Wednesday, January 30, 2008

The Eco-Philosopher

Lumo weighs in on the Fed.

As it happens, I share some of his concerns about being too quick to cut interest rates, but I'm more interested in some of his logic:

I want to say one more thing: a strategic, political observation. Friends of the U.S. are much more likely to hold the U.S. dollars while the U.S. enemies have a much higher probability to bet against the U.S. currency. By weakening the currency, the Fed effectively helps the enemies of the U.S. financially while it punishes its friends. It is a very bad evolution for the American (and not only American) strategic interests.

I wonder how likely that is. Sure, some people always bet on the home team, but I have my doubts that that plays a big role in the thinking of of the BOC or Saudi Arabia. Clearly, they both have an interest in a strong dollar, but does it go beyond political and economic calculation? I have my doubts. And that goes double for the trading desks at Goldman-Sachs et al.


I was sitting at the bar of a local bistro when an old acquaintance happened to come up. After a bit the the usual small talk (football, politics, string theory) he got this real serious expression on his face.

"I've got a tough choice to make Cap," he says. "I happened to help this guy out of a very tight spot, and in gratitude he wanted to offer me a reward."

So what was the problem, I wondered.

"It seems that he wasn't just any guy," says OA. "He turned out to be a Genie."

Maybe I snickered a bit here, because he rushed on:

"He told me that he was empowered to offer me a choice. He said he could offer me one of three second class superpowers. I was suspicious of course, but I parried by asking him what a first class superpower was. He gave me a haughty stare for a second, and then went on: 'Your first choice would be a permanent purse. Any time you reach your hand in, you can pull out a one ounce solid gold coin.'

"'You guys haven't converted to metric yet?' I asked. This got another stare. 'The purse has other advantages,' he says. 'If someone steals it, they can't get anything out, and as soon as they are out of sight, it immediately rematerializes in your pocket.'

"'The second choice is the ability to read minds, at ranges of up to 300 feet - that's about 100 meters. You can see others thoughts as they experience them, so if they think their thoughts in a foreign language, you might not be able to understand them. There are some obvious hazards - you can tell what people are really thinking of you.'"

Me: "So what do I think of you right now?"

"You think I'm nuts, but I didn't need a superpower to figure that out. Anyway, Genie goes on to explain the last choice: 'Finally, you can choose flight, on a broomstick, exposed to the weather. It's not tiring, but you are exposed to the wind, and need to be able to hold on. It's a bit like riding a motor cycle with no fairing and no handlebars. Most people find airspeeds over 70 miles per hour pretty challenging. So, which do you want to choose?'"

"It's a tough choice. What do you think?"

Me: "I'll ask around."

See poll.

Tuesday, January 29, 2008

HEP, HEP Hurrah!?

One little bit of the Prez's SOTU that I caught talked about doubling the budget for fundamental physics research. Is this restoration of the high energy physics funds that were cut? Something only for 2009?

Sunday, January 27, 2008

Knife, Fork, Gill and Wing

My thoughts upon reading Endless Forms Most Beautiful, by Sean B. Carroll

In the middle ages, says Prof Carroll, Europeans started eating with two knives, using one to spear their food and another to cut it. This redundancy opened an opportunity for one knife evolve to be more specialized for spearing, while sacrificing the cutting function. This division into knife and fork was followed by many more in sufficiently posh dining facilities - a veritable Cambrian explosion of cutlery.

A similar redundancy made room for arthropod specializations. Early arthropods had so-called biramous, or forked limbs, lots of them, but each fairly similar to all the others. Each consisted of a lower, leg-like limb used for walking, digging, or swimming, and an upper gill branch, used for absorbing oxygen.

The most dramatic arthropod changes have taken place in those who moved onto land. In the case of insects, only six legs have been retained, but many others have been converted to other uses: mouth parts, antenna, genitalia, etc. The gill branches took at least equally dramatic turns: in insects, two pairs of them became wings. In spiders, some became book lungs, others spinnerets, and still others, sex organs. The evolution can be traced because the developmental tool kit genes are conserved while the targets change dramatically.

Tool kit genes, recall, are turned on by a set of molecular switches, which are in turn controlled by the geography specifying genes. Such a gene can acquire new functions while keeping the old by acquiring a new switch. Thus, the distal-less gene whose original function was to declare "make a limb here", acquired a new function to "make a butterfly wing eyespot here" by adding a switch that was sensitive to the detailed geography of the developing butterfly wing.

Context is everything, though. How does distal-less tell developing scale cells to make suitable colors for eyespots instead of another leg in the middle of the wing? That requires still other genes and switches that know about the geographic location on the butterfly, and hence know that in this context the message is "form an eyespot" instead of "make a leg."

Happy SC Day!

A good weekend for the O-man and South Carolina - for Edwards, not so much. I think Edwards is done - done in by the press, done in by the haircuts, but mostly done in by being in between a charismatic candidate and the powers that be.

It would be hard to claim that our political process is likely to pick the best candidate or even a good candidate - but pick it does. Edwards had good positions on the issues, but clearly lacked the magic touch. One thing I don't see mentioned much, but that affects me, is the way he got taken to the cleaners by Cheney in 2000.

I don't like any of the Republicans, but with any luck the worst of them could be gone after Florida.

Friday, January 25, 2008

Say what?

Thomas Dent asks: Is this a reason to discard the theory?[ that contains
Boltzmann brains].

The best reasons for discarding a theory are: it
doesn't make testable predictions, or it makes such predictions but they are wrong. Try to stick that in your Boltzmann brain and see what it says.

LM: Dear pig, please, avoid these off-topic, superficial, uninformed, pig-like, Woit-like clichés that have been parroted by your likes
about 1,000 times. They are well below the level required at this blog.

Predicting a lot of Boltzmann brains is surely a prediction, whether folks like you understand it or not. Nevertheless, this prediction can't be used
to eliminate a theory.

If you have nothing to say about this particular
problem and if you (clearly) misunderstand all these questions completely, please shut your mouth or keyboard. Next time I will do everything I can do ban
your domains because I don't want this garbage to grow here. Go to Daily Kos or Woit blog or another place that is optimized for foam like you.

They did warn me not to annoy the crazy people.

Thursday, January 24, 2008

The Pig Studies Biology

Trying to read a little molecular biology again, I become aware of some habits of mind that unsuit me for the pursuit. I went through the citric acid cycle today, and found a couple of problems: my physicist brain wants to drill down to understand how everything works - why one molecular configuration has just so much more energy than another, and my stupid brain can't remember the names (much less molecular conformations) of all those intermediates.

