More on stained glass Necker cubes

A commenter below, RBH, told a great little story about a stained glass piece he made, which got into a curated show. I was already impressed, but now I know enough to be even more impressed.

my second was a 3-D wall sculpture (glass mounted to copper posts standing out from a plywood back, etc) that was a fool-the-eye, incorporating Necker Cubes in both 2-D and 3-D. That one got into a curated show at a gallery, and I promptly retired!

Trompe-l'oeil ("fool-the-eye") is a kind of art illusion, usually creating a very vivid depiction of 3D objects on a 2D surface, such as a painting or a mural, like below.



There are a lot of trompe l'oeil images used to illustrate points in psychology and cognition, because they provide interesting explorations in how the eyes and brain process information. I had to look up Necker cubes to make sure I was thinking of the right thing; here is an example (Mathworld is a wonderful resource for math definitions and bibliographies; both of these examples are from Necker cube there.):



and the following tile floor, excavated at Pompeii:



So from this, we can get an idea at a very low level of the basis of RBH's stained glass; no idea what colors he used, but the basic pattern is the 2D rhombi above and the 3D analogue.

Now for why I am further impressed--I went to the stained glass store where I take my lessons, and saw a Necker cube (2D only) piece for sale. The woman behind the register is the one who made it; it was one of her early pieces. I mentioned that I was struck by how easy it looked from the simplicity, yet how hard it must have been to make: the illusion is maintained by the precision of the lines and angles. It is not a forgiving design at all; my parrot, on the other hand, acquired some occasional curves it hadn't had, but absorbed them seamlessly. But this one--either the lines are perfectly straight, or you might just as well not bother.

Having developed a new appreciation of how the lead came can fight back through the time I spent trying to keep already-assembled pieces from escaping while I was adding new ones, I said that it must have been hard to assemble. It was--the precision required and the number of pieces to keep in their exact place made this a formidable project. If you just look at it as rhombi, it looks very simple; if you appreciate how much work it is to assemble the rhombi, it becomes clear that the simplicity is deceptive, and RBH's design becomes even more impressive (even without knowing all the details).

I can only extrapolate how much work it must have been to add the 3D Necker cubes to the 2D ones--RBH, if you have a picture of your piece, I'd love to see it! Even though it would be a representation in only 2D, still it would be cool.

Also, I have to wonder about something, and I'd love to check it out: the illusion of the 2D Necker cube stimulates our brains to see 3D. What do the 3D Necker cubes stimulate our brains to see? Even though we are restricted to 3D space, still, the illusion has to "flicker" through something as it changes, much like the 2D cubes "flicker" through the illusion of 3D. Although we cannot really see 4D, I would love to see what the illusion of it--created by a 3D Necker cube--looks like to our perception.

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Got thyroid?

Apparently, you can take the girl out of Alabama, but you can't take Alabama out of the girl.

Isadora has allergies (not cat allergies, we hope, since she is one!), so we took her to the vet today for treatment. While we were there, we met the clinic cat. In addition to being black, he has exactly the same air as our Diana as well, who is taking thyroid medicine to control an overactive thyroid, a condition which often affects older cats. It is a look which is scruffy but not totally randomly scruffy--like the fur is partly cleaned, but not totally, and the oil is causing it to form lots of tiny semi-clumps.

I was so surprised at seeing a cat who looked so much in every way like Diana that I blurted out "That cat got thyroid?"

Yes, I am a PhD candidate in a major university's School of Medicine. I grew up hearing medical vocabulary from my physician mother. I am well-versed in the latest literature on feline hyperthyroidism, since I am treating a cat living with the condition. Yet with all of that lexical overlay, under surprise, I revert to the language I heard around me growing up: "That cat got thyroid?"

I guess I should just be grateful she doesn't have "high blood" as well.

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Who Lance has got to beat

The Seattle Times: But if anyone can defeat Armstrong in July, it will probably be Armstrong himself.

Good point--how much motivation is a seventh victory?

Four men have won the Tour 5 times; only Miguel Indurain has won five consecutively, as Lance has:

Jacques Anquetil (France): 1957, 1961, 1962, 1963 1964

Eddy Merck (Belgium): 1969, 1970, 1971, 1972, 1974

Bernard Hinault (France): 1978, 1979, 1981, 1982, 1985

Miguel Indurain (Spain) 1991, 1992, 1993, 1994, 1995

This kind of streak has occurred roughly once a decade; Anquetil, Merck, Hinault, and Indurain are, respectively, the 60's, 70's, 80's, and 90's. But all these guys are retired (if not dead); none of them is ever going to threaten Lance's streak.

Additionally, Indurain's window was continuous and recent enough that not many others have had the chance to win between his streak and Lance's. After Indurain and before Lance, there were only three winners:

Bjarne Riis (Denmark): 1996

Jan Ullrich (Germany): 1997

Marco Pantani (Italy): 1998

So these guys are the only ones who have a chance a the moment of matching or exceeding Lance's streak. But any one of them would have to win 5 more to tie or 6 more to beat Lance, and that task is going to take a while. The fact that their victories are 7-9 years in the past is no help, either--this is definitely a young man's sport (for the most part; there are exceptions, of course).

Bottom line: Lance's record is going to stand for a long, long time, whether or not he makes #7. As a result, he just may not be quite motivated enough this year. But, as quoted yesterday, if the race is to be won in the mountains, that is on his home turf.

