A journal of cognition, computation, cartoons and cooking; physics and phonotactics; academia, art, alcohol and angst.

Monday, August 11, 2008

Cells, visualization, and quantum consciousness nonsense

I'm a big fan of computer visualizations in science, both for the general public and for science students themselves (researchers, too). One project that I've been hoping to get off the ground soon is to build virtual worlds in special relativistic and quantum mechanical domains to help in building the modern "physical intuition" that all us students seem to lack.

Anyway, a couple videos caught my eye that were linked on Brain Windows: I enjoyed the videos by Drew Berry immensely (see Aptosis), as well as Harvard's The Inner Life of the Cell. Many more videos are available at the main site. Berry's videos were especially nice because of the use of environmental sound: there is a lot of useful information that can be effectively transmitted by sound. Accurate or not (and it's not, but neither is the visual information, since the scales of these videos are well below 400nm), it immerses the viewer in the environment.

One thing that kind of got me chuckling was the visualization of cytoskeletal microtubules and cytoplasm ions. Cytoskeletons are a nice modelling problem in physics (and under a lot of research at that), but I also came across them a lot in some light cog sci reading on quantum consciousness, or quantum computation in the brain (sometimes people, especially researchers in the field, confuse the two).

Yes, light cog sci reading. I could put the sum of physics in quantum consciousness theories on a napkin. I've seen two theories dominating the "literature" in this "field", with some overlap. The first is called Quantum Brain Dynamics (QBD), which asserts that applying the wave equations to the water in the brain creates a model for EEG signals while also creating quantum effects of wavefunction collapse and superposition. Then people decided a more convincing, less pseudoscientific mechanism for quantum processes than "water, ordinary water (laced with a healthy dose of LSD)" would be that computation occurs in the cytoskeleton of brain cells.

I won't say anything about the physics, because all the math that they do is probably fine enough, just not very interesting and certainly not enough to draw any conclusions from. But many good scientists (key example being Roger Penrose, a proponent of quantum consciousness theories) can fall victim to biasing their opinions based on how they think things should be. In spite of there being no reason for us to suspect quantum mechanics plays a role in cognition (no evidence for humans being capable of quantum computation, for example, and plenty of evidence that classical mechanics can model many cognitive processes), QBDers invoke it because consciousness is "exotic". I suppose it's an important idea to play around in just because any idea is worth investigating, but without even a mechanism for communication of quantum states between cells in the brain, the attention is very unwarranted. I shouldn't even be calling it a theory, since it has no basis in experimental or theoretical principles and makes no predictions.

Also, I will punch the next person who tells me to watch What The Bleep Do We Know?

Sunday, August 10, 2008

Abortion and animal rights: the post that gets me pipe-bombed

Okay, so physics and philosophy isn't the most exciting thing in the world. Let's talk abortion! I just saw this video that asks abortion protesters whether women who have illegal abortions should go to jail. Most said something along the lines of that women who have abortions are "punished enough".

It's an important question, and has actually changed my mind: from a purely social-pragmatic standpoint, it seems clear that abortion has to be legal. Nobody is prepared to let poor people die on the street, so medical care must be socialized. Nobody is prepared to send desperate women to jail (except for one person in the video), so abortion must be legalized. Makes sense to me.

But I'm pretty terrible at political issues and often flip sides (or do what my brother, an army language/diplomacy officer with an economics degree, tells me). On the abortion issue I've always just stayed out of it - as a man, it's not my place to presume how women perceive life in their bodies, or how their psychology works (lord help us), or anything else about them for that matter. Ethically, I still feel that way - it's not my place to judge. But law must be pragmatic, not necessarily "moral".

But you didn't ask how I felt scientifically: in this sense I think that if it's okay to kill great apes, it's okay to kill fetuses and infants up to three months (or was it years? I can't remember the research) old or so, depending on when they reach a measurable state of self-awareness.

The point is that it's NOT okay to kill great apes, dolphins, elephants, or any other higher animal with demonstrable self-awareness. As said before, I think there may be a measurable phase transition of self-awareness, at which point we must step back and stop invasive testing.

