aaron.harnly.net » culture http://harnly.net Sì, abbiamo un'anima. Ma è fatta di tanti piccoli robot. Thu, 11 Mar 2010 14:01:56 +0000 http://wordpress.org/?v=abc en Great article on why we should restrict immigration http://harnly.net/2007/blog/culture/politics/great-article-on-why-we-should-restrict-immigration/ http://harnly.net/2007/blog/culture/politics/great-article-on-why-we-should-restrict-immigration/#comments Thu, 14 Jun 2007 10:20:13 +0000 aaronharnly http://harnly.net/2007/blog/culture/politics/great-article-on-why-we-should-restrict-immigration/ The Atlantic Monthly is running a really hard-hitting, pull-no-punches piece on immigration restriction, and why this is the right time to put the brakes on.

It begins by acknowledging the historical role that immigration has played in our nation:

From the beginning, it has been the policy of the United States, both officially and according to the prevailing sentiment of our people, to tolerate, to welcome, and to encourage immigration, without qualification and without discrimination. For generations, it was the settled opinion of our people, which found no challenge anywhere, that immigration was a source of both strength and wealth.

It goes on to note that support for immigration generally rests on two key ideas:

  1. Immigration boosts our population, which we need because our birthrate is lower.

  2. Immigration brings laborers that do work that Americans are unwilling to do.

These two opinions were, first, that immigration constituted a net reinforcement of our population; secondly, that, in addition to this, or irrespective of this, immigration was necessary, in order to supply the laborers who should do certain kinds of work,…

The article then dismantles each of these two ideas. First, on the idea that we need immigration because our birthrate has declined — in fact, the article shows, our birthrate has declined because of immigration:

The arrival in the United States, … increasingly, of large numbers of degraded peasantry created for the first time in this country distinct social classes, and produced an alteration of economic relations which could not fail powerfully to affect population. The appearance of vast numbers of men, foreign in birth and often in language, with a poorer standard of living, with habits repellent to our native people, of an industrial grade suited only to the lowest kind of manual labor, was exactly such a cause as by any student of population would be expected to affect profoundly the growth of the native population. Americans shrank alike from the social contact and the economic competition thus created. They became increasingly unwilling to bring forth sons and daughters who should be obliged to compete in the market for labor and in the walks of life with those whom they did not recognize as of their own grade and condition.

And second: the idea that we need immigrants to do work that Americans are unwilling to do — this too is turned on its head. In fact, Americans only become unwilling to do certain “degrading” labor only when new groups of immigrants arrive:

Does the Italian come because the Irishman refuses to work in ditches and trenches, in gangs; or has the Irishman taken this position because the Italian has come? The latter is undoubtedly the truth; and if the administrators of Baron Hirsch’s estate send to us two millions of Russian Jews, we shall soon find the Italians standing on their dignity, and deeming themselves too good to work on streets and sewers and railroads. But meanwhile, what of the republic? what of the American standard of living? what of the American rate of wages?

Finally, the article points out that we just don’t have the room to absorb this influx of immigrants any more:

First, we have the important fact of the complete exhaustion of the free public lands of the United States. Fifty years ago, thirty years ago, vast tracts of arable laud were open to every person arriving on our shores, under the Preemption Act, or later, the Homestead Act. A good farm of one hundred and sixty acres could be had at the minimum price of $1.25 an acre, or for merely the fees of registration. Under these circumstances it was a very simple matter to dispose of a large immigration. To-day there is not a good farm within the limits of the United States which is to be had under either of these acts. The wild and tumultuous scenes which attended the opening to settlement of the Territory of Oklahoma, a few years ago, and, a little later, of the so-called Cherokee Strip, testify eloquently to the vast change in our national conditions in this respect.

Finally, the author calls for a national “rest” from immigration, to give our country a chance to recuperate from its devastating effects, before more undesirables arrive:

For one, I believe it is time that we should take a rest, and give our social, political, and industrial system some chance to recuperate. The problems which so sternly confront us to-day are serious enough without being complicated and aggravated by the addition of some millions of Hungarians, Bohemians, Poles, south Italians, and Russian Jews.

And yes, it was written in 1896.

