Quick note: I’m experimenting with showing ads on the blog. In my time with scientopia, I dumped a frankly ridiculous amount of money into keeping things online – it ended up coming to around $4K/year. Obviously, this site is a lot cheaper, since I only need to support the one blog, but still, I’d like to get to the point where it’s self-supporting.
If the ads are annoying, let me know. I’m trying to strike a compromise. I’d like to get some money coming in to cover hosting costs, but I don’t want to degrade the experience of my readers. The way I’ve set it up, the ads shouldn’t have popups, and they shouldn’t have any interactive animations. If you see anything like that, please let me know as soon as possible, and I’ll do my best to get it fixed. At the moment, the visual appearance of the ads is less than idea, but I’ll be tweaking it until it’s reasonable. (For now, things are still in process with Google, so all you see is a big yellowish box as a placeholder; as soon as someone at Google gets around to approving it, that should be replaced by ads.
If ads are offensive, again, let me know. I don’t want to be giving exposure to blatantly offensive rubbish.
If ads are pseudoscience or that sort of thing, I don’t care. I believe that the people who read this blog are intelligent enough to realize what a sham that crap is, and I have no problem taking money from them – every cent they waste buying ads on my blog is a cent that they’re not using for something a lot worse!
My mom died last friday night, a little bit after midnight. I’ll probably write something about her, when I’m feeling up to it, but not yet. Being a jewish dad, when I’m depressed, what do I do? I cook.
Last year, for the first time ever, I made homemade gefilte fish for Pesach. If you didn’t grow up Jewish, odds are you’re not familiar with gefilte fish. It’s a traditional ashkenazi (that is, eastern european jewish) dish. It was originally a ground fish mixture cooked inside the body cavity of a fish. It evolved into just the stuffing mixture, simmered in a fish stock. These days, most people just buy it in a jar. If you grew up with it, even out of the jar, it’s a treat; if you didn’t, and you’ve been exposed to it, it looks and smells like dog food.
Honestly, I love the stuff. In general, I’m not a big fan of most traditional Jewish foods. But there’s something about gefilte fish. But even as I enjoy it, I can see the gross side. It’s crazy overprocessed – I mean, come on – it’s fish that will keep, unrefrigerated, for years!
But made fresh, it’s a whole different kettle of fish. This stuff is really good. You’ll definitely recognize the flavor of this as gefilte fish, but it’s a much cleaner flavor. It tastes like fish, not like stale overprocessed fish guts.
So this year, I’m depressed over my mom; after the funeral, I sent my wife out to buy me a bunch of fish, and I made up a batch. This time, I kept notes on how I did it – and it turned out even better than last year.
It’s got a bit of a twist in the recipe. I’m married to a chinese woman, so when the Jewish holidays roll around, I always try to find some way of putting an asian spin on the food, to reflect the nature of our family. So when I cooked the gefilte fish, instead of cooking it in the traditional simple fish broth, I cooked it in dashi. It’s not chinese, but it’s got a lot of flavors that are homey for a chinese person.
So… here’s the recipe for Mark’s homemade salmon dashi gefilte fish!
2 whole pike, gutted and cleaned, but with skin, head, and bones
2 whole red snapper, gutted and cleaned, but with skin, head and bones
2 pounds salmon filet
3/4 to 1 cup matzoh meal
salt (to taste)
2 sheets of konbu (japanese dried kelp)
2 handfulls dried shaved bonito
4 or 5 slices of fresh ginger, crushed
2 large carrots
(For the fish for this, you really want the bones, the skins, and the head. If you’ve got a fish market that will fillet it for you, and then give you all of the parts, have them do that. Otherwise, do it yourself. Don’t worry about how well you can fillet it – it’s going to get ground up, so if you do a messy job, it’s not a problem.)
First thing, you need to make the stock that you’ll eventually cook the gefilte fish in:
If the fish store didn’t fillet the fish for you, you need to remove the filets from the fish, and then remove the skin from the filets.
Put all of the bones, skin, and head into a stock pot.
Cover the fish bones with with water.
Add one onion, and all of the garlic and ginger to the pot.
Heat to a boil, and then simmer for two hours.
