Network biology and the holographic resilience of biological function - lessons from E. coli

A recent groundbreaking study on the genetics of schizophrenia found a varied pattern of large scale "sledgehammer" (as in whack the genes) mutations in many persons with schizophrenia. These are thought to affect varying stages of brain development.

Curiously, the researchers found the same problems in a minority of the "control" group of "normal" people:

Gordon's Notes: schizophrenia

One in twenty seemingly normal people have big, ugly looking mutations that ought to be messing up their brain development. Yet they seem "normal"...

Now another big study explains this strange normality (emphasis mine) ...

Zimmer - Wired 04.18.08

.... In the latest issue of Nature, scientists reported an experiment in which they wreaked havoc with E. coli's network. They randomly added new links between the transcription factors at the top of the microbe's hierarchy. Now a transcription factor could turn on another one that it never had before. The scientists randomly rewired the network in 598 different ways and then stepped back to see what happened to the bacteria.

You might expect that they all died. After all, if you were to pop open the back of an iPod and start linking its components together in random ways, you'd expect it to crash. But that's not what happened.

About 95 percent of the rewired bacteria did just fine with their new networks. They went on with their lives, feeding, growing and dividing. Some even performed better than microbes with the original wiring, under some conditions.

The tolerance these bacteria showed reveals something important about how evolution works. Humans can randomly rewire cells, and so can mutations. There's something about gene networks that allow them to thrive despite these mutations, and, in some cases, to even gain an edge in the evolutionary race.

But scientists don't quite know why a network like the one in E. coli can handle this rewiring so well. The source of their strength lies not in a single molecule -- DNA -- but in a complicated web of relationships. The network itself is the mystery for biologists in the 21st century...

This is of a piece with the discovery that DNA control system have complex topological components, my June 2007 essay on evolved circuits. and reading I've done over the past year on bioinformatics (systems biology) and the modeling of interacting protein networks (interactome) (example).

The blueprint for an organism is emergent. It "appears" through the interaction of the storage elements in DNA and DNA associated packaging, but, like a holographic image, it can "appear" even when pieces of the storage structure are absent or reorganized. This is a shared characteristic of evolved systems on every scale, we see hints of this even in evolved mechanical systems such as the freight train pneumatic braking system. Bacteria, of course, are the most "evolved" of all systems -- far more evolved than mere humans.

That's why major "controllers" of brain development can be disrupted, but, in many cases, the brain can still develop -- differently perhaps. In some settings, the differences might even be advantageous.

How will we understand this emergent control system? We will not be able to do perceive it directly. We will need computational systems to discern the emergent controllers, and to be able to relate a network level "control element" to the set of physical manifestations of the abstract control element in real-world DNA.

Sigh. It all looked so simple in the days of 'one gene, one protein' ...

Update 4/19/08: There's an obvious metaphor for the type of emergence we see here. An example that makes the problem transparently obvious for all of us.

Imagine that I want you to meet me by the science museum at 11:30 am. I could use English or French or draw a picture. In any spoken or written language I could use an enormous variety of words and word order and still communicate my meaning.

If we think of "the meaning" in cellular biology as that which arises from interacting protein networks, then by analogy we can understand that many different gene arrangements and even several somewhat different proteins could produce similar protein network interactions.

Marvelous Gail Collins editorial on Bush's greenhouse 2025 goal

Gail Collins channels the spirit of Molly Ivins...

The Fat Bush Theory - New York Times

...Suppose that two years after taking office, George W. Bush discovered that because of the stress of his job, he had gained 40 pounds and was tipping the scales at 220.

The real-world Bush would immediately barricade himself in the White House gym, refusing all human contact or nourishment until the issue was resolved. But imagine that he regarded getting fat as seriously as he regards melting glaciers, rising oceans and drought and starvation around the planet. In that case, he would set a serious, management-type goal — of, say, an 18 percent reduction in the rate at which he was gaining weight, to be reached within the next decade...