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Don Quixote of Paris, or Inverted Adaptations http://harnly.net/2005/blog/culture/don-quixote-of-paris-or-inverted-adaptations/ http://harnly.net/2005/blog/culture/don-quixote-of-paris-or-inverted-adaptations/#comments Tue, 24 May 2005 23:04:55 +0000 aaronharnly http://harnly.net/blog/culture/don-quixote-of-paris-or-inverted-adaptations I’m trying to think of adaptations (page to screen, page to stage, or any other) in which the adaptations does not merely alter some fundamental aspect of the original story, but indeed entirely inverts it.

Where this started: So Sunday Mrs. Prophet and I went to see the opera Don Quixote down here in Buenos Aires. We had a wonderful time marveling at the opera house and those within it, and by the fourth act really enjoyed the production as well.

But for the first twenty minutes, we both were simply shocked and dismayed. Because, as you probably remember, much of the action and humor of the book revolves around the fact that Quixote proclaims as his “beautiful beloved” a plain, coarse, peasant girl. Everyone else knows perfectly well that this woman is ugly, loose, ill-mannered and entirely undeserving of his title Dulcinea of Toboso. Yet Quixote composes endless love poems exalting her beauty, her refinement, and chasteness, while promising Sancho that he will share some part in her vast riches when Quixote has won her heart.

So we both a little, uh, surprised when the opera begins with Dulcinea, who is, in fact: rich, beautiful, chaste, and refined (though a bit mischievous). Apparently Jules-Émile-Frédéric Massenet, the silly Frenchmen who wrote the opera, had a favorite mezzo-soprano in mind for the part of Dulcinea, and it wouldn’t do well to launch her career playing an ugly wench, would it? So he tidied up the part by inverting it.

Now there are plenty of lousy adaptations out there. But what others can you think of pull this kind of inversion?

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In Which Mithras Does a Poor Imitation of *Far Outliers* http://harnly.net/2005/blog/culture/history/in-which-mithras-does-a-poor-imitation-of-far-outliers/ http://harnly.net/2005/blog/culture/history/in-which-mithras-does-a-poor-imitation-of-far-outliers/#comments Tue, 24 May 2005 22:13:19 +0000 aaronharnly http://harnly.net/blog/autobiography/in-which-mithras-does-a-poor-imitation-of-far-outliers Greetings to all from the Southern of our hemispheres!

Today we have a pair of readings, illustrating the alternately generous and brutal, ultimately xenocidic mindset of 16th century Argentina.

This first excerpt is from the account Voyage to Río de Plata and Paraguay by Ulderico Schmidt, a German soldier and adventurer, published in 1554. Do be patient and read all the way to the end, as it gets rather interesting.

There we built a new town and called it Bonas Aeieres, that is, in German, Guter Wind.

We also brought from Hispania on board the fourteen ships seventy-two horses and mares.

Here, also, we found a place inhabited by Indian folk, named Querandíes, numbering about three thousand people, including wives and children, and they were clothed in the same way as the Charrúas, from the navel to the knees. They brought us fish and meat to eat. Those Querandíes have no houses, but wander about, as do the Gipsies with us at home, and in summer they oftentimes travel upwards of thirty miles on dry land without finding a single drop of water to drink.

And when they meet with deer and other wild beasts, when they have killed them they drink their blood. Also if they find a root, called Cardos, they eat it to slack their thirst. This — namely, that they drink blood — only happens because they cannot have any water, and that they might peradventure die of thirst.

These Querandíes brought us daily their provisions of fish and meat to our camp, and did so for a fortnight, and they did only fail once to come to us. So our captain, Pedro de Mendoza, sent to them, the Querandíes, a judge, named Johan Pabon, with two foot-soldiers, for they were at a distance of four miles from our camp. When our emissaries came near to the Indians, they were all three beaten black and blue, and were then sent back again to our camp. Pedro de Mendoza, hearing of this from the judge’s report (who for this cause raised a tumult about it in our camp), sent Diego Mendoza, his own brother, against them with three hundred foot-soldiers and thirty well-armed mounted men, of whom I also was one, straightaway charging us to kill or take prisoners all these Indian Querandíes and to take possession of their settlement. But when we came near them there were now some four thousand men,for they had assembled all their friends. And when we were about to attack them, they defended themselves in such a way that we had that very day our hands full. They also killed our commander, Diego Mendoza, and six noblemen. Of our foot-soldiers and mounted men over twenty were slain, and on their side about one thousand. Thus did they defend themselves valiantly against us, so that indeed we felt it…

In due course God Almighty graciously gave us the victory, and allowed us to take possession of their place; but we did not take prisoner any of the Indians, and their wives and children also fled away from the place before we could seize them.


