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User Journal

Journal Journal: A couple brainstorms on theoretical biology 3

I recently blogged a couple brainstorms on potential tools in the field of phylogeny-

Long-term alternatives to our current common-descent model in contexts where horizontal gene transfer is significant;

Logarithmic Evolution Distance, an intuitive computational approach to comparing genomes.

They were a lot of fun to think about; perhaps they'd be fun to read if you like theoretical biology stuff.

User Journal

Journal Journal: Citizendium

I've posted a new blog entry on Citizendium, the Wikipedia competitor that Larry Sanger (co-founder of Wikipedia) is starting. It's probably the most effort I've put into a blog post yet, and there's a good discussion forming (Sanger is among the participants).

If you're interested in Wikipedia and alternative collaborative models, I encourage you to come on over and join in.

User Journal

Journal Journal: Blog Update 6

At long last I've gotten my science webpage/blog up and running- the address is It's currently a smorgasbord of topics, so if you're interested in science there's probably something for you there.

I plan to update it decently often, but my emphasis will be on quality science writing and thinking rather than regular posting.

As with any beginning author, I'm very eager for feedback. Come on over and say hello!

Update: Reworked the neurogenesis post for accuracy and clarity.

User Journal

Journal Journal: Less Than Words Can Say

I recently found a treasure of an online book, Richard Mitchell's Less Than Words Can Say. It's an always eloquent and entertaining- and often clear- critique of American illiteracy in all its varying forms and manifestations. As someone who tries (with varying success, I'm sure) to write well, and who values the attempt in others, I enjoyed it a lot.

If this is your sort of thing, I'd recommend reading it.

The book is available for free online; here's the text of the index, which is itself quite interesting.

Foreword "Words never fail. We hear them, we read them; they enter into the mind and become part of us for as long as we shall live. Who speaks reason to his fellow men bestows it upon them. Who mouths inanity disorders thought for all who listen. There must be some minimum allowable dose of inanity beyond which the mind cannot remain reasonable. Irrationality, like buried chemical waste, sooner or later must seep into all the tissues of thought."

1. The Worm in the Brain "The next step is not taken until you learn to see a world in which worms are eaten and decisions made and all responsible agency has disappeared. Now you are ready to be an administrator."

2. The Two Tribes "There is a curious thing about the way they use their verbs. They have, of course, both passive and active forms, but they consider it a serious breach of etiquette amounting almost to sacrilege to use the active form when speaking of persons."

3. A Bunch of Marks "An education that does not teach clear, coherent writing cannot provide our world with thoughtful adults; it gives us instead, at the best, clever children of all ages."

4. The Voice of Sisera "Jefferson must have imagined an America in which all citizens would be able, when they felt like it, to address one another as members of the same class. That we cannot do so is a sore impediment to equality, but, of course, a great advantage to those who can use the English of power and wealth."

5. "let's face it Fellows" "The questions are good ones. Who does hire teachers who can't spell? Where do they come from? The questions grow more ominous the more we think about them. Just as we suspect that this teacher's ineptitude in spelling is not limited to those two words, so we must suspect that she has other ineptitudes as well."

6. Trifles "Our educators, panting after professionalism, are little interested in being known for a picayune concern with trifles like spelling and punctuation. They would much rather make the world a better place. They have tried on the gowns of philosophers, psychologists, and priests."

7. The Columbus Gap "American public education is a remarkable enterprise; it succeeds best where it fails. Imagine an industry that consistently fails to do what it sets out to do, a factory where this year's product is invariably sleazier than last year's but, nevertheless, better than next year's."

8. The Pill "Thought control, like birth control, is best undertaken as long as possible before the fact. Many grown-ups will obstinately persist, if only now and then, in composing small strings of sentences in their heads and achieving at least a momentary logic. This probably cannot be prevented, but we have learned how to minimize its consequences by arranging that such grown-ups will be unable to pursue that logic very far."