Gail reminds us that Bush's 2002 "goal" was a voluntary 18% reduction in the growth of greenhouse gas emissions by 2012 (we won't achieve this). His 2008 "goal" is a voluntary 100% reduction in the growth of greenhouse gas emissions by 2025. This "goal" is not to achieved by “raise taxes, duplicate mandates or demand sudden and drastic emissions cuts.”

So Bush's reach goal is that the US stabilize greenhouse gas emissions at an level consistent with the complete melting of Greenland's ice cap. This goal will be achieved by technology alone. (Bush does not rule out tax reductions to support technology development.)

John McCain would be not any better.

The Economist on the food crisis

How many people live on $1 a day?

Food | The silent tsunami | Economist.com

...Roughly a billion people live on $1 a day. If, on a conservative estimate, the cost of their food rises 20% (and in some places, it has risen a lot more), 100m people could be forced back to this level, the common measure of absolute poverty. In some countries, that would undo all the gains in poverty reduction they have made during the past decade of growth...

Did you guess a billion?

In addition to the editorial, the Economist has essays on Bangladeshi and Chinese responses to food concerns. In the past the Economist has criticized China's insistence on food self-sufficiency, but they seem to have forgotten that.

They don't have any answers except the most obvious -- we need a billion in food aid quickly and stop the idiotic biofuel subsidies.

We need to a bit more creativity here ...

The infamous fake-Springsteen Vista video: we think it's kind of sweet

An internal Microsoft sales team mock rock video was leaked to the net, to general mockery and derision.

I've seen it 1.5 times, including a full sitting with my wife.

We think it's sweetly silly, though it's just musical enough to be disturbing. My toes almost started tapping, even as my teeth ached. The critics seem to think this was a serious marketing video, but they need a bit of sympathy for the Devil. It's obviously 50% self-mockery and 50% fun.

I wonder what Springsteen thought of it. The man has a sense of humor, but ...

Of course true geeks all want Microsoft to fail badly enough to crack their monopoly, but I really don't see that happening. They've got more cash than ever, they'll fix the worst parts of Vista, eventually the hardware will catch up, and Vista is far more virus resistant than XP. Unfortunately brighter days lie ahead for the sales team.

Do the sheep dogs think they are sheep?

My best explanation for the inexplicable survival of the east african plains ape is that the shepherds are keeping us around. (For mutton or for wool? The Bible is silent on that distinction.)

Shepherds, of course, make use of sheep dogs, which falsely think of themselves as more sheep than wolf.

I thought of that as I described John Halamka for a lecture I'm giving on technology for health record interoperability. From my graphic:

• "John D. Halamka, MD, MS, is Chief Information Officer of the CareGroup Health System, Chief Information Officer and Dean for Technology at Harvard Medical School, Chairman of the New England Health Electronic Data Interchange Network (NEHEN), CEO of MA-SHARE (the Regional Health Information Organization), Chair of the US Healthcare Information Technology Standards Panel (HITSP), and a practicing Emergency Physician"
• sleeps 4-6 hours a night
• wears an RFID chip in his shoulder
• climbs ice-covered cliff faces to relax
• flies 400,000 miles a year
• tries to be nice

Sounds like a sheep dog to me. I'm sure he thinks of himself as human though.

PS. I realized after posting that I should clarify that I'm a major Halamka fan and read everything he writes. It's actually kind of nice to have "the bar" set so high that I can relinquish any competitive aspirations.

Proud to be a geek: stackoverlow.com

At moments like this, I feel an undeserved and irrational pride in being of tribe geek:

stackoverflow.com - Joel on Software

Jeff Atwood and I ...  build a programming Q&A site that's free. Free to ask questions, free to answer questions, free to read, free to index, built with plain old HTML, no fake rot13 text on the home page, no scammy google-cloaking tactics, no salespeople, no JavaScript windows dropping down in front of the answer asking for $12.95 to go away. You can register if you want to collect karma and win valuable flair that will appear next to your name, but otherwise, it's just free...