Strain out all of the bones, and put the stock back into the pot and bring to a boil.
Add the kombu to the stock, and let it simmer for 30 minutes.
Remove from the heat, and strain out the kombu.
Add the bonito (off the heat), and let it sit for 15 minutes.
Strain out the bonito and any remaining solids.
Add salt to taste.
While the stock is simmering, you can get started on the fish:
Cut all of the fish into chunks, and put them through a meat grinder with a coarse blade (or grind them coarsely in batches in best food processor you can get your hands on.
Cut the onion and carrots into chunks, and put them through the grinder as well.
Beat the eggs. Fold the eggs and the salt into the ground fish mixture.
Add in maztoh meal gradually, until the mixture holds together.
Refrigerate for two hours.
Now you’re ready to cook the gefilte fish!
Heat the stock up to a gentle simmer.
Scoop up the fish into balls containing about two tablespoons of the fish mixture, and roll them into balls.
Add the fish balls into the simmering stock. Don’t overcrowd the pot – add no more than can fit into the pot in a single layer.
Simmer for 10-15 minutes until the fish balls are cooked through.
Remove the balls from the simmering liquid. Repeat until all of the fish is cooked.
Put all the cooked fish balls back into the stock, and refrigerate.
I’m coming in to this a bit late, but since I really do care about the online science blogging community,I still have something that I want to say.
For those who don’t know, there’s a complete horses ass named Henry Gee. Henry is an editor at the science journal Nature. Poor Henry got into some fights with DrIsis (a prominent science blogger), and DrIsis was mean to him. The poor little guy was so hurt that he decided that he needed to get back at her – and so, Henry went ahead and he outed her, announcing her real name to the world.
This was a thoroughly shitty thing to do.
It’s not that I think Isis didn’t do anything wrong. We’ve got history, she and I. My experience with her led me to conclude that she’s a petty, vicious bully that takes great pleasure in inflicting pain and anguish on other people. She’s also someone who’s done a lot of good things for her friends, and if you want to find out about any of it, go read another blog – plenty of people have written about her in the last couple of days.
If she’s so awful, why do I care that someone outed her?
Because it’s not just about her.
The community that we’re a part of isn’t something which has been around for all that long. There’s still a lot of fudging around, figuring out the boundaries of our online interactions. When people play games like outing someone who’s using a pseudonym, they’re setting a precedent: they’re declaring to the community that “I know Xs real name, and here it is”. But beyond that, they’re also declaring to the community that “I believe that our community standards should say that this is an appropriate way to deal with conflict”.
I don’t want that to be something that people in my community do.
People use pseudonyms for a lot of different reasons. Some people do for bad reasons, like separating unethical online behavior from their professional identity. But some people do it to avoid professional retaliation for perfectly reasonable behaviors – there are tenure committees at many universities that would hold blogging against a junior faculty; there are companies that don’t won’t allow employees to blog under their real names; there are people who blog under a pseudonym in order to protect themselves from physical danger and violence!
Once you say “If someone makes me angry enough, it’s all right for me to reveal their real identity”, what you’re saying is that none of those reasons matter. Your hurt feelings take precedence. Bloggeroid tells you how to blog successfully so you avoid all of this. You’ve got the right to decide whether their reasons for using a pseudonym areimportant enough to protect or not.
Sorry, but no. People’s identities belong to them. I don’t care how mean someone is to you online: you don’t have the right to reveal their identity. Unless someone is doing something criminal, their identity isn’t yours to reveal. (And if they are doing something criminal, you should seriously consider reporting them to the appropriate legal authorities, rather than screwing around online!)
But to be like Mr. Gee, and just say “Oh, she hurt my feelings! I’m going to try to hurt her back”! That’s bullshit. That’s childish, kindergarten level bullshit. And frankly, for someone who’s an editor at a major scientific journal, who has access to all sorts of information about anonymous referees and authors? It’s seriously something that crosses the line of professional ethics to the point where if I were in the management at Nature, I’d probably fire him for it.
But Henry didn’t stop there: no! He also went ahead and – as an editor of Nature! – told people who criticized him for doing this that he want “adding them to the list”.