Friday, August 8, 2008

Counting: science we can all count on

I'm browsing blogs regularly now to steal ideas, and this one caught my eye with a funny line from an actual scientific paper quoted in the New York Times:
While attending lectures on dementia, the doctors, Kenneth Rockwood, David B. Hogan and Christopher J. Patterson, kept track of the number of attendees who nodded off during the talks. They found that in an hourlong lecture attended by about 100 doctors, an average of 16 audience members nodded off. “We chose this method because counting is scientific,” the authors wrote in their seminal 2004 article in The Canadian Medical Association Journal. (emphasis added)
Is this the funniest thing ever in a scientific journal? There's the old tale of the paper with a one-sentence abstract, "No, it does not," but I think this is in a league of its own.

Now to over-analyze it with two related questions: is counting scientific, and is it science we can all agree on?

In the mathematics of set theory, we begin to answer that question. In logic, counting numbers is an extension of the propositional logic that is so familiar to lawyers in philosophers (hence, I don't like it much). Also, I've never formally studied logic, am not a logician, and can't do it justice. But being outside my specialty hasn't stopped me so far on this blog.
The counting numbers (integers) are called a mathematical group, while the real numbers as a whole are a field. The main property that defines these sets is closure under some operation, like addition or multiplication. This means that any elements of the set that are operated on will generate other elements of the set: add two numbers and get a number, multiply them and get another number, etc. You cannot add apples and oranges to get a pear is the point.

What is interesting about this subject is that our numbers are only one type of field. There's the complex field, the quaternions, the rationals, vectors, matrices, and all sorts of stuff that do not behave like "counting" should. In matrix multiplication, for example, A*B does not equal B*A: it is noncommutative (in the real world, this is why quantum mechanics works the way it does: the universe is not commutative).

But the concept of a field can be too restrictive. A while back some crackpot math teacher proposed adding a new number to math classes called "nullity." While I could analyze it briefly but incorrectly with my limited topology background, the idea is cleanly shot down by Cale. I would make a simple analogy: we count on a number line that extends to infinity in both directions. But what if we added an extra point to that line where infinity should be? Then we have a closed ring (reminds me of the temperature scale that includes negative temperature, actually). We can even add two more points above and below and get a sphere, or something even more exotic, leaving our simple linear counting structures far behind.

At the same time as we destroy the infallibility of counting, set theory reminds us that it's all good: through homomorphism, we can still understand systems in the real world by ordinary counting. Physics, even though it sees the world in exotic groups and complex fields, still works in a counting framework.

I will address briefly whether or not counting is a universal science. It is not. See an article on the Pirahã tribe for an example of people whose concept of integers fades at "3 or more" (see also the original paper, Nevins et. al.'s response, and Everett's response). And before anybody brings it up, Sapir and Whorf are still idiots. So is Stephen Hawking.

Several Amazonian and Austronesian tribesmen have settled in the cities, many with similarly exotic languages. The human mind can adapt - it's not a slave to language or culture - but you'd have to start learning by counting on your fingers by going back to kindergarten. I wonder again what logic is universal. Obviously it's not first-order or second-order, and I would still argue that it's not even basic propositional: according to me, all logic is learned from the environment.

Thursday, August 7, 2008

Epistemology, logic, and a quantum universe

I stumbled on this old blog post about people who argue that not reducing something to self-evident truths is equivalent to having a foundationless theory of circular logic that doesn't explain anything.

Philosophically, we observe something nice about the universe: symmetry. That is, if I observe some kind of process, then set up the same process some time later (or in some other galaxy somewhere) and observe it again, there won't be any difference. Observed phenomena are invariant in space and time: our universe is consistent. This is great because it gives us the power of prediction - without it, Tom Hanks could never say that "Tomorrow, the sun will rise!"

We need that to do anything in science, and, as I argued in a philosophy essay, symmetry combined with entropy could give rise to deductive logic (a "learned" trait among animal species, perhaps not instinctual?). That gives us the power of evidence and hence experimental science. Maybe other people perceive a different reality (hell, with enough shrooms, you can't count on anything being consistent in the world), so as I said in the last post, the question of who's right is open.