... Every week, Jeff and I talk by phone (he's in California, I'm in New York), and we're going to record those phone calls and throw them up on the web for you to listen in on, and call it a podcast. We have a lot of trouble keeping on topic, so the podcast may be interesting to you even if you don't want to hear about stackoverflow.com. The first episode is up right now. Eventually I imagine we'll figure out this newfangled "RSS" technology and you'll be able to actually subscribe and get fresh episodes delivered into your ears automatically. All in good time.

Jeff's Announcement

PS I'm still CEO of Fog Creek full time. StackOverflow.com is a joint venture between Fog Creek and Jeff Atwood. He's the full time CEO which means he's calling the shots. I'm sort of a consultant on this one.

From Jeff's description we see how inspiring 'experts-exchange' has been ...

Stackoverflow is sort of like the anti-experts-exchange (minus the nausea-inducing sleaze and quasi-legal search engine gaming) meets wikipedia meets programming reddit. It is by programmers, for programmers, with the ultimate intent of collectively increasing the sum total of good programming knowledge in the world. No matter what programming language you use, or what operating system you call home. Better programming is our goal.

I've followed Joel Spolsky's blog on business and software for several years, and Jeff Atwood's blog for over a year. They're both great writers and teachers with the geek compulsion to advance the world -- as well as their part of the world.

It's the bit about advancing the world that marks the noble geek. Karma counts. Fairness matters. You get and you give.

These two have millions of readers. By virtue of their considerable reputations earned through their writing, they may be able to make this work.

If it does work that will say something interesting about the power of the geek tribe, and of reputations developed entirely online.

Joel has a full-time job, but Jeff has only recently quit his programming job to work on independent projects. I wish him and stackoverlfow.com every success. At the moment the site is entirely audio oriented, so the best way to follow its development will be to subscribe to Jeff's blog.

Kateva.org may be blocked by some corporate filters

A reader tells me that she can't access Gordon's Notes following migration to kateva.org:

Blogger: Gordon's Notes - Post a Comment

My workplace blocks kateva.org (don't know why, I thought they only blocked porn and gambling sites) so I'll have to follow your adventures on my own time. Bummer.

This is indeed odd, since the only pages I've had at kateva.org have been my tech pages, which are pretty plain.

One workaround is to read the blog through a web-based blog reader, which is really the right way to read these things. I use Bloglines, and I also like Google Reader. So if you can get to them, just add http://notes.kateva.org to the reader, choose any feed, and read that way.

Kateva is a made up name we gave our dog, but maybe it's impolite in some language? Or maybe your employer is using a fairly dumb filter that gets fooled by spammers faking the domain name.

I'll ask around ...

Dyer - 4 new articles

Dyer has 4 new articles out:

• Maliki blinked: Sadr came out ahead, but it doesn't matter anyway. Soon America will leave and Iraq will be forgotten.
• Zimbabwe: I'd skip this one, nothing much in it.
• Olympics: The running of the torch was a Hitler invention. (!) Look for trouble in India, and mockery in Australia.
• Nepal: The Maoists won the election.
• Berlusconi; The best of this batch, see below ...

For example:

http://www.gwynnedyer.com/articles/Gwynne%20Dyer%20article_%20%20Berlusconi%20Is%20Back.txt

...To elect Berlusconi once, as Oscar Wilde might have put it, may be regarded as a misfortune. To elect him twice looks like carelessness. But to elect him THREE TIMES is beyond a joke, for he is the most transparent fraud to have held high public office in a major European country since the Second World War. He even makes the late Boris Yeltsin look serious and competent by comparison...

...

My country re-elected George Bush, so I have some sympathy for the shame and horror intelligent Italians must feel today. Between Italy electing Berlusconi, and Nepal electing Maoists terrorists, Democracy is looking a bit peaked.

Gordon's Notes: move appears to have succeeded

The move to notes.kateva.org worked this time. Now we'll see if the feeds are redirecting properly ...