(best name I've seen so far belongs to a 28-year-old Spaniard, riding for Spain on the Liberty Seguros team: Angel Vicioso)

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Nematode 911

Today I had a flashback to the rainy season, coming across a worm inching its way across the sidewalk. Usually, you don't see that very much in the summer, but it is a very common sight in the winter rains--I am told that they come up out of the soaked ground, so apparently they are on the sidewalks, parking lots, and streets trying not to drown.

The trouble is, there are many other things on the cement, none of them very good for little worms. That time of year, you see lots of squashed worms who got out of the ground to breathe, only to encounter a foot or a bicyle or a car, and that was the end of it.

Out of revulsion at seeing too many needless worm tragedies, I have become a worm rescuer of sorts, taking them out of the hostile environment and putting them back in their home. I used to just use whatever was at hand--a leaf, perhaps--to pick up the worm and return it to the grass. Then I began noticing likely sticks on my walks, and carrying them home to take with me prophylactically on future walks.

There is a very narrow range into which the perfect worm stick falls--too narrow, like a pine needle, and the worm just falls off when you try to pick it up. Too thick, on the other hand, and it's hard to get under the worm--you can inadvertently injure it that way. Also, the worm characteristically does not appreciate the help; you have to not only pick it up, but balance a squirmy animal while you carry it to its destination. A worm is not perfectly uniform along its entire length; there is a clitellum, or wide band, closer to the mouth end. So the center of gravity is not at (length of worm)/2; it is shifted forward, and a little experimentation will help you to estimate it successfully almost always, at least until it starts squirming too fast.

When he heard about my requirements for the perfect worm stick, my friend Dale made me a customized worm fork, pictured below.



Dale is a fine craftsman in wood, as well as in other venues such as horticulture; he has a nice eye for detail, and integrates function with symbolism in his work. (For the upcoming anniversary of the death of a young climber friend from cancer, he has made a clock out of a wonderful piece of old wood that looks just like a craggy rock face.) The specifications for the fork were my contribution; the leather handle for attaching it to a backpack, and the clitellum were totally Dale's ideas.

Now, thanks to Dale, I have a really nice stick for rescuing worms, although I have put it up for the season, not expecting to need it until the rains begin. But I do have a nagging question--is it really helping the worms to put them back in the grass? Apart from the obvious examples--for example, they need relocation because they're headed for the freeway on-ramp--it is the wet grass that they were escaping from in the first place, after all. I hope that in rescuing them from squashing, I'm not condemning them to drown. I'd welcome thoughts on the subject from anyone who knows more about worm anatomy and physiology than I do.

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Plus ça change...

In the sports section today, Lance Armstrong is quoted as saying "This year, the Tour will be won in the mountains.".

I am counting on it--Lance always gains time on the competition in the mountains, and if the past is any indicator, he will go into it somewhat behind, and then pull ahead on the ascent. If this year, the Tour is indeed to be won in the mountains, then I expect Lance to win an unprecedented seventh victory.

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Research on massage in pregnancy

Notes to follow.

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Score!

Woo-hoo! I just scored big.

I don't often get over there, but this morning, I went over to the biology building to meet my PI on the bear project. On the way in, they have a table where people dump journals, flyers, conference announcements, etc.--anything they don't want anymore is left there, free for the taking.

Today, I got there to find someone had cleaned a whole lot of monographs and journals out of their library and left them on the free table. As I've mentioned, my medical informatics research is in representing comparative anatomy in an information system. But a big problem in developing my system is getting a lot of data for it--much of the information doesn't exist online, but in the old journals and other print sources.

Back in the golden age of gross anatomy, people would record their findings in loving detail in these sources--they are actually a joy to read, not only for the information, but for the effort they put into the presentation. I had a bad inferiority complex when I took comp anat, and compared my pathetic squiggly renderings of what I observed to some of the old work. That is, I did until I found out that a lot of the old guys used camera obscura, tracing, and other technical drawing techniques to make their work look better--they were, after all, scientists, not artists.

Much of this work, as important as it is, has not been digitized, and so with a generation of practitioners who use mostly or only online sources, access to a great deal of the anatomical knowledge of the past has been effectively cut off. One of the purposes of my intended research is to bring it online, and standardize it so that we don't have one source for human, and a totally unrelated source for mouse, but rather that we can go seamlessly back and forth between any number of species.

So when I found these monographs just put out for the taking, it was like coming across a treasure! The only downside, and it is a minor one, is that I am currently working on mouse and rat, and none of these sources are about those species. Instead, they are all about different species of fish.

Never mind--I am a patient woman, and I am dealing with species that took millions of years to evolve. I will focus on the mouse and rat for now, and keep these precious written sources for the day that I actually do model the alewife.

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Transgressions

PZ Myers wrote a post that brings together many convergent threads. I had heard of parasitic twins and of teratomas before, though I was unaware of the medical term fetus in fetu.

Fetus in fetu can arise in one of two ways: an identical twin never fully develops, and instead is (literally!) incorporated into the surviving twin, OR, a teratoma (germ cell tumor, from the Greek word τέρας, "monster") forms, and, because of the nature of germ cells, differentiates into developed tissues. The effect is quite freaky--I have seen a picture (I think in Teratologies, by Jackie Stacey; I can verify that when I unpack my books) of a tumor with some teeth and hair--very disturbing!

I suspect that one reason it is so disturbing is that this kind of teratology forces us to confront how similar reproduction, aging, cancer, and death are at the cellular level. Normally, we think of these as very different from one another, divided by reasonably clear boundaries. Teratology trangresses, literally "steps across" these boundaries, and brings forward things we normally don't face.