What kind of list do you think Henry is adding them to? This guy who’s showed how little he cares about ethics – what do you think he’s going to do to the people who he’s adding to his list?
I think that if Nature doesn’t fire this schmuck, there’s something even more seriously wrong over there than any of us expected.
What’s a subset? That’s easy: if we have two sets A and B, A is a subset of B if every member of A is also a member of B.
We can take the same basic idea, and apply it to something which a tad more structure, to get subgroups. What’s a subgroup? If we have two groups A and B, and the values in group A are a subset of the values in group B, then A is a subgroup of B.
The point of category theory is to take concepts like “subset” and generalize them so that we can apply the same idea in many different domains. In category theory, we don’t ask “what’s a subset?”. We ask, for any structured THING, what does it mean to be a sub-THING? We’re being very general here, and that’s always a bit tricky. We’ll start by building a basic construction, and look at it in terms of sets and subsets, where we already understand the specific concept.
In terms of sets, the most generic way of defining subsets is using functions. Suppose we have a set, A. How can we define all of the subsets of A, in terms of functions? We can do it using injective functions, as follows. (As a reminder, a function from X to Y where every value in X is mapped to a distinct function in y.)
For the set, A, we can take the set of all injective functions to A. We’ll call that set of functions Inj(A).
Given Inj(A), we can define equivalence classes over Inj(A), so that and are equivalent if there is an isomorphism between X and Y.
The domain of each function in one of the equivalence classes in Inj(A) is a function isomorphic to a subset of A. So each equivalence class of injective functions defines a subset of A.
And there we go: we’ve got a very abstract definition of subsets.
Now we can take that, and generalize that function-based definition to categories, so that it can define a sub-object of any kind of object that can be represented in a category.
Before we jump in, let me review one important definition from before; the monomorphism, or monic arrow.
A monic arrow is an arrow such that
(That is, if any two arrows composed with in end up at the same object only if they are the same.)
So, basically, the monic arrow is the category theoretic version of an injective function. We’ve taken the idea of what an injective function means, in terms of how functions compose, and when we generalized it, the result is the monic arrow.
Suppose we have a category , and an object . If there are are two monic arrows and , and
there is an arrow such that , then we say (read “f factors through g”). Now, we can take that “≤” relation, and use it to define an equivalence class of morphisms using .
What we wind up with using that equivalence relation is a set of equivalence classes of monomorphisms pointing at A. Each of those equivalence classes of morphisms defines a subobject of A. (Within the equivalence classes are objects which have isomorphisms, so the sources of those arrows are equivalent with respect to this relation.) A subobject of A is the sources of an arrow in one of those equivalence classes.
It’s exactly the same thing as the function-based definition of sets. We’ve created a very general concept of sub-THING, which works exactly the same way as sub-sets, but can be applied to any category-theoretic structure.
A quick administrative note. For people reading this blog via RSS readers, there’ve been problems with LaTeX equations for a couple of months. I’ve set up a local tex server and tweak the configurations. Hopefully, now everyone will be able to see the math stuff.
As a test, . If you still get an error box instead of an equation, please drop me an email.
Just a quick administrative note. For the last few days, there’s been a huge increase in spam comments. As a result, I’m tightening up the spam filters to prevent them from getting posted even for a brief period. As a result, legitimate comments may take longer to appear. If you have a comment that should have appeared, and it still hasn’t shown up after a few hours, feel free to send me an email, and I’ll bounce over and release it as soon as possible.
So, via Panda’s Thumb, I hear that Granville Sewell is up to his old hijinks. Sewell is a classic creationist crackpot, who’s known for two things.
First, he’s known for chronically recycling the old “second law of thermodynamics” garbage. And second, he’s known for building arguments based on “thought experiments” – where instead of doing experiments, he just makes up the experiments and the results.
The second-law crankery is really annoying. It’s one of the oldest creationist pseudo-scientific schticks around, and it’s such a terrible argument. It’s also a sort-of pet peeve of mine, because I hate the way that people generally respond to it. It’s not that the common response is wrong – but rather that the common responses focus on one error, while neglecting to point out that there are many deeper issues with it.