The point I want to bring up is the origin of the universe, because such a scenario requires two assumptions (regardless of the theory used to generate it): quantum fluctuations and symmetry. Symmetry allows, by Noether's Theorem, all the a priori laws of mathematical physics (such as conservation of energy) to hold. But how are we so confident in the quantum nature of reality? I'd just look to the axioms of QFT for inspiration: anything that's not forbidden is required, or, you might say, "Sorry, but while you weren't looking, everything that could possibly happen, happened!"

I imagine the pre-universe to be completely undefined (because any definition means something specific is there), so of course there's symmetry in every metric you want (in any number of dimensions). Now it's just a matter of having something appear out of nowhere, and we have mountains of experimental evidence supporting the notion of a quantum reality. It's philosophically "nice" to have a free lunch appear in a blank-slate universe.

It's not a Q.E.D. moment, but I keep wondering what's Latin for "From nothing, everything," or perhaps more appropriately, "Science: it works, bitches!"

Note my possible circular logic: we observe symmetry, incorporate it in our logical thought, and then assert that it must always exist.

Wednesday, August 6, 2008

Atheistic cosmology does not imply atheism

To conclude my two posts below, I will talk about theism and consciousness. If we don't have or don't need a first cause, is there still room for god?

Incidentally, god is not throwing dice to make quantum mechanics work. It is simply not "how it works" - true randomness is the rule, not the exception. There is a multiverse interpretation of quantum mechanics that would contradict me, but I think that's a bit of a cop-out.

Anyway, I make room for the possibility of god, since other people seem to know god so well. I call myself ignostic, meaning I recognize I have no concept of what god is as other people understand it.

What keeps me from pure atheism is my understanding (or lack thereof) of consciousness. There are certain philosophical problems with it: consciousness is wholly our own phenomenon, yet other people have it, and we can never know for sure if it's the same as ours; it is immutable, in that there is no meta-awareness of a change in awareness; and it appears to have a mostly-definite transition point between consciousness and unconsciousness, a phase transition if you will.

The first two points seem unlike anything we have encountered, and are suggestive of the need for a new physics or an impenetrable barrier for physics (which may leave room for a god). The third point gives me hope that we can crack consciousness with ordinary physics, because we have a clear indication of something measurable that interacts with it.

I have faith in physics and objective reality, but there's little that can be argued against me saying that I may be the only person with true consciousness, or that someone's reality of knowing god is fundamentally and possibly even measurably different from mine.

You might say I am an atheist who believes in (or is at least agnostic about) a god that only others know.

The answer

What do most physicists believe the origin of the universe, or first cause, is?

First of all, I would like to say that if you want more information or need clarification, get it yourself. Wikipedia is an infinitely useful scientific research tool, even though the liberal-artsies hate it for some reason. Alan Guth also has a good, technical but math-light review article.

Assuming we have some familiarity with the Big Bang and evolution, most of the universe seems to work like clockwork if you take it back to 10^-34 seconds after the first explosion of a lot of mass-energy that was the Big Bang, which essentially started in an infinitesimal point, a singularity (which is a fancy word for our ignorance which will be resolved with a theory of quantum gravity).

Where does all that energy come from - what is the first cause, and how do we get something out of nothing? The simple first cause is quantum mechanical fluctuations in the vacuum. Energy can be spontaneously created from nothing, as can mass, as long as it's destroyed quickly. This is a theoretical and observational fact of quantum mechanics.

Quantum mechanics is weird stuff, I know, but if you don't know it and don't care to, all I ask is that you believe it. Believe it because it's the reason why MRI, electron microscopes, and lasers all work, and why we know mathematically how they work to a precision equivalent to knowing the distance from New York to Los Angeles with less than a human-hair's width of error (yes, this is all quantified).

So mass-energy gets created, as does the stuff to destroy it, in the middle of a perfectly symmetrical unscaled pre-universe which we can call the true vacuum, or the simplest state possible (It is only now that we need even consider the specifics of 4D spacetime - up to now all that we care about is symmetry, which ensures our math to work). This mass-energy is no longer vacuum, and so usually it's unstable and destroys itself quickly. But sometimes it's enough to climb into a new kind of stability called a false vacuum, a metastable state, where it can rest easily and not get destroyed. Here's the real kick - this mass-energy can be self-repulsive and actually expand out in the true vacuum, where it can spontaneously (because of quantum mechanics) have pieces break off, either collapsing into the true vacuum or some other, more stable false vacuum. These pieces are trapped inside this false vacuum bubble, and the break-off moment releases lots of energy, up to as much as was used to create this mega-universe in the first place. BANG!