I'm just guessing now, but I think this could account for something I observed while I was practicing massage more actively--some of the most touch-deprived patients I encountered were either terminally ill, had cancer, or both. I think that normally we can draw a mental boundary between cancer or death and us "healthy people"--and being confronted with those conditions makes that conceptual boundary harder to maintain. Once again, a "transgression" has taken place. In the rational, logical part of our brains, we know that neither cancer nor death is contagious, but unconsciously, we shrink from touching. As a result, a normal human need that we Americans are short on anyway becomes even more scarce for a population which, paradoxically, needs it perhaps more than ever.

I don't think it is wrong to have these feelings; it is perfectly understandable. But to take the extra step to get past them--to decide to acknowledge their uncomfortableness and reject them in favor of reaching out to someone--for me, that is a true mark of insight and kindness.

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Brillo bear

While I will miss the bears and other animals here, the Philadelphia Zoo does have bears, whom I will look forward to visiting.

I don't have any decent pictures of the spectacled bear or of the polar bear, but I like this one of the sloth bear:



I have actually had the opportunity to touch their fur--it is very coarse; Iain aptly calls them "Brillo bears".

They have a very interesting adaptation to their myrmycophagic, or ant-eating, lifestyle--because they "hoover" the ants out of dead and decaying logs, their lips are very supple and flexible, and they have no upper canine teeth or incisors.

A question that I am curious about is at what stage do they lose these teeth? Do the teeth never develop at all, or do they partially develop and then get resorbed? If so, at what stage? I am not likely to get answers to these questions soon--if ever--but still would really like to know.

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Research and evidence in massage

As a massage practitioner, I have always been interested in the intersection between practice and medical research. When I returned to grad school, it was an opportunity to learn more about evaluating research evidence, and to apply that to the body of research in complementary and alternative medicine (CAM).

One of the things I want to blog about is what exists in that intersection, as well as what remains to be done. Below are some slides from a PowerPoint presentation I gave recently; I'll go back later and fill in some explanatory notes.

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The teams and the route

The team rosters for the 2005 Tour de France can be found here. The race starts in Northwestern France (Fromentine to Noirmoutier-en-l'Ile) on July 2, and follows this route.

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Vive Lance!

Normally, the marriage of Mr. Raven and me is pretty much orthogonal, if not directly opposed, to traditional sex roles. For example, he is the domestic one who does most or all of the housework, and I am the one he catches eating out of the pan. When he goes out of town to visit his family, he returns to a domestic situation which, to say the least, has devolved in his absence, and he gets to spend a week just regaining lost ground--not that I do it on purpose; it's just absent the civilizing pressure, orbits decay. While we're pretty much opposite traditional sex roles on housework, in other areas of life, we're both pretty similarly androgynous.

The exception that proves the rule is sports--11 months out of the year, he is the avid sports fan, and I am the one who never can quite remember which team name belongs to the basketball team, and which to the baseball team. But July of every year--now that is a bicycle of a different color.

Every year at this time, I get totally caught up in the Tour de France (French here, English here). It's not particularly because Lance Armstrong is American; I'm not that much of a nationalist. Nor do I think I would particularly hit it off with Lance personality-wise; I lost an young, athletic, very vibrant friend to cancer; in the last year of his illness, he read my copy of It's Not About the Bike, and where I was willing to cut Lance a lot of slack, based on my ignorance of what it must be like to live with cancer, my friend (MF) ripped him several new ones about what a jerk his stories revealed him to be, cancer or no. MF's judgment in other things was good; I suspect my opinion would be the same as his, if I weren't so consciously not judging someone else's disease experience.

No, I think it is a synergistic combination of his being a cancer survivor recovered enough to compete professionally, and of his achieving six consecutive victories. Beating the odds on one front is compelling; on the second, it is more than twice as much--it's compelling squared. As unlikely as it is for me to be a sports fan, for one month out of every year, I am hooked on this combination of unlikeliness.

So, no, I don't have time for this; I'm not nearly ready to leave for Philadelphia yet--I've still got tons to do. But despite that, I will be tour-blogging in and around the move preparation.

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Here's to you, Chamah!

While going through some old boxes of paper to recycle, I found an old press release from Woodland Park Zoo, on the passing of their last male sun bear a few years ago.

"Chamah was a very handsome, intelligent and gentle old bear," said zoo keeper Cheryl Frederick.

Selamat jalan, beruang bagus baik. (UPDATE 6/29: I was trying to say in my rudimentary Indonesian "goodbye, good bear". There are two words for "good" in Indonesian, "bagus" and "baik", and I thought they were synonyms. Today I got a chance to talk to a native speaker about the difference, and learned that the "good" I meant--well-behaved, kind, good temperament--is actually "baik". "Bagus" is more like "good-looking, pretty". So I have changed my toast to Chamah accordingly.)

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This one's for you, Dr. Witherspoon

Posting's been light the last few days, as I do a major housecleaning and organization before I leave for Philadelphia in July. But this turned up at the bottom of a stack of papers, and as it's on the subject of my last post on teachers, I'll take a break to post it to my blog.

This was the introduction to a paper on apoptosis that I wrote for an assignment in one of my first informatics classes, "Biology for Informaticists" in Fall 2000. One of the aspects of informatics that I am very interested in researching is how we organize information. As apoptosis was a brand-new topic to me at the time, I began gathering information, and found that the differences between apoptosis and necrosis reminded me of a distinction I had seen drawn elsewhere, but in a very different context.

Raven's Apoptosis Paper: Introduction

When I began research for this paper, I did not really know anything about apoptosis, except that it was some kind of cellular suicide, and that it was a popular buzzword among people interested in cancer.

