort of the very best of them, just then as the era of the Death of the Novel was beginning in earnest.

The Death of the Novel has been going on for decades now and it gets more press these days than talk of the Great American Novel does. Well, of course, it's a terrible loss for all concerned, the Death of the Novel, and it's only fitting that anyone with any sensitivity at all should pause to say a few words over the corpus, which was such a fine fit art in its day, now dying off, killed by offspring, just as it assisted in its own day in the Death of Poetry. Ah, well, in all the decades since the conclusive end of the form was first discerned, many sobering words on the subject have been announced with all the niceties of thoughtfulness and remorse that the occasion requires, and many wonderful novels have been published, but mostly, it is taking so long to complete that the Death of the Novel, too, seems more likely a goal than a destination. Whether it can be reached before the Great American Novel is uttered remains an open question.

Arbitrary Animal Blogging

Brown Pelican, Santa Cruz, 2007


Golden Tamarin, Seattle Zoo, 2007

Water music

How alive this instrument is.

Over the course of nearly ten minutes, on its home acres, where influential heat may seasonably evaporate or effluential rain may fill to the lip the bowls of the jal-tarang, the tuning of each bowl must change as the amount of water in each bowl changes in the course of a performance. The tuning of each tune is itself liquid, in league with the liquid melody as made from the bowls that day. I suspect the jal-tarang player is intimately familiar with this eventuality, and has the well-trained knack for adjusting play accordingly.

Lionel Hamton must make do with a related instrument whose struck tones and intervals are at least nominally invariant:

Quotidian still not written in such a way as to be plainly understood, study says

Sad, really.

The selling price of number 762 has yet to be determined

Barry Bonds' No. 756 to be branded with an asterisk and sent to Baseball Hall of Fame

By RICK FREEMAN, AP Sports Writer
September 26, 2007

NEW YORK (AP) -- The ball Barry Bonds hit for his record-breaking 756th home run will be branded with an asterisk and sent to the Baseball Hall of Fame.

Fashion designer Marc Ecko, who bought the ball in an online auction, set up a Web site for fans to vote on the ball's fate, and Wednesday announced the decision to brand it won out over the other options -- sending it to Cooperstown unblemished or launching it into space.

Man Scorns What is Not So, Controversy Erupts

Mainly P.Z. Myers uses his web site Phayngula to bring down the hammer of thor on anyone god-deluded enough to offer up organized religious blather about evolution in public.

It's not uncommon for supportable facts about the one thing or the other to be challenged by the vigorous interposition of the immediate announcement of some unsupportable assertion about the matter springing from the resolute lips of those compelled for their own good and sufficient reasons to resist the fundamental imposition such facts represent on their understandably favored view of everything.

As a matter of practical humanity it's personally difficult to resist the inclination to adhere to the favored view, for all the good it generally does, with whatever amount of tenacity seems appropriate.

Those bothered most by assertions of supportable facts sense a threatening move on the part of those facts not only to shift the position of their favored view with those facts, an accommodation most people might begrudge is due, but to dislodge it entirely from what was previously understood to be its favored precinct, like an abalone in the shallows of the sea popped off its rock by the actively advanced pry bar.

Such is the case with people presently driven here in the United States to create their creation science or spawn their intelligent design in heartfelt reaction to the dull threatening realities of evolution by natural selection, hoping to see their beliefs substituted for the evidence at hand, particularly when it comes to the approved store of knowledges of the nation being parceled out to our nominally educable youth in public schools across the nation these days.

Supportable facts are always the rub in foundational arguments such as the ongoing foundational argument for evolution these days between people who know something about the supportable facts like P.Z. Myers, the biologists and geneticists and geologists and paleontologists and their kind, versus proud groups of god-deluded citizens who insist there must be somewhere in this fact-based narrative of life on earth to shoehorn in the unsupportable assertions of their own understanding of its creation as variously written in their variously holy books, none of which narratives of creation can be true unless all the others are false, creating a truly dramatic and admittedly absorbing Mexican standoff of unsupportable foundational assertions against which the supportable facts of people who know what they're talking about can easily enough go ignored at times unless they're promoted as vigorously as they are by folks like P.Z. Myers.