Bald Monstrosity

Olivia Judson's latest New York Times column/blog called The Wild Side talks about "hopeful monsters."

The term was introduced in the 1930s by a geneticist called Richard Goldschmidt. He was interested in the question of how radical changes in morphology evolve.
As an example of radical change, he gave flatfish — the flounder and its relations. These are descended from fish with the usual fishy symmetry: the same left-right symmetry that we have. Larval flounders have it, too. But as adults, flounders have a profound asymmetry — one side has been completely flattened. What’s more, they have deformed, twisted skulls, and an eye that has migrated from one side of the face to the other. It’s as though you had both eyes on the same side of your nose. How did they get this way?
Goldschmidt speculated that big changes like this could be caused in one step by a mutation acting on the developing embryo. Most such mutations, he suggested, would produce individuals that were plain monstrous, and doomed to die without issue. But every so often, one of these mutations would happen in an environment where it could be beneficial. Then, the individual sporting it would be a hopeful monster, because it might have an evolutionary future as the founder of a new lineage.

The idea came into disrepute because the probabilities didn't look right, and the steps looked to big. Evolutionary development had to be gradual, it was thought.

Judson wants a revival, and her starting point is the featherless head of the vulture. She is inspired to her view by the fact that there seems to be a point mutation of chickens that produces a featherless head.

She mentions some other examples, including some that are well-known to evo-devo, but not perhaps to her. In particular she talks about the classic case of the flatfishes, which, it happens, were very nicely discussed in some detail by PZ Myers, evidently taking a brief break from his frothings on religion.

It's an interesting topic, and an interesting blog, though I would like to have seen a more detailed discussion of the evo-devo, and especially, some mention of the critical role of genetic switches. Go to PZ for that.

Haloscan Seems to be Fixed

Thanks Khris.

Wednesday, January 23, 2008

Haloscan Comments Screwed

Haloscan comments seem to be screwed. Apparently new one can't be seen from other computers - but I can see them here. Not sure what is going on. More later.

Tuesday, January 22, 2008

Petraeus: One More FU

Joementum and Johnny Mac think we've already won in Iraq. General Petraeus is not so sure:

Gen. David Petraeus, however, appeared on NBC this morning and rebutted the declarations of mission accomplished and said that he’ll need at least another Friedman Unit before he can make a judgment:

We think we won’t know that we’ve reached a turning point until we’re six months past it. We have repeatedly said that there is no lights at the end of the tunnel that we’re seeing. We’re certainly not dancing in the end zone or anything like that.

Monday, January 21, 2008

Swimming with Stanley Fish, Public Intellectual

A public intellectual, so far as I can tell, is an English teacher with an audience beyond the immediate family. Stanley Fish is our nation's most famous English teacher and writes a frequent column/blog for the New York Times, so I have on rare occasions sampled his stuff. Today's contribution is Against Independent Voters.

So what exactly does Mr. Fish have against the indies? Mostly he just resents the fact that they get so much attention.

We’re in that season now when we hear the same things being said over and over again, and nothing is said more often by political pundits than this election (it doesn’t matter which one) will be decided by independent voters. Accompanying this announcement is the judgment – sometimes implicit, sometimes explicit – that this state of affairs is to be welcomed, even encouraged: it’s good that the independent voters are making themselves heard and forcing candidates to think outside their partisan boxes.

He doesn't like this, and he especially hates the idea of "voting for the man, not the party."

Floating independently above the fray and inhabiting the marketplace of ideas as if were a shopping bazaar rather than a battlefield is an unnatural condition. The natural condition is to be political. To be political is to believe something, and to believe something is to believe that those who believe something else are wrong, and after all you don’t want people who believe (and would do) the wrong things running your government. So you organize with other like-minded folks and smite the enemy (verbally) hip and thigh. You join a party.

This sounds sort of reasonable, but my bullshit detectors are screaming. Now it's probably true that I have a bit of hostility toward English teachers, but I'm working on that, and I don't really think that that's the problem. What's wrong with the idea that our job as voters is to join a tribe and commit fully to it?

A lot, I think, but let's give Mr. Fish a bit more line:

Now, voting the person rather than the party is about the dumbest thing you can do for a reason I elaborated in an earlier column (“Parties Matter”). The party affiliation of a candidate tells you what kind of appointments he or she is likely to make. Do you think that regulations of industry stifle productivity and damage the economy, or do you think that unregulated industries endanger the environment? Do you think that illegal immigrants are just that – illegal – and therefore should be deported when detected, or do you think that we should figure out a way to legitimize their status and make the best of what has already happened? Do you think that Iran poses a threat that must be countered before it is too late, or do you think that military action should be resorted to only after every avenue of diplomacy has been exhausted, even if it takes years or decades?

Why does Mr. Fish think that party or party history is a better guide to these crucial points than the character and personality of the candidate. Bill Clinton accomplished many things that Republicans talked about but never managed to do: a balanced budget and welfare reform. George W Bush appointed many of the same men his father appointed, but in the international arena made all the mistakes his father studiously avoided. The Republican candidates this year have changed their positions on most crucial issues more recently than their underwear.

I'm a strong, maybe even yellow dog Democrat myself, but it's obvious to me that the personal qualities of a president are more important than his party affiliation. At the moment, of course, all the main Republican candidates are profound losers, but the notion that voting for the party rather than the man is always a good idea is still idiotic.

Fish concludes with a bit of sophomoric sophistry:

In the end, there is nothing to be said for independent voters and a lot to be said against them. Remember, a bunch of them voted for Ralph Nader. Case closed.

The main thing to be said for independent voters is that their existence tends to force the political parties toward toleration, compromise and moderation, and without those democracy cannot function.

Whispering About the Apocalypse

The Fed and most mainstream economists, not to mention your friendly stock hustler, continue to say we aren't really in a recession, and probably won't be. Chronic bears, like yours truly, think that we hear whispers of the apocalypse amidst the cheery chirping. A rather loud whisper was heard this morning when Asian stock exchanges plummeted. A softer but still ominous hint comes from this Michael A. Fletcher story in the Washington Post. It seems that:

An unusually large share of workers have been out a job for more than six months even as overall unemployment has remained low, a little-noted weakness in the labor market that analysts said threatens to intensify the impact of the unfolding economic downturn.

The hollow core of the Reagan-Bush-Greenspan phony economy of borrow and spend is increasing exposed. The Republicans and their minions in the press are determined to stick the public with the bill, and no doubt they will succeed at least in part.

UPDATE: Department of heroic understatement. The WSJ speculates that the selloff in Asia and Europe reinforces fears that the Market might be tested on Tuesday. My utterly worthless prediction: DOW low, down 700; close, down 500.

