Fun Phonetics Quote

"When you release the nasal consonant, Boom! - that front cavity is there. Except "boom" is not the right word." - Ken Stevens, 2/22/07, on the absence of a salient burst in nasal stop releases.

The Rise of Neo-Aristotelianism?

My mom recently wrote an entry about "Spiritual Formation", and it got me thinking. It was Aristotle who thought that everything has a form which leads it to behave in certain ways in certain circumstances. The natural bent of that form could be thwarted or modified by certain accidences attendant upon it, such as its combination with some object of a different form (e.g. air might be mixed with water, keeping it from going upward to where all air is supposed to be; when the water is heated, the air escapes - of course we now know that this is just a difference between the liquid and gaseous states of the same water). By undergoing Spiritual Formation we are attempting to mold ourselves into a new form that we did not have before. This is why I put the "Neo-" in front of "Aristotelianism". I don't think Aristotle believed that an object's form could change. If it could, that would be a sort of transmutation (and now we're getting alchemical). And indeed, even Donne, who as far as I can tell was a good Aristotelian, seemed to think that our form was fixed - at least according to the poem that I love to put on my blogs:

Goodfriday, 1613. Riding Westward

LET mans Soule be a Spheare, and then, in this,
The intelligence that moves, devotion is,
And as the other Spheares, by being growne
Subject to forraigne motions, lose their owne,
And being by others hurried every day,
Scarce in a yeare their naturall forme obey:
Pleasure or business, so, our Soules admit
For their first mover, and are whirld by it.
Hence is't, that I am carryed towards the West
This day, when my Soules forme bends toward the East.
There I should see a Sunne, by rising set,
And by that setting endlesse day beget;
But that Christ on this Crosse, did rise and fall,
Sinne had eternally benighted all.
Yet dare I'almost be glad, I do not see
That spectacle of too much weight for mee.
Who sees Gods face, that is selfe life, must dye;
What a death were it then to see God dye?
It made his owne Lieutenant Nature shrinke,
It made his footstoole crack, and the Sunne winke.
Could I behold those hands which span the Poles,
And turne all spheares at once, peirc'd with those holes?
Could I behold that endlesse height which is
Zenith to us, and our Antipodes,
Humbled below us? or that blood which is
The seat of all our Soules, if not of his,
Made durt of dust, or that flesh which was worne
By God, for his apparell, rag'd, and torne?
If on these things I durst not looke, durst I
Upon his miserable mother cast mine eye,
Who was Gods partner here, and furnish'd thus
Halfe of that Sacrifice, which ransom'd us?
Though these things, as I ride, be from mine eye,
They'are present yet unto my memory,
For that looks towards them; and thou look'st towards mee,
O Saviour, as thou hang'st upon the tree;
I turne my backe to thee, but to receive
Corrections, till thy mercies bid thee leave.
O thinke mee worth thine anger, punish mee,
Burne off my rusts, and my deformity,
Restore thine Image, so much, by thy grace,
That thou may'st know mee, and I'll turne my face.

Regarding the question whether our form is fixed or not, I think both sides have something to offer - but how to bring them together, I don't quite know. On the one hand, we would like to say that we are all made in the image of God and that is something fixed and will never change. On the other hand, we would like to say that we are re-formed and made into a new creation in Christ. But I don't want to talk more about this at this time. Moving on...

It's interesting that the idea of a worldview, which as far as I can see is an idea that is on the rise - partly as a result of post-modernism, and partly as a reaction against it - also suggests the notion of an Aristotelian form. Our worldview is like the essense of our form, the thing that determines how we will behave, or how we will respond to certain situations, the thing that determines the way we think about things, the conclusions we draw, etc. Of course, in the post-modern world the nice thing about worldview is that it acts as a touchstone for our belief that who we are is a function of who we (or our parents, or the broader culture) have been. [Side note: I just realized that this is similar developments in Linguistics - namely, that what a language is is a function not only of natural laws of phonetics, etc., but also of what the language has been.] But again, we are Neo-Aristotelians in that we think that worldview can be changed, re-formed.