While the word α π ο π τ ω σ ι ς (from the root "to drop, to fall" [of leaves]) in the senses of bone dislocation or erosion, or of shedding of scabs, dates back to the writings of Hippocrates of Cos and of Galen (Mauro Dello Esposti, "Apoptosis and the Classics"), and "programmed cell death" at least back to the 1960s, the modern sense of apoptosis can be traced to the publication in 1972 in the British Cancer Journal of a seminal article by J.F.R. Kerr, A.H. Wyllie, and A.R. Currie. From that initial publication, the MEDLINE citations at last count have grown to 38870 items over the last 28 years. The size of that number--obviously prohibitive for researching thoroughly for this paper on the face of it--speaks simultaneously to the intense research interest in the topic, as well as to the need to develop a practical strategy to approach the body of literature in any meaningful way.

Although I did not yet have a conscious organizing strategy when I set out, the more I read and studied about apoptosis, the more I was stuck by the parallels among the cellular physiological processes taking place, and the events described in the Navajo origin story, Diné Bahane'[1]:

...For the Navajo, death of old age is considered to be both natural and highly desirable.

In Navajo mythology, Coyote, the philosopher, argued that death had to be a part of the scheme of this world. He argued that if death did not occur, the earth would soon be overcrowded, and there would be no more room for corn fields. He concluded that it was better for each person to live a limited time, and then leave and make room for the children. The people recognized the wisdom of his words, and agreed that it would be so. (Reichard, 1950a:42).

Birth and death are recognized as structural opposites; one cannot exist without the other. This is manifested in mythology when Monster Slayer, who is in the process of killing the enemies of the people, comes across Old Age with the intention of killing him.

Directly, Old Age spoke up, "In spite of all, I am going to live on, my grandchild," he said... "You have not the right thing in mind, I see," he told him. "Should you kill me, dying would cease," he said. "Then too giving birth would cease," he said, "and this present number of people would continue in the same amount for all time to come. While if I live on, old age will do killing and giving birth will go on in the future. As giving birth goes ahead, so deaths will go on in the other way," he said. "The various birth beings, all without exception, should continue to give birth in the future, every kind of moving being, none excepted," he said.

"Now think this over, my grandchile, you can see now how this thing is!" he told him (Wyman, 1970:573).

Life is considered to be a cycle which reaches its natural conclusion in death of old age, and is renewed in each birth. Death before old age is considered to be unnatural and tragic, preventing the natural completion of the life cycle. Whereas illness usually comes from various forms of disorder and disharmony, premature death usually results from malevolent intentions and deeds[2].

Hinted at in that description of events are analogies to the concepts explored in this paper of:

• apoptosis vs. necrosis as different mechanisms of cellular death: a peaceful, good death determined internally in the fullness of one's own time, as ultimately desirable, and as opposed to a premature, violent death at the hands of external forces such as accident, witchcraft, malevolent intentions and deeds, etc.
  
  
• the effects of each kind of cellular death on its immediate environment of its neighbors and the macro-organism at large: violent or premature death leaves ch’ỉįdii--angry, malevolent spirits who wreak havoc on the living, while a peaceful, fulfilled death of old age leaves behind no such ch’ỉįdii
  
  
• apoptosis as autodestruction
  
  
• the parallelism between apoptosis and mitosis at the cellular level
  
  
• the role of apoptosis in developmental embryology
  
  
• homeostasis
  

Obviously, it is possible to take any analogy way too far, and you have to be fastidiously careful not to distort the facts in order to wring a little more mileage out of the analogy. Certainly I am not arguing that the Navajo were actually observing and reporting processes at the granularity of cellular and genetic mechanisms--rather, I am simply suggesting that learning more about apoptosis opens the door to broader, more universal philosophical questions of the type that have been concerning people for millenia: questions on the nature of birth and its relationship to illness, old age, and death, the dynamic tension between individualism and interdependency, etc. It is this fundamental relevance of apoptosis to all of these processes which makes it such an important concept, especially--but certainly not solely--in research on the mechanisms of cancer, and its prevention and treatment.

I am not going to deal with these questions and paradoxes at the broader level any further in this paper--from here on, the focus will be on the cellular physiology level--but I just wanted to mention that the framework outlined in this creation story provided very useful conceptual hooks for me to approach what was initially a huge and confusing body of literature, and enabled me to begin to sort out and make some kind of sense of it.

[1] Much later, I discovered that I was by no means the first to draw such analogies between apoptosis in the cellular and the social organisms--the word "apoptosis", in the social and political sense, dates back at least as far as the writings of Marcus Aurelius--whose physician was Galen! (Dello Esposti, 1998)

[2] Witherspoon, Gary. Language and Art in the Navajo Universe, University of Michigan Press, 1977: pp. 19-20.

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On teachers

Just hanging out on the blogs today, I have had occasion to quote not only my professor of classical Hebrew (in discussion of the ramifications of the first word of Genesis for Biblical literalism versus science), but also my Navajo-language professor (for an analogy between Navajo views on different kinds of death and their parallels to apoptosis and necrosis). Both of these men were first-class scholars, and they bridged a huge conceptual divide, between English-speaking students and languages that share very little vocabulary and structure in common with English.

As I wrote elsewhere, it has been my privilege in this life to have many wonderful teachers, of whom these two are a representative sample. I am grateful to each of them in very different ways, for the windows onto the world that they opened for me.

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Paper accepted!