Saturday, January 19, 2008

Of Mice and Men

My thoughts upon reading Endless Forms Most Beautiful, by Sean B. Carroll

Where should we look for the well laid plans that sculpt mice and men so differently? Well in the genome, of course, but there we meet a problem. Men and mice each have about the same number of genes, about 25,000. The conundrum gets worse. The genes are not only the same in number, but for most purposes they are the nearly the very same genes, producing very similar proteins.

The answer to this and many other puzzles of development, form, and evolution seems to be that it's in the switches that turn those genes on and off. If we think of the genes as the keys on an old fashioned player piano, the switches are the piano roll. It's the sequence of switching that orchestrates the notes into the symphony of development. For the most part, man and mouse are built out of the same cell types and tissues - different architectures built out of the same old Lego blocks.

The Persecution and Execution of Joe Klein

Glenn Greenwald continues his dissassembly of Joe Klein and the examination of his entrails. Klein's problem is that he has a habit of misremembering history in a way that makes his part in it look less inglorious than it was. Unfortunately for Joe, the internet remembers what he wrote, and Glenn is annoyed enough and diligent enough to track down the details and hang him by them.

Gonna Build Me a Mountain/Some Assembly Required

Reading Endless Forms Most Beautiful, by Sean B. Carroll

Some unicellular creatures called dinoflagellates are remarkable for their ability to change shape and mode of existence in response to environmental conditions. Their shape changing skills are nothing compared to those of a more familiar cell, however. Each human (or mouse, elephant, or frog) cell has the instruction set for turning itself into a blood, bone, brain, or skin cell. The story of how they manage these feats is the tale of embryonic development, and it is a remarkable tale indeed.

When people set out to build something, we gather parts from afield, and bring them together in carefully (in my case, usually not carefully enough!)planned sequence and pattern, but an embryo assembles itself from the inside. The method is both elegant and instructive. First, the egg and early embryo establish a set of internal coordinates. These internal coordinates are specified in terms of chemical gradients, and are initially simple (up-down, forward-back, right-left), but as the embryo develops, are progressively refined by further chemical gradients to exquisite positional precision. The chemicals that make up these gradients are signals that turn on or off certain specified genes in the locations specified. Those genes, in turn, are controlled by a pattern of switches which can give them great specificity. A typical develomental gene has ten or more switches which turn it on or off in response to rather complex signals.

This fact gives rise to modularity and reusability for genes: the same bone morphogenesis proteins turned on in your finger bone were turned on in many or most of the other bones of your body, but the precision of control made possible by the the switch mechanism allows the tissues they produce to be sculpted and otherwise specialized for the specific uses intended.

Friday, January 18, 2008


Wall Street had a pretty bad week but the bad news just keeps on coming. The latest tremor seems to be the prospect of a downgrade of bond insurers. The money involved is huge - trillions. Kevin Drum summarises in the link.

Paul Krugman's column today has some insights into the bigger picture. The US has been playing a very familiar game, living high on the hog on borrowed money, and this story always ends the same way.

Mexico. Brazil. Argentina. Mexico, again. Thailand. Indonesia. Argentina, again.

The story has played itself out time and time again over the past 30 years...

To be more precise, some in the US have been living high, most of the rest of us are just getting by, but Cheney's Halliburton options are doing quite well, thank himself very much. Bush and his Congress has been spending like crazy though, and so have American consumers.

Fed Chairman Ben Bernanke looked at the phenomenon in his previous life and observed that it was OK though, because:

The global origins of our current mess were actually laid out by none other than Ben Bernanke, in an influential speech he gave early in 2005, before he was named chairman of the Federal Reserve. Mr. Bernanke asked a good question: “Why is the United States, with the world’s largest economy, borrowing heavily on international capital markets — rather than lending, as would seem more natural?”

His answer was that the main explanation lay not here in America, but abroad. In particular, third world economies, which had been investor favorites for much of the 1990s, were shaken by a series of financial crises beginning in 1997. As a result, they abruptly switched from being destinations for capital to sources of capital, as their governments began accumulating huge precautionary hoards of overseas assets.

The result, said Mr. Bernanke, was a “global saving glut”: lots of money, all dressed up with nowhere to go.

In the end, most of that money went to the United States. Why? Because, said Mr. Bernanke, of the “depth and sophistication of the country’s financial markets.”

All of this was right, except for one thing: U.S. financial markets, it turns out, were characterized less by sophistication than by sophistry, which my dictionary defines as “a deliberately invalid argument displaying ingenuity in reasoning in the hope of deceiving someone.” E.g., “Repackaging dubious loans into collateralized debt obligations creates a lot of perfectly safe, AAA assets that will never go bad.”


But guess who gets the bill?

For eight years the American public bought the free lunch fantasy the Republicans sold us, and now they are starting to pay. Have they learned anything yet? For sure the Republican party hasn't, because they are still selling the same old voodoo.

If we are quite lucky, we will shamble out of this sadder but wiser, bruised but still with a powerful economy. If we aren't, our children will inherit a much poorer and weaker country.

Loschmidt's Paradox

Charles University is the oldest university in central and eastern Europe, founded in 1348, so more than twice as old as William and Mary or Yale. It has a host of distinguished alumni, including several Nobel Prize winners, famous historical figures, Novelists Karel KapekČapek and Franz Kafka as well as Nicola Tesla, Ivana Trump and Lubos Motl. Einstein and Mach appear on the faculty list. (Though the place never entered my consciousness before the last named alum beat the crap out of me for dissing the joint).

Another student there was Johann Josef Loschmidt, who was the first to determine the number of molecules in a cm^3 of air, and made other contributions to Chemistry. He was a friend of Boltzmann's and contributed to the clarification of the foundations of statistical mechanics, notably through posing Loschmidt's Paradox, which is deeply connected to the Boltzmann Brain problem. (This is kind of a second indignity at the hands of history, since not only should Avogodro's number probably been named after Loschmidt, but Boltzmann's brain probably should be too.)

From the Wikipedia article:

Any process that happens regularly in the forward direction of time but rarely or never in the opposite direction, such as entropy increasing in an isolated system, defines what physicists call an arrow of time in nature. This term only refers to an observation of an asymmetry in time, it is not meant to suggest an explanation for such asymmetries. Loschmidt's paradox is equivalent to the question of how it is possible that there could be a thermodynamic arrow of time given time-symmetric fundamental laws, since time-symmetry implies that for any process compatible with these fundamental laws, a reversed version that looked exactly like a film of the first process played backwards would be equally compatible with the same fundamental laws, and would even be equally probable if one were to pick the system's initial state randomly from the phase space of all possible states for that system.