This might also be related to the debates over stem cell research. In an earlier entry (on Xanga) I think I raised the question whether it would be a helpful thing to consider an Aristotelian perspective - namely that an embryo has a certain form which it will naturally move toward becoming, i.e. a full-fledged human being. This way of thinking could potentially shed some light on the questions, especially since most the debate seems to be revolving around more Platonic questions - What is an embryo? Is it a life? Is it a ball of chemicals? When does one suddenly transform into the other? The Aristotelian concept of becoming as opposed to being is, I think, rather intriguing. And again, both have some Biblical merit - Jesus became better than the angels, but on the other hand Jesus is the second person of the Trinity. But there might be a problem here. Perhaps Aristotelianism is already breaking into the stem cell debates. One of the arguments in favor of doing stem cell research (on stem cells derived from embryos) is that the harvested embryo (harvested for whatever reason) is already no longer capable of becoming a person since it is not in an environment conducive to that development. The increasing awareness that an object is not defined solely without regard to its environment (perhaps this is remotely similar to Donne's assertion that "no man is an island") raises the question whether an embryo's form is constant between one environment and another, or if it changes.

And that raises another interesting question - whether the same emphasis on the dependency of an object on its environment might apply to the question about Spiritual Formation. In the absence of God, do we automatically have a different form than we have in the presence of God? For now I'll say that this sounds rather appealing to me, but I'll have to spend some more time thinking about it.

In the meantime... Is Neo-Aristotelianism on the rise? What does it mean?

Answering "The God Question", part 2

Last night I went to the second evening event of the Veritas Forum at Harvard. The topic at hand was "Dawkins and the Divine: Is God a Virus of the Mind?" Dawkins was not there (if I remember my "he saids, she saids" correctly, Dawkins follows S.J. Gould's advice not to engage in public discussions/debates about religion with religious people because deigning to do so simply legitimizes religion), but the discussion centered around Dawkins' new book The God Delusion. So unlike my last entry, this "God Question" really is about whether or not God exists and what He's like. Both sides had good things to say, and in the end I guess what was most strongly reinforced to me was the neccesity of falling back on Jesus as the foundation of our faith. What many atheists or agnostics seem to think these days is that among Christians faith is not something that goes above and beyond reason but that it contradicts reason. I think this probably has roots in 19th century American Christianity, but since I know virtually nothing about that, I will say nothing more about it. The point is that this is how faith is viewed today. And I think that the Church as a whole is responding - responding well, too - to this perception by talking more about how faith actually leans on reason an awful lot. We believe certain things about God - why? Because X, Y, and Z - we have reasons. I think the ultimate reason is the historicity of the ministry, crucifixion, resurrection, and ascension of Jesus. If those things actually happened, then everything else begins to fall into place. If those things did not happen, then like Paul, we have to say that Christians are the sorriest of people, and we should eat, drink, and be merry, for tomorrow we die.

All in all, a very good discussion last night.

Answering "The God Question"

In this case, The God Question has nothing to do with whether or not God exists or what He's like. It's a question that has been posed by my boss and others in the scientific world, and goes something like this: Suppose you are wondering what the answer is to some question. Now suppose that God comes down and tells you the answer so that you don't have to spend any time or money figuring it out. Now you've got the answer. So what?

That "So what?" is The God Question. And I've been trying to come up with an answer to that question with regard to the study of certain populations of cells in the vocal folds. As I wrote in my last entry, the interaction between epithelial and mesenchymal cells in the regulation of fibrosis seems to do the trick! But of course now I need to get much more detailed so that I know exactly why such and such an experiment moves us toward answering those questions about how things work. I think I will begin by looking into the literature on how mechanical environment affects fibroblasts. For instance, it would be good to know how vocal fold fibroblasts change in stiffness when their substrate changes stiffness, or how they change in stiffness when they are vibrated at high frequencies. It would also be good to know how fibroblast stiffness relates to the secretion of certain pro- and anti-apoptotic signaling molecules (are these cytokines?) into the ECM. Perhaps there is a feedback mechanism in vocal fold fibrosis in which increased ECM tension causes increased fibroblast stiffness, which causes increased anti-apoptotic signaling and ECM deposition, which causes increased ECM tension, which ... ???

Woohoo!! I'm becoming a biologist! (sort of)

A Place to Hang My Hat (both literal and figurative)

I finally have a place to hang my hat! Well, actually we've had this coat/hat stand in the corner of my office for a couple of weeks now, and it's been so nice to have it! I can hang my coat up and my hat & scarf, instead of always putting the coat and scarf on the back of my chair and my hat on my desk or bookshelf. I still put my backpack on the bookshelf, but...