And when we returned again to our camp, our folk were divided into those who were to be soldiers, and the others workers, so as to have all of them employed. And a town was built there… The town wall was three foot broad, but that which was built today fell to pieces the day after, so that they suffered great poverty, and it became so bad that the horses could not go. Yea, finally, there was such want and misery for hunger’s sake, that there were neither rats, nor mice, nor snakes to still the great dreadful hunger, and unspeakable poverty, and shoes and leather were resorted to for eating and everything else.

It happened that three Spaniards stole a horse, and ate it secretly, but when it was known, they were imprisoned and interrogated under the torture. Whereupon, as soon as they admitted their guilt, they were sentenced to death by the gallows, and all three were hanged.

Immediately afterwards, at night, three other Spaniards came to the gallows to the three hanging men, and hacked off their thighs and pieces of their flesh, and took them home to still their hunger.

After all this we remained still another month together in great poverty in the town of Bonas Aeieres, until ships could be prepared.

At this time the Indians came in great power and force, as many as twenty-three thousand men, against us and our town of Bonas Aeieres. There were four nations of them, namely, Querandíes, Charrúas, and Timbúes. They all meant to go about to destroy us all. But God Almighty preserved the greater part of us, therefore praise and thanks be to Him always and everlasting, for on our side not more than about thirty men, including commanders and ensign were slain.

– from The Argentina Reader, pp 22-25.

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Brother Spikey Mace of Mild Reason http://harnly.net/2005/blog/culture/religion/brother-spikey-mace-of-mild-reason/ http://harnly.net/2005/blog/culture/religion/brother-spikey-mace-of-mild-reason/#comments Thu, 14 Apr 2005 21:19:52 +0000 aaronharnly http://harnly.net/blog/culture/religion/brother-spikey-mace-of-mild-reason A new religious terror group has emerged. In a field crowded by Islamic radicals, Christian Identity bombers, and of course the various cultists, who else must we fear?

This the Unitarian Jihad. Their manifesto was recently published by Jon Carroll in the San Francisco Chronicle:

Greetings to the Imprisoned Citizens of the United States. We are Unitarian Jihad. There is only God, unless there is more than one God. The vote of our God subcommittee is 10-8 in favor of one God, with two abstentions. Brother Flaming Sword of Moderation noted the possibility of there being no God at all, and his objection was noted with love by the secretary… We are Unitarian Jihad. We are everywhere. We have not been born again, nor have we sworn a blood oath. We do not think that God cares what we read, what we eat or whom we sleep with… We are Unitarian Jihad. We will take over television studios, kidnap so-called commentators and broadcast calm, well-reasoned discussions of the issues of the day. We will appear in public places and require people to shake hands with each other. People of the United States! We are Unitarian Jihad! We can strike without warning. Pockets of reasonableness and harmony will appear as if from nowhere! Nice people will run the government again!

It think the world needs more martyrs for moderation. I might even be willing to commit an act of reasonableness for this outfit; recruiters, feel free to contact me.

Also, thanks to a loose coalition of affiliated cells, you can get your own Unitarian Jihad name.

-Mithras, aka “Brother Spikey Mace of Mild Reason”

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Church and State and all that http://harnly.net/2005/blog/culture/politics/church-and-state-and-all-that/ http://harnly.net/2005/blog/culture/politics/church-and-state-and-all-that/#comments Wed, 06 Apr 2005 13:07:29 +0000 aaronharnly http://harnly.net/blog/culture/politics/church-and-state-and-all-that Image hosted by Photobucket.com

Everyone is talking about Church and State these days. Is America a secular nation, imperiled by a new breed of religious radical? Or is our proud religious and Christian tradition under assault from an unprecedented liberal, anti-religious agenda?