Another way of dealing with Loschmidt's paradox is to see the second law as an expression of a set of boundary conditions, in which our universe's time coordinate has a low-entropy endpoint: the Big Bang. From this point of view, the arrow of time is determined entirely by the direction that leads to the Big Bang, and a hypothetical universe with a maximum-entropy Big Bang would have no arrow of time. The theory of cosmic inflation tries to give reason why the early universe had such a low entropy.

RIP Bobby Fisher

Bobby Fisher, the last chess genius, has died. He was a strange and tormented figure, the prototypical genius whose insanity took over at the moment of his greatest triumph.

Rest in peace.

Wednesday, January 16, 2008

Boltzmann Brain Update

My new model universe for Arun et. al. Consider a rectangular box, containing ten molecules. Here the ticks of the state change clock occur whenever a molecule passes from the left side to the right or vice versa. At some point we drop a partition down the middle and find that there are eight molecules on the left side and two on the right. We denote this macro state by (8;2). What is the most likely predecessor state (PS)?

Once again, there are just two possibilities: (9;1) and (7;3). There are 9 ways for the (9;1) state to go to the (8;2), but only three for the (7;3), so can we conclude that the (9;1) is the most likely PS? No, because the two states are not equally likely. There are only 10 ways to make a (9;1) state but 120 = (10x9x8)/(3x2) ways to make the (7;3) state.

No bit of probabilistic hocus pocus is complete without Bayes theorem, so, let A be the event that the initial state is (9;1), B that the initial state is (7;3), and C that the final state is (8;2). P(A)=10/1024, P(B)=120/1024, and P(C)=(10x9/2)/1024 = 45/1024. We have already seen that P(CA)=9/10 and that P(CB)=3/10.
Invoking Bayes Theorem the probability that the PS was A is P(AC)=P(CA)P(A)/P(C) = (9/10)(10/1024)(1024/45) = 1/5. Similarly the probability that the PS was B is
(3/10)(120/1024)(1024/45)= 4/5.

Consequently, it is 4 times as likely that the PS was the higher entropy state.


I think that the argument is quite general. What does it mean that a macroscopic system is far from equilibrium? It means that the ensemble of states corresponding to the system has a small (coarse grained) volume in phase space compared to the available volume. If we evolve the system forward it tends to spread out in phase space increasing its (coarse grained) volume because most trajectories from the volume spread out – that is the second law of thermodynamics.

Similarly, if we look at trajectories leading into the original volume, those coming from a smaller volume have higher probability of forming our original volume, but the overwhelmingly larger number of trajectories coming from larger volumes means that if you treat all possible predecessor states as equally likely then it is more likely that the PS had higher entropy rather than lower.

From the standpoint of Hamiltonian dynamics the situation is completely symmetric in time. There are a very small number of future trajectories for the ensemble which steadily decrease entropy. There are an identical number of past trajectories that do the same thing. We are used to ignoring this fact because low entropy situations of this type are usually not “found” but created by deliberate action, e.g., placing a cold reservoir in contact with a hot one. (If we put two warm reservoirs in contact and waited for one to get hot and the other to get small, we would have a very long wait, unless we made them very small – like my toy universes.) Even more important, the evolution of the Universe seems to have presented us with a situation a convenient distance from equilibrium – unless, as is a priori more probable, it’s all just a dream in a Boltzmann brain.

This problem was recognized by Boltzmann. The only known ways to overcome it are to either introduce an explicitly time asymmetric principle (like Boltzmann’s “molecular chaos”) or to assume that the whole shebang started out in a very low entropy state. My money is still on the latter, and if cosmological theories find that inconvenient, so much the worse for them. Subject to revision without notice.;)

Tuesday, January 15, 2008

The God of Low Entropy

Arun wants some justification for my claims in the Boltzmann's brain post (Ludwig's Revenge).

...pure statistics seems to imply that entropy should increase in the past as well as the future.

I definitely don't follow the argument.

Physically, if a low entropy state most likely arose from a high entropy state, then we should see a lot of that happening around us. We don't...

Both physically and statistically, a state of given entropy is much more likely to have arisen from a state of lower entropy (even though the number of states of high entropy which could have had a fluctuation to lower entropy is enormous, the probability of such fluctuations is even smaller - e.g., statistical partition functions wouldn't exist without that - the sums would diverge.)

Consider a simple universe consisting of ten distinguishable bits, with an evolution law such that at each time step exactly one randomly chosen bit is flipped. There are a total of 2^10 = 1024 such states, of which 10x9/2 = 45 of them have two bits set and the others all off. Define our coarse grained entropy to be the [UPDATE: the log of the number of microstates corresponding to a given] number of set bits. Thus our state is fairly low entropy.

What about the predecessor state? There are two (coarse grained) possibilities: the predecessor state (PS) had only one bit set (only ten ways to do this), or it had three bits set (10x9x8/(3x2) = 120 ways to do this). Not all of these states are eligible to be the PS, though. If the PS has one bit set, there are just two ways this can happen - the set bit has to be one of the two set in the current state and the switched bit is the other. If there were three bits set in the PS, two of them have to be the two set in the current state and there are eight possibilities for the third set bit, which must also be the switched bit in the transition. Thus, of the ten possible PS, two have lower entropy and eight have higher entropy.

The reasoning here is quite general, and is in fact identical to that leading to the second law of thermo, except for the time orientation. If the previous state is arbitrary, it is more likely to have higher entropy than lower.

So why don't we see that happening all the time? Because it works the same way into the future! For our mini-universe to evolve into the 3-bit set state the probability is 8/10, while it is only 2/10 for it to evolve into the lower entropy 1-bit state. If all possible future states are equally likely, then the future will likely have higher entropy. Ditto the past.

Maybe the following will clarify the point: However unlikely it is that a brain emerged fully formed from chaos (and it's very, very, very unlikely indeed), it is still more unlikely a priori that a whole cosmos just happened to be in an extremely low entropy state.

We don't know of any laws that specify that the universe started in a low entropy state, but none of our laws make sense unless it did. Some magic, some unknown law of nature, or some design did apparently start it off thus, and that's a puzzle.

Ludwig's Revenge

Dennis Overbye, writing in the New York Times, has a nice article today on the so-called Boltzmann brain problem in cosmology. It's a new incarnation of a familiar problem in statistical mechanics and the physics of time, the problem that pure statistics seems to imply that entropy should increase in the past as well as the future: it's a priori more probable that the present is a momentary fluctuation rather than part of a long history extending into the past. Overbye, like cosmologists, recognizes that this way madness lies - the question is what to do about it.