And I think I have finally found a place to hang my hat - figuratively speaking - with regard to my research as a post-doc. I've been struggling for a long time to find/define a project that made sense to me, where I could see what the big picture was, and where I could see some semblance of a connection to speech production. And the hat-rack/theme is: Fibrosis! I'm reading a bunch of papers on pulmonary fibrosis, and it's fascinating stuff. The reason this is particularly fascinating is because I've figured out that I can relate pulmonary fibrosis to vocal fold scarring/fibrosis. Pulmonary fibrosis has been studied a lot, but vocal fold fibrosis mechanisms at the cellular and molecular level have hardly been touched! So there's plenty of work to be done. But there's just enough known that I can read the pulmonary literature and be thinking of specific questions to ask about vocal folds - do they fibrose in similar ways to the lung? Are there similar mechanisms involved? So I can define a large set of experiments to study the mechanisms of vocal fold fibrosis, which is nice because it relates in some very clear ways to speech production - but in doing so I will also be able to relate vocal fold fibrosis to pulmonary fibrosis, which will keep me grounded in the world of respiratory physiology. This is very nice since I am in a respiratory physiology group, and I've been trying to come up with some way to relate my interest in vocal folds to the lung. Another nice thing about this project is that it involves a lot of molecular biology, and the biophysics have not really been touched upon, even in pulmonary fibrosis. So there is definitely room to relate fibrosis to biophysics. Furthermore, studying the biophysical properties of vocal fold epithelial cells and their contribution to vocal fold fibrosis will be useful for pulmonary fibrosis since it is difficult to study the biophysics of alveolar epithelial cells because they are ciliated (I think - maybe that's just bronchial/tracheal epithelial cells?).

Some example questions: Is there evidence of pro-apoptotic signaling in the epithelium of fibrotic vocal folds? Does the stiffness of the ECM affect the migratory and mitotic capabilities of epithelial cells? Do epithelial cells in fibrotic vocal folds have different stiffnesses than in normal vocal folds, and do these different stiffnesses translate to different stresses propagated through the ECM to the fibroblasts and myofibroblasts? How do different stresses on fibroblasts and myofibroblasts affect their function, the laying down of ECM, and the signals they send back to the epithelial cells wrt mitosis, migration, and other functions?

On the side, I have these questions: How do the mechanical properties of the ECM affect the generation of the mucosal wave? Is the stiffness and elasticity of the elastin and collagen in the longitudinal direction really relevant to this, or could it be the density of ECM fibers along the superficial-deep tissue axis, or the stiffness and elasticity of the anchor proteins that bind the epithelium to the ECM or other proteins running along the same (superficial-deep) axis?

Finally Making Progress with Oroqen

I've been making extremely slow progress (over the course of the last 19 months!) analyzing the Oroqen data that I recorded with LJW and FL. In the last few months I have been more aggressively analyzing (though still slowly, since it's all in my 'free time' - it's not part of my post-doc work), and in the last few days I have actually started writing! The paper still has a long ways to go, but at least I'm figuring out what kind of structure to give the paper, and getting some of the tables filled in (or at least started) and starting to figure out what figures to make & include. Given the huge time crunch (this should have been turned in about 3.5 months ago), there is a bunch of data that I will not be able to include simply because I don't have time to make all the measurements. But they will come in a later paper, and in the meantime I am feeling more optimistic about the potential for this paper, even though it will not be as complete and comprehensive as I'd like it to be. Funny, my dissertation was the same way - not as complete and comprehensive as I'd hoped - perhaps this is just the way academic publishing works, and something I need to get used to. In the meantime, I think this paper will be solid, and a valuable contribution to Tungusology and (acoustic phonetic) Typology. Right now this paper is my #1 publishing priority. When it's done... I'm not entirely sure what I will focus on next. I will probably bite the bullet and make a bunch new recordings/measurements of F2 transitions and then write up the locus equation paper that I have in mind. It's already partially written and I already have one bunch of data complete and ready to go, but I think I should replicate the same data with a different speaker whose subglottal resonances I already know by independent means. That will form a crucial control that I'm currently missing, and make the paper that much more convincing. After that? There are a few directions I could focus on, but I don't know yet which one I will work on first. I suppose I'll leave off that decision until I have to deal with it (after the locus equations paper is done). Hopefully I'll be working on a paper that is related to my post-doc work by that time! I'm rather looking forward to what I think my academic career is shaping up to be... A string of speech perception papers, a string of subglottal acoustics papers, a (small-ish) string of Oroqen papers, a string of vocal fold papers... They may not all materialize - "way leads on to way", you know. But I'm feeling better now than I was a month and a half ago about my prospects for developing and following up a coherent, interesting, and valuable line of research. For the time being, it's just hard enough to learn biology and condensed matter physics at the same time that I'm trying to follow up on those speech-y research projects... Don't get me wrong - I'm enjoying my post-doc work. But I'll be so glad when I get my first tenure-track faculty position! September 2009 sounds pretty good...