As the above straw men make clear, neither is true. This is a nation founded by and composed of mostly religious Christians, yet with a deeply secular governing tradition. Forces promoting and opposed to religion, and promoting and opposed to the mingling of church and state, have been battling for the past two centuries. These latest kerfuffles are pretty mild in the context of the controversies that have riven the nation before.

An early debate in the drafting of the Constitution in 1787 was whether and how a religious oath should be required of national leaders. The Massachusetts Constitution extended the equal protection of the law, and right to hold office, to any Christian (though Catholics had to swear to renounce papal authority “in any matter, civil, ecclesiastical or spiritual.”) The 1777 New York Constitution implicitly permitted Judaism, but required immigrating Catholics to renounce papal authority, and prohibited Catholics from holding office. The 1776 Maryland Constitution extended “protection in their religious liberty” to “all persons professing the Christian religion” but not Jews or deists.

Only Virginia’s constitution established complete freedom of religious opinions and belief, and explicitly separated civil duties from religion. So it was a matter of some controversy that the Constitutional Congress modeled the federal constitution after Virginia’s, explicitly stating in Article VI that federal officials “shall be bound by Oath or Affirmation, to support this Constitution; but no religious Test shall ever be required as Qualification to any Office or public Trust under the United States.”

In 1794, Thomas Paine, popularizer of the American Revolution, wrote The Age of Reason, a treatise on religion. While he disavowed atheism, he embraced a deist worldview and viciously attacked Christianity and clericalism of all stripes. This did not make him a popular man in America. The book was written in a French jail (where Paine sat because he rejected the overzealous heights of the French Revolution), and Paine stayed in France until 1802.

He returned at the personal invitation of Thomas Jefferson, who had been elected president in 1800. Jefferson himself was not a Christian — he wrote, but declined to publish, The Life and Morals of Jesus of Nazareth, a version of the New Testament with all miracles and theology removed. Paine’s reputation as a radical and anti-Christian preceded him; Jefferson came under furious attack from Federalists for his invitation:

If, during the present season of national abasement, infatuation, folly, and vice, any portent could surprise, sober men would be utterly confounded by an article current in all our newspapers, that the loathesome Thomas Paine, a drunken atheist and the scavenger of faction, is invited to return in a national ship to America by the first magistrate of a free people. A measure so enormously preposterous we cannot yet believe has been adopted, and it would demand firmer nerves than those possessed by Mr. Jefferson to hazard such an insult to the moral sense of the nation. If that rebel rascal should come to preach from his Bible to our populace, it would be time for every honest and insulted man of dignity to flee to some Zoar as from another Sodom, to shake off the very dust of his feet and to abandon America.

Makes Tom Delay look positively civil. (source: Freethinkers: A History of American Secularism by Susan Jacoby)

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While I’m not quite sure that I’m personally ready for such a step, I do find the work of Steve Haworth, body modification artist, quite inspiring:

Image hosted by Photobucket.com Image hosted by Photobucket.com

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A Better September 11 http://harnly.net/2005/blog/culture/history/a-better-september-11/ http://harnly.net/2005/blog/culture/history/a-better-september-11/#comments Mon, 28 Mar 2005 23:15:32 +0000 aaronharnly http://harnly.net/blog/autobiography/a-better-september-11 September 11.

For most of us, the phrase can only evoke September 11, 2001, and its attendant horrors. Perhaps for Chileans it still means September 11, 1973, and the violent end of Chilean democracy.

There is another September 11, however, and I hope to plant its seed within you, lest we think the day was always and only a sad one.

On that day in 1956, the field of cognitive science was born. The Institute of Radio Engineers, a gaggle of nerds of the finest caliber, held a “Symposium on Information Theory” at MIT. On our fateful day, the second day of the conference, three seminal papers were presented: First thing in the morning, Alan Newell and Herbert Simon (later a Nobel Laureate in Economics) presented “The Logic Theory Machine”, an automated theory-proving computer program. A little later, Noam Chomsky, age 29, presented “Three Models for the Description of Language”, which wrenched the study of language from mere sociology to a formal mathematical endeavor. And shortly after that, Princeton psychologist George Miller presented the instant classic, “The Magical Number Seven plus or minus Two”, demonstrating from multiple lines of evidence that our working memory can only handle that many items (a measly 3 bits) at a time.