It could be the weirdest and most embarrassing prediction in the history of cosmology, if not science.

If true, it would mean that you yourself reading this article are more likely to be some momentary fluctuation in a field of matter and energy out in space than a person with a real past born through billions of years of evolution in an orderly star-spangled cosmos. Your memories and the world you think you see around you are illusions.

This bizarre picture is the outcome of a recent series of calculations that take some of the bedrock theories and discoveries of modern cosmology to the limit. Nobody in the field believes that this is the way things really work, however. And so there in the last couple of years there has been a growing stream of debate and dueling papers, replete with references to such esoteric subjects as reincarnation, multiple universes and even the death of spacetime, as cosmologists try to square the predictions of their cherished theories with their convictions that we and the universe are real. The basic problem is that across the eons of time, the standard theories suggest, the universe can recur over and over again in an endless cycle of big bangs, but it’s hard for nature to make a whole universe. It’s much easier to make fragments of one, like planets, yourself maybe in a spacesuit or even — in the most absurd and troubling example — a naked brain floating in space. Nature tends to do what is easiest, from the standpoint of energy and probability. And so these fragments — in particular the brains — would appear far more frequently than real full-fledged universes, or than us. Or they might be us.

It seems that the current incarnation of this puzzle is somehow connected to the problem of dark energy, though I couldn't quite understand Overbye's discussion of the problem. I think I may need to go read Sean Carroll's discussion of the subject, if I can still find it.

Monday, January 14, 2008

Modularity and Symmetry

Wherein Captain Imperio meets evo devo (Hat tip to Changcho)

Modularity is the law in biology, and indeed in the universe. Somehow those ancient Greeks rightly guessed that the world was made of universal tinkertoys. The funny thing is that it works at seemingly every level. Everything is made of atoms, and atoms are made of even fewer and simpler parts: electrons, protons, and neutrons, each of which is identical to all the other members of its species. At larger scales are stars and their solar systems, which assemble to build Galaxies, which in turn form clusters. Above and below, we can't quite be sure - though protons and neutrons are made of quarks.

But this post is about life, because I have started reading Endless Forms Most Beautiful: The New Science Of Evo Devo And The Making Of The Animal Kingdom by Sean B. Carroll. All the life we know inhabits one planet around one star, and it, like everything else, is made of atoms, but there is a lot more to its modularity. All that life is made of cells, the atoms of life, and all those cells have an elaborate set of molecular tools and factories, the most crucial of which are common to all.

Carroll, so far at any rate, is mainly concerned with yet higher levels of modularity. Vertebrates, arthropods, and many other large life forms are built of multiple segments that show clear homologies within individuals and across species.

Modularity is a kind of symmetry, but it tends to be a broken symmetry. Fingers and toes are homologs but different. Ditto arms, wings, and fins. It's a fascinating story, and I'm just getting to the good part - I need to get back to it.

Clap Harder!

One plausible road to climate catastrophe would be a rapid rise in sea level. The IPCCs most recent report estimated a maximum sea level rise of a couple of feet this century, but put in a huge caveat: meltdown of Antarctica and Greenland was not figured in for lack of adequate data.

Data is trickling in, and the signs are ominous.

Climatic changes appear to be destabilizing vast ice sheets of western Antarctica that had previously seemed relatively protected from global warming, researchers reported yesterday, raising the prospect of faster sea-level rise than current estimates.

It has become much more plausible that the century's sea level rise might be measure in meters rather than inches. This would be catastrophic for several countries and devastating for coastal cities in much of the world.

Note to denialists everywhere: clap harder.

Sunday, January 13, 2008


Re: Conceptual Mathematics: A First Introduction to Categories (Paperback)
by F. William Lawvere (Author), Stephen Hoel Schanuel (Author)

Even genius has its limitations.
Stupidity is not thus constrained.

Unfortunately, I keep demonstrating the second half of the couplet. For some time I have owed Arun a response on his question, but have delayed out of feelings of guilt:

Did you get much beyond Brouwer's theorems?

A funny thing happened when I tried to do Exercise 1 in the Brouwer's theorem chapter. I hit a pole in my stupidity quotient. I am convinced that it is pretty easy, but every time I thought about it, my brain found a good reason to be somewhere else. So for a couple of months I just stopped.

I finally decided to just go on, and have worked about the next dozen or so exercises in Article III, but that's as far as I've gotten.

It is a very good book, but I'm unable to take any of the ideas and apply meaningfully to anything outside the book, and so am feeling a bit frustrated. Probably need to think a lot more and with more patience

I haven't found any real application either, but I have toyed with a couple of ideas. You might recall that Malcolm Gladwell, in his New Yorker article on IQs, mentioned that the KhoiSan, when asked to group objects, always picked functional relationships (knife cuts potato) rather than taxonomic (knife is like spoon). I think that that is analogous to the Category theoretic notion of emphasizing maps rather than sets.

Even a bit further out is the notion of relating forgetful functors to mutations in evolution. It may be silly, but I find it fun.

Saturday, January 12, 2008

Atmospheric Mixing

Our onetime blogging mentor and occasional critic Luboš Motl is doing some greenhouse warming calculations. This is good, since Lumo is a much cleverer fellow than the AGW critics that he likes to listen to, and he can hardly help but learn some important things by doing the math himself. In particular, he has now calculated the logarithmic dependence of the temperature change on the CO2 concentration. This is all to the good, as I said, but I would like to focus on one little mistake he made, not because it’s very important, but because it’s symptomatic of the flaws in his reasoning about AGW in general – he simply hasn’t mastered the relevant facts. Another reason I bring it up is that we clashed before on the same subject, and at that point I didn’t bother to understand exactly why he was wrong, and didn't follow up on his mistake.

What he does is assume that he can calculate the distribution with height of CO2 molecules based on the Boltzmann distribution for the CO2 molecules alone. This leads to a biased result, since CO2 molecules are among the heaviest common constituents of the atmosphere, and the atmosphere is in fact well mixed up to about 100 km (the so-called turbopause). The underlying assumptions leading to his result are two: that the atmosphere is a perfect gas, and that it is in thermal equilibrium. Both assumptions are slightly false, and the two conspire to make the atmosphere well-mixed for much of its depth.

If molecular diffusion were the only process occurring, the atmosphere would indeed assort by height, and the heaviest molecules (like CO2) would concentrate more at the bottom than the lightest (H2 and He) would. Really heavy stuff, like dust particles and sand grains wouldn’t get off the ground at all. In fact, the atmosphere is constantly stirred by turbulence, and when the turbulence is vigorous, dust and even sand get lofted.