People who know what they're talking about have been actively arguing evolution's merits on the internet, pushing back against a lot of compulsively spread hooey about the matter, for a long time. The Usenet forum talkorigins.org. began in 1986, and it's far from finished going on about evolution. Undeniably, if anyone is to say anything useful about evolution at all in light of all the argument about it collected there at talk.origins over the years, they should at least show that they're familiar with the collected shape of that argument, with what's been gone over again and again at talk.origins down the years, the supportable facts of the matter, unless of course understandably enough they merely wish to say whatever unsupportable something or other rushes to their lips in the heat of what they recognize as a fundamental assault on their favored view.

P.Z. Myers himself, aside from being a Professor … of Science!, is among those who's spent a good amount of time on the internet distinguishing the supportable facts from the unsupportable assertions of evolution by natural selection in the well-established argument laid out not only at talk.origins over the years, but, with the advent of the world wide web and blogging software and all, such sites as Panda's Thumb, where I suppose I first encountered P.Z. Myers's writing.

Panda's Thumb was and is a weblog published by a group of academics who have a command of the supportable facts of evolution by natural selection and a taste for laying into the claimed "science" of the proponents of Intelligent Design, which represents the latest expression of the continuing outcry of people really fundamentally challenged by the crimp all this evidence of natural selection puts in their favored god-deluded view. I suppose, without ever having bothered to find out, that the blog's name is a reference to Stephen Jay Gould's popular book of the same name.

Myers is a biologist, a professor of the stuff at the Morris campus of the University of Minnesota, giving him a vested interest in seeing that god-deluded claims don't interfere with the functioning of his profession. His blog Pharyngula is well-visited.

Often enough the comments attached to the regularly updated writing of Professor Myers posted there at Pharyngula are awash in outbursts of text from those who feel most keenly the contradiction to their favored view embodied in evolution by natural selection, outbursts dealt with summarily by P.Z. Myers and the band of others who've joined there in an ongoing correspondence, inhabiting a public space where the inevitable ongoing intrusion of unsupportable assertions into the argument for evolution by natural selection can be given the focused back of the public hand by those who know their supportable facts and all.



I admit I'm moderately uninformed on these matters myself.



Once in awhile P.Z. Myers puts down his cudgel and resorts to writing down the supportable facts of his craft, the science of biology. Some time ago he wrote what must have seemed to him a brief overview of the role of the hox genes in the structural development of embryos, no doubt gathered from all the notes he's piled up over the years representing his developing understanding of the subject, such as it may be. I'm not sure that Hox genes are the focus of P.Z. Myers's interest in biology. They may be just something he knows about as a matter of course, being a professor of the stuff.

It's just as well that he writes lucidly on the subject, because explaining the intricate workings of Hox genes involves marshaling a lot of complicated general knowledge, of DNA and chromosomes and embryos and such, and then adding to those complications the specific complication of how Hox genes themselves physically fit into that general picture, with all the basic good they do regulating the embryonic development of the physical framework of the beast that owns them. Hox genes ensure that the front of the beast and all its associated bits goes here, the mid goes here, and the back end with all its trailing matter goes back there behind, all according to the Hox genes owned by the beast.

The Hox genes, which are not one strand of genes, but a whole complex of sequentially linked chains of like genes on the chromosome, sit on the chromosome directing the eyeballs toward the head and the asshole toward the back as fits the generally understood development of the beast in embryo. The paired parts of the bilaterally organized beast, if so organized, are sent their respective way by the Hox genes as well.

Hox genes were first testified to by an observation of anomalies in their normal workings, in mutations that made an antenna where the leg of a fly should be (antennapedia), for example, or the eye of a crustacean replaced instead by an antenna, or where a petal should be, a stamen.

