Invisible Hand

Talisman: the Game

2012-02-14T16:29:00.001-05:00

When my son Daniel was 9 or 10, we played the board game Talisman with his friends. It was a lot of fun, and I was sad when I found out that it was no longer in print.

Well, I am sad no longer!

While browsing the ever enlarging Games section at Barnes and Noble, I noticed that Talisman is back on the shelves in a handsome new edition. Yay! As with the version we played, there are several add-ons for it as well. I didn't see Talisman Dungeon on the shelf, but it is available through Amazon.

According to reviews on Amazon, the rules have been tweaked slightly from the classic 2nd edition. For example, the mighty Prophetess no longer dominates the game as a character. Looks like a new generation is going to get hooked by this game.

Review: First Life, by David Deamer

2012-01-15T10:23:00.001-05:00

Just finished David Deamer's First Life.

The main point of the book is to expound on Deamer's theory that lipid based vesicles were important to the Origin Of Life (OOL). Lipids are the oils and fatty acids we use today as cell walls in our bodies. They are 'polar' molecules, with a different charge at each end of the chain of atoms. This makes one end attracted to water and the other end repelled by water (hydrophobic). When dispersed in water, the hydrophobic ends wind up crowded together, while the hydrophillic ends stick out, so the lipid molecules naturally form surfaces that are two molecules thick. Under the natural physical forces found in water, the most stable shape for these layers is a sphere -a vesicle or bubble.

A key property of these vesicles is that small molecules can work through the layer separating the inside from the environment, but a large molecule inside can't get out. Therefore, a chemical reaction that built up large molecules from small ones inside the vesicle would build up a concentration of large molecules far faster than the same reaction happening in the open, where the reaction products would get mixed and diluted quickly. It just so happens that life is full of these kind of reactions.

Having read a lot of pop sci literature (Zimmer, Ridley, etc.) it shows that Deamer is a working scientist, not a professional writer. At times the book felt padded by reviews of everything from the Big Bang onward, and an explanation of what name comes first in an article reference. And there was a fair bit of chemistry porn, in which the author gives a bit too much detail on lab procedures.

Deamer's take home message is that OOL requires some minimum complexity, and most scientists are not willing to attempt the messy experiments necessary. In a football analogy, grant funded science is a "three yards and down" ground game, and OOL needs some Hail Mary passing.

His last chapter describes his ideal update of the famous Miller-Urey experiment, which showed that a combination of small molecules and energy could lead to biologically important molecules such as amino acids. It's big, throws a lot into the mix, and would cost a couple million dollars to run. At the same time, he acknowledges that it would have to run over and over, with multiple changes in atmosphere, temperature, pressure, etc. which would increase the cost. But at the same same time, he mentions that robotic experimentation runs hundreds of experiments at the same time. However, the two ideas never connect - that you have to reduce OOL experiments to something that can be done on a microfluidics chip in large batches.

Recommended.

Vaclav Havel, RIP

2011-12-19T06:06:00.001-05:00

Vaclav Havel was one of the great men of the 20th Century. Like Nelson Mandela, he was jailed by the regime that he eventually replaced. He cared deeply for his country and the world.

Last night, I went with Blanka to light candles for Havel at Narodni Trida, the memorial to the Velvet Revolution that toppled Communism in Czechoslovakia. We walked around the old part of the city, and enjoyed the sites of the Christmas Market in Old Town Square. We eventually wound up in Wenceslas Square, another important site in the history of Havel and the Velvet Revolution. There, the statue of St. Vaclav had been turned into another candle draped memorial. I tried to explain to some French tourists what was going on, why students were reading from Havel's essays to the crowd. We lit another candle and returned home.

Remember him. He mattered.

Public reading by SFABC Writers of the Weird at The Fine Grind

2011-07-18T10:34:00.001-04:00

Congratulations to the Science Fiction Association of Bergen County's Writers of the Weird! Thanks to the organizational energies of Phil DeParto, the group of published and aspiring writers held a group reading at The Fine Grind (http://www.thefinegrindcoffeebar.com/) this past Sunday afternoon.

The Fine Grind gave us a warm welcome, with a space reserved for the expected group of writers and cheering section. We had six authors present seven short stories, tied together with introductions by Phil, and a pitch by John Adamus for the North Jersey Writer's Meetup group. John made his group sound awesome, I might check it out since it meets in my favorite Barnes and Noble in Paramus!

I enjoyed reading my own story, Molybdenum, for the group. I hope others enjoyed listening as much as I enjoyed reading!

If we repeat the experience (perhaps at a public library), I'll try to blog it in advance.

World's Best Computer Chair

2011-07-06T00:41:00.000-04:00

Staples Varretta high back mesh chair. SKU 865004. 'Nuf said.

The Facepalm of Compensation

2011-06-23T16:01:00.000-04:00

Readers here and elsewhere will know that Dr Granville Sewell thinks there is a problem with biology and the Second Law of Thermodynamics. He has written several versions of an argument claiming that the Second Law poses a problem for biology, especially the origin and development of life on Earth.

Dr Sewell is not alone in this concern. Generations of creationists have had this concern. However, the answer given is so obvious that even creationist bastions such as the Institute of Creation Research no longer recommend using this issue in debates. That answer is that SLoT only applies in closed systems, and the Earth is not a closed system. The surface of the planet receives energy from the Sun, energy from its core (from radioactive decay and residual heat of friction) and these sources overcome the trend towards higher entropy.

Dr Sewell has attempted to avoid this answer by arguing in several ways. One is to try to apply SLoT to an open system. Another is to attack the idea of compensation that appears in some elaborations of the answer given above.

Dr Sewell's argument is that even an open system MUST rely on passage through the boundary of anything that that is going to increase inside the system.

If an increase in order is extremely improbable when a system is closed, it is still extremely improbable when the system is open, unless something is entering which makes it NOT extremely improbable.

The above quote is from Dr Sewell's Can ANYTHING Happen in an Open System?

One of the biggest problems with this argument, which Dr Sewell has called his controversial tautology, is that it expands SLoT to cover any diffusion problem at all. We can break this down into two sub-problems, expanding SLoT and treating the issue as a diffusion problem.

Can SLoT be expanded to cover anything beyond thermal entropy? Obviously, Dr Sewell says yes here, and in his invocation of "X-order" in the AML paper. At the same time, in a later article he criticizes Dr Dan Styer for allegedly applying SLoT broadly. He has perhaps learned something, since most scientists would agree that you can't, willy nilly, go applying conservation laws wherever and whenever you feel like it.

Secondly, not all of the universe is a diffusion problem. Let's say that my open system of choice is a crowded bar, and I'm interested in the amount of whiskey in the bar as whiskey diffuses across the boundary I've drawn around the bar. Is the amount of whiskey in the bar solely dependent on the amount crossing the boundary? Obviously not, it also depends on the rate at which it is consumed within the bar, the rate at which sober customers (who are not, themselves, made of whiskey) arrive, and the rate at which inebriated customers (partially made of metabolized whiskey) exit.

What is true of whiskey is also true of cosmic rays, high energy photons, radioactive atoms, and many other things. They can enter through a boundary around an open system, but there are significant transformational processes that can occur within the system as well. So Dr Sewell's controversial tautology is neither controversial nor a tautology. It is simply wrong.

This is why Dr Sewell's argument fails at explaining photosynthesis. Similar to the crowded bar, we draw the boundary around the cell wall of a cyanobacteria. Light enters at one frequency, strikes various molecules, is absorbed, its energy is changed into thermal motion and the potential state of various electrons, sugars are produced and eventually a low energy infra-red photon exits the boundary. Sugar did not enter across the boundary. A low energy photon did not enter across the boundary. The quantity of high energy photons inside the boundary has not increased.

This brings us to compensation. We can say that the exit of the low energy photon "compensates for" the sugar. There is an energy difference between the high energy photon that came in through the boundary, and the sugar molecule. If we add in all the thermal motions and escaped photons, we should be able to make the energy equation balance.

But not the order equation. Even though the sugar molecule has lower entropy, the universe as a whole is worse off.

Dr Sewell seems to think that compensation can happen at a distance. It doesn't. Dr Styer says in his article:

Presumably the entropy of the Earth’s biosphere is indeed decreasing by a tiny amount due to evolution, and the entropy of the cosmic microwave background is increasing by an even greater amount to compensate for that decrease.

Does this mean that Dr Styer is engaged in some magical thinking that life here makes the CMB colder via some spooky action at a distance? No. Dr Styer previously wrote:

The Sun heats the Earth through electromagnetic radiation largely in the visible and near-infrared bands . The Earth radiates electromagnetic radiation largely in the far-infrared band into outer space, where it eventually joins the cosmic microwave background.

So it is clear that the CMB effect Dr Styer is referring to is based entirely on the passage of sunlight through the biosphere of the Earth. Yes, the CMB observed by someone distant from the Earth will have higher entropy than if the same sunlight had struck a dead planet of the same size and location.

Compensation is not action at a distance. You can always trace the interactions back to the point where one high entropy and one low entropy component were created, and see how the high entropy component escaped the open system. In considering the overall accounting for entropy in the closed system (the Universe) within which our open system is embedded, the escaped component is compensation for the low entropy component it left behind. It is only in this overall perspective that we need to worry about compensation, since it is only in this closed system that we need to be concerned with SLoT.

These misunderstandings and logical fallacies have led Dr Sewell to embarrass himself once again, by writing to the journal that published Dr Styer's article, the American Journal of Physics. In a blog entry on Uncommon Descent, Dr Sewell calls AJP a "major physics journal". In fact, it is a journal for articles related to teaching physics to high school and college students. The rejection message he received makes that clear, as well as making clear the overall high crank science level of his writing.

Model Madness: Axe vs. Lynch and Abegg

2011-06-20T17:05:00.000-04:00

I recently blogged about a paper by Lynch and Abegg 2010, which I thought was an important paper. It showed that, yes, there was time enough for evolution, mainly because neutral and even maladaptive variations could accumulate in sufficient numbers until they finally coalesced into a new beneficial function.

Douglas Axe, a leading scientist within the ID community, responded to the challenge inherent in this paper. Axe's position and research agenda has long been that there is not time enough for evolution.

At this point, I have to say that even though I disagree with Dr Axe, I give him credit for being the most professional and rigorous pro-ID scientist I have ever read. Yes, professional scientists can work themselves into a corner that eventually becomes crank science as they refuse to abandon a position - witness the Rubin group at the University of Oregon on "birds are not dinosaurs". Yes, I do think Axe is in this position, but he is trying in a principled, scientific way to address the issues. As such, he has demonstrated far more professional integrity than Stephen Meyer or William Dembski, neither of whom is a scientist.

Axe's response is The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations, which attempts to criticize Lynch and Abegg and to propose an alternative model.

For now, I'd like to focus on the differences in the models. Lynch and Abegg use a model assuming sexually reproducing diploid populations. Axe tries to refute them with an asexually reproducing haploid island population model. Are those differences appropriate?

One way to answer would be to look at the biochemistry that is being discussed, and ask when did it evolve. Is it eukaryotic or prokaryotic in origin? As I pointed out in my last post on this, eukaryotic sexual species with large populations have been around for a billion years. The larger portion of the biochemistry we operate with is eukaryotic - not shared with bacteria.

That calls into question the basic assumption of Axe's model. Another way to look at the issue is to question the realism of the asexual population genetic abstraction. We now know that in real life, as opposed to the test tube or a mathematical simplification, bacteria exchange genes rapidly. The process might be based in conjugation, or it might be through viral infection. In either case, the binary fission model of where genes come from isn't relevant.

Axe's model also incorporates an effective population size that is quite small - 10^9, a billion bacteria. This is justified by appealing to the island model dynamics of Maruyama and Kimura 1980. Even accepting these dynamics, a gene's eye view of the world has to incorporate the reservoirs afforded by other species and viruses. So I would argue that Axe's effective population size is too small.

New York-New Jersey Trail Conference - You Rock!

2011-06-10T03:38:00.000-04:00

I recently took a hike in the Ramapo Reservation without a map, and had a less fun time than I hoped for. The natural surroundings were great, but there are many trails, and I could not find what I was looking for.

To the rescue - trail maps by the NY-NJ Trail Conference. Great color and BW maps printed on Tyvek, so they won't rip. NYNJTC does great work for hikers in the area of New York City. Buy their stuff.

(A shoutout of thanks to Danny Chazin, who has worked tirelessly for TC, the Scouts, and his synagogue over the years.)

Hypothesis: Reordering typical GA operations opens up new opportunities

2011-06-09T07:54:00.000-04:00

One of the truisms of the area of evolutionary computation is that time spent on the evaluation of the fitness function dominates the the total resource budget of the run. Therefore, we should want to allocate trials as efficiently as possible, even more so as we are using a method which will inevitably allocate trials to poor choices as part of the exploration of the parameter space.
When GAs are introduced, the fitness function evaluation is typically a single test case, for example evaluating f(x) for some x, which is the phenotype constructed from the individual's genotype. The population might have genotypes of binary strings, these strings then become phenotypes of real numbers, and the phenotypes are evaluated.

For more 'real world' problems, the phenotype has to be evaluated across multiple test cases, perhaps thousands of cases. The outcome of all of these test cases contributes to the overall fitness measure of the individual. As noted in this early paper, the test cases can vary greatly in their discriminant utility. The basic idea here is to break down the test cases into a population of individuals that will co-evolve with the population of possible solutions.

My idea is somewhat simpler. Typically, one individual is tested across all test cases, and a cumulative fitness score generated. In my reordering of operations, all of the new population members are generated, then each member is evaluated on the first test case, then all on the second, etc. We stop the evaluation process at some point to compute a partial fitness score. On the basis of this score, we abandon some members of the population and delete them, replacing them with perturbations of high scoring members.

In terms of the biological analogy, reordering the test case evaluations allows us to select from the population at multiple points in each individuals "lifetime", where the lifetime is the sequence of test cases.

The hypothesis is that this reordering, partial fitness selection, and reward of well performing members will lead to more efficient allocation of trials in problems that are amenable to this reordering.

Time Enough for Evolution: part n++

2011-06-08T11:32:00.000-04:00

The Rate of Establishment of Complex Adaptations
Michael Lynch, and Adam Abegg 2010

Several points about this important paper:

The concerns of evolution critics are addressed in the scientific literature. The paper mentions the critique of Behe and Snoke (2004) as a motivation.
The particular set of population genetic models discussed are based on sexual reproducing populations of diploid chromosomes. We are familiar with sexually reproducing organisms as large plants and animals, and therefore the charts in the article which show effective population sizes up to 10^11 individuals may seem alarming. But consider that there are many single celled sexually reproducing plants, animals, and fungi (protists, generally), and that even one trillion (10^12) eukaryotic cells take up less space than the human body.
Single cell protist sex has probably been around for a billion years.
The evolutionary features we find most striking are at the edges of the vast conserved biochemistry of life. We look at changes in timing and rate of developmental signals that can change a tapir into a giraffe, but these don't require new biochemistry.

Taking these points together, this paper is an important answer to the 'no time for evolution', bignum crowd.

Granville Sewell's SloT article: Zombie or Persistent Vegetative State?

2011-06-08T06:19:00.003-04:00

I've been apprised that the 15 seconds of Internet fame alloted to this blog has arrived, in the form of a link from John West's blog entry over at Evolution News and Views. As welcome (in the 'just spell my name right' way) as that may be, it seems that John and/or lawyer Pete Lepiscopo are confused about the issues.

Here's the text of my letter to Dr Rodin, the editor at AML.

Dr Rodin,

I am appalled to see a preprint, apparently from Applied Mathematical Letters, of the often repeated and often refuted nonsense of Granville Sewell on an anti-science web site.
http://www.uncommondescent.com/intelligent-design/elsevier-publishes-granville-sewells-latest-on-the-second-law/

Dr Sewell, whose expertise lies in partial differential equations, has writen several times on the relevance of the Second Law of Thermodynamics to the topic of evolution. Each time he makes poor arguments that do not show any understanding of the physics or chemistry involved, clearly contradicting the philosophy of your journal.

A concise refutation is
http://ajp.aapt.org/resource/1/ajpias/v76/i11/p1031_s1

The reputation of AML will be harmed by publishing this article by Sewell.

Yours,
David vun Kannon

You might notice that I don't make any request of Dr Rodin, specifically, I don't ask him to not publish. Nor do I base my argument on my own reputation in the field of evolution or thermodynamic studies (fields where my reputation is at least equal to Dr Sewell's). Rather, I supply Dr Rodin with a link to an article published in 2008.

American Journal of Physics -- November 2008 -- Volume 76, Issue 11, pp. 1031
Entropy and evolution
Daniel F. StyerDepartment of Physics and Astronomy, Oberlin College, Oberlin, Ohio 44074
Abstract:
Quantitative estimates of the entropy involved in biological evolution demonstrate that there is no conflict between evolution and the second law of thermodynamics. The calculations are elementary and could be used to enliven the thermodynamics portion of a high school or introductory college physics course.
© 2008 American Association of Physics Teachers

The above article is far more persuasive than a letter referencing it. While Sewell's lawyer might think an e-mail from a nobody blogger can move an editor to extraordinary actions, I think the credit fairly belongs with the scientific literature that was cited.

West then follows lawyer Lepiscopo into an odd series of quotes and links. For example, West states:

According to the journal's editorial policies, acceptance of an article cannot be rescinded once an author has been notified of its acceptance, and accepted articles are supposed to be withdrawn only "under exceptional circumstances" such as fraud, errors, ethics violations, and the like.