In a truly perfect gas, molecules don’t notice each other at all. Each species passes through its fellows and other molecules completely unhindered. In the surface level atmosphere, though, the mean free path for an air molecule is about 1 micrometer = 10^-6 meters. This means that two molecules that start out together take along time to wander apart by diffusion. Meanwhile, winds and turbulence, large scale collective motions, sweep whole large chunks of atmosphere from one point to another. Turbulent stirring of the atmosphere, which doesn’t care about individual molecular masses (only the mass of the parcel of which it is a part) dominates until reduced density makes the mean free path of molecules longer than the mixing length (the average distance an air parcel travels while maintaining its identity). This doesn’t happen for Earth until you get to about 100 kilometers up. Above this turbopause, diffusion takes over, and molecules tend to stratify in the heterosphere.

Book Review: The Emergence of Life on Earth, by Iris Fry

Iris Fry's book The Emergence of Life on Earth: A Historical and Scientific Overview is a detailed but non-technical account of attempts to explain how life emerged from non-living material. I have posted a number of articles on the book and closely related subjects here.

I liked the book a lot, and much of the material was new to me, even though I have long been interested in the subject. Fry is a clear and careful writer, and there are endnotes enough for any scholar - the book includes a sixteen page bibliography. At first I was a bit suspicious of her historical and philosophical point of view, but in retrospect, it is an excellent vantage point. Although a good portion of the book is "ancient history," that is, prior to 1953 and the molecular biology revolution, the majority is focussed on the developments since.

She excels at concisely presenting the perspectives and starting points of major investigators, and they are highly various. Like the fabled blind men of Benares confronting various parts of an elephant, the origin of life investigators are forced to reach for similes, and all of them seem to fall short of capturing the essence.

A couple of thousand years of progress in biology since Aristotle have brought us a great deal of knowledge about how life works, but so far that knowledge hasn't seemed to bring us any closer to the solution of the mystery of mysteries of the origin.

The last chapter of her book is devoted to the possibilities of extraterrestial life, which she(and I) find highly promising. Of course if such life could be found in the solar system, it could hardly help but clarify the puzzle of origins.

This is a story that does not yet have a proper ending. Neither an understanding of the origin of life nor any especially promising approach is yet on the horizon. Nonetheless, information accumulates and many interesting experiments wait to be done. This is long shot science still, but the payoff could be huge.

Steve Weinberg's Big Picture

For physics students of my generation, there were three new General Relativity textbooks: Gravitation by Misner, Thorne, and Wheeler; The Large Scale Stucture of Space Time, by Hawking and Ellis, and Gravitation and Cosmology by Weinberg. Each became an instant classic. Hawking and Ellis is a somewhat specialized and advanced treatise but the others were wide ranging texts with lots of cosmology in them.

Thirty-five cosmologically eventful years have passed since then, and there are a few new and notable books on GR and cosmology on my bookshelves, but perhaps this is a good time for Weinberg's forthcoming new book (listed for May, 2008) Cosmology.

Weinberg has a lucid and penetrating style and is a prolific and graceful writer of both classic textbooks and popular science, not to mention a Nobel Prize winning physics god. I haven't seen or ordered his new book yet, but the prospect looks inviting. Besides G&C he has previously written a terrific popular book on cosmological origins called The First Three Minutes

Uh Oh

Blogs by people who know something are great, and the blog world is valuable, especially if it pushes a story forward. But the blogs of people who simply write what they are thinking are not particularly valuable.

....................James Collins, who has written a new novel (Beginner's Greek).

Friday, January 11, 2008

Billions and Billions

Wolfgang has a post from a couple of months ago on an interesting puzzle. I think it has something to do with the way SIVs and CDOs are valued.

Thursday, January 10, 2008

The Diebold Effect

Following up on some links provided in the comments by Kurt L., I looked at some oddities in the New Hampshire vote count. All the NH ballots are paper ballots, but about 80% are counted by Diebold optical scanners, while the rest are counted by hand. Now here is the oddity: percentagewise, obama does much better on the hand counted ballots and Hillary does much better on the machine counted ballots. The percentage discrepancies for other candidates are all smaller. Similarly, on the Republican side, Romney does much better on the machine counted ballots, while Huckabee, McCain, and Paul all do better on the hand counted ballots.

Is it just coincidence that the two machine candidates, Hillary and Mitt, got a little boost from the machine counters? The referenced links have detailed data by candidate, town, and counting method.


With Bush and the Neocons, Paranoia may be the only rational response.

UPDATE: Critique and response.

From the comments, WB says:

This story names only one name in an official position: "assistant secretary of state for European affairs under the Clinton administration and undersecretary of state for political affairs".

So why do you have Bush and NeoCons in your one-line post?

The post I linked to mentions no names, but it does have four secondary links, which I will call A, B, C, and D in order of their appearance. Secondary link B links to a tertiary link, and quotes from it. No names appear in the tertiary link quote either, but it did reference an unnamed high official. Following that, secondary link B claims that the official in question is Marc Grossman, a Clinton appointee. It goes on to mention a number of other officials allegedly involved or on the fringes: Paul Wolfowitz, Doug Feith, Richard Perle, and Eric Edelman, all of whom are former very high Bush administration names. I can't verify any of these particular charges, but I stick by my characterization of the Bushies as justified paranoia inducing.

Secondary link C contains a reference to the part played by George W. Bush.

Are the Clintons part of the vast right wing conspiracy too?

A few years back I would have said no, but now that Bill and Richard Mellon Scaife are BFBs, who can say? Hillary and Murdoch seem pretty tight also.

Tuesday, January 08, 2008

Fear and Loathing in NH

26 % of the votes in and it's starting to look pretty bleak here in Obamaville. Confident predictictions of a crush seem out the window. At this point, any victory for Obama will be great, but it's starting to seem unlikely. For Hillary, living to campaign again seems certain. A grim prospect of Hillary vs. McCain and another Republican President looms.

UPDATE: Hillary wins. The Bradley effect wins. Bush's war wins. The bullshit pollsters lose big. I suspect Edwards is done, but this is a season for surprises, so who knows.

Did Hillary benefit from the universal media prediction of her demise? Probably. Did she benefit from a sympathy vote? Who can guess? Did she benefit from New Hampshire contrariness? Maybe. Is the race now wide open? I think so.