I imagine generations of post-docs have played this trick and others like it on drosophila lineages, breeding whole misshapen batches of the things, putting an antenna where the leg should be or displacing the eye from here to there on the little beasts to confirm their own understanding of the techniques available to their craft which make it possible to reveal the curious play of the Hox genes in regulating the general disposition of the bodyparts, fore, mid and aft. The weight of supportable facts about Hox genes engendered by all these intrusive observations into the formal structure of drosophila is considerable, from what I understand.

Speaking of history, one of the things we can do with a phylogenetic analysis of the Hox cluster is see fascinating aspects of our ancient history. Since the genes are conserved, we can map correspondences between them within a lineage and in comparison with other lineages. We can surmise where duplications and deletions occurred, and most interestingly, since the genes are associated with morphological regions of the organism, we can speculate about how new additions to animal morphology occurred.
— P.Z. Myers at Pharyngula, on useful speculations

I do wonder about the ocean sunfish, though.

On my first marveling view of the beasts at the Monterey Bay Aquarium recently, I couldn't help but think of the first of the two posts written by P.Z. Meyers on the subject of Hox genes, which I'd idly glanced at and most certainly only partly comprehended some time before going to the Aquarium, and idly speculated while I watched them circulate in their huge tank of water, based only on my glancing familiarity with the facts of the matter, that the Hox genes of ocean sunfish must have some say in the abrupt wrapping up of the beast's form, which by most accounts of a fish would taper off to the agreeable formality of tail, but instead in the ocean sunfish comes to its curious bulbous compact halt just where the finality of a tail and all its associated bits might be expected to begin in what we commonly presume to be the layout of a fish. That the ocean sunfish has no scales is only a subsidiary marvel compared to its unique aft. It's just not a tail back there at all, by any measure.



But I don't really know if this truly marked divergence in the sunfish reaches right back into the nature of its Hox genes, snipping off the tail right there in the process of resolving the most basic inclination of its oriented parts, diverging before the tail even has a chance to be a place to put parts on a sunfish, or whether the tail that might be advanced by those genes is turned to its other end by the intercession of the successful play of some other bunch of genes, Hox or not, going on about their own simultaneous chemical business there in the embryo. If it's the Hox genes that are responsible, I can only say that the ocean sunfish must carry a highly distinctive bunch of them to do the remarkable job of rounding off it does.

Veterans Day Observed

The price of war is tallied one heartbreak at a time.

leafpile one and two

Moderately Uninformed

I know little enough of science. I have a small store of the basics, but with all the distractions have never delved deeply into any of its parts. I can express the distinction regularly, if somewhat elliptically, between the accelerations of Newton's Second Law of Motion and the dissipations of the Second Law of Thermodynamics, and "iff" pressed can perform many of the basic operations of algebra, Euclidean geometry, and sums. I can listen to the arguments being successfully carried along in their discourse by scientists who seem to know what they're talking about with what I consider passing comprehension, to the point of getting the drift of the thing pretty much, the gist which, without further study on my part, I'm happy enough to carry away from any of science's bailiwicks.

From time to time the gist of what I've brought away of the drift of the argument of scientists exposes some prior misapprehension of fundamental processes of nature on my part which has led me to entertain up to that point counterfactual suppositions about the the way things actually work, suppositions which must be sloughed off of course if the gist of what people who seem to know what they're talking about is to be entertained instead. But most often there is no prior misapprehension to contend with at all, since I lack prior thought on the matter brought to my attention by the discourse of scientists to begin with.

I find all this talk of evolution, for example, with its entailed stuff of natural selection, plausible enough. Much of what I've ever read about evolution was written by Stephen J. Gould, the late paleontologist and popularizer of science. His monthly essays for Nature magazine, collected over the years in a number of books, are a marvel of American literature, spinning out in an episodic way the history of the idea of evolution from its first bruiting about to its abrupt efflorescence in the work of Darwin and Wallace in the mid-1800's, and on even unto the contested fruit of the mature idea of it in our own present day.