I just got word that our paper "Of Mice and Men: Design of a Comparative Anatomy Information System" was accepted to AMIA 2005. Due date for revisions is July 15; since I'm leaving for the East Coast on the 7th, I just got even busier in what I need to get done before I leave. Still, in the past I've been too busy with work I love, and too busy with work I hate, and I know which one I prefer! I am not complaining about this addition to my to-do list.

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Bear meat

So last year, I was coming back from a medical informatics conference with a group of my fellow graduate students. We were a large enough group that we couldn't all get a table together in the bar while we waited for our flight, so I was sitting with Donna, Aaron, and Andrea, sipping beer and laughing, when this guy comes over and starts chatting to me. He greets me, and asks me where I'm from.

I thought it was a little odd, to approach a stranger engaged with a group of friends and just interrupt like that. Having been raised in the South, though, I'm terminally polite, so I answered "Seattle", and then, not knowing what to do, asked him where he was from. He answered that he was from Manitoba.

Now it was starting to get kind of awkward, with him just standing there having brought our previous conversation to a halt, and since I couldn't think of anything to say, I just added "Ah, you have lots of bears there.". His face lit up, and he started talking about how great the bear-hunting was, and how I really ought to come up to Manitoba for the hunting.

I heard Donna suck in her breath behind me. She and Andrea exchanged looks as the guy kept rambling on, as if they weren't sure what was going to happen next, but it was certainly going to be bad. Fortunately for the guy, though, I never start anything in airports anyway, and he certainly wasn't worth getting on a blacklist over. I put on the Southern icy-polite face--let him run out of steam, and then figure out that this conversation wasn't going anywhere and excuse himself.

On the flight back to Seattle, I was teased about could this guy have picked a worse way to try to impress me than with bear hunting, and how he doesn't even suspect what a narrow escape he had.

So that's how I feel about hunting bears.

Given that, I was a little taken aback to read this story: Juneau homeless shelter stops serving bear meat, The Associated Press

JUNEAU, Alaska — A Juneau homeless shelter has stopped serving donated bear meat after learning the state prohibits nonprofit groups from accepting wild game meats such as bear, fox and walrus. "We didn't know that it is illegal," said Jetta Whittaker, executive director of the Glory Hole. For years, the Glory Hole accepted bear meat to supplement its meals for the homeless. The meat went into many recipes, including burgers, casseroles and spaghetti. But last year, Whittaker learned that serving it was contrary to rules set by the Alaska Department of Environmental Conservation. This year, it has meant turning down five offers of bear meat. "That was 250 pounds of ground meat I could use for spaghetti sauce," said Bob Thompson, operations manager of the shelter. "We are protein-poor."

So the state of Alaska has chronically-nutritionally-compromised people on the one hand, 250 pounds of ground meat on the other, and a rule forbidding the obvious next step.

Part of the concern is that the bear meat could transmit trichinellosis (a PubMed search on "bear AND (trichinella OR trichinellosis)" yields 106 articles). I thought that, as with pork, proper cooking kills the trichinella larvae, but the state claims that the difference between how pork and bear meat are raised and processed makes it too unsafe. I am not sure that that is a convincing argument--either cooking kills the larvae or it doesn't, and if it doesn't, then our pork industry has major problems. If it does, then why not strictly regulate how bear meat can be prepared and served?

A nonprofit with a yearly budget of $193,000, the Glory Hole has only $4,500 to churn out 54,000 meals a year for the homeless.

That comes to a grand total of $0.08 per meal in Juneau, where everything is more expensive, because it is brought in by air or ship. Given that constraint the shelter has, it is a shame to have to turn down free meat, even if it is bear meat.

The bears are dead already, after they are hunted. Not permitting the shelter to use the meat means that it is just wasted. If, as a society, we are going to decide that bear hunting is acceptable, we should at least mitigate it by allowing the meat to go to people who depend on shelters for their food. I hope that Alaska is able to resolve this soon in a way that makes the bears' sacrifices mean something more than pure waste.

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Sky sounds

Previously, I have recommended Iain's radio program, but tonight's should be especially worth listening to. 12 midnight to 3AM Monday on KBCS 91.3 FM Bellevue/Seattle, or streaming here.

From his email:

"Maps of the sky--pieces of music that are somehow related to the constellations and other lovely patterns we project into the heavens."

One of my favorites is in the lineup, although I don't know what time he will play it: "Grande Ourse (The Great Bear)", by Iancu Dumitrescu.

Next week, I will be a guest in the studio for his "Animal Sounds" program. More details to follow. UPDATE: 6/20--Maybe. The program may be rescheduled until November, after I get back from the East Coast. More info as I know it. UPDATE: 6/26: It is definitely postponed, because another source is unavailable. Iain will reschedule it for after my return at the end of October.

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Father's Day

Thank you, Dad.

Love,

Raven

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Modeling correspondences among Hox genes and their resultant structures

PZ Myers has another great biological post this morning (I know, that's redundant). It's about how the interactions among Hox genes create structures. As he writes, "The message of which I try to always remind myself (not always successfully) is that genes don't make things, interactions between collections of genes and the environment make things. Biology arises out of the processes, not the structures; it's the reactions, not the end-product."--in other words, there is not a 1:1 correspondence between genes and products, nor between genotype and phenotype.

This is where my a big part of my research lies--I'm essentially trying to represent comparative anatomy 1) in a way the computer can understand, while 2) not misrepresenting the subject through oversimplification in doing so. There's a lifetime of fascinating research questions in undertaking this task.

So up to now, we've explored what we are comparing (referents), and on what basis (homology). While we haven't yet gotten into the details of how we compare them, PZ's post provides a great excuse for one of my favorite examples of a modeling problem. Like PZ's post, it deals with structures resulting from Hox genes, but the species I am looking at are more familiar to most of us: the mouse and the chick.