Um, yeah. Follow that "cannot be rescinded" link and you arrive at a page describing the Elsevier editorial process, which is not relevant to the situation after acceptance. Even so, the page states:

Editors with the appropriate EES permission* can rescind (undo) a decision before or after the Author has been notified, or after the final disposition has been set to Reject.

Notice the "can rescind" verb? West and lawyer Lepiscopo appear to have read that as "cannot rescind" for some reason, perhaps a reason favoring their position.

West and lawyer Lepiscopo continue by noting that errors are a valid reason for withdrawing a paper. Well, that is really the point, isn't it? While people familiar with Sewell's Johnny-one-note attack on evolution know he has been singing the same song for years (as Weseley Elsberry showed), more to the point for AML is that this version of the paper does not address the literature, specifically the 2008 paper cited above.

I am not privy to any agreement, certainly less so than John West seems to be. If Elsevier has made a pragmatic choice to buy off a nuisance lawsuit, I understand it from a business perspective. I hope it might make them review the business process that led to this fiasco, a 'rapid review' editorial workflow. I'm glad to hear that Dr Sewell is welcome to submit future articles to AML. This is a privilege that is shared by most of the population, including myself, John West, and lawyer Lepiscopo.

And what of the paper itself? According to West, it can join several of it's kin on Dr Sewell's web site. It might even say 'accepted by AML' on it. But it remains comatose. If John West wants to see how Dr Sewell and I discuss his ideas, he can look at my comments (under the pen name Nakashima) on the various threads on Uncommon Descent where the same thoughts have been floated in the past.

Spetner, Wilf, & WEASEL

2011-05-30T08:00:00.006-04:00

Last year, a short paper was published in the Proceedings of the National Academy of Sciences (PNAS) entitled "There's Plenty of Time For Evolution". (Link goes to arXiv version of the paper.) It wasn't the best of all possible papers on the subject, and some people seriously questioned why it got published by PNAS.

The paper, by Wilf & Ewens, attempts to address the 'bignum' argument frequently used against evolution. Bignum arguments usually run along the lines of: a functional protein enzyme is at least 150 amino acids long, but if you just tested strings of length 150 with any sequence of 20 amino acids, that is equivalent to searching through 20^150 strings. Even if the universe were filled with testing apparatus working since the Big Bang, not enough time would have passed to find a single functional protein. Therefore, evolution needs the assistance of an Intelligent Designer to nudge things in the right direction, or perhaps create everything already working perfectly.

Bignum arguments have been around a long time, and they were famously taken down by Richard Dawkins in his popular book, The Blind Watchmaker. In that book, Dawkins shows that cumulative selection is the natural process which allows evolution to proceed faster than the random search model. Dawkins does this with a little computer program that has come to be known as WEASEL.

The WEASEL algorithm was simple. Generate a population of random strings. Measure their fitness. In WEASEL, this was done by comparison to a fixed string. The fittest of the population is the only one allowed to reproduce. It does this by copying itself until the population is the same size again. However, each time a copy is made, letters have a chance to change. Repeat this process for as long as you like.

The WEASEL algorithm could find strings much faster than the random model, of course. The key is remembering your good choices. The second key is using a population to test multiple possibilities at the same time.

To rebut WEASEL, anti-evolutionists have made two critiques. The first is that WEASEL uses a fixed target string. This, they say, is 'sneaking in information'. No, this is just making the example easy to understand. You can write a WEASEL-like program with a different fitness test that does not involve a fixed string. An example would be the Traveling Salesman Problem (TSP), where the fitness is the shortest path through all the cities.
The second critique is that the program protected its good choices from ever changing again, which was not a good model of mutation in a genome. A careful reading of Dawkins' description shows that he did not make this mistake. It is a side effect of using a population based model that reversions from correct letters rarely happens, but it can happen at high mutation rates in small populations.
Neither of these critiques go to the heart of the issue, that a population based model with cumulative selection is a better approximation to real biology than a random search model.

The reason for this lengthy diversion into WEASEL lore is that anti-evolutionists are not the only folks to get the algorithm wrong. Even academics trying to demonstrate evolution occasionally code it wrong by protecting the correct letters. This brings us to Wilf & Ewens.

Wilf and Ewens do use a model which protects good choices. However, what they are modeling is very different from the WEASEL model. In WEASEL, the objects were individuals in a population. In Wilf & Ewens, the object is a population itself. In a population, the process of fixation is the analog of protecting the letter. This isn't well explained in the paper. Essentially, instead of counting generations, the 'rounds of guessing letters' are rounds of selective sweeps and fixations in the population. Each of these could take many generations. Since the paper is directed at the mistakes of non-specialists, all of this should have been made much clearer.

Now along comes Dr. Lee Spetner. Spetner is a well known and well respected name in the anti-evolution field. He is an MIT Ph.D, so he has credentials that command respect and attention. Spetner has written a critique of Wilf & Ewens, but PNAS has refused to publish it, so it has been posted on Uncommon Descent instead.

Spetner's first critique is that Wilf & Ewens are attacking a mislabeled problem. According to Spetner:

They gave no reference for such a model and, to my knowledge, no responsible person has ever proposed such a model for the evolutionary process to “discredit” Darwin. Such a model had indeed been suggested by many, not for the evolutionary process, but for abiogenesis (e.g., [Hoyle & Wickramasinghe 1981]) where it is indeed appropriate. Their first goal was not achieved.

First, lets thank Dr Spetner for pointing out that evolution and abiogenesis are two different things, two different issues. Many are the anti-evolutionists who cannot make this distinction. However, the bignum argument has been used often against evolution, also. For example, Douglas Axe, Michael Behe, and Stephen Meyer all use it. These people are not 'responsible', apparently. Spetner should inform the Discovery Institute of this!

Since we see that bignum is used against evolution, Spetner's own first critique fails.

Spetner's second critique is more serious. According to Spetner, the selective sweep and fixation of one improvement cannot be achieved until the last sweep is finished. Therefore, fixation of multiple genes must proceed in series, returning us to a bignum argument.

I think a big part of the disagreement here is that Spetner is assuming an asexually reproducing population, while Wilf & Ewens are assuming a sexually reproducing population. Neither the original paper or the critique make this point clear, but that is the simplest reading to me.

You can go on to question Spetner's reasoning, even in the asexual case. First, lateral gene transfer means that in reality, even asexually reproducing bacteria have many 'parents', so genes mix much more quickly than a pure, asexual, mutation driven process on paper. But even in the pure case, assume that a mutation is present in 90% of the population - it has almost taken over, but not quite. Certainly, a new mutation of another gene could arise within that 90% and begin a new selective sweep of its own. How would it 'know' to wait?

Spetner's argument is also couched in terms of the individual, not the population, so it seems that he has missed or ignored the issue of what is the object.

(A much more interesting criticism (to me) assumes that in an asexual population two different good mutations of two different genes arise in different individuals. Now their sweeps are competing with each other. It is a random walk as to which will prevail, and then the losing mutation will have to develop again.)

So Spetner's second critique also fails. He makes a fling that Wilf & Ewens have ignored Fisher, and the chance that even a good mutation can get lost, but this is unfair, since the original paper says:

In practice further modifications are needed to the calculations since, because of stochastic events, only a proportion of selectively favored new mutations become fixed in a population.

Spetner has also posted a version of his correspondence with the PNAS Board, to support a contention that his critique was rejected unfairly. It seems to me that the reasons given don't align with the real issues with the critique.

How the Earth Was Made, reviewed by David vun Kannon

2011-05-29T23:10:00.002-04:00

I picked up Seasons 1 and 2 of this History Channel series at Barnes & Noble recently.

This is excellent science television. Season 1 takes the viewer through a history of the Earth from its formation to the arrival of Mankind, sort of like the original conception of Fantasia's Rite of Spring. I was most interested in the first episodes that dealt with the formation of the Earth until the beginnings of life. Was there an era in the past when the seas were green and the sky pink?

Season 2 focuses of specific features or events and explains them in depth. I was very impressed by how the series showed the experimental evidence for each idea and tied it to the facts observed. A large variety of working scieintists were showcased. Even one from my alma mater, Hofstra University! Talking about rocks that I've visited!!

Worth watching, worth owning.

Signature in the Cell, reviewed by David vun Kannon

2011-05-28T22:54:00.003-04:00

I won my copy of Signature in the Cell in an essay contest on the intelligent design advocacy blog, Uncommon Descent. I didn't even pay for shipping.

I made a strong attempt to read it through in order to write a review of the book for UD. Sadly, that blog often bans dissenting voices, so my review will have to be published here instead.

The book is too long for its stated purpose. For its unstated purpose, it is about right. The stated purpose is to review the history of DNA science, and Meyer's own life, as a framework to explain the inadequacy of naturalistic explanations of the genetic code. The unstated purpose is to throw a lot of basic history and science at the reader so that when the science becomes merely 'sciencey' most will not notice the transition. The result is that three small books (DNA for Dummies, My Life, and ID, the Theory That Couldn't) have been woven together and sold as one.

On p. 143, Meyer tells us that "The idea of design helped liberate Western science from such fact-free reasoning." "Such" reasoning belonged to the Greeks that argued from first principles, and purely from logic, to the actual state of the world. Signature in the Cell almost immediately falls back into that error when Meyer argues purely from logic, analogy, and common sense instead of experiment and calculation.

This abandonment of experiment is what most clearly justifies calling the book non-scientific, and even anti-scientific. A good example is Meyer's treatment of Michael Polanyi's arguments on pp 237-243. Meyer is convinced when Polanyi 'argues', 'insists', and 'concludes' all without doing a single experiment. It is the logical structure that is convincing. This is a retreat from science.

Polanyi's argument is central to many claims of ID, so lets talk about it a bit deeper. Polanyi makes the claim that to function as a code, the order of the bases can't be forced by potential energy. ATC and G must be free to come in any order. This is argued by analogy to human communication systems.

However, we already know there are exceptions to such rules. In English, Q must be followed by U. And yet, we somehow stumble forward using English to communicate. Similarly, there may be slight influences in base to base sequence.

Polanyi was writing when almost nothing had been sequenced, today we have thousands of complete genomes to test the idea. But testing the idea is irrelevant if Meyer is already convinced by the logic.

Since Meyer is focused on the genetic code, Polanyi's argument is a major intellectual roadblock. Sequence independence of symbols is far less important than the translation from one symbol system to another, in understanding what a code is and how it functions. DNA is a code for protein (and RNA). Sequence independence means random sequences can acquire meaning slowly and stochastically, not that the entire code was graven on tablets of stone before the world's creation, and then delivered from heaven by a choir of angels.

This process of "acquiring meaning" in the case of the genetic code means narrowing down the association of each triplet of bases from any random amino acid to a specific amino acid. There is a lot of evidence that this process is at least in part driven by the laws of physics and chemistry, contra Polanyi's pronouncements of 40 years ago. But you are not going to learn that from Signature in the Cell.

Meyer also indulges in a 'big number' argument about the size of proteins (and RNA polymers). Starting from an assertion that we need 150 amino acids for functionality, and old and often refuted argument follows that the universe doesn't have the resources to find even one such protein. Sadly no. Meyer ignores all evidence that vastly smaller fragments of protein have useful function.

Function in proteins is often associated not with a specific arrangement of amino acids, but with the polar/non-polar nature of the amino acid. (If you want to think in terms of symbols, this is cutting down the number of symbols from 22 to 2.) While the universe can't explore 22^150 sequences, it certainly can explore 2^15 sequences, then use two of the best 15-length sequences together in a 30-length sequence. Etc, Etc. But Stephen Meyer is not going to tell you that.

Signature in the Cell is padded with a lot of historical information. Dr Meyer can claim that it is included to show that he is giving every argument a fair opportunity. Exactly the opposite is true. In chapter 14, pp 296-297, Meyer recounts an exchange with Dr Kenneth Miller over his coverage of the RNA world in an article from 2000.

The article, DNA and Other Designs, is still available on the Discovery Institute web site. I recommend reading it, since it says just about everything that Meyer says in this large book, and for free. But just as Signature in the Cell recapitulates and expands on that article, it recapitulates the error of that article as well. As Dr Miller complained in 2000, Stephen Meyer lies by omission by "not having the space" to mention 20 years worth of research in the RNA World hypothesis. Now it is 28 years, and the page count of Signature in the Cell spent on long forgotten theories crowds out discussion of current theories and work that directly undercuts the main ideas of the book.

There is no mention of the work of Michael Yarus' lab, no mention of the stereochemical hypothesis in the origin of the genetic code. This is the key work that Meyer has to come to grips with if his whole facade of looking into every possibility is to have any credibility at all.

It might be an acceptible debating technique to dodge your opponents best arguments until the time runs out, but that kind of rope-a-dope argumentation isn't science. That is the bottom line verdict on this book. It is not looking at everything and arguing to the best explanation. It is picking and choosing, retelling lots of old stories, personal stories, and some basic science, while avoiding the experiments and evidence that would challenge ID, and collapse its claim to be the best explanation of anything in the universe larger than Stephen Meyer's paycheck. ID explains that perfectly well.

Great Falls, Paterson

2011-05-24T18:22:00.002-04:00

I've never been to Great Falls before, but I thought that the heavy rain we had gotten for the past week would make them worth photographing. I was right!

Marjorie Grene, and the fate of the Faith of Darwinism

2011-05-23T12:26:00.002-04:00

I didn't know much about Marjorie Grene until a few weeks ago, and I admit I still don't. However, she has suffered the ill fortune, shared by not a few, that in death she has been taken up by creationists as supporting their cause against Darwinism.

My own interest was peaked by a reference to her work with Michael Polanyi. I think Polanyi is the intellectual mother lode of all the thinking that underlies the intelligent design movement, and most of that movement would agree with me. That is why Dr. Dr. William Dembski named his ill fated foray onto the Baylor campus the Michael Polanyi Center.

Grene's fame with the ID crowd rests on an essay she wrote in 1959, The Faith of Darwinism. Even the title is quote-minable! The style of the essay is the overheated, bombastic rhetoric that philosophers often use against each other. Unfortunately, she frequently conflates neo-Darwinism (the science) with "Darwinism", a reductionist philosophy she doesn't approve of.

Her attacks on the science are of the form, 'sure it works, but Eminent European Authority X has his doubts', and 'it might explain all of that, but it hasn't yet explained this, and its supporters are too smug in their expectation that it will.'

From our vantage 50 years later, having seen evo-devo and gene regulatory networks answer the doubts of Authority X, and learned that new forms of variation, and acceptance of genetic drift, expand the explanatory power of the core theory, it is too easy to be condescending. We have 50 years more fossils, 50 tremendous years of growth in molecular evidence.

But even Marjorie Grene realized later that she had overblown her statements and position. The essay was collected into a book "The Knower and the Known" as chapter 7. In 1974, Grene wrote in the preface to the paperback edition:

Were I to write this book now, I would perhaps tone down the rhetoric and would certainly (in chapters 7 and 9) separate more prudently than I did then the strictly empirical scope of evolutionary theory from its metaphysical associations or implications.

and further

I would still stand by the criticisms made in Chapter 7 of ambiguous and overambitious evolutionary thinking, and of course by the main theme of Chapter 8; but I confess to having been unfair to the stricter evolutionists who have always seen clearly what they were not explaining, and to having overestimated the relevance of teleological thought for evolutionary theory - which I would now place at zero.

But with juicy quotemines comparing Darwinism to a religion and a religious orthodoxy, you can't expect creationists to read the preface.

And Polanyi? Grene did work with him, and had this to say about the experience later in an interview with The Believer magazine in 2005:

BLVR: Was there any relation between your project with Polanyi and the later philosophy-of-biology work?

MG: Not directly. But OK, yes, continually, in the sense that he had asked me to look up heresy in evolutionary theory, because he hadn’t a clue about evolutionary theory. He didn’t think that neo-Darwinism could be right at all. He was very silly about it, evolutionary theory in general. He said natural selection was like catching two tigers and letting one go! He just had no understanding of evolutionary theory. What he wrote about it was just terrible. He had a friend, a clergyman, who tried to get him to change it. He was just as shocked as I was, this clerical guy. But it was really bad. I think that’s when I started looking through the literature, to help him out. Even before that, my work on Aristotle started because I was asked to teach Greek philosophy at Belfast, and I didn’t know anything about it so I had to start studying him.

But it matters not. Google "Grene faith Darwinism" and the first page of results is taken up by creationists quoting her rhetorical flings of 1959.

PotC: On Stranger Tides, reviewed by David vun Kannon

2011-05-23T08:28:00.001-04:00

Turning a theme ride tie-in into a continuing series is a dangerous gambit, though it has undoubtedly been a lucrative one so far.

In this installment, very few of the characters from the previous three films carry over. There is a small plot connection via the map that Jack Sparrow has which shows the location of the Fountain of Youth. (Jack's enchanted compass also makes an appearance.) The action shifts back and forth among several groups racing to find the Fountain. The Spanish start first, with the help of a completely improbable and poorly motivated event. But the focus shifts quickly to Jack, sorry, Captain Jack Sparrow, in London to find out who is impersonating him. For those who like the transgendering effect of Jack's eyeshadow, the sight of Penelope Cruz in a moustache will be appealing. Cruz play Angelica, Jack's old flame. Their relationship is highly reminiscent of Indiana Jones and Marion Ravenwood from Raiders of the Lost Ark. With eyeshadow.