UPDATE II. Curiouser. All pre-election polls showed Obama with a substantial or even huge lead. Exit polls showed him winning more narrowly. But Hillary wins decisively. The Bradley effect? What kind of voting machines does NH use, I wonder? (Paper ballots, it seems).

Sunday, January 06, 2008

Can There be Only One?

The toughest problem in defining a general theory of life is the paucity of examples. That statement sounds like an oxymoron - isn't life famously diverse? Man, elephant, mouse, carrot, redwood, mushroom, coral, sponge, and bacterium seem pretty darn different. At the molecular level, however, they aren't. The most essential machinery at the molecular level is almost exactly the same.

They all use the same genetic code, and the same basic mechanisms for the most basic operations of life. These commonalities, and the patterns of both commonalities and differences constitute the most dramatic proof of the fact of common descent. However all that common machinery came into existence, it all seems to have existed in the most recent common ancestor of all known Earthly life.

Despite a large number of apparently contingent and arbitrary elements in life, exceptions are not known. Proteins and complex sugars have definite chiralities but we don't know of any fundamental reason why life based on the opposite chiralities couldn't exist. The particular amino acids from which are proteins are built are just a small subset of many similar amino acids. So why couldn't a different set of twenty, or thirty have been chosen. Many other possibilities for the genetic code would also seem to be possible.

We wind up knowing about only one kind of life, and the mystery of how all that elaborate and apparently necessary machinery of life developed seems at least as mysterious as ever.

This hasn't stopped speculation about other possibilities. The cover story of the December Scientific American was on the possibility that there might be Alien life among us but undetected - probably small bacteria like cells with a different hereditary and metabolic history. (An online version here) Well maybe, but of course there is no evidence.

Suppose we find life elsewhere in the solar system. That should be completely different, right? Again, the answer is maybe. Most scientists are doubtful that the ballyhooed meteorite from Mars, AH84001, really demonstrates Martian life, but it would seem to show that if life developed in one part of the solar system it might have made the interplanetary trip to other planets.

Robert Shapiro and physicist Gerald Feinberg have suggested that life might be much more exotic still - perhaps based on ammonia on cold planets or substituting silicon for carbon on a very hot planet, or even being encoded as patterns in the plasmas in stars or interstellar clouds.

In any case, discovering any other form of life would seem likely to clarify the thorny questions of the hows of the emergence of life on Earth.

View From the Pew

The Republican Debates

It's just possible that I have a slight prejudice here, but were the Republican candidates a bunch of scuzzy old whores or what? Ron Paul excepted, of course, but every time he said something intelligent, the stupidocracy, led by Romney, shouted him down. Giuliani is the sleeziest, and McCain is the oldest, but Romney valiantly tried too.

Pretty much the whole message of these louts (Ron Paul - you should keep better company) is fear mongering. The Islamic bogeyman poses an "existential threat" says the McCainbot - (I prefer to think that the real John McCain is being held prisoner somewhere, while this dopey Republibot campaigns). Pull - f*****g -leeze! The entire Islamic world has little technology, little military power, and is largely allied with our ruling Republicrooks.

The country does face some serious threats - the disregard for our constitution, the erosion of individual liberty, the destruction of the economy by Republican borrow and spend, and the alienation of friends and allies through reckless arrogance and stupidity. There are plenty of other challenges as well: the external competition from India and China, the failure of our education system, the absurd inefficiency and exorbitance of our health care system, and numerous and potentially catastrophic threats to the environment.

Health care was the only one of these to appear, so far as I can tell, and what was said about it only reveals an even more serious threat to our country: You apparently can't get nominated as a Republican for the Presidency without lying through your teeth and/or being a more or less total idiot.

The current Republican incumbent excels in both regards, and it was striking how reluctant the current crop of candidates was to let a hair's breadth of difference appear with the most unpopular President in generations. Bush's only serious competition for worst President ever is Dick Cheney, and only Ron Paul dares to challenge him in any respect.

Friday, January 04, 2008

Wisdom of Pundit Crowds

Glenn Greenwald gleefully assembles the just pre-Iowa predictions of our fearless punditocracy. A true Christmas in January for all the Joe Klein, Glenn Reynolds, Mike Allen, etc. haters of the world.

A small sample:

Joe Klein, Time, December 31, 2007:


Des Moines

Just when you think the Republican presidential race can't get weirder...Mike Huckabee holds a press conference here to announce that he'd just made a last minute decision not to air a negative TV ad slamming Romney.

That sound you hear rumbling out of Des Moines appears to be a monumental implosion.

There is much, much more from the wing-nut crowds.

Never Mind

Every year Edge asks the Dyson family and a few dozen notable others some philosophically tinged scientific question. This year the question was: "What have you changed your mind about?"

Your humble correspondent is much too humble to be among those interrogated, but I have heard of many of them, and one or two have even deigned to address me on occasion. Some of the notables have blogs: PZ Myers, Sean Carroll (the Caltech astrophysicist Sean Carroll, that is), and John Baez.

It turns out that most of the things these people change their minds about are pretty boring. Richard Dawkins used to think some theory of peacocks tails was wrong, but now he doesn't. PZ Myers works on problems slightly different from those he started with. Lots of others claim to have changed their minds about things quite some time ago, but I suspect that they were always heretics - I'm thinking Rovelli and Smolin for example.

Emboldened by these bits of mundania, I started thinking about questions that I might have changed my mind about. Boxers or briefs, for example? Or should I have invited Linda T to the high school senior prom? Chocolate or vanilla? As far as I can tell, I haven't really changed my mind about any of these.

Sometimes evidence can help. I guess I've changed my mind a few times about whether Snape is evil. Freeman Dyson's mind change on nuclear war seems to have changed for similar reasons. Ditto Roger Schank on Artificial Intelligence.

A few have something to say. I liked and agreed with Frank Wilczek for example. Check them out - you might find something interesting.

Kindness of Strangers

The current US economy is highly dependent on the willingness of the big international dollar holders - China, the Gulf States, Russia, Japan, and others - to lend us money at cheap rates. So far, this has been a dubious financial decision for them, since the decline of the dollar means that they keep losing money.

Brad Setser takes a look at some historic parallels. They aren't entirely encouraging. Surprising enough, owing a lot of money has a way of weakening your status and bargaining position. For the present, and for the foreseeable future, we are addicted to that cheap Chinese and oil exporter crack. The only things likely to improve our international standing are cutting back on our oil use and balancing the budget.


I have been an Obama supporter for some time, so naturally I'm gratified by the Iowa result. Being the sort of conflicted individual that I am, I'm also a bit nervous. Is he ready? Are we making a mistake in throwing out Hillary? Wouldn't we be better off with the more liberal Edwards? Conventional wisdom says Edwards is likely done. Hillary is poised on the knife edge, but still leads New Hampshire and national polls.