These disparate papers had a common thread. As Miller wrote in a 2003 reminiscence:

I left the symposium with a conviction, more intuitive than rational, that experimental psychology, theoretical linguistics, and the computer simulation of cognitive processes were all pieces from a larger whole and that the future would see a progressive elaboration and coordination of their shared concerns.

In this new synthesis, psychology, linguistics, mathematics, and the still-infant computer science could be seen not simply as distinct fields sharing a few common elements, but rather as different approaches to a common goal: understanding the information processing in the human brain.

Today cognitive science is recognized as an endeavor unto itself. For some wandering souls like mine, it is the ultimate goal of life, heeding Socrates’ injunction that the unexamined life is not worth living; for what could be more worth examining than precisely this core of our humanity?

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symbolic incoherence http://harnly.net/2005/blog/culture/politics/symbolic-incoherence/ http://harnly.net/2005/blog/culture/politics/symbolic-incoherence/#comments Fri, 25 Mar 2005 12:56:00 +0000 aaronharnly http://harnly.net/blog/culture/politics/symbolic-incoherence So by now we’ve probably all seen the photos of the Terri Schiavo protesters with tape over their mouths:

I’m not going to get into the utter tragedy that is this case. I just want to register my confusion and disappointment at this protest imagery.

Image hosted by Photobucket.com

What is this image supposed to mean?

  1. I am censored by LIFE?
  2. LIFE is the duct-tape of oppression?
  3. Free Terri from LIFE?

Now, if these protesters wore a T-shirt that said LIFE, and then covered their mouths with duct tape on which was scrawled, JUDICIAL TYRANNY, or CULTURE OF DEATH, well, I might disagree but at least it would make sense.

See, this peace protester is using the image correctly:

Image hosted by Photobucket.com

I thought these pro-life types were pretty experienced and savvy protesters, but apparently they need an aesthetic advisor.

Okay, enough snark for the day.

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Network Motifs http://harnly.net/2005/blog/culture/science/network-motifs/ http://harnly.net/2005/blog/culture/science/network-motifs/#comments Fri, 25 Mar 2005 07:39:00 +0000 aaronharnly http://harnly.net/uncategorized/2005/03/network-motifs After a month-long hiatus, thought I’d return with an exposition of a very, very neat paper I read recently. This takes us into the still-inchoate world of computational biology, at the intersection of the platonic mathemtics of computer algorithms and the messy junkyard of cell biology. If you’re not versed in the language, try to hang in there, because it’s all rather interesting.

The paper is Network motifs in the transcriptional regulation network of E. coli, by Shai Shen-Orr, Ron Milo, Shmoolik Mangan, and Uri Alon at the Weizmann Institute in Israel. It was published less than three years ago in Nature, and has already been cited by more than 150 other papers; clearly, the ideas it introduced have caught the imaginations of other researchers.

Before jumping into the paper though, let’s begin by framing what a network is.

Networks A network (also called a graph) is a collection of two things:

  1. nodes, which are some entity that you care about, like people, places, times, or genes.
  2. edges, which express some relationship between nodes. Edges can express a symmetric relation such as “are friends” or “are neighbors”, or a one-directional relationship such as “loves”, “hates”, or “is built from.” We call a network with symmetric relations “undirected networks”, and the other a “directed network” (or graph).
    For example, using characters as our nodes, and love-relationships as our edges, we can draw a small directed network representing the love triangle in Shakespeare’s Twelfth Night:
    Image hosted by Photobucket.com Or, more prosaically, researchers have built a network representing the core connectivity of the Internet: Image hosted by Photobucket.com