Some thoughts about post-modernism and science

I've been thinking a lot about post-modernism and its influence in the sciences lately. In ways, it's almost paradoxical. Here we have science, which really started developing quickly into its current form as a result of the Enlightenment and its emphasis on observation and reason. This way of thinking was refined over time and led to positivism which claims that we can't know anything except by our own experience - and particularly that all of our experience is derived from sense-perception. This develops in two different ways: First, it acted as a forerunner to post-modernism because of its claim that all we can know is what we sense-perceive. This is very individualistic, and meshes well with post-modern ideas of individuality plurality, and even relativism since what you experience (sense-perceive) is different from what I experience (sense-perceive) and how can anyone say that one set of experiences is better than another? Sense-perception is inherently individual and inherently neutral. Second, the focus on sense-perception as the only way to know anything was paralleled by work in mathematics which was trying to ground itself on a specific and small number of basic axioms. Could such a set of axioms be defined? Could these axioms be facts of the world that were sense-perceivable, or did they have to be divorced from the material world and simply posited? Kurt Gödel's work showed that a totally consistent and complete system of mathematics could not exist, and that we therefore had to live with the fact that we couldn't know all things by reason alone. [This is very messy exposition, I know, but...] This also played a role in the development of post-modernism. It's no longer ok to work from a given set of assumptions (e.g. F=ma, or conservation of mass, or...), because there may be truths out there for the finding, but not with your particular set of basic axioms/assumptions. So the need for creativity and a multitude of perspectives is emphasized. This is perhaps most easily seen in the humanities and social sciences, or even in current American politics. It forms a part of the argument for quotas in college admissions and in immigration; it is in the rationale behind bipartisanship in Congress (even if it doesn't get carried out in practice); it is in the notion that a book is to be judged by what it means to individual readers; it is in the conception of all religions as equally containing some but never all Truth.

And in science? It seems to me that the emphasis on creativity in the sciences is sometimes overblown. Is creativity important for good scientific work? I think it is. But where does that creativity come from? What role does it actually play in research? One hundred years ago and more people talked about creativity somewhat as though it were simply luck - with statements such as "fortune favors the prepared mind" (Pasteur) and "genius is 1% inspiration and 99% persperation" (Edison). True, these things were said before post-modernism came onto the scene. But sometimes I get worried about the current state and future of science when I hear things like "the point of science is to challenge authority". This sort of statement has been made recently in regard to claims that the Holocaust wasn't so bad, or it was the Jews' fault, or that 9-11 was the Jew's fault, or it was a U.S. conspiracy, or other crazy stuff like that. This argument isn't made in the hard sciences so much, but an analogue to it is very common although usually not explicit. There's "something in the air" that makes young researchers (like me) feel that they have to say something provocative just for the sake of being provocative. (Actually, the claim that scientists need to do provocative research *is* very common and even rather explicit, at least in some fields - and it does make sense to some degree, insofar as it helps to get attention and funding, but it also commonly goes beyond that to being provocative for the sake of being provocative.) There's almost an unspoken law that scientists need to focus on coming up with crazy and provocative ideas and that the rest will then follow. This is played out in a variety of ways, but one way in which it is played out is when the scientist says "I've come up with this radical new theory that accounts for all (or a lot) of the data". Nevermind that the fundamental premises may or may not be hard to swallow (and that is sometimes the point of being provocative), but we often stop after stating the theory and do very little high quality real research to shore up or dismantle the theory. And why not? All of the money and all of the glamour is in the provocative theory itself. There's no glory in the steady stream of technical papers published in less flashy journals, no matter how solid the research actually is.

And here's the paradox... The development of science played an important role in the development of post-modernism, but post-modernism in large part undermines the foundations of science.

So what's going to happen to science? How do we in the sciences (or academia more generally) go about doing excellent science? How will this whole conflict play out over the next 50 years (when people in my generation, who I think are arguably among the first true post-moderns - at least in the sense that I've been thinking about it - will be "taking over" responsibility and leadership from the previous generation(s) of scientists? And what is the role of engineering in all of this? If I might make a prediction, I'd say that the engineering-research schools (MIT, CalTech, etc.) are going to become increasingly prominent, as will engineering-research departments in all schools. Because solving engineering problems is practically-oriented, it must be focused on the rigorous, solid research that will lend itself to developing real applications. No engineer wants to challenge authority unless he has to - it's enough to let Newton remain a major authority figure. I think this also connects with the major developments of funding and research in the biomedical world - it is extremely practically-oriented stuff.

Ok, this is a *way* long enough entry. Some thoughts....some more clearly organized and expressed than others....but some thoughts, all the same.

My New Home

Almost a year later, my second entry here is to announce that I plan to move my blog permanently from Xanga to Blogger. Stay tuned for more entries...