Way too many things blow up, too many fights break out for no reason, and too many swords get pointed at the audience just to prove you are watching in 3D. (I was.) Blackbeard is the Monster of the Week, a fearsome pirate with voodoo powers and a magic sword that lets him control his ship. Stuff happens, some involving mermaids. The mermaids are the most original part of the movie. I found Ponce de Leon's ship the most interesting visual, and Ponce himself was amusing.

Oh yeah, it all turns out fine. You wouldn't expect a Disney theme ride to dump its paying customers over a cliff, would you? You wind up where you started, exit to the left, and don't forget your packages that you brought with you. In the next film (and you know there will be one) Sparrow and Gibbs will be fighting Barbosa for control of the Black Pearl - the only lasting theme in the PotC mythology.

Metamorphosis, a new Illustra film

2011-05-20T08:36:00.003-04:00

Illustra is a film production group that makes high quality films for Christian apologetics such as intelligent design. They've produced several films that adapt the look and feel of science documentaries for the purpose of spreading the Gospel.

Just announced, Illustra's newest effort will focus on Monarch butterflies as iconic species for The Argument Regarding Design (TARD). The Discovery Institute has already begun flogging the video.

Monarch butterflies have long been a creationist favorite, for three reasons. They are beautiful delicate creatures. They migrate absurdly long distances. They have a complete metamorphosis that transforms them from larval caterpillar to adult butterfly.

I'm not going to say anything against the creationists and their sense of wonder at Monarch butterflies. It is a good thing, a trait they share with the rest of humanity. Sadly, I'm sure there is a sect out there that thinks butterflies are the work of Satan, and looking at butterflies might lead to evils like dancing. (An application of the internet meme Rule 34 to the religious tendency to hate.)

How about migration? Currently Monarch butterflies migrate north and south across North America every year, a process that lasts generations! Their winter resting site is a small patch of pine forest in Mexico.

It is a dramatic story, but is it a challenge to evolution? The butterflies are doing something completely natural, following their food sources. Their navigation is based on the chemistry of their brains and antennae, which is determined by their gentics.

At the end of the last Ice Age, Monarch butterflies, a species that preceded them, must have lived far to the south of Mexico. That inference is simply based on temperature. This species might not have been migratory at all. As the Americas warmed, their range expanded northward through Central America. After a point, though, they can't follow the climate change northward, into the huge new areas of open ecological niches, without migrating back south for the winter.

This could have begun with seasonal migration north and south within a single lifetime. The navigation based on the sun and the circadian clock could develop gradually. (I also don't know the extent of the wintering forest back then, but it could easily have been much larger than it is today.)

The real innovative part of Monarch butterfly migration is its multi-generational aspect. The genes that help navigate the butterfly back south have to be carried by several generations of butterfly for which that specific package of genes does no good whatsoever.

This a great example of what Richard Dawkins called the Extended Phenotype. The bodies of the butterflies (their phenotypes) are just carriers for the selfish genes. What matters is not that the phenotypes make the round trip, but that the genes make the round trip. If a reproducing buttefly suffers a mutation or other variational event on the way north in the springtime, its children might not have the genes to fly back. That variation might expand slightly for the two or three generations of butterflies that live over the summer, but in the fall they die faster than other butterflies (selection on variation) because they are not migrating, not migrating as fast, or in the wrong direction.

So our amazement at Monarch butterfly migration shouldn't lead directly to "Goddidit, therefore Jebus." There are amazing, but completely natural and material, explanations for the behavior. Explanations being elaborated by scientists who don't stop at "Wow", but go on to "How?"

And metamorphosis? Again, for the creationist there is no need to ask how, because Jebus is the Answer.

But for everyone else, metamorphosis is one of the coolest things around!

Lets remember that metamorphosis has been around for a long time. Crustaceans in the ocean do it. It has clear evolutionary value by letting a species exploit two (or more) different niches at different times during the life of an individual.

A very common process during development is the creation of a sheet of cells, and then the destruction of a large group of those cells via a planned cell death (apoptosis). For example, humans have webs between their fingers and toes at a certain point in our embryonic development, and then these webs die back. Cool, but natural - guided by chemical signals guided by genes collected by evolution.

What is happeneing inside the butterfly's coccoon is much the same, though the ratio of surviving and dying cells is very different. Inside the coccoon, most of the cells are dying, giving up their resources and energy to allow other surviving cells reshape the larva into an adult form.

Compared to insects that don't undergo a complete metamorphosis, those that do (like Monarch butterflies) seem to have shifted the timing and extent of hormone releases, a very typical path to speciation known as heterochrony. Heterochrony happens because of variation in gene regulatory networks. Variation with material causes and material effects.

So there is nothing in the history of insects over the last few hundred million years that would suggest that an Intelligent Designer had intervened in the natural processes. It has been said of God that He must love beetles, having made so many of them. But for all that love, he seems to have let all the species of beetle develop the process of metamorphosis just once, in a distant ancestor, and then diversify naturally, almost as if he wasn't involved at all.

It would be great if Illustra's new video intrgated all of this knowledge, and showed how changes from millions of years ago (the origin of insect metamorphosis), climate change (the origin of migration), and ecology united to give us this beautiful, brightly colored animal to share our world with us - and why it was important to preserve the Mexican wintering grounds threatened with deforestation, and provide resting stops along the migration routes stocked with plants that are nutritious to Monarch butterflies. But somehow, I'm afraid the wonder, the sheer wonder is going to dominate.

Rarity vs. Isolation, a problem for Intelligent Design

2011-05-16T10:19:00.006-04:00

Douglas Axe is a scientist, and a creationist, judging from his affiliation with Biola University. (Biola requires signing a faith statement.) He has occasionally published studies relating to the occurence of protein folds, using mutation as a way to determine the frequency of functional folds. His overall research program is to show that functional folds are so rare in nature that they could not arrive by chance mutation from an existing fold (killing evolution) or by chance from random polypeptides (killing abiogenesis).

Axe's most recent peer reviewed work is Axe 2004. Of course, anything even mildly supportive of ID in the peer reviewed literature gets a lot play, and this did. It has recently gotten some more, as Doug has blogged about some reactions to it from Steve Matheson and Art Hunt. Here are some of my observations.

Side point 1 - As with Guillermo Gonzales, advocating creationism seems to be negatively correlated with publishing. Gonzales couldn't get tenure because his publishing and grants dried up, and Axe publishes very infrequently.

Side point 2 - Axe's argument is essentially a variation on the argument from improbability - the universe doesn't possess the time/resources required for evolution to work. As such, it is a "bignum" argument, and the most important bignum in the ID memenet is Dembski's Universal Probability Bound. This UPB is usually stated as the odds of something happening have to be greater than 10^-150 before an ID supporter will allow that they might have natural causes. Well, Axe's work is well within that bound. The number usually plucked from Axe is 10^-77 as the "chance" for a functional protein. That is 80 orders of magnitude more likely than UPB, so Axe is really not supporting ID if these folks could keep their bignums straight.

The main point - rarity is not isolation. Even if we grant for the purposes of argument that Axe's rarity number is correct, that doesn't mean proteins, and the genes that make them, are isolated.

Here's an analogy. Gold is rare. But on land, gold is not isolated. If I find a piece of gold in one spot, my expectation (hope) is to find another piece of gold nearby. Lots of people will come and try to find gold nearby. Now there might actually be more gold in the ocean than on land, but if I find one gold atom in a bucket of seawater, I'm not going start my next gold mine where I found that one gold atom.

The difference is the distribution, and isolation is far more about distribution than it is about rarity. Gold on land is very unevenly distributed, rare but not isolated. Gold in seawater is evenly distributed and isolated. At another level, nucleons are extremely rare within the volume of an atom, but not isolated at all. They are all in one lump in the center of the atom.

Of course, there is an underlying process that accounts for this uneven distribution. And if you want to challenge evolution or abiogenesis, you have to challenge the underlying processes, not make hand waving arguments that always assume a uniform distribution. Rarity is not isolation.

Quintessence of Dust: Exploring the protein universe: a response to Doug Axe: "http://disqus.com/forums/quintessenceofdust/exploring_the_protein_universe_a_response_to_doug_axe/trackback/"

Barry Malzberg and the Immortality of Winston K Marks

2011-05-15T10:26:00.001-04:00

Barry N Malzberg was the guest speaker at this month's meeting of the Bergen County Science Fiction Association.

Barry was slow to warm up to his audience. He read a short (900 word) piece and insisted that anyone wanting to know the most cursory details of how he began in science fiction should look up his autobiographical essay, more of a biography of the Scott Meredith Literary Agency, published several years ago in F&SF.

After this abortive attempt to be gruff, surly, and uncommunicative, Malzberg settled down to an engaging hour and half's conversation on science fiction, his own, its history and probable fate.

Malzberg's basic thesis was that science fiction is a literary genre that was explicitly and deliberately created by Hugo Gernsback. It had foreshadowings in European (Verne, Wells) literature, but as a genre existed to educate the reader in the process of thinking that would be most helpful in a technologically driven society. Society might not have known it needed this education, might have turned up its nose at the field, but science fiction nevertheless succeeded wildly. This 'purpose' beyond entertainment has allowed science fiction to survive, while other forms of genre fiction (Malzberg noted gothic, nurse, and western in particular) have died. However, the genre is threatened, deeply threatened, by several factors.

The first is the success of fantasy, and space fantasy edging out science fiction. This Malzberg encapsulated as "Tolkien, Star Trek, and Star Wars." But the fact that the market for these products exploded doesn't explain why.

Here Malzberg sees two trends. One is that science (and science fiction) succeeded. (Malzberg dates this to the moon landing.) Technology has become such a mainstream concern it is almost unnecessary as a separate field. (So Michael Crichton, Robin Cook, and Tom Clancy are mainstream authors, not SF.) If I read Wired, do I really need Analog? Secondly, the editors of science fiction magazines, books, and anthologies have developed different tastes than the mass-market.

Let me give my own example. Bride magazines can reprint the same 100 articles over and over, because they know that no-one reads a bride magazine for very long. The editor of a bride magazine is actually perfoming a public service to all brides by finding the best set of advice articles and constantly refining and updating them with new artwork, or links to current fashions. "Choose the Wedding Music That's Right For You!" is as valid editorially in 2011 as it was in 2010, 2009, 2008,....

But science fiction magazines that cater to long time readers are different. At least in the minds of their editors, they are. The difference is the difference in desire between wanting to publish the next robot/space ship/alien story and wanting to publish the next _kind_ of robot/space ship/alien story. The trouble is that there are many fewer kinds of stories than there are stories. If your editorial appetite for an entire kind/style/manner of story is exhausted by the first one, you quickly move into a very esoteric and rarefied space.

Seen as a business strategy, it is the difference between selling to an established base and selling to a steady stream of new customers. Even the established base will get fed up and leave (or die) if the editor chooses to please themself rather than the market.

So I see the Malzbergian malaise as an unwillingness or inability to track the Gernsbackian market segment. There will always be smart, introverted 15-30 year old nerds, just like there will always be brides. Rework the publishing channel however is necessary, a story a day downloaded to their cell phone, whatever it takes. Track that market and science fiction can live forever.

Barry also noted that even classic sf has a chance to live forever. As a working example, Barry gave Winston K Marks. Marks published a substantial number of stories in the 40s and 50s, mostly in second tier magazines. Malzberg was undoubtledly correct that until he mentioned his name, no one at the meeting had ever heard of, or read, Winston K Marks. "But if you Google him, you get 10,000 hits!"

A brief digression. The number of hits reported on the first page of a Google search is an approximation. When I first Googled "Winston K Marks", I got 24,000 hits. I went to page 2 of the listing, and the number went up to 64,000. But I know that this number is bogus, because even for a quoted string, Google will start finding partial matches eventually. So I jumped deeper into Google's results. It seems that there are many 'torrents' of science fiction collected from Project Gutenberg and other sources, which you can download if you don't mind also infecting your computer with malware.

At page 24, Google fessed up the truth. There are only 234 references to Winston K Marks on the internet, though publishing this blog entry will change that. As a matter of fact, this entry is destined to be one of the leading references to Winston K Marks, because he is mentioned in the title and very often in the text.

Marks currently has 11 stories available through lapsed copyright on Project Gutenberg. I went there and read "Mate in Two Moves", originally published in the May, 1954 edition of Galaxy. It was a fun and entertaining story. The science was dated but the story was still good.

So Malzberg is right. Lapsed copyright and content piracy will keep the work of Winston K Marks in circulation until the extinction of the species. And if it does that for Winston K Marks, it will also do it for Barry N Malzberg.

There was a lot more to the evening. Barry was a wonderful speaker, encyclopedic in his knowledge of science fiction. His analogies to musical periods and composers were well thought out. Isaac Asimov as the central voice of sf, in the same way as Bach. As Phil DeParto said at the end of the evening, it would have been easy to spend many more hours talking together.

Calculating the Hoyle state of carbon-12, from first principles

2011-05-11T18:23:00.000-04:00

http://www.sciencedaily.com/releases/2011/05/110509113254.htm

Calculation of the "Hoyle nucleus" of Carbon

The Hoyle nucleus is that state of the carbon nucleus with very similar energy to three helium nuclei. The similarity allows fusion in stars to create carbon readily, and from there, the rest of the larger atomic nuclei up to iron. (Nuclei bigger than iron only get formed when stars explode.)

Sir Fred Hoyle considered the similarity to be an example of cosmic fine tuning when he first predicted it in 1954, without which we would not exist. As this article points out, this was pretty much an assertion for the last 50 years, but now we are in a position to actually calculate whether it does depend sensitively on other physical constants, and if so, what they are and over what range.

Several years ago, I asked an astrophysicist if the resonance was necessary or just helpful. In our normal model of stellar evolution, as the star ages and uses up hydrogen in the core, it starts fusing helium nuclei. Two He-4 nuclei form an unstable Beryllium-8, but if another He-4 comes along they can form a stable C-12. Everyone agrees the process proceeds faster because of the resonance. My question was - if the resonance didn't exist, would a similar amount of carbon be formed, just later, when the core had reached a higher temperature?

If you do have to wait, that by itself would knock down the total amount of carbon in the universe, since some smaller stars would never reach that temperature without the help of fusing larger and larger nuclei. Their fusion process would stall, and they would evolve towards red dwarfdom, as small stars do in the real physics of our universe. But we are the result of large stars blowing up, so I discount this effect in deciding whether there would be enough carbon for life.

On the other hand, you can't just tinker with the resonance without explaining why it would be different than it is. Changing whatever underlies the resonance of C-12 and 3 He-4 would necessarily change other things as well, perhaps in the direction of producing Carbon by a different route through a new or strengthened alernative resonance. This is of course never considered by fine tuning enthusiasts. Now we are starting to put the tools together to test these ideas

http://physics.aps.org/pdf/10.1103/PhysRevLett.106.192501.pdf

The main article is available for free at the above address.

The money quote, at least for Hoyle worshipers:

We note the 17 MeV reduction in the ground state binding energy and 12 MeV reduction for the Hoyle state while less than half as much binding correction for the spin-2 state. This degree of freedom in the energy spectrum suggests that at least some fine-tuning of parameters is needed to set the Hoyle state energy near the 8Be-alpha threshold. It would be very interesting to understand which fundamental parameters in nature control this fine-tuning. At the most fundamental level there are only a few such parameters, one of the most interesting being the masses of the up and down quarks.

Emboldenation by mois.

OK, I hope you don't think I'm being a dick about this for going on for so long, but I think this is important.

Why? Because of Hoyle's approach and use of anthropic reasoning, and the subsequent uptake by fine tuning anti-science folk, that's why. Besides, this is damn hard for me to understand, and I'd like to make sure I do understand it.

So, Hoyle says this resonance _must_ exist because we exist, and further, this shows that the universe has been mightily fine tuned.

So what is this amazing fine tuning?

Look at table 1 in the paper.

Be-8 + He-4 = -84.8 MeV
C-12 = -92.16 MeV

Difference? 8%

As a result of which, 4 out of 10,000 Be-8 and He-4 collisions go on to become C-12.

I gotta say, I'm way disappointed. I thought I was going to hear that the difference was only 0.000000...8%, not 8%, and that C-12 production was 9,000 out of 10,000, not 4.
What is Hoyle saying? If it was 8.00001%, then the successful collision rate would crash to 4 in a billion? If it was 7.9999999% the rate would shoot up to 4 out of 10? That in one case no star could synthesize carbon, and in the other the universe would be awash in carbon? I've never heard a numerical guess like that attributed to him, just that the existence of the resonance convinced him a deity exists.

The paper does speculate that the resonance depends on the ratio of the mass of the up and down quarks. Cool, that is a step towards understanding it. But if we imagine the fine tuning in these terms, changing this ratio will also change the energy levels of Be-8 and He-4. A resonance at one energy level might disappear, while one at another level will be created. Hoyle didn't work all that out, did he? No, he just asserted that changing some unknown parameter by any amount would wreck the known resonance, and nothing would replace it.

That is not science.

Thor, movie review by David vun Kannon

2011-05-08T23:57:00.001-04:00

Thor is an entertaining film. There, that is all that really needs to be said.

OK, in a little more detail, Thor is an origin film that re-imagines the Marvel superhero The Mighty Thor. Thor's enmity and continuing battle with Loki, his brother, is established, as is his love for Jane Foster (Natalie Portman). Anthony Hopkins is more believable as Odin than he was as an aging werewolf. Stan Lee got his cameo, but only about half the audience knew who he was. Stellan Skarsgard pitches in, and Tom Hiddleston as Loki looks way to much like Commander Data. Loki is the only interesting character, everyone else is too flat. Even Thor stops being arrogant too quickly. What hapened to that Marvel specialty, the flawed hero?