9. A Handout of Material "The propensity for borrowed jargon is always a mark of limited ability in the technique of discursive thought. It comes from a poor education. A poor education is not simply a matter of thinking that components and elements might just as well be called factors; it is the inability to manipulate that elaborate symbol system that permits us to make fine distinctions among such things."

10. Grant Us, O Lord "One of the most important uses of language in all cultures is the performance of magic. Since language deals easily with invisible worlds, it's natural that it provide whatever access we think we have to the world of the spirits."

11. Spirits from the Vasty Deep "Bad writing is like any other form of crime; most of it is unimaginative and tiresomely predictable. The professor of education seeking a grant and the neighborhood lout looking for a score simply go and do as their predecessors have done. The one litanizes about carefully unspecified developments in philosophy, psychology, and communications theory, and the other sticks up the candy store."

12. Darkling Plain English "The bureaucrats who have produced most of our dismal official English will, at first, be instructed to fix it. They will try, but nihil ex nihilo. That English is the mess it is because they did it in the first place and they'll never be able to fix it."

13. Hydra "At one time I thought that I was the victim of a conspiracy myself. I was certain that the Admissions Office had salted my classes with carefully selected students, students who had no native tongue."

14. The Turkeys that Lay the Golden Eggs "The minimum competence school of education is nothing new. We've had it for many years, but we didn't talk about it until we discovered that we could make a virtue of it."

15. Devices and Desires "If you cannot be the master of your language, you must be its slave. If you cannot examine your thoughts, you have no choice but to think them, however silly they may be."

16. Naming and Telling "Two things, then, are necessary for intelligent discourse: an array of names, and a conventional system for telling. The power of a language is related, therefore, to the size and subtlety of its lexicon, its bank of names, and the flexibility and accuracy of its telling system, its grammar."

17. Sentimental Education "The history of mankind hasn't yet provided any examples of a decrease in stupidity and ignorance and their presumably attendant evils, but we have hope. After all, history hasn't provided anything like us, either, until pretty recently."

Critical Bilbliography "I should say, for those who might think these things unusual, that they aren't and that they weren't difficult to find."

User Journal

Journal Journal: When mod points count

As most of you have undoubtedly seen, Slashdot is gathering questions to submit to Wikipedia's Jimmy Wales. I respectfully suggest that, if you have mod points, use them in said story. He's an important, smart person whose answers to these questions will (hopefully) inform Slashdot discussion about Wikipedia in the months to come.

His answers, however, will only be good as the questions posed to him, and one of Slashdot's warts is that the first comments to a story get a disproportionate amount of the moderation. That's where those of you with mod points come in.

Since this (in contrast to most Slashdot discussions) is more-or-less a zero-sum game, I'd suggest being free with the downmods as well as the upmods.

And here's a link to the questions themselves:

User Journal

Journal Journal: Stanford content (free) on iTunes 4

Stanford just put up a bunch of faculty lectures, discussions, interviews, and student-created music up on iTunes. There's supposedly some video up too, though I haven't found that yet. Free as in beer. Content to expand in the coming months.

Although select lectures will be restricted to tuition-paying students, I think this is really cool. It's nice to see land-grant universities such as Stanford actively and boldly contributing to the public good.

I'm currently listening to "Stress and Coping: What Baboons Can Teach Us" by Robert Sapolsky. I can't say that I agree with all of it, but it's interesting.

User Journal

Journal Journal: MGM v. Grokster: working off steam with Lessig

Today the justice system sent a strong message to citizens: promote something by encouraging people to break the law with it, and you're going to get burned. This was in the context of a movie company suing a peer-to-peer company for distributing software that people could use to download movies (illegally)- the court ruled that, insofar as grokster (the p2p company) promoted their software as a tool that could be used for copyright infringement, they were liable for their users' actions. It now goes to a lower court for a ruling on whether grokster actually promoted it as a tool for breaking the law.