In case you’ve been hiding under a rock, the creationist argument is basically:
The second law of thermodynamics says that disorder always increases.
Evolution produces highly-ordered complexity via a natural process.
Therefore, evolution must be impossible, because you can’t create order.
The first problem with this argument is very simple. The second law of thermodynamics does not say that disorder always increases. It’s a classic example of my old maxim: the worst math is no math. The second law of thermodynamics doesn’t say anything as fuzzy as “you can’t create order”. It’s a precise, mathematical statement. The second law of thermodynamics says that in a closed system:
is the entropy in a system,
is the amount of heat transferred in an interaction, and
is the temperature of the system.
Translated into english, that basically says that in any interaction that involves the
transfer of heat, the entropy of the system cannot possible be reduced. Other ways of saying it include “There is no possible process whose sole result is the transfer of heat from a cooler body to a warmer one”; or “No process is possible in which the sole result is the absorption of heat from a reservoir and its complete conversion into work.”
Note well – there is no mention of “chaos” or “disorder” in these statements: The second law is a statement about the way that energy can be used. It basically says that when
you try to use energy, some of that energy is inevitably lost in the process of using it.
Talking about “chaos”, “order”, “disorder” – those are all metaphors. Entropy is a difficult concept. It doesn’t really have a particularly good intuitive meaning. It means something like “energy lost into forms that can’t be used to do work” – but that’s still a poor attempt to capture it in metaphor. The reason that people use order and disorder comes from a way of thinking about energy: if I can extract energy from burning gasoline to spin the wheels of my car, the process of spinning my wheels is very organized – it’s something that I can see as a structured application of energy – or, stretching the metaphor a bit, the energy that spins the wheels in structured. On the other hand, the “waste” from burning the gas – the heating of the engine parts, the energy caught in the warmth of the exhaust – that’s just random and useless. It’s “chaotic”.
So when a creationist says that the second law of thermodynamics says you can’t create order, they’re full of shit. The second law doesn’t say that – not in any shape or form. You don’t need to get into the whole “open system/closed system” stuff to dispute it; it simply doesn’t say what they claim it says.
But let’s not stop there. Even if you accept that the mathematical statement of the second law really did say that chaos always increases, that still has nothing to do with evolution. Look back at the equation. What it says is that in a closed system, in any interaction, the total entropy must increase. Even if you accept that entropy means chaos, all that it says is that in any interaction, the total entropy must increase.
It doesn’t say that you can’t create order. It says that the cumulative end result of any interaction must increase entropy. Want to build a house? Of course you can do it without violating the second law. But to build that house, you need to cut down trees, dig holes, lay foundations, cut wood, pour concrete, put things together. All of those things use a lot of energy. And in each minute interaction, you’re expending energy in ways that increase entropy. If the creationist interpretation of the second law were true, you couldn’t build a house, because building a house involves creating something structured – creating order.
Similarly, if you look at a living cell, it does a whole lot of highly ordered, highly structured things. In order to do those things, it uses energy. And in the process of using that energy, it creates entropy. In terms of order and chaos, the cell uses energy to create order, but in the process of doing so it creates wastes – waste heat, and waste chemicals. It converts high-energy structured molecules into lower-energy molecules, converting things with energetic structure to things without. Look at all of the waste that’s produced by a living cell, and you’ll find that it does produce a net increase in entropy. Once again, if the creationists were right, then you wouldn’t need to worry about whether evolution was possible under thermodynamics – because life wouldn’t be possible.
In fact, if the creationists were right, the existence of planets, stars, and galaxies wouldn’t be possible – because a galaxy full of stars with planets is far less chaotic than loose cloud of hydrogen.
Once again, we don’t even need to consider the whole closed system/open system distinction, because even if we treat earth as a closed system, their arguments are wrong. Life doesn’t really defy the laws of thermodynamics – it produces entropy exactly as it should.
But the creationist second-law argument is even worse than that.
The second-law argument is that the fact that DNA “encodes information”, and that the amount of information “encoded” in DNA increases as a result of the evolutionary process means that evolution violates the second law.