Like us, mice and chicken are vertebrates; we have a spinal column made up of vertebrae surrounding and protecting a major part of the nervous system. This high-level abstract similarity among all three species is part of what the old anatomists called the vertebrate Bauplan, or "building plan". From the 30,000-foot point of view, we all have a dorsal vertebral column bisecting the body, with a head at one end, a tail (admittedly vestigial in our case) at the other, and two limbs off either side in between.

That is the kind of thing we mean by anatomical similarity. But when we look at it more closely, differences emerge as well. Here, we will take our vestigial tails and leave the discussion, to focus more specifically on the mouse and the chick.

One of the differences we notice right away is that although they both have vertebrae, they are distributed differently: the chicken has a long neck, while the mouse has a short one; conversely, the mouse has a long tail, while the chicken's is very short. Although we are not comparing them quantitatively, qualitative differences such as "long" and "short" are exactly the kind of thing we will be looking at.

To avoid a perceptual confusion, though, let us first do one thing with our model that, sadly, PZ cannot do in his lab: we normalize the chicken and mouse to the same size.



The reason we do this is so that the vertebrae we are comparing will also be the same size, and so we know that many vertebrae in a line will be longer than fewer vertebrae. Otherwise, we could have a situation where many tiny mouse vertebrae are still shorter than fewer chicken vertebrae. By normalizing the size of our models, we have now robustly connected relative length of chain of vertebrae to number of vertebrae.

On our mouse and chicken, we now draw their vertebrae, indicating each different region with a different color.



The red line segment is the cervical (neck) vertebrate; green is thoracic (chest); pink is lumbar (lower back); dark blue is sacral (sacrum); and light blue is coccygeal or caudal (tail).

Now we drag our line segments off the drawings and juxtapose them to compare them directly to each other.



We see that while the chicken's neck is much longer than the mouse's, the mouse has a much longer tail segment, thoracic segment, and lumbar segment, while the sacral segments are pretty similar. Because of the step where we normalized the size of the models, we know that that means that the chicken has a greater number of vertebrae in the neck than the mouse does, while the mouse has a greater number of vertebrae in the tail, and so forth. However, the overall number of vertebrae (disregarding the segment they belong in) appears to be roughly comparable.

So it would seem that, rather than having lots more vertebrae to have several longer sections, the mouse and the chick have roughly the same number of vertebrae, and these vertebrae are distributed differently.

Let's check out that idea. In order to do so, we go back to the embryological structure from which vertebrae arise, the somite. The drawing below shows the correspondence between somites in the chick (yellow circles) and the mouse (gray circles). The two-headed arrows indicate the correspondence across species.



At this point, we (rightly) cannot see a lot of difference, except for species. The somite has the potential to become any different kind of vertebra; what kind of vertebra it will become depends on the interaction among the Hox genes. And indeed, the mouse and the chick both have the same (stipulating different species) Hox genes (again, yellow for chick and gray for mouse).



To be totally consistent, this drawing should have two-headed arrows between the Hox genes across species as well. However, it is about to get out of control real fast anyway without them, so we'll just say right up front that for the sake of simplicity, we are leaving out some relationships from the drawing.

What kind of vertebrae somites become is not controlled on a one-to-one basis by the Hox genes, but rather by their interactions. (Actually, there is not even a one-to-one correspondence between somites and vertebrae; the back half of one somite joins with the front half of the somite behind it to become one vertebra.)



While Hox 5 controls the development of cervical vertebrae, the interaction of Hox 6 and Hox 9 control the development of thoracic vertebrae, and Hox 10 controls the development of lumbar, sacral, and caudal vertebrae--hardly a one-to-one correspondence. Additionally, the Hox genes have to coordinate with each other to "know" where one set of interactions leaves off and the next begins. It is a real challenge to represent this complexity on a 2D sheet of paper (or in a computer, for that matter), and these diagrams are greatly simplified.



Ok, for the space allowed in a post, this drawing now seems to be too complex to get all the details in. We do note, however, that between somites and vertebrae (colored squares), there are two correspondence lines, indicating that a vertebra develops from neighboring halves of two somites. Additionally, all the vertebrae across species are connected by a simple black line, indicating that the correspondence is no longer exact--in terms of vertebra number it is similar, maybe even the same, but in terms of what segment it belongs to, it can be very different.

And this is only a simplified representation of the relationships; there are many more that were left out of the drawings. This is the raison d'être of my work: there is so much emerging information in biology, and the relationships are so complex, that computers are necessary to manage the sheer volume of data. Peter Karp asks what happens when an idea is too big for one human to grasp--that is why we need computers in biology.

At the same time, computers are stupid, or perhaps it is fairer to say "overly literal". To represent these ideas in a form the computer can understand, we run a real risk of oversimplifying them. There is an Italian proverb "Traduttore, traditore", or, "who translates, betrays". If, to get the biology into the computer, we misrepresent it--betraying it--not only have we not advanced knowledge, we have even set it back. My research concerns how we can take such complex work, and represent it truly and meaningfully for the computer to be able to manage it.

PZ finishes his post with "Evo-devo is really moving fast to leave the ghosts of molecular preformationism behind, and our vision of how developmental biology works is becoming progressively more strange and abstract. Give us a few more years, and developmental biology is going to be as weird and mind-bending as modern physics.". That is so true and totally cool that nothing I say can add to it, except maybe just that I am thrilled to be involved in my research at such an exciting time in biology.

