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.

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.

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.

Chipping Away at the Wierdness

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

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.

Why Now?

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.