Asgard is nicely imagined, though dominated by a golden pyramid closely resembling that huge garish hotel in Pyongyang. Why does all pseudo-triumphalist architecture come out looking the same, and boring?

I saw it in Imax 3D, which was probably overkill for this movie. Certainly the noise level was too high.

Some funny 'fish out of water' moments for Thor when first arrives on Earth had the audience laughing out loud.

Trailers:
Transformers: Dark of the Moon looks loud and confusingly shot, continuing the poor tradition of the first two films.

Cowboys & Aliens (extended trailer) looks like a lot of fun. Daniel Craig, Harrison Ford and some nasty aliens kidnapping people.

Pirates of the Carribean - Can the series continue without Keira Knightley and Orlando Bloom? Johnny Depp, Geoffrey Rush and Penelope Cruz will help us find out. Looking for the Fountain of Youth, mermaids, etc... only tracking 50% likelihood of going on my personal buzzmeter (still better than Transformers...)

Super 8 - a new film by JJ Abrams. Trailer has some very Spielbergian elements, looks interesting.

The Unfinished Clue, By Georgette Heyer reviewed by David vun Kannon

2011-05-08T14:16:00.001-04:00

Georgette Heyer wrote almost 50 genre novels - Regency romance, historical, and detective fiction. The Unfinished Clue is a classic English country house murder detective story. First published in 1934, the story features contemporary characters packed into the country home of General Sir Arthur Billington-Smith, a right hard bastard that no-one is sad to find dead, except for those trying to get his money. With lots of motive, and no clear alibis, the guests are stuck hanging about the Grange, as the mansion is called, while a Scotland Yard detective is put on the case to interview them one-by-one.

The characterizations and dialog are sparkling. Heyer includes a sub-plot of romance for the one known innocent, Miss Dinah Fawcett, a 'spinster' (in her own words) at twenty five. The game of guess the murderer is kept going up to the last few pages, befitting any good mystery. Any devoted reader of mysteries knows to throw out the obvious choices, including the butler, right away. Choosing an unlikely character with no clear motive at the start of the novel pays off in the end, when the author reveals that you were correct in your guess.

Of course, the combination of unlikable bastard victim, unlikable minor character responsible and brought to justice, and successful love affair for main character makes this a novel that is not going to challenge the reader significantly. This is not hardboiled detective noir. You are here to get entertained in an enjoyable way, not forced to think deeped than 'whodunit?' And I did enjoy reading The Unfinished Clue. Heyer sends up English manners, skewers affectations, and pops the bubble of the pretentious with relish. Her strong central female could use a little more witty repartee and smoldering glances before falling into the arms of Inspector Harding (and she doesn't solve the case before he does), but on balance this is a minor issue.

If you are interested in genre writing, I would recommend reading more of Georgette Heyer. Certainly I plan to populate my Nook with more of her stories. As Isaac Asimov's R Daneel Olivaw detective stories show, it is possible to transplant some of the conventions of country house mystery to fantasy and science fiction settings. Heyer is also lauded for her historical research and detail, and credited by some with inventing the Regency romance category in the 20th century.

Fun, and recommended.

New York Botanical Garden - Beautiful!

2011-03-20T11:05:00.001-04:00

We went to the NY Botanical Garden yesterday. It was gorgeous, except the wind chill. It was a first time experience for me, 50 years of living around NYC and had never been there before. Highly recommended, I'll probably go there again for the blossoming of the cherry trees. And again, and agian! It was easy to get to, becoming members felt like the right thing to do, to help green the city.

The Retraction of Granville Sewell

2011-03-17T15:36:00.001-04:00

Followers of Uncommon Descent and other Intelligent Design websites may be aware that recently there was a triumphalist announcement by Dr. Dr. William Dembski of the acceptance for publication of a paper by Dr Granville Sewell, a math professor at University of Texas, El Paso. It was exactly the kind of premature "Waterloo" announcement that has backfired on Dembski in the past, and it did this time as well.
Applied Mathematics Letters had accepted the paper, but not yet published it. Dr. Sewell had a prepublication version up on his own site, to which Dembski's UD post was linked.
The paper itself was a repetition of Sewell's argument that SLOT disproves TOE. Sewell's argument is more like FOOT in MOUTH, though that hasn't prevented him from repeating it nearly word-for-word over the years, as Wesley Elsberry showed in a posting on Panda's Thumb.
Looking up the editor of AML, I took it upon myself to apprise him of the error of his ways.

Dr Rodin,

I am appalled to see a preprint, apparently from Applied Mathematical Letters, of the often repeated and often refuted nonsense of Granville Sewell on an anti-science web site.
http://www.uncommondescent.com/intelligent-design/elsevier-publishes-granville-sewells-latest-on-the-second-law/

Dr Sewell, whose expertise lies in partial differential equations, has writen several times on the relevance of the Second Law of Thermodynamics to the topic of evolution. Each time he makes poor arguments that do not show any understanding of the physics or chemistry involved, clearly contradicting the philosophy of your journal.

A concise refutation is
http://ajp.aapt.org/resource/1/ajpias/v76/i11/p1031_s1

The reputation of AML will be harmed by publishing this article by Sewell.

Yours,
David vun Kannon

Dr. Rodin's response was swift and has been published elsewhere. AML retracted publication. Science wins!

A big shoutout of thanks to Dr. William Dembski, whose premature ejaculations helped avoid even more severe embarrassment for AML.

Battle Royale (manga), reviewed by David vun Kannon

2011-02-02T00:43:00.001-05:00

This is an extremely graphic manga, containing frequent scenes of violence, murder, and death. There is also a lot of nudity, 'fanservice' and explicit sex, supposedly of 9th grade students.

The plot is easy to summarize. In a dystopian near-future Japan, a fascist government has created a gladatorial comabt in which a 9th grade class is abducted each year and forced to kill each other until there is only one survvivor. The students are given different weapons, ranging from Uzis to forks and boomerangs. The manga follows the 42 students of one class as they battle each other. The flavor is of a teen slasher horror movie where Freddie and Jason are your classmates.

Chapter arcs alternate between scenes of combat of the students trapped on the island arena and flashbacks to the normal life they led before "the Program". Several protagonist groups develop of students trying to avoid "playing the game", in some cases trying to actively destroy the Program itself. Several other major characters are students that embrace the amorality of the Program, and seek to win by killing off weaker classmates.

Still, even with three major good groups, two major antagonists, oodles of supporting characters, and flashbacks of everyone, the manga is padded with very repetitive philosophical conversations. The major group of protagonists does basically nothing but sit and talk until practically everyone else is killed. As in operas where characters take fifteen minutes to sing a final aria while mortally wounded, characters continue to ponder their existence and reminisce for pages and pages after their brains have been blown out.

And blown out they have been, in lyrical, explicit detail. The art is exceptionally graphic, going to pornographic at times, in the level of detail lavished on violence and harm to the body. At the same time, the sex scenes continue to dance around the idiosyncratic rules of Japan on the display of the genitals. (You'll also see a strong resemblance between one of the main characters and the style of the great Osamu Tezuka.) But the art is really focused on a fetish for bullets leaving gun barrels, brains, blood, and eyeballs not right in their sockets. Most characters display an excess of bodily fluids in the form of tears, mucus, blood, semen, and the ubiquitous "sweat drop".

Most characters are one dimensional, and wind up as cannon fodder to the two most evil and sociopathic of the students. The fate of some other students is study in paranoia. The male Big Bad has a pile of unfair advantages (genius, can learn any physical skill if he sees it once, etc.) on top of being a sociopath and drawing an Uzi. He is, of course, supernaturally hard to kill, and is drawn with a cape that hovers around his body no matter what fantastic martial arts moves he is pulling.

After lavishing over 100 chapters of attention to violence, the manga ends on a note of "love and hope and faith in human nature can conquer all" which even the characters realize is unrealistic. I am reminded of the moral ending tacked onto "Golden Lotus", the great erotic novel of China.

In the language of tvtropes.com (a great site), Battle Royale is high octane nightmare fuel from beginning to end. If you liked 1984, Lord of the Flies or A Clockwork Orange, you'll find the descent into paranoia, animalism, and ultraviolence familiar. It is up to each reader to decide if the author and illustrator are indulging themselves or using a legitimate device to explore the human condition. I vote for indulgence.

TRON: Legacy, reviewed by David vun Kannon

2011-01-17T10:16:00.001-05:00

I saw the original TRON in 1982, motivated mostly by a desire to see computer graphics on the big screen. The story was secondary, and the plot device that actually transported the action from the real world to the virtual world was less believable than the twister from the Wizard of Oz. I didn't care, I still wanted to see computer graphics on the big screen. This was because I was a computer science grad with an interest in computer graphics.

I went to see TRON: Legacy motivated by pretty much the same thing.

TRON: Legacy chose to cast many of the same stars as the original TRON into reprises of their roles. Jeff Bridges is Kevin FLynn and Clu, a program that has taken over The Grid, the virtual world of TRON. Bruce Boxleitner is Allen Bradley, Flynn's friend, and the voice of Tron. Other characters are new. Michael Sheen is fun as flamboyant bar owner, Zuse. (The name is homage to Konrad Zuse, creator of one of the earliest electrical computers.)

Since I mentioned the Wizard of Oz, I should say that the plot of TRON: Legacy uses the same trope - how to get back home from an alternate world? But that plot is subsidiary to a series of set piece scenes the display the wonders of CG. I did not see the movie in 3D, though you can. Here, the movie is caught on the horns of a dilemma. It really really wants to go back and show light cycles and solar sailers, the state-of-the-art of 1982 computer graphics that fanboys demand. It also wants to show of its own cutting edge chops, so the clean room perfection of The Grid is rendered in 3D, blurred with smoke and the haze of digital memory.

This doesn't evoke the "sense of wonder" that the producers were aiming at. In the post-Avatar world, computer graphics has crossed over the 'uncanny valley' that caught Final Fantasy: The Spirits Within (the first full CG feature film). The original TRON did not aspire to having its digital world be mistaken for the real. It couldn't, with that technology, so it didn't try. TRON: Legacy does try, and comes up short as a result. The homages are so close that the modern CG of smoke, explosions, and flame seems inappropriate. Only the work on Jeff Bridges, letting him play a much younger face as Clu, is so good you don't know how they did it.

TRON: Legacy ends happily, and set up for a sequel. Nobody important dies on-screen. That's too bad, since it is just another way life is sapped from the plot.

Bottom line - limited appeal to anyone outside its core audience.

PS - the trailers!

Cowboys and Aliens - this looks fun. Daniel Craig and Harrison Ford together, woot. From the trailer, it would seem that Craig is a bad guy, was abducted by aliens, escaped or was released, and now must join forces with Sherriff Ford who wants to hang him, in order to save a western town from flying saucers. Or something.

Green Lanten - nice visuals, but might suffer as do all superhero origin stories.

Born to be Wild - baby orangutans and baby elephants! OMG can you get any cuter! Based on the First Looks segment shown in the theater before the movie, the 'making of' feature on the DVD for this film will be awesomely funny.

Real Steel - giant robo fight movie. Very "Transformers" feel to the robots. I'm hoping for a Rock-em-Sock-em Robots tie in, becuase that is all this movie is.

MtG AI: The Opening

2010-08-24T12:58:00.002-04:00

In the previous post, we saw that for an AI program the major difficulties in Magic can be broken down into two areas, generating legal moves, and scoring the game state. The score might be simplified for now as life points plus mana or something, but the major difficulty remains of generating legal moves.

Ever turn, there's the chance of a player playing any one of hundreds of cards that are legal to play at that point.

To do a good job of looking ahead, we need to prune down the number of possible moves as much as possible.

The beginning of the game has a maximum of possibilities and a minimum of information.

AI programs for games such as chess deal with this problem in the same way as human players. They make several moves out of a "book" of already worked out opening moves.

Personally, I doubt the relevance of this strategy to Magic. If the AI "knew" that a deck was designed for a particular playing style, such as aggressive, control, or combo, there might be some standard opening plays. But at least in the initial stages, the decks constructed by the deckbuilding algorithm are not going to fall into clear categories.

MtG AI: Playing the Game

2010-08-20T15:36:00.002-04:00

My take on MtG deck construction was pretty straightforward from an AI perspective, even though it was very different from the way a human player thinks about the process. But now that we have a deck, how do we play it with an AI?

While the complexities of 11,000+ cards and changing rules might lead to some initial frustration, let's review what is in our favor in trying to build an AI for the game.

Magic is a two person game. The players take turns making plays. If one player wins, the other loses. The game always has a specific state. All of those things are also true of chess, checkers, go, and many other well studied games. So we really do have a lot going for us in terms of theory and ideas.

Two person games of this type are playable by an algorithm called minmax, or alpha-beta pruning. The basic idea is to start from specific game position. Assuming this position is not itself a win for one player, the opposing player has to move. First make a list of all of the players legal moves. Now change the game state (as if they had taken that move) and re-evaluate the state. Is it a win for either player? If not, score the position in terms of relative advantage for one player or the other. Repeat the process, this time scoring eac of the replies of the player to each of the possible moves. And on. And on.

This process builds a tree of game states, as many moves into the future as you have time to evaluate, each one of which has a score. The AI will choose the play at the first level which leads to the best score for it, as far into the future as it can see, assuming that on the player's turn, the player is doing the same thing.

This is a very well understood algorithm in computer science. It depends on two things - being able to generate a list of legal moves for each player, and a way to score game states. It is in these two areas that the complexity of Magic rears its head.

Legal moves

For all the complexity of the Magic turn structure, it really is a game where players strictly take turns moving. You can see this is true because any time Alice takes an action, Bob her opponent can play an 'instant'. So each players legal move list is changing as the game runs through its different phases and turns, but it always includes "play instant from hand". The trouble is that 'instant' is not just one thing, but a whole class of things that or might not be in the hand. But hey, we're already in a lot better position than assuming that at any point in the game a player can play any one of 11,000+ cards!

This is a great reason to start with a very restricted set of cards to play with. For example, the recent computer game "Duels of the Planeswalkers" for Xbox 360 and PC has a game playing AI. This AI doesn't have to deal with 11,000 cards, only the ones allowed in the specific decks of the game itself.

The number of choices for legal move is called "fan out". Both Go and Magic have a big fan out, and that makes it difficult for a computer program to look very far into the future. In comparison, in a game such as checkers the program can analyze the tree many layers forward (actually, in the case of checkers, all the way to the end). The depth of this lookahead is what makes a game AI smart (or dumb).

A way to look deeper is to not look at all the choices at each level. The program can sort the list so that it is looking at the likeliest moves first, and also "prune away" whole sections of the tree that lead to bad results. In AI programming, these are standard ways to speed up and look farther ahead.

Game state evaluation

Each position needs to be scored in order to use our algorithm. Again, this might sound very complicated for Magic, since the "game state" includes the visible cards, the probabilities of the cards not seen, and even the rules themselves (which can change as different cards are played). However, we can start with some very basic scoring based simply on life points, perhaps with some modifiers for mana pool, tapped/untapped cards, etc. All of these are known to both players at all times.

Most of the time, we want our evaluator to be fast rather than accurate. For one thing, it is hard to be accurate. For another, this algorithmic approach relies on evaluating many, many positions to choose the best play.

Summary

Even though Magic is not a game of "perfect information" (unlike chess, where both players have all the information and the same information) we can still analyse it using a standard game algorithm of minmax, looking at legal moves and scoring them. This is all a program has to do to play the game.

MtG AI: Deck Construction

2010-08-17T14:23:00.001-04:00

Magic is played with decks of cards, 60 or more, chosen from a pool of legal cards.

Walk Before We Run - ignore sideboard issues

WBWR - make the pool of legal cards small to test the code, add to the pool later.

I'd attack this problem with something like a genetic algorithm. A GA has a simple algorithm:

Create a population, give each member a score.
For as long as you want:
Choose high scoring members, modify them, score the new version, and add them to the population.
Take out members of the population based on some criteria (such as a low score).

Several modifications are usually allowed. Mutation changes a population member slightly. Crossover mixes two members of the population.

Lets make Magic decks our population members. Each member is just a list of card numbers, drawn from the list of legal numbers. Mutation might mean switching a number for another legal number. Crossover might mean choosing a number, N, between 1 and 60, and taking the first N cards from one member, and rest up to 60 from a second member. There are more sophisticated versions of these genetic operators that can be invented, as well.

Since we are constantly testing new decks that are similar to our high scoring members, and throwing away poor decks, the overall population is expected to gradually improve its score. If the poopulation is small, we can also expect it to converge on a single solution, a "killer deck" that is better than all the other decks tested. (Is this a killer deck in real life? No way. It is just good in the metagame that our population represents.) There are also ways to encourage the evolution of 'species' - several different decks that remain in the population for long periods.

Of course, the above description is hiding a big issue behind a "Separation of Concerns" wall. How do we score decks? Well, the best thing to do would be to have a huge round robin tournament, and the score for each deck would be its wins minus its losses. Now you can see why I thought "Self Play" was an important heuristic!

Until you get your game play AI running, you can substitute other scoring methods. Invent some way of assigning points to a deck. If a deck with a creature that requires some color, doesn't contain land of that color, then give that deck a penalty. If the same keyword appears on more cards (so the deck has a 'theme') give the deck a bonus. This kind of quick and dirty scoring is also useful in the beginning of a run of deck development. If our first set of decks is generated by just throwing 60 random numbers together, over and over, those decks are going to be really bad. It might save time to not even bother playing these decks until they reach some basic level of sanity.