There is reason to be a bit cheerful about Huckabee's victory as well. He is the second most authentic Republican candidate and not quite as scary as Ron Paul. The phony Romney and his money went down, and the ultra scary Giuliani finished fifth. McCain and Huckabee now look likely to duke it out, though Romney and Giuliani probably can't be counted out yet - and Paul could still make some big noise in libertarian New Hampshire. It should stay interesting for at least another five days.

Thursday, January 03, 2008

Simple Academic Fairness

Every university worth its ivy has a college or school of liberal arts, but how many colleges have a college of conservative arts? This is an extreme example of American academia's left-wing bias. In simple fairness that needs to be remedied, and correcting that terrible injustice is the primary mission of Reagan Memorial University.

Because entrance to RMU is purely on a merit basis (if you've got the cash, you merit admission), some remedial courses in basic conservative principles are offered. Liberals are admitted too, of course, but they will be promptly mugged, ergo ... Basic preparatory work consists of principles of illogic, rationalization I, lying, cheating, and stealing. More advanced techniques are covered in the upper division courses - ballot tampering, vote suppression, and the ever popular torture but we don't call it torture.

The college of Conservative Arts is the capstone of RMU, but other traditional disciplines are represented as well. We also offer degrees in anti-environmental studies, Darwinian denial, and religious fanaticism. Minors are available in a wide variety of related fields.

RMU discriminates on the basis of race, religion, national origin, sex, and IQ.

Closeted gays and lesbians are welcome.

Wednesday, January 02, 2008

The Pardon Pen

Bush has been exceptionally stingy with pardons and commutations so far, but it looks like it might be time to fill the old pardon pen inkwell. Thomas H Kean and Lee H. Hamilton, the bi-partisan co-chairs of the 9/11 commission, have written an op-ed in today's New York Times bluntly accusing the CIA and White House of obstructing their investigation.

The commission’s mandate was sweeping and it explicitly included the intelligence agencies. But the recent revelations that the C.I.A. destroyed videotaped interrogations of Qaeda operatives leads us to conclude that the agency failed to respond to our lawful requests for information about the 9/11 plot. Those who knew about those videotapes — and did not tell us about them — obstructed our investigation.

There could have been absolutely no doubt in the mind of anyone at the C.I.A. — or the White House — of the commission’s interest in any and all information related to Qaeda detainees involved in the 9/11 plot. Yet no one in the administration ever told the commission of the existence of videotapes of detainee interrogations.

When the press reported that, in 2002 and maybe at other times, the C.I.A. had recorded hundreds of hours of interrogations of at least two Qaeda detainees, we went back to check our records. We found that we did ask, repeatedly, for the kind of information that would have been contained in such videotapes.

It is hard to conjure up a scenario under which the concealment and destruction of the tapes was not a criminal act. George Tenet, Alberto Gonzalez, and David Addington are clearly in the cross-hairs, and Cheney and Bush are highly suspect. Glenn Greenwald has a detailed analysis in his post 9/11 Commission: Our investigation was "obstructed."

Attorney General Mukasey has begun an investigation, but the appointed prosecutor lacks independence - contrary to department guidelines - so the reality of the investigation is in doubt. If a real investigation ensues, there is likely to be blood, or at least pardons. Can the President pardon himself? Or he could imitate his father and just pardon enough to keep them quiet about his own crimes.

When Fembots Attack

You, says David Levy, can be replaced. You, here, would be pretty much everybody.

Tuesday, January 01, 2008

Chicken, Egg, and Soup

Comments upon reading Iris Fry's The Emergence of Life on Earth Chapters 9-11

Which came first: the chicken or the egg? That is the fundamental question in the origin of life. Evolution manages to kick this can down the road a bit: the chicken and egg evolved together from earlier egg layers which in turn evolved from more primitive reproduction schemes. We even have samples of the more primitive reproduction schemes around to encourage us.

The discovery that life processes could be reduced to biochemistry, together with the Oparin-Haldane hypothesis positing a reducing atmosphere for the primeval Earth, encouraged origin of life researchers to believe that organic chemistry might naturally produce the molecules of life. However, developments from 1960 to the nineteen-eighties put a couple of severe dampers on such optimism.

First, and probably most grievously, explication of the mechanisms of heredity and metabolism revealed an intrinsic complexity that seemed guaranteed to prevent any easy synthesis of the substrates. Life as we know it depends critically on two very specific and chemically delicate types of polymers: proteins and nucleic acids. More crucially, proteins can't be made without nucleic acids, and nucleic acids can't reproduce without proteins. This presents us once again with the chicken and egg problem in a more fundamental form.

The second new problem was that the notion of an early Earth with a reducing atmosphere became dubious. It now looks likely that CO2 and H2O were the common molecules in the early atmosphere instead of NH3 and CH4. This makes early organic synthesis much more difficult and calls into question the notion of a rich prebiotic organic soup.

A third constraint also appeared. The early Earth was bombarded with a heavy rain of plantesimals that melted the surface and almost certainly made the place uninhabitable until about 3.85 billion years ago, but evidence of fairly sophisticated microbial life is clear by 3.5 billion years ago, and suggestive much earlier, perhaps 3.8 billion years ago. This appears to show that life arose very fast.

The idea of the "naked gene" arising from an "organic soup" was a clear casualty. There was no obvious way it could arise, and even if it did, no plausibility that it would survive and reproduce.

This crisis produced some new ideas. One of them is the idea of hetero cycles, collections of fairly small molecules catalyzing each other. Another biggie was RNA world. RNA plays at least three essential roles in mediating the conversion of DNA's information into proteins. Is it possible that RNA came first, before DNA and before proteins?

The components of RNA are somewhat simpler to synthesize than those of DNA. Unlike DNA, RNA tends to fold up in ways that suggest that it could have catalytic activity. The discovery of ribozymes - enzymes that are RNA instead of protein - confirmed that insight and quickly became a major focus of research. It too hits a very hard barrier though - initial formation of a set of ribozymes precise and complex enough to replicate seems too improbable to be credible.

Many became discouraged enough to adopt the counsels of despair - perhaps life did not originate on this planet, but somewhere else. Maybe primitive bacteria arrived on comets or on interstellar space craft. Clearly each possibility is very close to surrender to intelligent design.

To be continued...


It seems that the Lumonator is publishing a book. Unfortunately, it appears that it will be in French. Maybe Peter Woit can be talked into reviewing it.