(this post is based on a couple of animated PowerPoint slides from my thesis defense, and the material on which I developed the slides came out of notes from my comparative vertebrate embryology class. I need to go back to primary sources to get some references for this post, and will do so, modulo time constraints in getting ready to move; I was just so excited to see PZ's post on this topic this morning that I couldn't wait to write it.)

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Well, heck

I missed posting this, because I was so busy :(.

My friend George directed a staged reading of a chapter of Ulysses in celebration of Bloomsday, and our friend Lyndol was the pianist. George also used XML to make updating the scripts easy and quick. Unfortunately, the event was last night, and I'm just now posting this.

Oh, well, consider this a very early invitation to watch this space for Bloomsday 2006...

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On similarity

We have established (ok, stipulated more than formally proved, for the moment) that we can use a number line as a similarity metric. Now let's pin down what we are measuring--in other words, what we mean by similarity.

I've seen this diagram in tons of comparative anatomy books, so I'm not bothering to attribute it--I think it's pretty standard as common knowledge in the field, and it was intuitive enough to come up with from memory rather than looking it up.



It illustrates the three kinds of similarity that comparative anatomists have traditionally considered: homology, or similarity of evolutionary origin; homoplasy, or similarity of appearance; and analogy, or similarity of function.

(Actually, it's even more complicated than that--remember the pesky homonymy problem I referred to in my earlier post? Well, when it comes to "homology", there are differences even among biologists in what they mean by it. Molecular biologists talk about genetic homology in quantitative terms, and I really don't want to get into that right now. We use the term homology in the traditional way that morphologists have used it to indicate evolutionary relationships between gross structures, where they are either homologous or not, but in no case, for example, "80% homologous".)

Naturally, these similarities are not mutually exclusive, so any two structures being compared across species may have 0, 1, 2, or 3 of these similarities.

0: the mammalian nipple and the fish gill do not look alike, function alike, or have the same evolutionary origin.

1: the three tiny bones in our ear have a common origin with certain bones in the jaws of snakes, although they no longer either look like them or function like them.

2: the "torpedo" body shape shared (more or less) by the tuna, the dolphin, and the ichthyosaur look alike (roughly a cylinder tapered at each end), and function alike, aiding swimming by reducing hydrodynamic resistance, but each of them got their similar body shapes in a different way (convergent evolution, rather than shared evolutionary origin).

3: Human, dog, and mouse hearts: except for scale (remember, we are not being quantitative), one mammalian heart is pretty much like another in origin, function, and appearance.

Ongoing research is being done in description of anatomical appearance and function, but for now, we are concentrating on structural descriptions alone. For this reason, we examine similarity of homologous structures only, and describe their similarity or difference in terms of their distance on the number line. The next post will discuss how we do so.

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Identical, same, similar, different

Well, it's been a busy week preparing to move to Philadelphia for a while, but now I have to write--it's bugging me too much not to! My graduate research is in the informatics of comparative anatomy, specifically in the validity and implications of comparing model organisms, and I feel like writing about that tonight.

First of all, a meta-observation: because my work is at the intersection of biology (anatomy), computer science, and mathematics, I have a pesky homonymy problem--a lot of the terms I use have one meaning in biology and a different one in mathematics or knowledge representation or computer science or whatever. For example, "model", "homology", "topology"--all of these are terms whose meanings vary depending on context. So if I seem to spend an awful lot of time up front defining terms, it's only partly because of my inherent pedantry--it's also very important to make sure that we're all on the same page about what things mean as we proceed. My PhD committee has 3 computer scientists, a vertebrate embryologist, and a comparative genomicist on it--so we definitely use words differently sometimes.

For instance, in biology a "model" is an organism--in this case an animal, such as a mouse or a zebrafish. In knowledge representation, on the other hand, a "model" is a simplified representation of a real-world object (or referent). My work is based on the Foundational Model of Anatomy, a model (in the second sense) of human anatomy for the computer. I used the previously-developed human anatomy model as a template for representing mouse anatomy. But because the mouse is used in medicine as a model (in the first sense) for human disease, that makes my work a model of a model. That kind of homonymy happens a lot in my work, so we'll spend time up front establishing some definitions, so that later we can make faster progress.

In order to talk about comparing anatomy across species, we'll need to have some kind of metric for comparison. Obviously (or maybe not so obviously, so we'll stipulate it), it's kind of silly to talk about anatomical similarity in quantitative terms (what would it mean to say that the human prostate is 20% similar to the mouse prostate?). If we are describing anatomical similarity, we use qualitative terms such as "identical", "same", "similar", or "different". Given that, how do we establish a metric for comparison?

We can talk about distance along a number line, even without assigning exact quantities to each property. It would look something like this:



(ok, this ASCII art has to go, because those dots to force it to do space right are just confusing. consider this a placeholder for the moment, till I can whip out something in PhotoShop. UPDATE: done)

So if we can set up such a line, we can compare similarity, even without assigning quantities to the anatomical structures under comparison. The more similar two things are, the closer they are on the number line, and the more different they are, the more distant they are. The example above is a representation that the mouse heart is more similar to the human heart than the mouse prostate is to the human prostate--the hearts are close to each other on the line, while the prostates are relatively far apart.

That will be our basic modus operandi; now we have to establish what we compare, why, and how.

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Busy

I haven't forgotten to blog this past week; I've just been crazy busy on a couple of fronts. The biggest is that it seems I will be spending 3 months in the metro Philadelphia area, and so I am frantically preparing for such a big trip on such short notice. It's a very good opportunity that came up at literally the last minute.