Update 4/15/08: Of course it didn't really work. Google changed the format of RSS feeds from blogspot to the custom domains, and so old RSS feeds don't work. I'm not sure any feeds, Atom or recent vintage RSS subscriptions, are forwarding correctly. Blogger is showing a very odd set of "recent" posts even with the new Atom feed.

Gordon's Notes to move to notes.kateva.org: Take II

The last time I tried to change the url for this blog the move failed. Google says the problem is fixed, so as before ...

Gordon's Notes: Gordon's Notes to move to notes.kateva.org: In theory, no changes required

... The address, however, is about to change to notes.kateva.org, where it will join Gordon's Tech which has been tech.kateva.org for about a year. It will still be published through Blogger, kateva.org is a Google "custom domain"...

... In particular Google doesn't redirect for some legacy Blogger (working) feeds, only for the current feeds.

So if you find this post in your Feed, and then no "it worked" post after it, you should be able to find Gordon's Notes at notes.kateva.org. The Kateva.org main page will also have news of the move.

Most blog readers will reset your "unread" count to 10 posts.

Wish me luck, I'll make the 2nd attempt to relocate tonight April 15th.

Scientific American on compact fluorescent light bulbs - toxic waste or not?

We'd be using compact fluorescent bulbs -- except I'm kind of clumsy. I break a few bulbs every year. According to the EPA a broken bulb is a toxic waste spill. The incongruity of one part of government advocating fluorescents, and another department warning against them, made me dig in my heels ...

... A commenter pointed to this Energy Star Canada document. It's deeply "schizophrenic" in the non-medical sense of term. On the one hand it says:

• These are perfectly safe for your baby's bedroom. Don't worry about them. You could break one a day for the rest of your days and not have a problem.
• They must be disposed of as toxic waste. Vacuum up carefully and then drop your vacuum off at the toxic waste site ...

I'm joking about the vacuum. Sorry, this still doesn't make sense. Either the mercury content is harmless and they're not toxic waste, or they're toxic waste. (My bet is they're not really toxic waste, but I'm not buying 'em until we get the regulators to be internally consistent.)

Recently Scientific American covered this topic. Some highlights (emphases mine):

Are Compact Fluorescent Lightbulbs Dangerous?: Scientific American

... Compact fluorescents, like their tubular fluorescent precursors, contain a small amount of mercury—typically around five milligrams.

As effective as it is at enabling white light, however, mercury—sometimes called quicksilver—is also highly toxic. It is especially harmful to the brains of both fetuses and children. That's why officials have curtailed or banned its use in applications from thermometers to automotive and thermostat switches. (A single thermostat switch, still common in many homes, may contain 3,000 milligrams (0.1 ounce) of mercury, or as much as 600 compact fluorescents.)

Jim Berlow, director of the U.S. Environmental Protection Agency's (EPA) Hazardous Waste Minimization and Management Division, recommends starting by opening the windows and stepping outside. "Any problems at all frequently are handled for the most part by quickly ventilating the room," he says. "Get all the people and pets out of the room for 15 minutes and let the room air out. If you have a central heating system or an HVAC [heating, ventilating and air-conditioning] system, you don't want it sucking the fumes around, so shut that down."

... After airing out the room, the larger pieces of the bulb should be scooped off hard surfaces with stiff paper or cardboard or picked up off carpeted surfaces with gloves to avoid contact. Use sticky tape or duct tape to pick up smaller fragments; then, on hard surfaces, wipe down the area with a damp paper towel or a wet wipe. All materials should be placed in a sealable plastic bag or, even better, in a glass jar with a metal lid.

...Vacuums or brooms should generally be avoided, as they can spread mercury to other parts of the house.

Intact bulbs can be a headache to dispose of, too. In many locales it is illegal to throw fluorescents out with regular garbage, but the closest recycling or take-back facility may be miles away...

"Our first preference is not to see them go into landfills," Berlow says. "Recycling really closes the loop on this as best we can right now. But on the other hand, we also don't see huge risks from them going into landfills, either."

So the authorities aren't budging on the toxic waste cleanup routine, and legal disposal of even an intact bulb requires a significant trip (I have years of toxic waste dump material in the garage waiting for me to schedule that trip).