I wouldn't overdo the scoring heuristics, though. One of the best things about a GA is that it can find a solution to a problem that a human would never think of. Using a lot of heuristics to score decks, instead of letting them compete head to head, is forcing the algorithm to follow your way of thinking.

So that is my approach in nutshell. Self play involving a variable population which improves over time.

MtG AI: First thoughts

2010-08-17T12:01:00.002-04:00

Yes, the complexity of Magic is overwhelming! Where do we start?

Let's start by laying down some well tried heuristics (rules of thumb) for the development process.

Walk Before You Run - this means we might have to try to solve a simpler version of the problem first, learn some lessons, and then attack the bigger problem we really want to solve. Sure we want to play any kind of Magic game out there, but starting off by staring at 10,000+ card descriptions just leads to drooling. Think about ways to cut the problem down to size. Work with only the cards of a recent core set, for example, instead of every card ever made. How about limiting the number of colors? Eliminate enchantments or some other aspect of the game, until later. Even programming some BabyMagic game is going to be a challenge, so start easy. You won't get discouraged (so fast).

Separation of Concerns - this means not trying to solve everything at once in one ball of wax. Magic naturally falls into separate areas, such as deck construction and play. There are even areas such as the metagame and trading values that I won't try to talk to right now. You can attack deck construction separately from play, even if you want to integrate them eventually.

Self Play - the interface of your system should allow the system to play against a copy of itself, not just a human being. The computer can play thousands of games while you sleep, improving it's algorithms, databases, etc. Self play assumes that your AI is written so that learning/improvement can be scored independently of a human. A genetic algorithm is an example of that.

I'm sure we can come up with other high level heuristics like these, but for now this will do nicely.

Magic the Gathering, why no AI?

2010-08-17T11:27:00.002-04:00

On my mind recently, the lack of good AI for MtG.

Why is this so? It seems that everyone is put off by the bewildering complexities of game mechanics that change the rules as each card is played.

I agree that Magic is more complicated than the sorts of boardgames that are the traditional targets of AI, such as chess. But if you can write game AI for an RTS (Real Time Strategy) game, you should be able to write an AI to play Magic. Given that position, I'd like to write a few posts here on what I think would work for Magic, if you were to go about building an AI for it.

SFABC Writers group

2010-08-17T10:50:00.001-04:00

Just gotta say, this is a great group!

Review: Toy Story 3

2010-06-21T19:08:00.002-04:00

Pixar is now, what, 11 for 11?

As a sequel, TS3 does suffer from replaying various bits of shtik that you've seen before. But the whole framing story works well, and the last scene is a bit of a tear jerker. There are also several laugh out loud moments in which I think the whole audience was laughing at once. No mean feat, that.

I saw the film in 3D. I can honestly say that I did not see one case where 3D was used obtrusively, as a gimmick, an effect you were supposed to notice. Neither was the film flat. I think the filmmakers hit an effective balance. (The same cannot be said for Avatar, for example.)

Pros:
Spanish Buzz
Ken
Totoro as Miyazaki homage

Cons:
"Night and Day", the short before the main film, was not as strong as previous films. I know, I'm reaching.

Review: Legion

2010-06-21T18:29:00.002-04:00

I saw this on the small screen of an airplane. That is about what it deserved.

The story is a combination of Terminator (imminent end of the world, the baby must die, pursued by unstoppable big guy) and "X of the Dead" (small group of strangers trapped in the house by zombies) movie.

It doesn't really work, since running away from the Terminator was the only effective strategy.

Pros:
None

Cons:
laughable CGI
you can tell an angel by their British accent

What was the early earth really like?

2010-06-21T16:36:00.003-04:00

I've been trying to collect some facts/factoids about what the environment of the Archaean Earth might have been like, in order to organize some of my thinking about origin-of-life scenarios.

Sun:

70% weaker in total(?) radiation - weaker at least in the visible by that much.
higher activity in UV range
spinning faster - like the Earth and the Moon, before they all traded rotation for distance.
larger magnetic field - from the faster spin.
bigger solar gamma and x-ray bursts - from the larger magnetic field.

Earth:

6-12 hour rotation period - if you back up from current conditions of the Earth-Moon system, this is what you get for the time right after the Moon reformed after the impact of some Mars-size planetoid with the proto-Earth.
3x current heat flux from the interior due to more radioactives.
thick atmosphere of CO2 (like Venus today) - there is a huge amount of CO2 buried today as rock formed by life.
no oxygen, so no ozone to stop UV from reaching the surface - an incredible 10^30 more! That is a mind boggling amount of radiation, which the ozone layer currently keeps at bay.
tides are 1000 times higher! (if moon is 10x closer)
winds are very strong, east-west bands - due to rapid rotation.
no large continents
low levels of cloud cover -no nucleating particles.
high level of infall of cometary organic material - inner solar system still full of debris

Moon:

much closer (10x closer?) - that is inside Earth's geosynchronous orbit. We have satellites that would have been further away!
spinning itself - not yet tidally locked
covering a huge piece of the sky - because of being so close
collisions that make moons such as ours are rare but not completely unlikely - they might happen in 5-10% of solar systems with rocky planets
30 (out of 300) gas giant exoplanets discovered so far orbit in their star's 'habzone' - even if the planet is too big for life as we know it, it could have life bearing moons

Put some of these together, and you get a recipe for incredible weather. We often think of the ancient Earth as tropical volcanic islands being lapped gently by tides that swish warm and shallow waters of a lagoon containing a dilute organic soup.

Think again. Think howling winds blowing endlessly around the world, as they do between Antarctica and the southern continents. Think waves pushed by that wind and tides the size of the World Trade Center towers, rushing over flat landscapes to crash like tsunamis and run inland for miles, or entirely across the landscape to the next shoreline. Every 3 hours.

Think of the hurricanes. Clouds and rain nucleate around dust and organic chemicals floating in the sky. Not much of either would be available, so those heaving oceans just evaporate, and the amount of water in the atmosphere just keeps building up. And up. And up until it supersaturates. And then finally the rain starts to fall in huge fat drops. The storm grows, the quickly whirling planet triggers a spiral, an eye.

But there is no landfall to dissipate this hurricane. There is just the wind howling around the planet, and isolated islands being drowned by the tides. The hurricane could spin like Jupiter's Great Red Spot, around the world and then back over the same ocean that spawned it.

What are some of the Origin Of Life (OOL) implications?

High UV levels striking the ocean surface, where water and CO2 are present, can rapidly build many organic molecules. Some people fear that the UV would break big molecules apart faster than they could form. Luckily, that is not true. Long chain molecules, such as RNA, can 'quench' the high energy photon before it heats up the entire molecule, or breaks a single bond. The heat drains away into the ocean. So the high UV works in life's favor to build up lots of the chemicals of life.

Those winds? It turns out that the top layer of the ocean, a skin only a few millimeters thick, has its own dynamics. Evaporation raises the concentration of other chemicals just below the surface. And the wind whips the surface into masses of bubbles - spindrift. These bubbles trap chemicals together for long periods.

The tides? The endless pounding that landforms received was insurance that all kinds of useful chemicals were ground up and dissolved in the ocean, as rapidly as the volcanoes brought them to the surface.

It is also true that the endless cycling of tides and drying out is a natural form of what we call PCR - a way to duplicate organic molecules

No continents also meant that there was a much larger network of undersea cracks in the crust, where seawater and lava could meet. Today these conditions exist in fewer places, creating the 'black smokers' and 'lost cities' that support life without light. They would have been far more common in the ancient past.

Bottom line - as truly alien as our planet must have been three and a half billion years ago, it was still a setting in which life blossomed almost as soon as it was able. Some of the most important reasons are all based in the existence of the Moon as the large close companion of the Earth. Life may come up out of the depths, or at the surface, but the Moon donated the rocks and created the stirring motion of our oceans.

Review: The Digital Plague, by Jeff Somers

2010-01-09T11:08:00.001-05:00

I bought this book to read on the plane. It was a good value for the price.

The cover advertises it as 'nano-noir', a term I would agree with. It is science fiction with a hard boiled detective edge, and a good dose of humor.

The lead character and narrator, Avery Cates, is a successful assassin. Cates and his world were introduced in Somer's previous novel, The Electric Church. I have not read that book, but as in all sequels much of the plot and characters in that book are quickly sketched in this one.

The book is fun and fast-paced. Its problems are relatively minor, but the editor was asleep at the wheel a few times.

My big issue with the book is that it tries to put too many ideas forward at the same time, instead of limiting itself to the exploration of one idea fully. One key idea in particular is terribly motivated, and even the characters agree is inexplicable. It appears to exist only to punch up flagging adrenaline levels and created scenes that might be more cinematic if filmed.

Good entertainment value at the paperback price. I will go back and buy the first book, and the next in the series as well.

Review: Daybreakers

2010-01-09T10:48:00.001-05:00

Daybreakers is an Australian-made vampire film that explores some traditional vampire tropes in unconventional ways by taking them to their logical limits. Set in the near future, it has science fiction and horror elements skillfully mixed. Except for Willem Dafoe, I did not recognize the cast.

The premise is ecological. In a predator prey-relationship, if the population of predators goes above the level that the prey population can support, it will crash. Not enough antelope = starving lions. The mathematics (called Lotka-Volterra dynamics) are very beautiful.

Many vampire stories assume that vampires will carefully cultivate the human population they feed on. Not Daybreakers. This movie introduces a destabilizing idea - that vampires will 'promote' many humans instead of feeding on them, for essentially loving reasons. Done with the best intentions, but in the future of Daybreakers, ten years after a vampire plague of unspoken origin, most of humanity are now the immortal undead, kings and queens of the night.

For the sake of argument, if a vampire needs 60 humans as a stable blood farm to provide a renewable resource of one pint a day, you can see how converting 90 percent of the humans to vampires is going to lead to 'instabilities'. There is just not enough blood to go around. Blood is both food and currency in this future.

The premise is inventive. The details are worked out nicely. The film is a good blend of horror and s-f. Those who are fans of traditional effects, as opposed to CGI, will be happy. My main quibble is that it solves the main problem twice, apparently for cinematic rather than in-story reasons. I enjoyed the music quite a bit.

Recommended.

Review: Sherlock Holmes

2010-01-09T10:09:00.000-05:00

I saw Sherlock Holmes last night with my son.

Likes:
Title design
Set dressing
Irene Adler
Humor

Dislikes:
That same washed out color palette you've seen in other recent films.

For those who enjoyed Robert Downey Jr. in Ironman, Sherlock Holmes (the film) has a bit of steampunk Tony Stark to the character Sherlock Holmes. Jude Law plays Dr Watson very well in my view. Rachel McAdams plays Irene Adler, the moral, comic, romantic, and intellectual foil (and equal) to Downey's Holmes.

One of the joys of detective fiction for a reader is to see if they can solve the mystery before the main character. This is difficult in film detective stories, but this film does honor the trope by at least letting you see the clues, even if they whiz by too fast to process until the requisite flashback at the end.

Holmes and Watson as the bickering odd couple got old fast, though it was better than the fawning hero worship versions of Watson in other films.

The least likable parts of the film are the fight scenes. Holmes does have a reputation 'in canon' as a boxer and martial artist, so I am not objecting that they are out of character. Rather, they are filmed in gratuitous slo-mo intercut with sped up footage on some very cluttered sets. The result is some very muddy views of the action - who is hitting whom how.

Recommended - a well made 'reboot' (though not 'origins') genre film. Strong detective, minor steampunk notes, and no bitter aftertaste.

Jump the Hybrid!

2009-09-18T14:03:00.003-04:00

Actually, jump from the hybrid. Nathan left the lights on in the old Altima, and the battery (a brand new battery) couldn't start the car, plus the alarm was tripped. (This is the second time that running down the battery has tripped the alarm.)

Because of the alarm issue, Nathan couldn't get a jump from helpful strangers. They tried, but the engine wouldn't start, just beep, beep, beep. Dad to the rescue.

I had researched the alarm system of the 98 Altima on the web, and tried the secret handshake with the key in the driver's door, two lefts, then two rights. That seemed to have cleared the alarm issue.

Now for jumping - the new Altima is a hybrid. We looked in the owners manual and you can indeed jump start a hybrid from another 12 volt battery. The manual said nothing about jumping another car from the Altima, but we decided to give it a shot.

Open the hood. Under the hood are some large boxes. I'm stumped. Henry Ford would be stumped. Saved by the owner's manual. It has an illustration of where to attach the cables. Negative to ground, positive to a bolt exposed in what otherwise looks like the fuse box.

The moment of truth. I push the button to start the hybrid - which starts in all electric mode. No sparks, flames, or explosions. I take this as a positive sign. Finally the gas engine starts, and I rev the engine like normal and tell my son to try to start the other car.

It works!

OK, maybe a blog entry about jumpstarting a car is thin gruel for you. But at the time, it felt pretty cool.

Review: G.I. Joe The Rise of COBRA

2009-08-22T08:18:00.003-04:00

Let's get this out of the way - this is one silly film. Silly in the way of '60s era films deconstructed by The Incredibles, played straight. It reminds me strongly of the story lines constructed by seven-year olds when they are playing on the floor with their toys -

"Bang! You're dead!"
"You missed so my guy is still alive!"
"OK, but then the whole place explodes! Whoosh!"

Now some people might say that this is appropriate for a GI Joe film, but with ticket prices what they are, I was hoping for something more. Alas.

Deep silliness. When the ebbil viwans (BWAHAHAHA!) blow up the ice pack over their undersea lair, the huge chunks of ice fall ponderously through the water to crush the base. Falls. Through. The. Water. ICE!!

I have to admit that by the time this happens in the film, you are ready for silliness. So much silliness has preceded it.

Upsides:

In the future, Jonathan Pryce will be President.
breast accentuating bodysuits
decolletage to China for the bad girl
kissing (in a film meant for small boys)
Dennis Quaid striking poses last seen in green plastic figures

Downsides:

Undersea battle as WWII dogfight
dialog delivery last seen during the silent film era
dodging rocket fire in slo mo
Mach 6 aircraft chases down missile over Moscow and then catches missile over Washington DC!
trashing Paris

Interestingly, the only intelligent line in the film is delivered by one of the villains, over the issue of human jealousy. Homer did a pretty good job with that, but in this film it just gets blown away. Wait for the DVD, and then don't buy it.

District 9 review

2009-08-19T10:03:00.003-04:00

Peter Jackson employs his awesome CGI talent to bring us a wicked satire and cautionary, somber tale about race and discrimination, constructed a very new cast and director. However, the story is told in a mixture of cinema verite clips from the cameras ever present in our society and traditional storytelling that I found to be an uneasy blend.

Twenty years ago, a giant spaceship coasted to a stop over Johannesburg, South Africa. It did nothing for a month. and humans cut their way in after getting impatient. They found the prawns, slightly more than man sized aliens, mostly dazed, confused, sick, and malnourished. First contact immediately became a disaster relief effort. The million odd prawns were transfered down to a sprawling tent city that quickly became a slum, with an especially nasty Nigerian crime lord preying on the Prawns as they pick over mountains of garbage and squabble over cow heads and cans of cat food. Human/alien tensions are constant and high. Now the relief agency MNU wants to relocate the prawns of District 9 to a new area, further away from Jo'burg.

The public face of the relocation effort is chosen to be a hapless civil servant, Wikus van der Merwe (Sharlto Copely), a clueless bureaucrat whose main qualification seems to be his marriage to the daughter of the head of the agency. While he is casually racist and ignorant himself, he seems to be honestly unaware of the darker death squad/concentration camp guard mentality of the armed forces who regularly confront the prawns.

Things never go right as our antihero is filmed going door to door through the slum, knocking on the doors of shanties and trying to get uncomprehending aliens to sign away their civil rights in a forced relocation. For an American, a lot will resonate with our government's repeated treatment native Americans.

He finds gun caches, an illegal egg hatchery (which is casually incinerated), and stumbles finally into the shanty of the only intelligent prawns around, who have been trying to cobble together a repair for their ship for the last twenty years. Wikus confiscates their fuel source, in the process exposing himself to a powerful mutagen that begins to turn him into a prawn.

For Wikus, things go downhill from there. The last half of the film is a lot ordnance exploding, a lot of bodies and heads exploding, as Wikus tries to save himself and make the switch from antihero to hero, which will necessitate the choice to save someone besides himself. There is humor and it is black. The film owes much to our experience of Uprisings, Intifada, and Iraq on TV and in previous movies.

There are issues of course. Aficionados of the X Files will be muttering "Black oil" to themselves before their popcorn is cold. A major plot point is forcing Wikus to fire alien weapons that only respond to prawn DNA, why this never was done with prawns themselves is unexplained. Why the mothership is not full of human scientists is never explained.

As a morality tale, Peter Jackson' team is working the same ground as JK Rowling. His tale is a far more adult, violent, bloodier version, of course. Pureblood and mudblood, wizard and Muggle, human and Prawn, why can't we all just get along? See it.

Review - I Sell The Dead

2009-08-15T09:42:00.003-04:00

My son Daniel and I went see this at the Quad Cinema on 13th St., the only place it was showing in NYC.

This film was a lot of fun!

A real horror/comedy with a good script and many funny moments. The movie is told as a series of flashbacks interspersed with present time dialogue. The dialogue is a bit slow, and had the filmmakers had more money, would have done better and quickened the pace as voice over narration. The take on many tropes of horror is quirky and funny. The ending ties up many story threads in a satisfying way. I was worried while watching the film that the anecdotes would be simply disconnected short stories, but the script brings most of them together by the end.