Often enough Gould's essays recount stories of scientists whose ideas were influentially misconceived to begin with or influentially misrecieved by the intended audience when finally communicated, and all the bother entailed by either alternative. I just generally like this kind of story, and have been pleased to follow Gould's tellings even through the choking thicket of unavoidable terminologies that spring up everywhere in them, being stories of science and all.

My wife, noticing that I've collected most of Gould's popular writing over the years, bought me Punctuated Equilibrium for Father's Day. Many of the arguments made favoring the idea of punctuated equilibrium in that book are anchored in just the sort of unavoidable terminology that shows up in his writing for a general audience, except here, being an excerpt from an even more compendious attempt to summarize with some rigor the view of evolution he argues for in a book called The Structure of Evolutionary Theory, the unavoidable terminology is unceasing. It's in every paragraph.

Gould and his partner, Niles Eldridge, the fellow who actually had the idea of punctuated equilibrium but wisely left the writing of it up to Gould, published a famous paper in 1972 that set a good fundamental argument going in the natural sciences about the true shape of evolution.

Gould came up with the catchy phrase "punctuated equilibrium" to formalize the understanding of data collected over the last few centuries by paleontologists, data derived from all the rocks with remaining bits of evident forms of life stuck in them that have been exhumed from the ground and examined with the clever methodologies of the natural sciences over the years. Gould and Eldridge pointed out that paleontologists have always known, but until then never willingly brought up the crucial but widely recognized detail apparent to all those familiar with the fossil record: over the course of unimaginably long periods of time, most Metazoan species remain identifiably the same, they do not gradually turn into something else as those who do not know the fossils might suspect based on then-current understandings of the processes of natural selection.

The fossil record is a record of stasis with respect to speciation, according to the data of the paleontologists, who have catalogued and shelved a wide ranging if recognizably incomplete record in rocks of the prodigious variety of remains of living things down the ages stuck there in those rocks, confirming evidence of what once flourished and then faded into rock in profuse and lasting numbers over immensely long periods of time past, living things remaining fundamentally the same over all those vast lengths of time, and leaving fundamentally similar remains all the while. Very occasionally these periods of recorded stasis are punctuated by the appearance of new, related species. Gould and Eldridge proposed that this model, the model of prolonged, potentially punctuated stasis, founded on what can be gleaned from an examination of the source material of paleontology, is an accurate model of how most species come to be, at least in the realm of the Metazoans, home to our own sweet species itself.

This claim sets up an interesting argument with people who's understanding of evolution is anchored in the standard evolutionary perception of incessant indifferent inexorable processes of natural selection working their gradual wiles, accumulating profound changes in populations in a species over time until those changes add up to something new, what Gould calls here gradualism: origin by "anagenesis."

And Gould acknowledges that in some clear cases anagenesis is exactly what the record shows, a species gradually transforming itself over some great length of time from one distinguishing shape and size to the next. But Gould submits that this is not the history of most species at all. Most species don't participate in any meaningful way in the self-improving gestures of anagenesis, but rather go on and on lounging around some mean of their own disposed values for millions upon millions of years until given some reason to cease.

Darwin himself had proposed, and subsequent evolutionists long accepted, that lack of overwhelming evidence for anagenesis in the remains was to be expected considering the incomplete record of geology, cutting off any contrary talk on the part of paleontologists about what was evident to them from what they'd managed to collect and analyze over the course of more than a century of assiduously sifting through all crusts of earth from sea floor to mountaintop: stasis, potentially punctuated by the appearance of new species, is what the data shows. The species remains significantly the same for all the long time of its existence, not turning slowly to some other form as anagenesis requires, but remaining the unique beast it always was from first to last, punctuated on special occasions in the record by the relatively sudden appearance of new, related forms.