I'm waiting for the LEDs.

PS. I'm sure as heck not touching that thermostat switch ...

Condolezza Rice and Torture

Rice is said to be maneuvering to be McCain's VP.

Rice authorized torture. In detail. Repeatedly.

ABC has the story. Note that Ashcroft, who's reputation has been on the rise for a few years, was disturbed. Tenet wanted to be sure Cheney and Rice were implicated in the torture decisions, he didn't want his agents to take the fall alone. The torture proceedings are probably still continuing -- as indicated by the Goss transition.

Emphases mine.

Sources: 'Principals' OK'd Harsh Tactics

By JAN CRAWFORD GREENBURG, HOWARD L. ROSENBERG and ARIANE de VOGUE

April 9, 2008—

In dozens of top-secret talks and meetings in the White House, the most senior Bush administration officials discussed and approved specific details of how high-value al Qaeda suspects would be interrogated by the Central Intelligence Agency, sources tell ABC News.

The so-called Principals who participated in the meetings also approved the use of "combined" interrogation techniques -- using different techniques during interrogations, instead of using one method at a time -- on terrorist suspects who proved difficult to break, sources said.

Highly placed sources said a handful of top advisers signed off on how the CIA would interrogate top al Qaeda suspects -- whether they would be slapped, pushed, deprived of sleep or subjected to simulated drowning, called waterboarding.

The high-level discussions about these "enhanced interrogation techniques" were so detailed, these sources said, some of the interrogation sessions were almost choreographed -- down to the number of times CIA agents could use a specific tactic.

The advisers were members of the National Security Council's Principals Committee, a select group of senior officials who met frequently to advise President Bush on issues of national security policy.

At the time, the Principals Committee included Vice President Cheney, former National Security Advisor Condoleezza Rice, Defense Secretary Donald Rumsfeld and Secretary of State Colin Powell, as well as CIA Director George Tenet and Attorney General John Ashcroft...

... this is the first time sources have disclosed that a handful of the most senior advisers in the White House explicitly approved the details of the program. According to multiple sources, it was members of the Principals Committee that not only discussed specific plans and specific interrogation methods, but approved them.

... Tenet, seeking to protect his agents, regularly sought confirmation from the NSC principals that specific interrogation plans were legal.

According to a former CIA official involved in the process, CIA headquarters would receive cables from operatives in the field asking for authorization for specific techniques. Agents, worried about overstepping their boundaries, would await guidance in particularly complicated cases dealing with high-value detainees, two CIA sources said.

Highly placed sources said CIA directors Tenet and later Porter Goss along with agency lawyers briefed senior advisers, including Cheney, Rice, Rumsfeld and Powell, about detainees in CIA custody overseas. ..

... Then-Attorney General Ashcroft was troubled by the discussions. He agreed with the general policy decision to allow aggressive tactics and had repeatedly advised that they were legal. But he argued that senior White House advisers should not be involved in the grim details of interrogations, sources said.

According to a top official, Ashcroft asked aloud after one meeting: "Why are we talking about this in the White House? History will not judge this kindly."

The Principals also approved interrogations that combined different methods, pushing the limits of international law and even the Justice Department's own legal approval in the 2002 memo, sources told ABC News.

At one meeting in the summer of 2003 -- attended by Vice President Cheney, among others -- Tenet made an elaborate presentation for approval to combine several different techniques during interrogations, instead of using one method at a time, according to a highly placed administration source.

A year later, amidst the outcry over unrelated abuses of Iraqi prisoners at Abu Ghraib, the controversial 2002 legal memo, which gave formal legal authorization for the CIA interrogation program of the top al Qaeda suspects, leaked to the press. A new senior official in the Justice Department, Jack Goldsmith, withdrew the legal memo -- the Golden Shield -- that authorized the program.

But the CIA had captured a new al Qaeda suspect in Asia. Sources said CIA officials that summer returned to the Principals Committee for approval to continue using certain "enhanced interrogation techniques."