The main characters are interesting and sympathetic enough, and enough of the cast is still around by the end that a sequel would be doable. If you are in New York, go see it while you can, otherwise look for it on video. A worthwhile diversion.

It's a HYBRID!!!

2009-08-15T09:18:00.002-04:00

How time flies. Just yesterday, it seems, I was seeing my son Nathan for the first time, a pudgy five month old straight off the plane from South Korea. Now he's starting college in September.

Since he has to drive to school, I'm giving him my old car, an Altima with over 100,000 miles on it. Still works fine, but definitely old. So I got a new car for myself.

Normally, I would never buy a new car, I'd buy a newer used car. I hate the car buying/selling experience. My father taught me to buy from a fleet owner - the price is fixed, the car is well maintained. No hassle. That's how I got my old car.

But I wanted to reduce my carbon footprint, and after reading The Weathermakers I was convinced that the best way to do that was to make my next car a hybrid. So I bought one.

Softening the blow is that the Altima hybrid still qualifies for a tax credit. It is not sold everywhere, only six states in the US. Since I wasn't trading in, I couldn't get the cash for clunkers incentive also, but that was ok. (I know, a big part of the carbon reduction is supposed to be taking the old car off the road. Ooops.)

Anyway, after 3 weeks of new car ownership, I have to say that I love this car. The hybrid engine is very powerful on acceleration, the regenerative system contributes to powerful braking also. My average MPG is now up to 32. The instantaneous MPG feedback is helping me to learn to drive "greener".

The nice folks at Hackensack Nissan sold me a great car. Thank you!

Review: Harry Potter and the Half Blood Prince

2009-07-19T08:45:00.004-04:00

I was thinking of a snarky title for this, like "Harry Potter and the Half Dead Series", but decided against it. Yes, it was that hard to generate any enthusiasm for the film.

It is impossible to consider any HP film on its own merits. They will always stand in reference to the books that spawned them as derivative media properties. In this case, the film comes off as a Cliff Notes/ADD (Shiny!) version of the book.

Details, details:

The Weasley twins' joke shop seems to have taken over the Gringotts Bank space on the Diagon Alley set. The twins speak in unison, which is less amusing than their previous style, but in the rush-rush pace of the movie probably saves a few seconds. A poor trade-off.
Much of the film has the same washed out, over-exposed color palette and photography that marked Terminator Salvation and bits of Star Trek. I hope this is a fashion that soon passes in Hollywood.
(I just realized that Twilight had a good bit of this also. As a film, it is really sad that HP6 is closer to Twilight than anything else.)
JK Rowling invented a huge number of interesting characters, and even the books had a hard time fitting them in. Now even substantial characters such as Neville Longbottom are reduced to cameos. Luna Lovegood comes off much better and has some of the funniest lines and deliveries. (Her name has that James Bond female sidekick quality, is there any Bond/Potter fanfic out there?)
Rupert Grint and Daniel Radcliffe both have a chance to chew the scenery, which they never had before. The audience greatly enjoyed both. Emma Watson (grrr) had less opportunity to shine, being reduced to crying, hitting Harry over the head and staring into the sunset. Her arch comments of previous films and great talent with magic are sorely missed. I can only hope that the next two films, based on the last book, will give her more space (since Ron Weasley is offstage for a good bit of time).
Quidditch scenes are handled very well. 'nuf said.
Helena Bonham Carter, another standout scene chewer as the psychotic Bellatrix Lestrange. She is given screen time instead of the character Rufus Scrimgeour. So the whole political subplot is lost, sadly.
Alan Rickman has been one of the most reliable actors in the HP stable, but his delivery of the revelatory "I am the half blood Prince." line is a major disappointment. The counterspell to Sectumsempra was also supposed to sound like singing, if I recall the book correctly, but Rickman doesn't come close to that.
The Muggle waitress in the opening subway sequence was a nice innovation. Just eye candy, but welcome nonetheless. (And yes, there is such a thing as product placement in an HP film!)

The big news, of course, is how different the denouement sequence is from the book. In one sense it is actually better, since it demands that Harry actively trust Dumbledore rather than just being a witness. But it has many other failings, including failing to be the "trash the Hogwarts set" that it should have been. This does not bode well for the final movie. But the real flaming mutual hatred of Harry and Snape does not come to the surface. That will greatly diminish the next films.

With an extra six months from the delayed release date, they could have done a lot. I'm disappointed if all they did was 12 minutes of IMAX 3D work.

The film is state of the art Hollywood, meaning high production values and absolutely formulaic. It will be a hit with its fan base.

Taking Input From Depositors

2009-06-19T10:58:00.003-04:00

A long time ago, I had the idea that a new form should be added to the income tax return. Rather than being a burden on the individual, it would be an opportunity to provide input on how they wanted their money spent.

It would basically expose the top categories of the federal budget and allow the taxpayer to allocate, by percent, how they want their money spent. At least in the beginning, it might be non-binding, just an informational tool. It would help our government know what we the people really wanted our money spent on.

Even if some people put down 100% of their taxes to spent towards the Defense Department, you'd have another person who might allocate 100% for HHS, or for paying down the national debt. Other people might be more nuanced and thoughtful in their choices.

The IRS obviously has the technology to handle this sort of thing. It is just a question of the government actually wanting detailed feedback directly from the public.

If it looked like it was working (not leading to huge skews in the budget from year to year, or only making up a fraction of the overall budget in size) then it actually could be made binding. Then people who made allocations would actually feel much happier about their tax payments.

I recently had an update of this idea while driving to work. Something similar could be done by banks for depositors. Listen to depositors about how they want their money put to use. Do they want it left in the vault? Do they want it lent to persons or businesses, locally or globally? Do they it used to buy or create derivative instruments?

Just listen, for a start. Any bank could do this without a regulator forcing them. It would make that bank seem to be a much more responsive and concerned institution.

Terminator Salvation Review

2009-05-25T07:14:00.002-04:00

I saw the new Terminator movie last night in Manhattan. The theater was sold out, several showings were sold out that night. Memorial Day, Fleet Week, and you are surprised?

Much of the movie is shot in this overexposed, greyed out palette that is supposed to suggest the whitening bones of the human future. or whatever. I took it as evidence of just how much of the movie was done in front of a green screen. It had a very PS3/Final Fantasy quality to it.

Christian Bale plays John Connor, resistance leader. Somehow, between the end of the previous movie and the start of this one, the remaining professional soldiers have taken over organizing and leading the resistance to the machines, and Connor is just a small unit commander.

Sam Worthington is Marcus, a Death Row murderer who donates his body to science in exchange for a kiss from scientist Helena Bonham Carter. Marcus wakes up in the future, takes clothes off of a corpse, and wanders into LA. (By the magic of cinema, the VLA radio telescope is now walking distance from the LA basin.)

Wandering into LA, Marcus almost gets cut down by a Terminator, but is saved by Kyle Reese (Anton Yelchin) and a mute girl, who are the LA branch of the resistance. As it happens, Skynet is looking for Kyle. Somehow, Skynet knows that Kyle is the one that will draw out John Connor.

Much shooting of things later, we finally learn that Marcus is a new kind of Terminator. Kyle has been taken by Skynet to its headquarters in San Francisco. Why does a self aware computer network build a 200 story headquarters skyscraper and major industrial complex on the San Andreas Fault? Dunno.

Connor goes in to rescue Kyle singlehandedly, 'cuz thats heroic, after letting Marcus go in and find him. In the process he gets beaten up by a voiceless CGI Arnold Schwarzenegger. Doing a convincing, moving Ahnuld was obviously too difficult/expensive, so the film burns his skin off, allowing them to go back to animatronic/shiny metal that is much easier to render.

The film ends with Kyle rescued, Connor mortally wounded, and Marcus feeling bad about being a murderer saved and turned into killing machine. Marcus donates his heart to save Connor, which transplant is done in a field hospital by Connor's pregnant wife (who you recall from the previous movie is a veterinarian).

Of the three male leads, Marcus is the most interesting, followed by Reese, followed by Connor. Marcus is Frankenstein's Monster, updated. He is wonderfully conflicted in his history and motivations, far more interesting than the G.I. Jesus that John Connor is supposed to be. It is really too bad his character is dead at film's end, he would have been a valuable franchise character.

I enjoyed the film, especially so because my son Daniel paid for my ticket! But seriously. when the film is exploring the Frankenstein angle, its very good. When the focus is on Connor, its flat. Lots of robots, lots of things exploding, lots of inexplicable puddles of fire. A summer movie for men.

State of Play (BBC production) DVD review

2009-05-23T09:44:00.003-04:00

I don't buy a lot of TV series on DVD (read, any). Dang, that's not true. On the back of a pleasant evening in the theater with State of Play, I bought the BBC mini-series on which it is based.

All I can say is, wow. A much better all around production. Six hours gives a lot of time to develop characters. The series is much more journalistic-procedural than the film, which is good. Excellent music. I love Kelly Macdonald's accent. Bill Nighy is amazing as usual.

Solid drama, worth your money over the film version. The film has some elements in its favor, such as the old media/new media tension, and Helen Mirren. That's not enough in the end. The original is better.

Angels and Demons - movie review

2009-05-23T08:22:00.004-04:00

Last night I wandered into a showing of Angels and Demons, not expecting much. I was not disappointed.

Good points:

Large Hadron Collider - you sexy beast!
some cool CGI
Ayelet Zurer as strong woman scientist
Rome

Bad points

Science and Religion as non-overlapping magisteria
Ayelet Zurer demoted to female sidekick of Tom Hanks
Idiotic plot

I do like the combination of Illuminati and antimatter. The problem is that the whole film is built on the bait-and-switch. Don't filmakers as practiced as Ron Howard know that audiences hate this? This is an entirely separate point from a final plot twist. This is the kind of audience trickery of "and it was all a dream" variety. No excuse that Dan Brown makes the same mistake in his novel. The same mistake is not made in Da Vinci Code.

Oh, yes, and the physicist turns out to be a toxicology expert also, how convenient. And that car bomb? Completely obvious. And who set it BTW? It seems you've just traded one conspirator for another.

The film almost acheives the quality of a Woody Allen film about New York, where the city becomes a character. If only they had gone that direction!

If you follow the evo-creo wars, the editorializing on the proper relations of science and religion will all be sadly familiar. Yawn.

Whither Stress Testing?

2009-05-20T08:08:00.003-04:00

OK, the stress of stress testing has come and gone, now what? If that is the first and last time we do this, it was a meaningless PR exercise.

Stress testing needs to be put on a solid, repeatable, and repeated basis.

First - Publish the stressors. What was the formula used to compute capital adequacy? Can I have that in XBRL, please?

Second - This is fun, let's do it every quarter! How long have people been complaining about financial statements being retrospective instruments? We need to embrace forecasting fully. We need to build up a body of time series of these things. Published in XBRL with no tweaking by the Fed. Transparency rocks!

Third - What's the error bar? Let's say I got my wish, and every quarter every bank in the US reported a matrix of capital adequacy forecasts across some increments of inflation and unemployment. Is that enough? No. We also want the probability assigned by the bank to each cell, and the uncertainty band around their reported figure.

Fourth - Why stop at banks? In this era of large companies sucking at the government teat to survive, we should be able to demand similar forecasts of other recipients. The capital market needs to eventually take up the responsibility of holding public companies up to a requirement of disclosure, not the regulators. In the meantime, regulators should prime the pump, and establish the set of data items to be provided. Standard setters, make some standards for prospective disclosures, please.

Capsule Reviews

2009-05-20T07:32:00.002-04:00

Seen recently:

Inkheart - Good solid fantasy fare. What Brendan Fraser gets paid to do nowadays. Helen Mirren and Jim Broadbent should have gotten more screen time, and their characters should have wound up together at the end, a missed opportunity IMHO. Some potential sequel material.

Twilight - Why did I bother? SFX pretty cheesy, but the target audience won't notice. A very good teen angst romantic vegetarian vampire movie. A little unclear if Edward, who vamped out in 1918, has actually killed people, not really motivated to find out.

Transporter 3 - my first view of the series. Anti-hero with a heart of gold Frank Martin is forced to break his rules, transport skanky Ukrainian teenager across Europe, a trip with curiously few difficulties at border crossings. Car/train sequences at the end are fun.

Body of Lies - Crowe and DiCaprio. Not as noir as a spy thriller should be, too much an actioner. Crowe is Mr Ugly American, action at a distance puppeteer. DiCaprio is the humint, constantly frustrated by his handler's ham handedness. Every bit of local color that DiCaprio befriends dies for their trouble, except the beautiful, saintly Iranian nurse (Golshifteh Farahani). If this was a real spy film, she would have bought it. Upbeat ending = torture is worth it? Maybe in the Bush Era. Actually, the torture in the film never works, but somehow that doesn't stop the people using it.

Star Trek movie review

2009-05-11T15:26:00.003-04:00

Yes, I was going to go eventually, but my son Daniel deserves the credit for pestering me to go this weekend to an IMAX showing of Star Trek. It was an 11 PM show, so it was almost the full geek experience possible.

I agree with a lot of other people, this is definitely worth your popcorn money, and IMAX is the way to go.

Likes-

mix of old and new
plenty of homage to TOS (the original series, for the non-Trekker), to the level of some audio cues
humor
Zoe Saldana's way retro outfit
Zoe in general
Zoe in specific
Zoe Zoe in a bar
Zoe Zoe in a car
Zoe and Green Eggs and Ham (or whatever that girl's name was)

Dislikes

way too much lens flare
naval tactics of the WWI era
Romulan mining vessels that look like goose roadkill
destroy two planets (Vulcan and Romulus) and stick us in an alternate universe
Scotty's mascot - should get an award for Establishing Annoying Alien Sidekick Persona In the Fewest Scenes
all the Star Wars homage, i.e. Ice Planet, there's always a bigger fish, Kirk as Han Solo punching bag, planet destroying ship, older Spock as Obi Wan

I don't think the big open sets made sense as the machinery spaces of the Enterprise. No one would build a military spaceship that way.

By far, the best line in the film is "Your father was captain of a starship for twelve minutes, and saved 800 lives."

I like the set up of the Kirk/Spock/Uhura triangle. As a reboot, I would have been happier if the creative team had just established that much in this film. The film crowds in all of the basic characters, and is a bit too hyperactive in doing so. In comparison, the Bond reboot is two films old and we still haven't met Moneypenny and Q.

Bottom line: Go!

State of Play movie review

2009-05-02T17:20:00.003-04:00

An enjoyable journalist-politician potboiler in which Ben Affleck does not suck. Helen Mirren and Russel Crowe are not overshadowed by the lack of suckage from Affleck. A good updating of the old newspaper flick tropes which I remember best from All the President's Men. Now mentioning that movie will bring up inevitable comparisons. To my mind one of the failures of State of Play is the willingness to kill people. We can't motivate viewers with anything less???

I suppose I'm going to have to watch the BBC TV mini-series now.

Wolverine movie review

2009-05-02T11:27:00.003-04:00

I saw the new X-Men Origins: Wolverine movie last night, an early Friday night show. My showing was half full, later shows looked much more full.

I enjoyed the movie, and felt I got my money's worth of entertainment. The opening credits reminded me of the opening of Watchmen.

I am not a Marvel fanboy by any means. The anti-military tropes of the Cold War and the Viet Nam war are really really dated. Last year's Iron Man was a good attempt to move on from these.

Deadpool as a wiseass was better than the finale's Deadpool-I-Have-No-Mouth-And-I-Must-Scream.

Why oh why does Wolverine have to stop and monologue in New Orleans before offing Creed? Oh, I forgot, its a superhero movie.

Professor X showing up at the end was a bit creepy. 'Nuff said.

What do I want next from Marvel? A Magneto/Iron Man team up. The two best acted roles in the Marvel film universe. Its such a natural! But it has to include Mystique, because, well, do I have to explain?

Death By Success - A Threat To XBRL?

2009-04-22T14:54:00.003-04:00

Talking to my friend and co-worker Yossi Newman, he brought up an interesting concern. Would the increasing use of XBRL cause a chorus of nay-sayers to form that could seriously threaten XBRL's path to ~~world domination~~ ubiquity?

Umm, no.

I think the number of applications of XBRL around the world has already put us past that possibility. Failure in one market could affect acceptance in that market, but that will only put that market behind others, which will eventually put pressure on them to catch up.

My larger concern along similar lines relates to asset bubbles. Our long run of good news ( no nuclear war, pandemic, global famine, etc.) has created a huge amount of investment funds chasing investments. This leads to asset bubbles. Any advantage will be pounced upon in the search for 'alpha'. XBRL is just such an advantage. The result could be that enormous pressure could be put on the vendors and supply chain of XBRL quite suddenly, too suddenly for them to adjust. A classic case of 'be careful what you wish for'.

The Great Taxonomy Landgrab

2009-04-22T14:45:00.002-04:00

With the SEC mandate on the use of XBRL arriving in June, it is almost time for XBRL's 15 minutes of fame and buzzword status.

One aspect of that moment in the sun that I anticipate is an outpouring of taxonomies foisted on an unsuspecting public, by organizations with tenuous-at-best connections to the subject matter of the taxonomy. I believe this will follow the pattern of the flowering of XML Schemas earlier in the history of the web.

This will all shake itself out in a few years, but for a while it will be a rough ride. I'd like to think that this will make XBRL acknowledgement by XII process more valuable, but at the same time it challenges the meaning and governance around that process.

