Monday, December 19, 2011

Vaclav Havel, RIP

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.

Monday, July 18, 2011

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

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.

Thursday, June 23, 2011

The Facepalm of Compensation

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.

Monday, June 20, 2011

Model Madness: Axe vs. Lynch and Abegg

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.

Friday, June 10, 2011

New York-New Jersey Trail Conference - You Rock!

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.)

Thursday, June 9, 2011

Hypothesis: Reordering typical GA operations opens up new opportunities

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.

Wednesday, June 8, 2011

Time Enough for Evolution: part n++

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?

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.





Monday, May 30, 2011

Spetner, Wilf, & WEASEL

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.


Sunday, May 29, 2011

How the Earth Was Made, reviewed by David vun Kannon

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.

Saturday, May 28, 2011

Signature in the Cell, reviewed by David vun Kannon

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.

Tuesday, May 24, 2011

Great Falls, Paterson



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!

Monday, May 23, 2011

Marjorie Grene, and the fate of the Faith of Darwinism

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 piqued 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

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.

Friday, May 20, 2011

Metamorphosis, a new Illustra film

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, or 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.

Monday, May 16, 2011

Rarity vs. Isolation, a problem for Intelligent Design

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/"

Sunday, May 15, 2011

Barry Malzberg and the Immortality of Winston K Marks

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.
 

Wednesday, May 11, 2011

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

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.

Sunday, May 8, 2011

Thor, movie review by David vun Kannon

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

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 deeper 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.

Sunday, March 20, 2011

New York Botanical Garden - Beautiful!

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.

Thursday, March 17, 2011

The Retraction of Granville Sewell

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.

Wednesday, February 2, 2011

Battle Royale (manga), reviewed by David vun Kannon

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.

Monday, January 17, 2011

TRON: Legacy, reviewed by David vun Kannon

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.