Then-National Security Advisor Rice, sources said, was decisive. Despite growing policy concerns -- shared by Powell -- that the program was harming the image of the United States abroad, sources say she did not back down, telling the CIA: "This is your baby. Go do it."

Rice, Cheney, Rumsfeld, Power, Tenet and even Ashcroft will need to be very careful about where they vacation for the rest of their lives. There are many nations which may be obliged to arrest them in the future.

If McCain accepts Rice as VP, he will be continuing a long repudiation of the values he once defended.

The Consumerist

A blog dedicated to consumer activisim: The Consumerist. It includes the Chinese poison train section. The world needs China to be enormously successful, in an ideal universe the Chinese government would be funding publication of "The Chinese poison train".

From the about stream:

7. Who is responsible for this?

The Consumerist is published by Gawker Media, the folks also responsible for Gizmodo, Fleshbot, Defamer, Idolator, Jalopnik, Gridskipper, Wonkette, Kotaku, Screenhead, Lifehacker, Valleywag and Gawker.

I can't get their feed to work with Bloglines at the moment.

Lester Brown, Julian Simon, the UNFPA, Malthus, and, again, the Food

I heard Lester Brown on NPR this morning.

That took me back 27 years. Bear with me, there's a reason to start then.

Once upon a time I was a covert intern at the UNFPA officers in what was then Bangkok.

In those days we thought of the "FP" in "UNFPA" as "family planning", though I think it stood for "Fund and Population". The UNFPA was all about changing fertility behaviors and accelerating the transition in family size from agrarian to industrial norms. Thailand, Taiwan, and Bangladesh were success stories. Rwanda was a worrisome failure. Afghanistan was on the map because of its ecological collapse.

In those days Lester Brown, the Worldwatch Institute, and Malthus were in the ascendancy. My UNFPA mentor and I leaned towards Malthus, and so I wrote essays for him attacking the optimistic economist Julian Simon, whose views were well summarized in his NYT obit:

... The essence of Mr. Simon's view of man and the future is contained in two predictions for the next century and any century thereafter that are in ''The State of Humanity,'' a book he edited for the Cato Institute.

''First,'' he wrote, ''humanity's condition will improve in just about every material way. Second, humans will continue to sit around complaining about everything getting worse.''

He argued that mankind would rise to any challenges and problems by devising new technologies to not only cope, but thrive. ''Whatever the rate of population growth is, historically it has been that the food supply increases at least as fast, if not faster,'' he said in a profile published in Wired magazine last year.

Mr. Simon's views were widely contested by a large coterie of the academic and scientific community, many of whose members believe that more people create more problems, straining the earth and its resources in the process.

''Most biologists and ecologists look at population growth in terms of the carrying capacity of natural systems,'' said Lester R. Brown, president of the Worldwatch Institute in Washington. ''Julian was not handicapped by being either. As an economist, he could see population growth in a much more optimistic light.''...

It's generally assumed now that Simon was right, but a pessimist would say it's too soon to tell. As DeLong and Krugman have pointed out, most of the human race was in a Malthusian trap from 6000 BCE until the time of Malthus himself. Rwanda, as feared in 1982, did experience a classic Malthusian collapse, though its subsequent recovery is much faster than the pre-industrial record. Afghanistan's fragile ecology collapsed in the 20th century, and we know how that story turned out.

Many things have happened since those days in Bangkok. Outside of Africa most of the world, especially China and India, followed the predictions of Simon rather than Malthus. On the other hand, world population growth has also followed the more optimistic projections of the 1982 UNFPA.

Given my historic roots, it's not surprising then that I would call the Simon vs. Brown battle a draw. On the one hand the Green Revolution worked, cheap energy meant cheap food, and worldwide trade combined with the kind of worldwide productivity growth Simon expected. On the other hand there were also near optimal changes in fertility behavior across many nations. The net effect was that a year or two ago we though that obesity might become a bigger public health problem problem than malnutrition in many once poor nations.