That's fine, but given the specific case, I'm a little disappointed. The unfortunate part about this is that the chilling effect of this ruling, and more importantly, the misinterpretations of this ruling, will probably cast a pall over innovation for years and years to come. As many have said, by this standard, Apple would have never dared to make the iPod (you're marketing it as a device that can hold 5,000 songs? Of course you're encouraging people to download music illegally to fill it). It's a shame the court didn't have a different set of priorities. And that they had Souter, the one justice that still refuses to use a computer, write the opinion-- presumably to send some kind of a message. I'm pretty discouraged about it.

I'd like to invite anybody that wants to work off some steam to help revise Lessig's "Code and Other Laws of Cyberspace". You can find the wiki, with more information, here. It's a cool way to run a project to begin with, and maybe some future chief justice will read the book that you helped revise.

Information about the community revision of Code, lifted from the linked webpage:

"Lawrence Lessig first published Code and Other Laws of Cyberspace in 1999. After five years in print and five years of changes in law, technology, and the context in which they reside, Code needs an update. But rather than do this alone, Professor Lessig is using this wiki to open the editing process to all, to draw upon the creativity and knowledge of the community. This is an online, collaborative book update; a first of its kind.

Once the project nears completion, Professor Lessig will take the contents of this wiki and ready it for publication. The resulting book, Code v.2, will be published in late 2005 by Basic Books. All royalties, including the book advance, will be donated to Creative Commons."

The Courts

Journal Journal: Supreme Court ruling in favor of eminent domain

My first reaction to this major supreme court ruling was that the bad guys won. I think, though the court had a point when it said local officials are in a better position to decide when eminent domain should and should not be used, Sandra Day O'Conner said it best with,

"Any property may now be taken for the benefit of another private party, but the fallout from this decision will not be random. The beneficiaries are likely to be those citizens with disproportionate influence and power in the political process, including large corporations and development firms."

It's naive to think that said local officials will not tend to unduly ignore the 'little guy' in favor of well-connected development interests with the ability to oil the various bureaucratic wheels of government. I'm not sure I trust my local official more than some remote judge to impartially and effectively decide when eminent domain should be employed, and to compensate fairly those impacted.
My considered reaction is that perhaps, just perhaps, this precedent is much larger than anyone is imagining.

There's nothing necessarily limiting this ruling to land property, or even physical property. What happens when some organization with nominal jurisdiction claims eminent domain over some intellectual property? Could a city council reassign music copyrights from local record labels back to local artists? Could some governmental body grab a patent from one entity and sell it to another?

Could Brazil use this SCOTUS decision to reassign the brazillian patents for various AIDS drugs from U.S. companies to the brazillian public domain, in the name of the public good, without the hassles of nationalization?

Here's what I'll say: this thing is bigger than it appears, and I don't know what's going to happen.

I invite you to leave your comment.

User Journal

Journal Journal: For the layman interested in physics 1

I stumbled across a perfectly wonderful homepage the other day- it has not only the hands-down best introduction to string theory I've ever read (various levels available- learn how your universe works!) but a lot of other content and a lot of 'good feeling'.

At the bottom of the homepage he writes in hindi(?) and english, "May everyone be happy". Indeed.

User Journal

Journal Journal: George Washington 3

I'd just like to leave you with an excerpt of George Washington's farewell speech. It's a portion that seems rather applicable to present-day politics.

"I have already intimated to you the danger of parties in the State, with particular reference to the founding of them on geographical discriminations. Let me now take a more comprehensive view, and warn you in the most solemn manner against the baneful effects of the spirit of party generally.

This spirit, unfortunately, is inseparable from our nature, having its root in the strongest passions of the human mind. It exists under different shapes in all governments, more or less stifled, controlled, or repressed; but in those of the popular form it is seen in its greatest rankness and is truly their worst enemy....

It serves always to distract the public councils and enfeeble the public administration. It agitates the community with ill-founded jealousies and false alarms; kindles the animosity of one part against another; foments occasionally riot and insurrection. It opens the door to foreign influence and corruption, which finds a facilitated access to the government itself through the channels of party passion. Thus the policy and the will of one country are subjected to the policy and will of another.