FreeRisk Bait and Switch

2009-04-15T21:50:00.003-04:00

Thanks to my friend John Turner, I just watched the video of a presentation about FreeRisk at O'Reilly's ETech conference.

The presentation listed a few problems in our current system of rating credit and investing in debt.

grade inflation in debt rating as NRSROs attract business with generous ratings
funds forced by law to invest according to ratings from only a few agencies
meaninglessness of the rating itself
opacity of the rating model
lack of diversity in modeling

They propose FreeRisk as a solution to the problems, which they have flipped into a set of requirements.

accessible
open
diverse
transparent

Cool, but how does that actually solve all of those problems identified earlier?

Grade inflation - FreeRisk models are still opaque, so we don't know if a company has bought special preference or not.
Forced acceptance - FreeRisk needs legislation to eliminate the privileged position of established NRSROs, and/or privilege some part of its own leaderboard as an NRSRO.
Meaninglessness - Models are still opaque, so scores are still meaningless.
Opacity - Continues.
Diversity - With continued opacity, we have no clue whether models are diverse or not.

So on my analysis, FreeRisk isn't doing to well at solving the problems it wants to solve, mainly due to model opacity. Solving model opacity isn't easy.

The first problem is that the market will pay handsomely for good models, so there is a clear incentive to keeping them opaque. FreeRisk must be assuming the OSS model will transfer to finance, a big assumption.

The second problem is knowing where to stop in the desire for transparency. Let's take a simple model such as the Altman Z-Score as an example. I'm not happy just getting a real number in a certain range for an answer. I ask for the model. I get a formula using certain financial accounts and weights. Where did the weights come from? Why those accounts and not others? I need to know the design methodology of the model, and the database used to derive the parameters.

FreeRisk currently supports an API that allows for scoring based on a single period's data. Even the Piotroski Score needs two periods of data to work. More troubling, the simple Piotroski and Altman Z methods touted during the presentation are methods for evaluating the corporate entity, not the debt instrument. The debt instrument has to be evaluated for its terms and conditions. We are still very far away from having public T&C databases available in XBRL and Common Logic.

More troubling still is the belief that all credit scoring is model based. This is certainly not true today. It won't be true even when T&Cs are in XBRL and CL. There is still an element of judgement, of interviewing senior management, of reading the news on a company, that comes into play.

There is a lot of free floating moral outrage powering the FreeRisk presentation. But we should step back from that and think dispassionately about changes to our financial system. Should NRSROs really be expected to be aware of bankruptcy before it is announced? To whom do NRSROs owe a fiduciary obligation to force companies into bankruptcy by downgrading their debt? Do we really want debt market volatility similar to equity market volatility based on quicksilver changes in ratings?

Here are some of the things I took away, even if they were unsaid.

we need finer grained ratings than the current scales provided
we need to take named NRSROs out of legislation
some funds should create softer cutoffs for investing
the buy side should fund the NRSROs, not the issuers

The last is the most important. It removes one of the largest reasons for distortion of ratings. It aligns the interests of the NRSROs with the capital markets.

It would be great if the buy side funded the public company financial statement audit as well!

Bell, Book, and Candle

2009-04-06T12:19:00.002-04:00

I watched Bell, Book, and Candle this weekend on DVD. I thought is was a fun film. I liked the interplay between Kim Novak and Jimmy Stewart. The supporting cast was a lot of fun also.

You can see how this movie was an inspiration for Bewitched on TV, but it all seems to go back to Thorne Smith's Passionate Witch. I've got a copy on order!

IEEE Computational Intelligence Symposium

2009-04-01T21:54:00.003-04:00

I spent Monday and Tuesday of this week in Nashville, Tennessee. Well, not really. In a hotel just off the runway is more like it, the Sheraton Music City was the venue for the IEEE symposium of the title. It was OK, but the food was terrible. Since we weren't downtown there was not a good chance to get out and experience more of Nashville.

But the science was great! I was there to speak on two panel discussions in the financial engineering track. I actually spent most of my free time in the A-Life track. By pure coincidence, I met up with Wes Elsberry of MSU. Wes is a key figure in the fight against intelligent design and anti-evolutionary creationism.

I thought Wes' talk on his research using Avida to explore the evolution of motion strategies was very interesting.

I made two points I think are worth repeating here. The research opportunities I think will be most helpful to the financial world are ontologies for law, accounting, and financial regulation, and agent based modeling as a way to escape the failed Rational Man hypothesis. One point raised by an audience member was that US federal level financial regulators should be supporting more academic research. I completely agree. Given the billions that are being thrown at problems, it wouldn't hurt to support some hard thinking.

Deceptive genomes

2009-04-01T21:50:00.002-04:00

Having worked out the kinks in my BinInt problem, I got my Deception code working also. As with BinInt, I've now scaled the output fitness to adapt to the number and size of subproblems. This isn't important in any one run, or averaging runs with constant parameters, but it does make it easier to compare runs with different parameter choices. I'm happy!

Jean Renoir - Whirlpool of Fate

2009-04-01T21:30:00.003-04:00

I took advantage recently of a Barnes and Noble sale on art films, and picked up a boxed set of Jean Renoir. The first one I've watched is his 1925 silent film, Whirlpool of Fate (English title). The film was interesting on a few levels. One was the view of contemporary French life. Horsedrawn barges cross the countryside, and the rich play with motorcars. The second level wsa the mechanics of the film-making. Renoir used many storytelling techniques, and there is a delightful special effects sequence in the middle of the film.

By modern standards, the final resolution might not seem very cathartic. The foul uncle of the damsel in distress is knocked into the river and swept off shaking his fist, and said damsel is taken along on a trip to Algeria by the family of her wealthy benefactors. But has she actually married the handsome young scion? To me it is unclear. Perhaps to contemporary audiences, her change of dress, and riding with the family in their carriage are sufficient clues that she is now a part of the family by marriage. To me, the fact that the film skips any explicit symbols of marriage, even a swinging church bell, leaves it ambiguous whether love has successfully bridged class differences.

While I greatly enjoyed the special effects sequence, for me the greatest enjoyment in the first few seconds of the film after the titles. Leaves flashing on the trees just out of sych with the film rate create this impressionistic shimmer on the screen that immediately transported me to another place and time, not only of story, but of story-telling.

BinInt, finally!

2009-03-28T21:39:00.002-04:00

After much delay, I finally got my BinInt GA problem running successfully in ECJ. Part of the issue was setting everything up again on a new laptop, part also was moving to ECJ 18, and part was my own stupidity. But it looks like it is all working now.

BinInt takes the same bit vector as MaxOnes and divides it into several subproblems. Each subproblem is treated as a binary integer, hence the name. The key new feature of this problem is the introduction of exponential scaling. Some bits are worth a lot more than others.

I wrote the fitness function so that it scales the fitness according to the size and number of subproblems. Best fitness is always 1. this way, we can vary the size and number of the subproblems and directly compare the trajectory of different parameter choices in solving the problem.

Watchmen Re-review

2009-03-28T21:15:00.002-04:00

OK, so now I've read the complete graphic novel of Watchmen, and I'll try to do the fanboy comparison of the book and the movie.

Overall, the movie is a pretty fanboy-ish production. The dialog, a lot of the visual blocking is taken straight from the panels of the novel. What's changed is the double layer of subtext in the newstand/Black Freighter plot, the chapter breaking texts, and the final plot device. As for the first two, that's the price of going from one medium to another. The final plot device (FPD) is actually an improvement. The material in the book supporting the FPD is weak, tenuous, and undercuts some of the suspension of disbelief. The movie's FPD is a tighter construction that helps motivate the self-exile of Jon Osterman, which is still the major plot problem of the whole story.

Watchmen is a wonderful comic book that is in love with the American comic book tradition and is speaking to it, playing with its conventions, and retelling its history. There is no way a movie can do all of that and still be a commercial success. However, the deep ethical question still shines through. Because they operate outside the law, are vigilantes in danger of becoming outlaws? Do they, in the end, become outlaws necessarily?

Ozymandias subscribes to the "shock and awe" theory that led to the bombing of Hiroshima and Nagasaki. To this, Watchmen adds the Big Lie and Orwellian Memory Hole. How many of us would choose that combination over the unflinching stance of Rorshach?

Watchmen review

2009-03-15T00:43:00.002-04:00

I watched the film without having ever read the graphic novel, so I've tried to think about it simply as a film. As such, I prefer V for Vendetta, which covers most of the same points.

Nixon's makeup was awful. The initial shot of Nixon from a distance had the best voice impression, from there it went downhill. Even in 1985 we knew Nixon was much more obscene out of the public eye, so his dialogue was as rubbery as his makeup. This Nixon is still the anti-communist cold warrior of the 1960 election, not the President who went to China and toasted Chou En Lai.

I thought the movie was effective at trying to give the feeling of simultaneity of experience that Dr Manhattan felt, by cutting back and forth in time. It also did acheive the effect of convincing me that anyone with God like powers is going to be aloof and apathetic to the human condition, that vigilantism becomes thrill seeking too easily. The other supers were more then Batman-esque characters. I think the movie is pretty clear that Ozymandias is both super-smart and super-fast, for example. They all can take a lot more punishment than the normal folks they beat up.

I enjoyed Rorshach's voice overs and dialogue, but as I said earlier, preferred V doing the same schtick. So V for Vendetta will remain my favorite Alan Moore adaption for a while. until they make a trilogy out of Lost Girls!

Alegria

2009-03-15T00:33:00.002-04:00

I was just listening to some Cirque du Soleil again. I love the voice of Francesca Gagnon, the White Singer of Alegria. It's got that smoky quality that makes the performance very intimate. I wish more of her music was available through iTunes. Does she remind you of Edith Piaf?

Folding Progress

2009-03-12T17:17:00.002-04:00

I'm quite enthusiastic about Folding@Home. My own folding just passed a milestone that means something, at least to me.

F@H awards points for finishing work units (WUs) on time. You can sign on with a user name, even join a team, and watch your individual contribution to science grow. Are points really pointless? Yes, but they appeal to our competitive urge, so they help keep people participating.

So my personal milestone - my number of points is now more than my standing on the leader board! Yes, comparing to different quantities, I know. It happened somewhere between 65,000 and 70,000. Since there are more than 1.2 million folders (not all active right now), I'm in the top 5% of contributors to F@H. Yeah, me! Also, Team Deloitte is in the top 5% of all folding teams. Pretty good for only three guys.

Actually, there are two other lessons you can draw from this progress. 1 - most people who do fold, fold anonymously. 2 - a lot of people tried folding, then forgot about it.

Wrestling with a superhero origins story

2009-03-09T13:36:00.003-04:00

Since joining the SFABC and the excellent Writers of the Weird writing group, I've written two SF stories which I'm quite happy about. I've collected one polite rejection, which is also ok.

Now I'm thinking about a new story that is actually a comic book superhero story! I'm not a real spandex-clad fanboi, so this is something of a departure for me.

All I've got right now is the gimmick that creates Our Hero. Our Hero is actually a mild mannered nobody-in-particular until they die, and then are saved by an emergency heart transplant. The gimmick is that they receive the heart of a dead superhero!

So far the dead hero is named Aurion. I don't know much about him so far, except he has golden blood, psionic powers and he's dead. Oh, he's also from somewhere in the EU, because he's a member of a Euro supersquad. Other members

Bruit - think Thing, but French. "Bruit, le smash!"
Accelerondo - think Flash, but Italian.

Need more Euros, right?

ps - don't take this too seriously!

The Origami of Life

2009-03-09T13:12:00.001-04:00

I just wanted to share my experience with this participatory science project.
Folding@Home is a protein folding research project that is part of Stanford University. While understanding how proteins fold up into their three dimensional shapes is very important, it is also very difficult. The process in the cell takes place in microseconds as the proteins are synthesized from the instructions in messenger RNA (copied from the DNA in the nucleus). Therefore the method of choice today is to simulate the motions of the atoms using computers.
Obviously, this takes a lot of computer power. More than even the largest supercomputer, in fact. So the only alternative is to reach out to thousands of PCs and borrow their spare CPU time. Modern computers are idle most of the time. Even when browsing the web and listening to music through your computer, its processor is just idling away. Distributed computing, also called grid computing, is a way to use those spare cycles to do some good.
Folding@Home is the largest distributed computing project in the world today. Anyone with a PC, laptop, or Sony PS3 and an internet connection can join. The joint efforts of hundreds of thousands of volunteers create a computing engine that is currently five times faster than the biggest supercomputer!
I recently joined, and it is very satisfying to know that for the cost of the electricity to leave my PC on, I am contributing in a significant way to curing Alzheimer's Disease, Mad Cow Disease, Huntington's Disease, studying cancer, and advancing basic science.
To join, I went to the F@H web page http://folding.stanford.edu/English/Download to download and install the right F@H client for my machine and operating system. Now F@H just sits in the background while I use the PC normally. Because F@H only uses the spare cycles on the machine, it never interferes with other uses. I can also pause F@H whenever I want.
As you might expect of a grid computing project, the security of the software is a top priority. The software has been downloaded over 800,000 times, and no one has ever gotten a computer virus from joining F@H.
Anyone reading this message probably has all that it takes to participate in F@H. Please try it. It's fun and rewarding to see the molecules your PC is working on, and to earn points for completing work. But the real reward is knowing that you are helping to make life better, one spare cycle at a time.

ps - SETI@Home is a similar project aimed at detecting signals in radio waves collected from the Arecibo radio telescope.
pps - This is not meant to be an internet chain letter, but obviously a volunteer grid computing project grows mostly by word of mouth. If you try F@H and like it, you have my permission to forward this message to your friends, or use parts of it to convince the powers that be at local school districts and college campuses that F@H is safe, fun, and something that can make kids excited about science. PCs in classrooms are exactly the kind of underutilized resource that would greatly benefit Folding@Home.

Catching up - SFABC

2008-12-24T10:09:00.003-05:00

First order of business - catching all of my faithful readers up on my life.

Science Fiction Association of Bergen County - a great group of folks I met in July at a Barnes and Noble in Paramus. Thank you, BN for hosting that meeting! I'm now a regular member and a member of their writers group. I'm very happy to be writing fiction again!

New job, new post

2008-12-23T20:27:00.002-05:00

Hey, it's been a while.

My only excuse for my long absence is that I've been in process of changing jobs for most of 2008. I've left PricewaterhouseCoopers and joined Deloitte and Touche.

So I hope to be sharing more with you, and more consistently, into the future.

Topping the charts

2008-02-21T14:53:00.005-05:00

Long time no blog, sorry!

So what have I been doing? Well, what I'd like to share with you is some hacking of the charting facility in ECJ.

ECJ's distribution contains some references to the inclusion of JFreeChart and iText, which will enable the production of "publication quality charts". OK, I'm all for it, but then come the caveats. "We don't use the Console app much." "We don't really use that."

So what we've got is the linkage to a good free package for charting, but only the sketchiest pointers on how to integrate it into your ECJ experiments.

There were two things about "publication quality" charts that I wanted to do right away. First, charts in journal articles often show multiple data series on the same chart. Second, data published in journal articles is usually averaged over a significant number of GA runs. ECJ doesn't contain an example of either of these things out of the box.

I've hacked together an example of the first functionality. Now I can chart the best of generation, worst, mean, and standard deviation all on the same chart.

I ran my BinInt experiment with the new chart to show that it worked. Wow! So much nicer than looking at the simple statistics!

One thing that jumps out immediately is that the experiment is wasting more than half its function evaluations because the population has converged. While we can guess this is happening when we see the best of generation fitness stall at a particular value, charting the worst, mean and standard deviation makes it completely obvious that before generation 45 (of 100) the entire population is a single genotype.

(Remember, this is a selectorecombinative GA experiment, so there is no mutation to rescue the population. We expect the population to converge well short of the optimum due to domino convergence and drift, and it does.)

Function evaluations are the currency of evolutionary algorithms. While many systems (including ECJ) let you stop a run if a known optimum is reached, stopping on a convergence criterion seems to be just as useful. I'm not sure why this is not more common, since the bookkeeping necessary is not that great an overhead. In general, you can trust the computational cost of the function evaluations to swamp the cost of the algorithm itself.

Now I'll start tinkering with the second issue, averaging over several runs. I'm going to hack this using the subpopulation mechanism of ECJ. Each subpopulation will be an independent run with a different random seed. However, the statistics gathering (and charting) mechanism can look across the values of each subpopulation and collect the statistics and average them. Is this the right way to do this? I'm not sure, but I'll try it!

The Illusion of Life

2008-02-12T21:07:00.001-05:00

The Illusion of Life is actually the name of a beautiful book about the classic Disney style of animation and how it was acheived.

I'm going to use the phrase as a jumping off point to talk about GAs. Genetic Algorithms are explicitly designed to imitate the successful process of optimization seen all around us.

Simple GAs try to tear down the bells and wistles of real biology and use just the core ideas of evolution. Take a finite population, evaluate the fitness of each member. Preferentially select higher fitness members to reproduce or be copied forward. Allow some source of variation to create new population members during reproduction. The most common reproductive operators are mutation and crossover.

A choice of population size, selection algorithm, operators and representation that all work together will take even a simple GA a long way. But GAs are sometimes criticised as being unable (even in principle) to replicate the diversity we see in the natural world.

Most GAs working on an optimization problem are like a microbe evolving drug resistance in a test tube environment. No one is even attempting to recreate the variety of species and niches of real life.

Here are some things that are sometimes brought up as examples of how GAs can be made more "biological", in the belief that this will somehow make them better:

haploid genomes
inversion operator
introns

Now it may be that there are specific optimization problems where each of these tricks might be helpful, but none of them has been shown to be extremely useful.