During this time the UNFPA, like all great bureaucracies, evolved to fill new niches. Now it's the "United Nations Population Fund - UNFPA" and all the links on the public page are about reproductive health and fighting HIV. The words "family planning" do appear, though they are a bit hidden.

Twenty-six years later, though, the wheel may have turned again. Simon died young at 65, but Lester Brown is still alive, and again on NPR. The reason, of course, is that classic collapse factors are again in play ...

Grains Gone Wild - Paul Krugman - New York Times

... Over the past few years the prices of wheat, corn, rice and other basic foodstuffs have doubled or tripled, with much of the increase taking place just in the last few months...

There have already been food riots around the world. Food-supplying countries, from Ukraine to Argentina, have been limiting exports in an attempt to protect domestic consumers, leading to angry protests from farmers — and making things even worse in countries that need to import food.

... First, there’s the march of the meat-eating Chinese — that is, the growing number of people in emerging economies who are, for the first time, rich enough to start eating like Westerners. Since it takes about 700 calories’ worth of animal feed to produce a 100-calorie piece of beef, this change in diet increases the overall demand for grains...

Second, there’s the price of oil. Modern farming is highly energy-intensive...

Third, there has been a run of bad weather in key growing areas. In particular, Australia, normally the world’s second-largest wheat exporter, has been suffering from an epic drought....

... Where the effects of bad policy are clearest, however, is in the rise of demon ethanol and other biofuels...

We need to dial way back on the biofuels experiment -- it's not working. Unless we figure out how to process cellulose it's an energy negative process. It should be a research project, not a production enterprise. Biofuel production happened prematurely because of US domestic politics (including, most shamefully, the actions of Minnesota's senators including the sainted Paul Wellstone).

The other problems are far less tractable, they'll persist even if we eliminate biofuels and lessen the direct competition between our mobility desires and food production.

So the EU, US, China and India could be simultaneously enlightened and decide to eat less meat, drive less, institute a carbon tax to fund research into alternative energy sources, and forswear biofuels. Or we could discover a something like "cold fusion", except it would have to work. Or we could ...

I'm out of ideas right now. Any suggestions?

It is worth remembering, in case anyone needs motivation for new ideas, that any local Malthusian collapse is likely to lead to the vengeful use of inexpensive weapons of mass havoc.

So we all have "skin in the game" -- beyond mere compassion.

Best explanation of the Monty Hall problem (Bayes)

John Tierney has been playing with explanations of the "Monty Hall" (Bayes theorem) problem for 17 years. That might be why he's provided the most succinct explanation I've come across ... (note: Monty knows where the car is, he can't open the door you picked, and he won't open the door for the car. That's important -- his actions provide new information. He's not picking randomly.)

Cognitive Dissonance in Monkeys - The Monty Hall Problem - New York Times

...Here’s how Monty’s deal works, in the math problem, anyway. (On the real show it was a bit messier.) He shows you three closed doors, with a car behind one and a goat behind each of the others. If you open the one with the car, you win it. You start by picking a door, but before it’s opened Monty will always open another door to reveal a goat. Then he’ll let you open either remaining door.

Suppose you start by picking Door 1, and Monty opens Door 3 to reveal a goat. Now what should you do? Stick with Door 1 or switch to Door 2?...

...You should switch doors.

... when you stick with Door 1, you’ll win only if your original choice was correct, which happens only 1 in 3 times on average. If you switch, you’ll win whenever your original choice was wrong, which happens 2 out of 3 times...

Probability problems are often asymmetric, they can be hard to solve in terms of the "correct choice", but easy to understand when considered when re-expressed in terms of the "wrong choice" (or vice-versa). That's what we see here.

Tierney's paragraph is a great example of expressing simple algebra in sentence form, but the key thing to recall is that Monty is adding new information because he doesn't choose randomly.

I'm fascinated by Bayesian probability. The mathematics is very simple, yet it can be very challenging to map correctly to the physical universe. On the other hand even a trivial understanding would greatly improve government and law enforcement. What a marvel!