There is an opinion that parties in free countries are useful checks upon the administration of the government, and serve to keep alive the spirit of liberty. This within certain limits is probably true; and in governments of a monarchical cast patriotism may look with indulgence, if not with favor, upon the spirit of party. But in those of the popular character, in governments purely elective, it is a spirit not to be encouraged. From their natural tendency it is certain there will always be enough of that spirit for every salutary purpose; and there being constant danger of excess, the effort ought to be by force of public opinion to mitigate and assuage it. A fire not to be quenched, it demands a uniform vigilance to prevent its bursting into a flame, lest, instead of warming, it should consume.

It is important, likewise, that the habits of thinking in a free country should inspire caution in those intrusted with its administration to confine themselves within their respective constitutional spheres, avoiding in the exercise of the powers of one department to encroach upon another. The spirit of encroachment tends to consolidate the powers of all the departments in one, and thus to create, whatever the form of government, a real despotism.... If in the opinion of the people the distribution or modification of the constitutional powers be in any particular wrong, let it be corrected by an amendment in the way which the Constitution designates. But let there be no change by usurpation; for though this in one instance may be the instrument of good, it is the customary weapon by which free governments are destroyed. The precedent must always greatly overbalance in permanent evil any partial or transient benefit which the use can at any time yield."

-- George Washington, September 17, 1796

Excerpted from

User Journal

Journal Journal: The single-issue voter

Even though a canidate's position on a single issue, copyright/patent law, will definitely sway me to vote for or against him/her, I don't think I'm a single issue voter because I feel their approach towards this issue highlights a pervasive, systemic attitude toward issues in general. If they are against my opinion in this realm, even if I agree with them almost everywhere else, it strongly implies that there's some deep flaw with that politician that is brought to light in this issue.

And... if I actually took this position I'd almost certainly be wrong- people can have differences in opinion on an isolated issue but still share a philosophy on most other issues.

Most single issue voters don't think they're single issue voters because they're mislead by this illusion, and vote worse because of it.

The Courts

Journal Journal: A small patch to the US's legal system

In any lawsuit, both sides should be required to keep track of their legal costs and once a verdict is reached, the losing side should be required (in addition to the judge's verdict) to remit an amount equal to their total legal expenses to the winning side.

Hypothetical situation: Boeing bought land near my house and started pumping out manufacturing pollutants and I sued them over it. I hired a moderately-price lawyer, and they hired 20 high-price lawyers. If they win, I'd fork over an amount of money equal to the money I've payed my lawyer. If they win, they'd fork over an amount of money equal to the money they've payed their 20 lawyers (in addition to carrying out the court's verdict).

This would considerably reduce frivolous lawsuits (as if a plaintif lost there would be consequences), encourage people to follow through with lawsuits in cases where they believe they are in the right, and create a more even legal playing field between those with resources and those without.

You heard it here first.

Edit: Perhaps let's limit this to civil cases. It'd be absolutely perfect in tort cases, for instance.

I think one could easily ask for this in a settlement, even if it's not made law (though only if you're the plaintiff in a case): some people include recouping their legal fees in requested settlements; I think folks could deem this "Reverse Legal Fees" and ask for this in addition to the court's verdict, instead of asking for regular legal fees.

Journal Journal: CmdrTaco Journal- Right on.

Whether this will get back to CT I don't know- but I'd like to give a big thanks to CmdrTaco for his recent journal entry thoughts.

In the journal entry before last I expressed some concerns about Slashdot, and how I didn't think I was alone in them- this update makes me think that these concerns are know about and, eventually, will be dealt with.

After thinking about it, I'd also like to apologize for my potshot at the editor michael.

Ok. Before this journal turns into a lovefest, I'm out to play some frisbee.


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Is it possible that software is not like anything else, that it is meant to be discarded: that the whole point is to always see it as a soap bubble?