Random Networks When scientists wanted to study the behavior of networks, they traditionally assumed that a typical “random graph” had characteristics like a Erdös-Rényi graph, a theoretical construct invented by a pair of fine Hungarian mathematicians; essentially, you start with a bunch of nodes, then flip a (weighted) coin to decide whether to draw an edge connecting each pair of nodes. This process produces a network that looks something like this (figures from Barabási & Oltvai 2004): Image hosted by Photobucket.com If you make a plot of the degree distribution, i.e. how many nodes have 1 edge connected, how many have 2 edges, etc., you get a histogram that looks like this for an Erdös-Rényi random graph: Image hosted by Photobucket.com So the principle characteristic of these Erdös-Rényi random graphs is that most nodes have roughly the same number of edges, equal to the average number of edges per node. These networks are fairly uniform-looking; most nodes are about the same as most other nodes. As a real-life example of such a network, you might imagine people sending a chain letter in a small town; most people with send it to five others, but some might send it to more or fewer.

Scale-free networks Now this is all very well, but when people looked more closely, they began to realize that many real-life networks do not have the characteristics of these Erdös-Rényi random graphs. Rather than having a whole bunch of nodes that are roughly equally likely to have connecting edges, many of these networks are highly non-uniform: they have a small number of highly connected nodes, and a very large number of nodes that just have one or two edges. A typical scale-free network might look like this: Image hosted by Photobucket.com Can you see the “important nodes” in blue? Sometimes those are called “hubs”, just like with “hub cities” for the networks of airlines. And this is the corresponding degree distribution: Image hosted by Photobucket.com This peculiar degree distribution gives these networks the name scale-free, for there is no “typical” node, and the degree distributions follow a power law; there are exponentially more nodes with a small number of edges than those with a great many edges. The Web has been found to be a scale-free network; there are a few pages that have a great many links, and a vast number of pages with very few links. (The connectivity of Internet routers shares this property as well.) And perhaps thanks to the Hollywood star system, the network of actors co-starring in movies in the IMDB is also scale-free.

It turns out that many biological networks are also scale-free; the neurons of C. elegans, the gene regulatory network of E. coli, protein-protein interaction networks in yeast, among many others, are all scale-free.

Scale-free networks can be modeled, or randomly generated by several methods, all different than the procedure described above for producing an Erdös-Rényi random graph. One simple method is to add a new node, and preferentially connect that new node to the more highly connected nodes that already exist. For example, when you create a new web page, you might tend to create links to sites that already have many links to them, because you will have heard about these sites.

Motifs So terrific: Scientists now have a better model for real-life networks. But is it sufficient to know that these real-life networks are scale-free? Can we do mathematical exploration of the characteristics of random scale-free graphs, and apply the lessons learned to the real-life networks? Or do the real-life networks have further unique characteristics that a simple model doesn’t capture?

This is the question that Shen-Orr et al. set out to ask in this interesting paper; the answer, as we shall see, is yes, real-life networks are not just random scale-free networks.

Shen-Orr chose as their first example the gene regulation network of E. coli; it’s a fairly small and well-understood network, so it was a good first target. In this network, each node represents a gene; an arrow is drawn from gene A to gene B if the protein that A encodes acts to alter the rate of expression of gene B (regardless of whether A upregulates or downregulates B).To answer the question of whether random scale-free networks are a good model of this network, they generated thousands of random networks, each of which had the same degree distribution as the original, real network. That is, each of these networks had 178 nodes with one edge, 54 nodes with two edges, etc., just as the original did, but which actual nodes were connected to which was randomized.

Shen-Orr et al. then searched each of these networks for subgraphs, which are just networks within the network, of a certain size. For example, in a directed graph (in which the edges are arrows), there are thirteen possible subgraphs of size three: Image hosted by Photobucket.com They then compared the frequency of occurrence of each of these types in the real network and in the many random networks. This is the fascinating result: Of all those 13 subgraphs of size three, one occurred much more frequently in the real network — number 5 in the diagram. Image hosted by Photobucket.com They dubbed this subgraph a “feed-forward loop”, because if you arrange its nodes like this: Image hosted by Photobucket.com you can imagine gene X exerting influence on gene Z by two pathways: one direct, and one indirect, by regulating gene Y which in turn regulates gene Z. This result means that there is probably some biologically useful property of this type of subgraph. It has been speculated by others that this type of subgraph is a more stable transmitter of information from gene X to gene Z than other possible arrangements, but the role of the feed-forward loop is not yet clear.