This scenario is quite nice, in that it explains a lot more about the universe than what I've mentioned here (see the WP article on cosmic inflation). It requires two theories: quantum field theory and general relativity, the former of which is the most accurate description of nature ever, and the latter is widely accepted with only some points contested on the largest and smallest scales. One consequence is that it opens the door to multiple universes with differing fundamental constants of nature. It has many flaws, however, which are not addressed and likely won't be addressed until the particles involved in this theory are sorted out and we understand quantum gravity. Another bad point is that since we're in a metastable state, there could be a true vacuum seed that wipes out the entire universe at the speed of light, the ultimate catastrophe. Whatever, you won't feel a thing.

To summarize: quantum mechanics allows for something out of nothing, which can find itself a stable home and with general relativistic theories of gravity will expand out and form Big Bang universes.

A question about life, the universe, and everything

Do regular people know that we're pretty sure what the origin of the universe is? Like, not the Big Bang - that's observational fact - but rather, the origin of the Big Bang and everything that we see and know? Do you realize that we don't need God as even a deistic first cause anymore (though we may need him for other stuff, as I'll explain later)?

I'll explain it all in the next journal post, but I'm curious what non-physicists have to say on this. Do you know that we know, and do you want to know?

(If you're curious and want to Wikipedia it already, I'm referring to Cosmic Inflation, which is a string-theoryless, Hawkingless, and thus very successful model)

Tuesday, August 5, 2008


I came home today to find Patches (my cat, whom I adopted off the street a month and a half ago only to find out she was pregnant) a lot thinner than usual. Sure enough, she had a surprise waiting in my closet behind a bunch of boxes. I'm leaving most of the boxes there for tonight so that they have some security, but I have some low-light pictures posted.

Five kittens: three tabbies, one brown-on-black patches (like Patches, the mother), and one white-on-black splotches (like who I think the father is, another stray who won't come near me).

Name suggestions will be considered, though Maggie (Magnetism) and Tessie (Tesla) are already taken.

Monday, August 4, 2008

Stephen Hawking is to blame for all science misconceptions

A couple weeks ago, I was discussing what I do with a friend. After the usual "wow, physics, that's intense" reaction, he asked how it was going. I told him how classes were becoming annoying, and he said...

"Yeah, I guess at that level it's mostly philosophy anyway."

What??? Is that what people think about modern theoretical physics? Well, I think if you did a properly-formatted survey, the answer would be yes. I doubt there are many people who know that all theoretical physics is applied mathematics and that facts and hypotheses are all in the equations. Who's to blame? who's responsible for this horrible misunderstanding of the most fundamental of sciences? Who wrote bestseller after bestseller implying that unfounded hypotheses in string theory were scientific fact, and that scientific facts could be effectively reduced to cute allegories without a single equation ever printed?

Stephen Hawking.

See - tech - astronomy

Bonus points for who gets the title of this post, a reference to one of the greatest movies of all time (with the greatest Sydney Poitier role of all time!).

So I finished teaching the last AST104 lab on Thursday, which was quite a lame but quick one. It's amazing how much we're able to cram into these non-science kids' heads in a 6-week summer course, but my hope is that they come out of this with two things: first that they appreciate the artistic beauty of what's in the universe, and second that they have some understanding of how science works. For most of these people, this will be the first, last, and only science course they will take in college, so it's absolutely critical that they get particularly the second point.

Now I love astronomy. Always have. But I'm also a physicist, so it makes it easy for me to appreciate it. How about the non-scientists who can get into this stuff - what motivates you? What is it about astronomy that you find interesting, that you'd like to learn more about? The students have a week left of class and then they're done with science for good, but many of them will still be coming to observation nights with me and turning in labs, so I'd like to be able to give them some final word to take home.