This absolutely doesn’t require bringing in any open/closed system discussions. Doing that is just a distraction which allows the creationist to sneak their real argument underneath.
The real point is: DNA is a highly structured molecule. No disagreement there. But so what? In the life of an organism, there are virtually un-countable numbers of energetic interactions, all of which result in a net increase in the amount of entropy. Why on earth would adding a bunch of links to a DNA chain completely outweigh those? In fact, changing the DNA of an organism is just another entropy increasing event. The chemical processes in the cell that create DNA strands consume energy, and use that energy to produce molecules like DNA, producing entropy along the way, just like pretty much every other chemical process in the universe.
The creationist argument relies on a bunch of sloppy handwaves: “entropy” is disorder; “you can’t create order”, “DNA is ordered”. In fact, evolution has no problem with respect to entropy: one way of viewing evolution is that it’s a process of creating ever more effective entropy-generators.
Now we can get to Sewell and his arguments, and you can see how perfectly they match what I’ve been talking about.
Imagine a high school science teacher renting a video showing a tornado sweeping through a town, turning houses and cars into rubble. When she attempts to show it to her students, she accidentally runs the video backward. As Ford predicts, the students laugh and say, the video is going backwards! The teacher doesn’t want to admit her mistake, so she says: “No, the video is not really going backward. It only looks like it is because it appears that the second law is being violated. And of course entropy is decreasing in this video, but tornados derive their power from the sun, and the increase in entropy on the sun is far greater than the decrease seen on this video, so there is no conflict with the second law.” “In fact,” the teacher continues, “meteorologists can explain everything that is happening in this video,” and she proceeds to give some long, detailed, hastily improvised scientific theories on how tornados, under the right conditions, really can construct houses and cars. At the end of the explanation, one student says, “I don’t want to argue with scientists, but wouldn’t it be a lot easier to explain if you ran the video the other way?”
Now imagine a professor describing the final project for students in his evolutionary biology class. “Here are two pictures,” he says.
“One is a drawing of what the Earth must have looked like soon after it formed. The other is a picture of New York City today, with tall buildings full of intelligent humans, computers, TV sets and telephones, with libraries full of science texts and novels, and jet airplanes flying overhead. Your assignment is to explain how we got from picture one to picture two, and why this did not violate the second law of thermodynamics. You should explain that 3 or 4 billion years ago a collection of atoms formed by pure chance that was able to duplicate itself, and these complex collections of atoms were able to pass their complex structures on to their descendants generation after generation, even correcting errors. Explain how, over a very long time, the accumulation of genetic accidents resulted in greater and greater information content in the DNA of these more and more complicated collections of atoms, and how eventually something called “intelligence” allowed some of these collections of atoms to design buildings and computers and TV sets, and write encyclopedias and science texts. But be sure to point out that while none of this would have been possible in an isolated system, the Earth is an open system, and entropy can decrease in an open system as long as the decreases are compensated by increases outside the system. Energy from the sun is what made all of this possible, and while the origin and evolution of life may have resulted in some small decrease in entropy here, the increase in entropy on the sun easily compensates this tiny decrease. The sun should play a central role in your essay.”
When one student turns in his essay some days later, he has written,
“A few years after picture one was taken, the sun exploded into a supernova, all humans and other animals died, their bodies decayed, and their cells decomposed into simple organic and inorganic compounds. Most of the buildings collapsed immediately into rubble, those that didn’t, crumbled eventually. Most of the computers and TV sets inside were smashed into scrap metal, even those that weren’t, gradually turned into piles of rust, most of the books in the libraries burned up, the rest rotted over time, and you can see see the result in picture two.”
The professor says, “You have switched the pictures!” “I know,” says the student. “But it was so much easier to explain that way.”
Evolution is a movie running backward, that is what makes it so different from other phenomena in our universe, and why it demands a very different sort of explanation.
This is a perfect example of both of Sewell’s usual techniques.
First, the essential argument here is rubbish. It’s the usual “second-law means that you can’t create order”, even though that’s not what it says, followed by a rather shallow and pointless response to the open/closed system stuff.