Looking at four-node subgraphs, of which there are 199 possible, it was found that the real network had a much higher-than-random frequency of this subgraph, dubbed the “bi-fan”: Image hosted by Photobucket.com Again, work is just beginning on understanding the function of this subgraph, and why the cell apparently considers it so useful. These unusually common subgraphs are called “motifs”, by analogy to the repeated patterns in art, architecture, or gene sequences. Once Shen-Orr et al. prompted people to look for them, people have discovered motifs in all kinds of networks, from a wide spectrum of biological networks, to human-made ones like electrical circuits. Why do biological networks have these motifs? Work is just barely beginning to work out plausible explanations.

One interesting result has to do with a closer look at the “feed-forward loop” motif we saw above. In the context of gene regulation, each edge can either represent a positive or negative effect on the expression of the downstream gene. That means that a feed-forward loop can be one of two types: coherent, or incoherent. A coherent feed-forward loop is one in which the direct path from X to Z has the same net effect as the indirect path; i.e. either both have a positive effect, or both have a negative effect: Image hosted by Photobucket.com

In an incoherent feed-forward loop, the effect from one direction is contradicted by the effect from the other direction: Image hosted by Photobucket.com

Shen-Orr et al. found that 85% of the feed-forward loops in the E. coli regulatory network are coherent. Why should this be? It makes a certain amount of “sense” that you’d want to have the overall regulatory effect of turning on gene X be coherent, but there’s still lots to learn. One recent paper out of India has found that theoretically, one particular type of coherent feed-forward loop is a more stable transmitter of information from X to Z; and indeed, that particular type is the most common. So evolution appears to be selecting for good information flow in her networks, perhaps not surprising, but very interesting.

Conclusions Overall, these results (which have been extended to many other biological and non-biological networks) mean that investigating the mathematical properties of random scale-free networks won’t model the behavior of the E. coli gene regulatory network, or many other biological networks, very well, because they is significantly different than random networks.

Of course, a “random” network is simply one generated by some stochastic process; different processes will produce different types of “random” networks. So far no one has found a simple generative process that produces networks that preferentially contain feedforward-loops and bi-fans, but if someone does, that might yield insights into the function and evolution of biological networks.

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Merry Candlemas! http://harnly.net/2005/blog/culture/history/merry-candlemas-2/ http://harnly.net/2005/blog/culture/history/merry-candlemas-2/#comments Wed, 02 Feb 2005 15:45:00 +0000 aaronharnly http://harnly.net/uncategorized/2007/02/merry-candlemas-2 Merry Candlemas everybody. As apparently only devoted churchgoers, beekeepers, and aging revolutionaries and their game show hosts still remember, it has been 40 days since Christmas (if you’re not a Julianist), and hence time to celebrate the fact that Mary completed her 7 days of uncleanliness, plus her 33 days of continuing in the blood of her purifying, and so brought Jesus into the temple for the first time.

Catholic tradition, established in the 11th century, is to hold a procession of beeswax candles, representing the entry of Light of the World into the Temple.

In England, begining in 1709, personal (private?) candlemaking was forbidden, licenses issued separately to tallow and beeswax chandlers, and a tax applied to the chandlers. In 1834, the candlemaking regulations were lifted, which kicked off an era of innovation, beginning with Joseph Morgan’s 1834 invention of a continuous candlemaking machine, using a piston to eject candles as they solidified. His invention could produce 1500 candles per hour, no doubt causing the unemployment of many a member of the Chandlers Guild.

Alternate history: if Jesus had been a woman, then following the edicts of Leviticus 12:5, Mary would have been unclean for 14 days, and have continued in the blood of her purifying for 66 days, putting Candlemas on March 15.

That most famous March 15 preceded Mary’s by 44 years, of course. But had everyone been observing Candlemas at this time, perhaps Czechoslovakia would have been a nation for one day longer in 1939, or — ironically — Germany forced to wait one more day before achieving formal independence from the Four Powers in 1991. Small changes, small ripples.

best to all

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