Notice that these ideas focus on the nitty-gritty of DNA. I have my own list of things I think might be important to bring in to our GA models from biology, but these aren't on my list. Instead, here is my list:

embodiment - in time and space
coevolution - a fitness measure in which the other members of the population are explicitly considered, including the possibility of parasitism
development - genetic cascades, and some form of lifetime fitness measure
self regulation - in the form of hormones or neurons
sexual selection

I'm much more interested in the possibilities of a boost from ecology than biology. It may be that one day, very powerful GAs will drop some things that are now considered "essential" such as the population itself! Estimation of distribution algorithms are a step in that direction. Until then, I think we do have a lot to learn from Mother Nature, but I think we need to look in some different directions.

Sex, Lies, and Genetic Algorithms

2008-02-11T21:51:00.001-05:00

Moving on from the BinInt problem, the next basic research problem to code in ECJ is the classic "deceptive" problem. In this kind of problem, the optimum point is surrounded by very low fitness points, while the points furthest from the global optimum have the second highest fitness. A hill climbing algorithm is tempted to follow the slope away from the global best towards the suboptimal points.
However, a selectorecombinative GA is not a hill climber. Its ability to find the optimum point is based on shuffling combinations of alleles, trying to find good sets.

If the deceptive subproblem is too big, the GA has little better than random chance of finding the optimum, so here also we will rely on building up a problem by concatenating several subproblems.

Based on calculations shown in The Design of Innovation, p. 160, I verified that my code for the trap function was in fact deceptive. Then I looked at a few other sources, including Franz Rothlauf's Representations for Genetic and Evolutionary Algorithms, and I saw that my code for the trap was basically the same as his.

Testing my BinInt implementation

2008-02-05T15:14:00.000-05:00

As a sanity check, I scaled the size of my subproblems down to 1, and compared the performance of the BinInt and MaxOnes problems with identical parameters. Ta dah! Exactly the same results, as you would expect.

Now I'm dialing up the BinInt size gradually. The effect of scaling is obvious, as many bits converge too early, carried along on the coattails of the high value bits. This series of experiments is with a 0.0 mutation rate, to test the powers of a selectorecombinative GA in isolation. In a problem l bits in size, with population and number of generations also held at l for l^2 function evaluations in total, the best fitness over a run is not even reaching half the known optimum.

I'm also still learning lot's of basic things about ECJ, such as how to chart statistics using the gui console. Woot!

ECJ - building a BinInt problem

2008-01-31T16:06:00.000-05:00

I've gotten a little farther with my learning of ECJ.

The tutorial 1 provided with ECJ uses the MaxOnes as a sample problem. MaxOnes simply adds up the number of "1" bits in the genome of an individual to create a fitness for that individual.

BinInt changes the problem by reinterpreting the genome as a binary integer. In my version, I've written it so that you can cut the genome up into several integers. For example, a genome of 150 bits can be interpreted as 30 5-bit integers, 5 30-bit integers, or even 16 9-bit integers with one 6-bit integer.

BinInt is a class of problems that imposes two new kinds of difficulty on the GA. First, BinInt shows scaling. Different bits are worth exponentially more than other bits. Secondly, bits are related to each other to form sub-problems. All the bits of a particular sub-problem contribute to the solution of that part of the overall problem.

Scaling in particular challenges a GA. The large fitness contribution from just a few bits can cause individuals lucky enough to have those bits turned on early in the run to quickly dominate the population, even before the population has found the best arrangement for the other bits. This problem is called premature convergence.

I had fun building the BinInt problem in ECJ. It was straightforward to modify the MaxOnes problem fitness evaluation function. The learning came in when I wanted to create a custom parameter to control the sizes of the integers. I invoked the OTSOG (On The Shoulders Of Giants) principle, and asked for help from the ECJ discussion list, with very helpful and immediate answers. Thanks guys!

Sketch of comics hero team

2008-01-24T15:43:00.000-05:00

Oh yeah, I like comics and manga, too. Sorry I forgot to tell you earlier.

I visited an Oscar site yesterday, and was happy to see that Cate Blanchett was nominated for Elizabeth: The Golden Age. I feel really stupid for not realizing that this movie is a sequel.

Anyway, it got me thinking about a hero team set in the Elizabethean Age.

In the backstory, Elizabeth really is the Faerie Queen. The last test of a new Queen of Faerie is to seduce a mortal lover, but Elizabeth instead falls for the mortal and renounces her throne in Faerie. This choice angers a large number of powerful spirits, who were planning on using Elizabeth's control of two thrones (Faerie and England) to transform England into the New Atlantis. (Not the New Atlantis of Bacon, sorry.)

Our heroes:
Gloriana - Queen Elizabeth in disguise. Or is Elizabeth the disguise, and Gloriana her real identity?
Sir Francis Walsingham - the spymaster of Elizabeth in real life. Here, a bit more "hands on".
Dr. John Dee - a link between the scientific and the supernatural. Capable of a bit of wizardry with the help of the right artifacts.
The Golem of Prague - on loan to Dee from the Maharal of Prague, who made him. Think Ben Grimm with a Yiddish accent.
Thomas Phelippes - asistant of Walsingham. Inventor, cryptographer, etc. The Q to Walsingham's M. Deciphered the Book of Soyga for Dr Dee.

Our villains:
Phillip II of Spain - wants to conquer England and create his own version of the New Atlantis.
Duetia - beautiful faery, would be Queen of Faery if she could eliminate Gloriana.
John Kelley/Talbot - worked with Dr Dee but has fallen under dark influences.
Quetztlcoatl - the Aztec god, making a deal to stay alive in the New World's New World Order.
Talus - a mechanical man/animated suit of armor. Sometimes comic relief for being too literal.

I know you're asking already, who would win a Golem vs. Talus smackdown. Is the occult science of Dr Dee any match for the pure pagan fury of a God? Can Walsingham outwit Phillip? Can Gloriana save England from drowning beneath the waves if Duetia has her way? And what about Naomi?

Find out in our next issue!

ECJ - tutorial 1

2008-01-22T21:58:00.000-05:00

I set up the Evolutionary Computation in Java (ECJ) system to run under Eclipse. Here is a brief report on using it to run the first tutorial provided with the system. This is the same tutorial covered in the YouTube videos mentioned previously on this blog.

The tutorial description assumes that you are typing in every line of the tutorial1.params file, but since it is provided I went straight to tweaking the different parameters.

The optimization problem in this tutorial is trivial to state. The genome is a set of unrelated bits which are counted, so maximum fitness occurs when all bits are 1, hence the name MaxOnes. As trivial as that sounds, a lot of basic research in GAs is conducted on this and similarly simple functions.

Out of the box, the parameters of interest are

crossover probability = 1.0 (we will always cross to get a new individual)

mutation probability = 0.01 (every bit has a 1% chance of changing)

genome size = 40 bits

population size = 40

generations = 100

With this setup, we get

Generation 32
Found Ideal Individual

It took 32*40=1280 function evaluations to find the ideal individual of all ones.

Upping the ante, if we double the genome size to 80

Generation 87
Found Ideal Individual

We found it, but doubling the size of the problem more than doubled the effort to solve it. It almost tripled it. That is disturbing.

Doubling once again to a genome of 160 bits, and the system cannot find the ideal individual, even in 1000 generations. Even if the population size is quadrupled to 160, the system fails.

What has happened? Have we reached the edge of evolution already? Is this all that GAs are capable of, solving trivial problems?

Happily, the answer is no. We are very far from the edge of evolution (if there is such a thing), but we are at the beginning of understanding how GAs work.

One of the great themes of search and optimization algorithms is the tradeoff between exploration and exploitation. When do we look in new areas for an optimum, and when do we try to find the best value in the local area of a solution we already know is "pretty good"?

In GA work, the operators of crossover and mutation are often characterized as typifying exploration and exploitation, respectively. I think this is an acceptable characterization wrt mutation, though it isn't the greatest way to think about genetic operators. Another way to think about mutation is to look at it as a kind of heat source, as in simulated annealing.

What happens if we scale back the mutation rate to 0.001 and go back to our original population size of 40?

Generation 219
Found Ideal Individual

Very interesting! What was happening in our earlier runs? The mutation rate was 1 out of 100. When the genome size was less than 100 bits, individuals could get crossed and then never suffer mutation on their way into the new population. But when the genome size went to 160, we were almost guaranteeing that every individual would suffer, on average, 1.6 bits changed. So the population was constantly dancing around the optimum, but never hitting it exactly.

If there is a final lesson to be drawn from this small example, it is that GAs are not about parameter tweaking. There is always a coupling between the probem and the parameters that needs to be understood.

Chipping Away at the Wierdness

2008-01-22T17:41:00.000-05:00

Over at the Mindful Hack, Denyse O'Leary defends the study of prayer thusly

Anyone familiar with the placebo effect would consider $2.3 million to
study the power of prayer money well spent.

How should we understand this? Does Denyse really think God is nothing more than the placebo effect? If intercessionary prayer "works", there should be some measurable difference between the placebo effect and people who are prayed for.

I think Denyse would like to help people believe in the objective reality of God. She is, after all, not a journalist but an apologist. This kind of post does not advance that agenda.

However, it is interesting when looked at in the context of many of Denyse's posts on Mindful Hack, Uncommon Descent, and her Design of Life blog. In posts where Denyse tries to channel Carl Zimmer to actually write about science, she winds up writing sentences that carry assumptions such as the reality of deep time, an old earth, and common descent. Is she with Michael Behe on this, and against most of her crank readership?

Also more out of the closet recently is DaveScot, Uncommon Descent's resident dominatrix. Dave fessed up to the same trio in a few posts over there recently, but has saved his crank street credibility by backing some form of front loaded evolution.

Are we seeing some of the loudest cheerleaders of ID talking themselves down? One can only hope.

A Model of Error

2008-01-22T13:04:00.000-05:00

Over at UD, math (sic) professor Granville Sewell resurrects one of the silliest posts of 2006, Gil Dodgen's misapprehension of what makes a model. No, the errors in our OS are not part of the model, any more than they are part of your PDE solver or Dr Dembski's MESA or Dr Marks' EIL work.

It is however true that if you are running intense numerical calculations, you need to take into account the quality of your (pseudo)random number generator, your floating point hardware's aptitude for error due to heat, cosmic rays, bad programming by Intel, etc. Taking these things into account is very different from intending them to be part of the model system. No one is going to be impressed by results that need to be run on Windows ME with a lump of uranium lying on the desk next to the CPU.

But it is from this support the Dr Sewell makes a sweeping statement, "Unintelligent forces simply can’t do intelligent things..." Sorry, Dr Sewell. In the words of the prophet, pwned! May I be the first to introduce you to the Humies.

If you're not following the link, I'll just summarize that the Humies are cash based awards for achievement equal or better than human at some intellectual task, by an EA based system. That we can give away awards like this is a testament to the power that GA, GP, etc have already achieved.

Paprika

2008-01-20T11:51:00.000-05:00

I'm not a complete otaku, which is probably why it has taken me until now to notice this movie.

If you appreciated the way The Matrix played with "is this reality?" than you will love++ this anime. The mix of traditional cel animation and cgi was well done and the music was excellent. The playfullness of the OP (opening credits) was amazing and set the tone for the whole movie. Buy it on DVD!

Can't wait for Spring!

2008-01-20T11:23:00.000-05:00

My recent look into science standards here in New Jersey popped up the factoid that the Garden Sate has a state dinosaur (as do several other states). Now I've found that the best place to look for fossils here is Poricy Park. Thank you NJGS!

Since you have to wade out into the stream to seive for fossils along the sandbanks, I'll have to wait for the spring before dragging the family out for the fun. This is gonna be great!

Looking back into ANAS

2008-01-18T20:55:00.000-05:00

ANAS is John Holland's 1975 monograph, Adaptation in Natural and Artificial Systems. I went back to it recently to review the history of the thinking about linkage learning from the very beginning.

I was struck that Holland's first presentation of a simple genetic algorithm, called a reproductive plan in ANAS, is a steady state GA. In steady state GA, a single individual is replaced at a time in the population. This means that new mixes of genetic material is made available immediately for selection.

I had mis-remembered this. I thought that historically GAs started as generational models in which the entire population was replaced at once, and that steady state GAs were due to Grefenstette.

Similarly, ANAS considers the possibility of evolving algorithms, not just parameter sets. This is the basic distinction between genetic algorithms and genetic programming, which most people attribute to John Koza.

There is a phrase in Pirkei Avot (Ethics of the Fathers) "hufach bo v'hufach bo d'kulla bo." Turn it over, turn it over, because everything is in it. I think it applies just as well to basic texts in the sciences as it does to the Talmud.

NJ ASK - WTF?

2008-01-17T13:44:00.000-05:00

So I was watching (via PT 'natch) the slow motion train wreck of Florida school districts signing up to stupidity, consigning a generation of graduates to burger flipping and telemarketing hell.

(Btw, if they ever figure out how to outsource burger flipping to India, we are toast. That is, until they figure out how to outsource toast to India...)

So there I was, all smug in my insufferable suburban Yuppie way, when it suddenly occurred to me that the fair state of New Jersey has its own share of rural ignorance, people from one end of the state who impose blue laws on the other end, teachers in Kearny that lecture kids on their private religious beliefs, etc. Perhaps I should check out how my own state is doing?

The good news - New Jersey has some (IMHO) appropriate core content standards in place for life science education in evolution. New Jersey got an A while Kansas was getting an F- (pwned!) a couple years ago when KS was devolving into BS. The standards went into effect in 1996 and are reviewed every five years. Testing shows that even economically disadvantaged kids are scoring above 50% "proficient" at all grade levels.

The better news - we have a state dinosaur! (OK, OK even Florida has a state fossil.)

Back to smug complacency until 2011, when our standards come up for review...

Why Now?

2008-01-16T09:14:00.000-05:00

In the interests of full disclosure, let me admit that I have been banned at Uncommon Descent. It is something of a badge of honor...

So one of the reasons for this blog is to provide a platform for comment and Kremlinology on the denizens of UD and the discussions there.

This time around, let us wonder at the recent post by Dr. Dembski himself. Yes, what is the predictive power of ID?

cue crickets chirping...

Well, that wraps up our program for today!

Now, for the Kremlinology portion of our show - what is the subtext of this message?

First, it is a way to say "I am important". Normally, important people don't have to broadcast that fact, so this is really telling us that Dr. Dembski's importance is falling rather than rising.

Second, it tells us that someone in the media is actually taking Darwin Day seriously. There is no other reason that anyone would take Dr. Dembski seriously enough to put him on TV (other than with Steve Colbert). Dr. Dembski is the "counterpoint" position for a Darwin program. Well, for a Fox program he might be the "point" position...

Third, it says Dr. Dembski's estimation of his chances of actually getting on the program are low. After all, actually appearing on the show is much more impressive than telling your friends that you might be invited on the show. But if this is as good as it is going to get, he's got to go with it.

Fourth, what is it with WaD and premature ejaculation? The guy cannot keep his mouth shut until the real results come in, he has to start blabbing at the very beginning. If you want other examples, look at the Polya Center and EIL fiascos. The guy knows how to kill his own prospects with ill timed PR better than anyone I know.

What Part of Evolution Don't You Undertand?

2008-01-15T18:41:00.000-05:00

We're coming up on the Darwin Bicentennial, hooray! In honor of the occasion, I'll throw out my own little explanation of evolution for the sake of anyone dazed and confused by the massive amount of misinformation wandering the Internet.

Evolution is the name of a process. It is what happens when the following are all true for some period of time.

There is a population of individuals, and these individuals have traits.

The traits influence the success of the individuals in reproducing.

There are limited resources available for reproduction.

Not everyone that wants to reproduce will get the chance.

Chances depend on traits.

The traits can vary when individuals reproduce.

If we compare the population after some long period with the initial population, the frequency of the traits will have changed. Traits that helped reproduction will have increased their frequency at the expense of alternatives.

There is nothing in this that limits evolution to biology. The whole point of a field like Genetic Algorithms is that I can set up those conditions in software and evolve data. This is a very successful part of computer science, with many commercial applications.

Of course, it does happen that evolution applies to the biology that we see around us. If you don't think it does, you'll have to point out which of the above conditions doesn't hold in the real world.

Getting back into GAs

2008-01-15T11:36:00.000-05:00

I don't remember how I discovered genetic algorithms. At some point, I got a copy of David Goldberg's book, Genetic Algorithms in Search, Optimization, and Machine Learning. It was a great book, and I had a lot of fun writing my own GA package in C (the code in the book was written in Pascal).

Goldberg's next book, The Design of Innovation is even better. The discussion of how to make GAs a principled engineering approach to solving problems, rather than a black box with too many knobs and levers, really energized my interest.

So now I'm learning the ECJ system using Eclipse. With the help of some nice YouTube tutorials on setting up ECJ with Eclipse, I'm off to the races!

Hello World

2008-01-15T11:11:00.000-05:00

Don't expect much from this blog. I'm not huge on reguritating my life into an open diary, and I'm not the author of bons mots every day.

I'm going to try to focus the blog on the intellectual areas I care most about. Right now, this means genetic algorithms, cryptography, defending evolution from misguided attacks, XBRL, and a very small dab of politics. Arts and letters will get a passing mention. I'm interested in comics (and manga, and anime), backing into the subect from the perspective of UI design, Tufte, Scott McCloud and Takahashi Rumiko.

Thanks for reading! I hope you'll be back.