And the second part is what makes Sewell Sewell. He can’t actually make his own arguments. No, that’s much too hard. So he creates fake people, and plays out a story using his fake people and having them make fake arguments, and then uses the people in his story to illustrate his argument. It’s a technique that I haven’t seen used so consistency since I read Ayn Rand in high school.
I had to close down the original comment thread discussing my rant about the crankery of Chris Langan’s CTMU.
The cost in server time to repeatedly retrieve that massive comment thread was getting excessive. All of Scientopia’s server costs are still coming out of my pocket, and I can’t afford a higher server bill. Since the server usage was approaching the point at which we’d need to up the resources (and thus, the bill), something had to be done.
So I shut down comments on that post. Interested parties are welcome to continue the discussion in the comment-thread under this post.
One of the most unusual things about category theory that I really love is category diagrams. In category theory, many things that would be expressed as equations or complex formulae in most mathematical formalisms can be presented as diagrams in category theory. If you are, like me, a very visual thinker, than category diagrams can present information in a remarkably clear form – and the categorical form of many statements of proofs can be much clearer than the alternatives because it can be presented in diagram form.
A category diagram is a directed graph, where the nodes are objects from a category, and the edges are morphisms. Category theorists say that a graph commutes if, for any two paths through arrows in the diagram from node A to node B, the composition of all edges from the first path is equal to the composition of all edges from the second path. (But it’s important to note that you do need to be careful here: merely because you can draw a diagram doesn’t mean that it necessarily commutes, just like being able to write an equation doesn’t mean that the equation is true! You do need to show that your diagram is correct and commutes.)
As usual, an example will make that clearer.
This diagram is a way of expressing the associativy property of morphisms: . The way that the diagram illustrates this is: is the morphism from A to C. When we compose that with , we wind up at D. Alternatively, is the arrow from B to D; if we compose that with , we wind up at D. The two paths: and are both paths from A to D, therefore if the diagram commutes, they must be equal. And the arrows on the diagram are all valid arrows, arranged in connections that do fit the rules of composition correctly, so the diagram does commute.
Let’s look at one more diagram, which we’ll use to define an interesting concept, the principal morphism between two objects. The principle morphism is a single arrow from A to B such that any composition of morphisms that goes from A to B will end up being equivalent to it.
In diagram form, a morphism m is principle if , the following diagram commutes:
In words, this says that is a principal morphism if for every endomorphic arrow , and for every arrow from A to B, is is the result of composing and . There’s also something interesting about this diagram that you should notice: A appears twice in the diagram! It’s the same object; we just draw it in two places to make the commutation pattern easier to see. A single object can appear in a diagram as many times as you want to to make the pattern of commutation easy to see. When you’re looking at a diagram, you need to be a bit careful to read the labels to make sure you know what it means.
One more definition by diagram: is a a retraction pair, and A is a retract of B (written ) if the following diagram commutes:
In my oh-so-abundant free time, I’ve been working on my own little text editor. And one of my motivations is TECO: one of the oldest, and one of the very best, ever written. It’s both a text editor and a programming language – and, in fact, that’s exactly what made it such a brilliant tool. So much of the drudgery of programming is stuff that really could be done by a program. But we’ve spent so much time learning to be fancy that we’ve lost track of that. Nowadays, you can write an emacs lisp program to do the stuff you used to do in TECO; only it’s awkward enough that you usually don’t.
The problem, though, with just re-implementing TECO with a modern UI is that it was designed in a different time. When TECO was written, every byte was critical. And so the language, the syntax, the structure, it was completely ridiculous. And, as a result, it became the world’s most useful pathological programming language. It’s a glorious, hideous, wonderful, horrific piece of computing history
TECO is one of the most influential pieces of software ever written. If, by chance, you’ve ever heard of a little editor called “emacs”; well, that was originally a set of editor macros for TECO (EMACS = Editor MACroS). As a language, it’s both wonderful and awful. On the good side, The central concept of the language is wonderful: it’s a powerful language for processing text, which works by basically repeatedly finding text that matches some kind of pattern, taking some kind of action when it finds it, and then selecting the next pattern to look for. That’s a very natural, easy to understand way of writing programs to do text processing. On the bad side, it’s got the most god-awful hideous syntax ever imagined.