What this means practically is that I will get around to blogging everything intended; just not as quickly as originally planned. Oh, well, to paraphrase one of my profs, if we knew how it was going to turn out, it wouldn't be life, after all!

Cranking on a grant, organizing data, and packing up the house this week, but I should have more time to blog at the weekend and after.

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In the home stretch!

I patina'ed the parrot tonight, and now it is sitting for 24 hours awaiting final wax, and it's done! I'll put up a picture when I have waxed it. I hope to present it to my friend Lisa as a housewarming present this weekend.

It turned out very nice, despite times along the way when the whole thing just seemed hopeless. Now that I better understand the process, I will document my third project from beginning to end, so that the steps will be represented accurately.

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More on concept, referent, term

A commenter asks in the thread below:

"I'm not sure I see how this would be a "triangle". If there's a real thing (an actual bear), what I think about bears (presumably somewhat idiosyncratic, though also presumably coloured by society &c to some debatable degree), and some linguistic intermediary I use to work between one and the other, that seems like a straight line. Everyone could have their own straight line between their thoughts and the bear, perhaps, but I don't see the triangle."

I've put up a couple of illustrations, but haven't yet gotten them to work in Blogger. One issue is that they are too big. I can shrink them in PhotoShop when I go in to school tomorrow, but for the moment, I'll just put links to them. Sorry that they take so long to load; that will be fixed tomorrow.


The first illustration is of the semantic triangle after Ogden and Richards. But the commenter raises a very good question: why a triangle? We could draw a straight line with the concepts on that line; wouldn't that suffice?

Let's try it and see. First of all, we'll make a minor change to the illustration, by changing the representation from a triangle to a concept graph. In my discipline, biomedical informatics, concept graphs are used frequently to illustrate structures, relationships, processes, and more. A concept graph consists of nodes (also called vertices), which are the circles representing entities, and of edges, which are the lines between nodes, representing relationships.


So converting the semantic triangle to a concept graph, we get this illustration. The entities are concept, referent, and term, and the bidirectional labeled edges a, b, and c are the relationships among them. For example, the referent may inform the concept by demonstrating an extremely protective maternal instinct, leading us to think of bears as fierce yet good mothers. That concept may inform the referent when, out of that concept, we pass laws forbidding the killing of mother bears with cubs. The referent may inform the term, as for, in example, the Russian медведь, which comes from "honey-eater" (cf. our English word mead. Similar relationships can be drawn so that each of the elements of meaning can be shown to inform each of the others in some way.

So now that we have the concept graph representation of the triangle, let's try the straight-line representation, to see if they are equivalent.



Notice that I have placed "concept" between term and referent. That implies that the referent informs my concept, which informs my term, and vice versa. The commenter asked the question in such a way that the term forms an intermediary between the concept and the referent, a perfectly good alternative way of arranging the three points on a straight line. The other alternative, where the referent is the intermediary between the concept and the term, is perhaps a little harder to visualize in terms of the physical world, but is, strictly logically, just as viable as the other too.

So we have three unique possible straight-line representations, as follows:

1) Referent <== a ==> Concept <== c ==> Term

2) Referent <== b ==> Term <== c ==> Concept (Update: this arrangement mirrors the strong form of the Sapir-Whorf hypothesis. Benjamin Lee Whorf: "We dissect nature along lines laid down by our native languages. The categories and types that we isolate from the world of phenomena we do not find there because they stare every observer in the face; on the contrary, the world is presented in a kaleidoscopic flux of impressions which has to be organised by our minds - and this means largely by the linguistic systems in our minds. We cut nature up, organise it into concepts, and ascribe significances as we do, largely because we are parties to an agreement that holds throughout our speech community and is codified in the patterns of our language. The agreement is, of course, an implicit and unstated one, but its terms are absolutely obligatory; we cannot talk at all except by subscribing to the organisation and classification of data which the agreement decrees.")

3) Term <== b ==> Referent <== a ==> Concept

Notice that rotation of any of these yields the an equivalent line--we can also write 1) as Term <== c ==> Concept <== a ==> Referent. There is no physical reason why either representation is more correct, so we consider the rotation of any line above to be the equivalent of the line. The only way to get a uniquely different line is to change which of the three entities is at the center.

Notice that while any of the straight lines manages to account just fine for all three entities, it only accounts for any two sets of relationships, but not all three. That is why Ogden and Richards used a triangle (a 2-dimensional representation)--in order to be able to account for three different kinds of relationships among the entities. A line (a 1-dimensional representation) does not have sufficient power to represent the relationships among all the entities, just among any two which are connected to each other.

But perhaps there is a way in which this line representation can work. In this illustration, I have drawn the b relationship in. Now all the relationships are accounted for, although the representation is no longer 1-dimensional, but now 2-dimensional, like the triangle.



Is our new representation the same as the triangle, then? Well, yes and no. Geometrically, it is very different. Topologically,, however, it can be proved to be the same. Further, if we take any of our 3 unique lines described above, and add the missing relationship, we can prove that they are topologically no longer unique, but are equivalent to each other, as well as to our original triangle.

So if geometry says that they are different, and topology says that they are the same, how do we know which one to go with? The subject matter is the deciding factor. Geometry is a very numeric branch of mathematics, which deals with exact lengths, angles, and such. Topology, on the other hand, looks at those non-numeric properties which remain invariant under transformation. Since the relationships we are talking about, such as how a term influences a concept, are very non-numberic, topology seems like a more appropriate domain--and indeed, the topology of graphs and networks is a very big research area in computer science and bioinformatics.

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