Anyway, Gould makes his argument for the contentious concept of punctuated equilibrium and finds it serviceable enough in the final analysis. Well, it's his book, and I have no way of judging whether he's given short shrift to cogent arguments against the idea and all it entails for understanding natural selection, but even lacking a true grasp of all the terminology, still, I can see what he's driving at, and it all seems likely enough as far as I can tell —which distance isn't all that far into the matter, admittedly. I stumble along just next to the cartload of knowledge needed for comprehension of a lot of what Gould has to say. Here's an example:

I fall far short of understanding this

Something's odd about this table. Look up at the top there where the abbreviated names of the geological ages go trundling across. See? SIL>|<DEV >|<CARB … Now, look below at the corresponding ages in millions of years down at the bottom.

I don't believe the Devonian age fell in the years indicated here, and I don't think the Silurian should even be mentioned in a table that only goes back 350 million years. So the data points on the chart, assuming they're being associated with the same Silurian and the Devonian everybody else means, are being compressed in some odd way that deforms the curve Gould points to repeatedly in his argument for punctuated equilibrium.

What's up with that? I fall short of knowing.

Tectonic shift

My wife and I got cellphones this week. I'm of two minds about being instantly available by telephone, influenced in part I admit by my experience working the evening shift as a PBX operator in a Pacifica, CA medical center years ago. Ah, well. I was a poor choice for a bad job, in retrospect, and as the telephone played a necessarily central role in the work, I've been for some time leery of reengaging the technology I failed so miserably those many years ago.

It was my poor adaptation to the irreducibly interruptive nature of the job of switchboard operator that made a ruin of my work there, I admit. There I'd be in the little closed parenthesis of a receptionist's cubicle in the post-office hours medical building making my $1.65 an hour. Upstairs there were the patients in a long term care facility, and out there were the people in the world who might want to talk to them, and of course the doctors on call out on the town at some fancy restaurant or other, I the one standing in the way of these people having the same instant telephonic connection with one another as that enjoyed with the whole world by everyone with a pocket to spare for a mobile phone these days.



Suddenly, arbitrarily, there'd come a call. Interrupting my credulous coursing through Nietschze as translated by Kauffman, I'd turn to the PBX machine and see if I couldn't deflect the interruption quickly along its proper path, some relative connected to an old one housed upstairs, some plaintive patient seeking a soothing something from a doctor.

At the time my underdeveloped ability to constantly initiate a new task in the midst of another, to be torn suddenly from whatever it was I was about to attend to, to some intruding new unscheduled something or other, often enough resulted in the incompletion of one or both of the tasks in the event. Before long, in the face of successive failures in this regard, an unwillingness to be interrupted in my reading grew like a carapace around the body of my work at the PBX, benefiting no one, it must be acknowledged.

I recognize the utility of immediate telephone contact encased in this compact little tool of a mobile phone, and the concievable but unlikely to be utilized utility of the text messages and photographs it makes possible, too. But I drag along with me my unwillingness to hear the interruptive phone ring at all, an abreaction developed to a fine if unhelpful sensitivity at that job long ago.



Along with the mobile phones, we were delivered an earthquake this past week. It lasted suprisingly long, the land rolling under our house in Santa Cruz for nearly 20 seconds after the initial jolt that announced it. I immediately wondered where it was centered. For all intents and purposes the quake in 1989 along the transverse section of the San Andreas Fault that passes through the northern part of Santa Cruz County was centered directly underneath our house, but I guessed that this week's earthquake wasn't so local, wondering as it went on if what we were experiencing wasn't the distant report of the dramatic lurch of the Hayward Fault everyone recognizes must come some day.

We had no damage, and except for the framed print of this image, which fell harmlessly from a bookshelf onto the ironing board below, nothing was dislodged by all the earthquake's extended roiling.

It didn't occur to me to use my new mobile phone, which, as it turns out, would have been useless in the immediate aftermath of the earthquake.