And as far as the tech goes, a college education cannot be complete without learning computer operation and basic programming. There is nothing more fundamental to the understanding of logic and scientific thought, and nothing more useful to every field. Programming should be a part of every student's computer education, especially since most students don't need basic computer operation in the first place since they probably know more about them than their teachers.

Common underrated veggies

I'm going to recommend five fruits and vegetables that are underused in American cooking, but often available at grocery stores and absolutely delicious.

1. Jicama - like a carrot, but sweeter and juicier. Can be deep-fried like a healthier french-fry, or just eaten raw with or without dip. Makes great salads and stir-fries as well.

2. Habanero peppers - I spent all last summer making salsas, and habaneros were my favorite pepper not because of their legendary hotness, but just due to the sheer amount of flavor they pack. Carefully remove seeds and the whitish lining inside before using, and use sparingly since they have an awful lot of flavor (and some residual spice), but put it in omelettes, stir-fries, sauces, or anything that you want a summery mexican feel to.

3. Olives - Kalamatas have a very acquired taste to them, and even I really can't stand eating them plain (though canned black olives are fine for me). But like a habanero, they just have a very concentrated flavor and need to be added sparingly - in proper quantities they will add a new dimension to omelettes and salads - another great summer fruit.

4. Artichokes - one of these days I'll use the leaf scrapings as a curry base. These were always my favorite vegetable as a kid - I demanded to have them for my 6th birthday dinner. The hearts are well-known, but the full vegetable makes a great meal - simply steam/boil for an hour, let cool, then pull off leaves and use your teeth to scrape the meat off the inside of each leaf. Finally, you get to the heart and the very best treat at the end. Serve with butter or mayo.

5. Avocado. Christ, need I say more? It's not so underrated, but I may have to spend a month in Mexico this year just so I can eat them every day. Use in everything in large portions. Hell, just plop one on my plate for dinner, I don't care!

The corner grocery birthday cake

It was my birthday a bit more than a month ago. I was waiting for the weekend to party, but as I was talking to my mom on the phone she insisted I spoil myself with a cake. It was 9pm - I wasn't about to make it from scratch. More importantly, my roommates had all moved out a couple days earlier and took all the baking pans.


Trip to corner grocery store: a tiny, tiny place that overcharges on bare essentials for the local hippies who lack cars. I go in looking for something to bake in. The only thing they have a is a chocolate-graham-cracker pie crust. Fine.

Need something for cake. I have an unopened box of spice cake mix - sounds better than mixing my own. That just leaves frosting. I have powdered sugar lying around, and I have cream cheese in the fridge - five minutes later I've got cream cheese frosting. This is starting to sound good...

Pie crust is ready to go, about half-full with batter, in the oven for 20 minutes. Pull it out - now what the hell do I do? I do the obvious thing - I flip it over onto a plate and frost the crust which is now face-up. It's the most geometrical tank-like cake I've ever frosted.

Friends are outside. Moment of truth. We're all taking bites. "Holy s***", someone says, "This is the best cake I've ever eaten". Sure Enough, I finish one piece and I feel like I've eaten the richest thing my stomach could take. Everybody else was floored, too. Not bad for 20 minutes prep. It also looks like it was very difficult to prepare, since it's so perfectly shaped and intricately layered.

Got the idea? Spice cake + chocolate graham crust + cream cheese frosting = win.

Origins: choose your coordinate system carefully

The first post must be a meta-post.

Riv-bar is a kanji mistranscription of my last name, given to me when I competed in my first kendo tournament. I used it as the title for this blog because it reminds me of Planck's constant, h-bar, which describes the scales at which systems behave quantum-mechanically.

This blog will be a dumping ground for recipes, research notes, cartoons, cognition, and admittedly angst, at least until I figure out what kind of posts get the most attention.

My background: I graduated from Case Western Reserve University in 2007 with a BS in Mathematics and Physics and a BA in Linguistics and Computation (self-declared). I finished my first year of grad school in theoretical biophysics, but am taking the year off because I am totally burnt out and am in an identity crisis. As I seek employment in some mathematical field, I also hope to continue exploring the world of research in my area of interest: brain and network theory.