Sunday, December 14, 2014

Information, Physics Envy, and Vitamin D

Aside from the rhetorical work around the possible suspension of living processes (as presumably  overthrowing a vitalistic notion that a lack of motion somehow means the organism is no longer alive), this observation from David Penny is interesting:
In reality, we already know that there is nothing in biology that is inconsistent with physics, chemistry and mathematics.  In one of the most fundamental biological experiments in the twentieth century, Harold Morowitz and colleagues took cysts of the complex multicellular brine shrimp Artemia down to 2.2 degrees Kelvin (less than –270 °C), left them for six days, then slowly warmed them to room temperature, where they revived, grew and reproduced.  At such low temperatures, information on energy levels, positions and velocities of electrons is lost; the only information left is about the chemicals and their relative positions.  This tells us (as discussed in Penny D (2005) Biol Philos 20: in the press) that the composition and organization of chemicals is all that is required for a system to be alive. [emphases mine]
The composition and organization of the biochemical machinery in the cells is the embodiment of information.  Information that is independent of the energy levels, positions, and velocities of electrons, much as would have been predicted by Polanyi's "Life's Irreducibility."  Polanyi agreed that life was not inconsistent with physics and chemistry--but it wasn't explained by them.  Aside from the insight of the experiment (as opposed to the lesson drawn by Penny), the reductionist fallacy is unhelpful:
The low-level information of particular particles turns out to be unnecessary for the organism to recover its machine-like thermodynamic process.
Therefore, organization is sufficient for life. 
Life can be suspended, therefore it is limited to a particular kind of organization (the kind that is presumably measurable). Reminds me of the reasoning that missed the early discovery of vitamin D.  If a human being could be frozen in the same way, would that mean that there is nothing more to persons than their observable structure?  Organization could be sufficient for the simplest examples of life.  Or not.  But the reasoning seems terribly flawed and overweening.  Non-simulated "artificial life" has always involved already living cells.

Penny seems to be replacing physical reductionism with biochemical reductionism.  It all reduces to structure.  No need for physics envy here:  My biochemistry is bigger than your physics.  Ahem.  Here's what you can do with your electrons.

The low-level information of electrons turns out to be so much noise, compared to the functional information stored in the organism's structure.  I'm skeptical about much else beyond that significant observation, but then in this day and age any skepticism about orthodox precepts can make you a "denier."

It's interesting from the standpoint of this question:  What sort of dissipative systems are as dependent (fundamentally) on the thermodynamic state (distribution of energy levels and particle momenta) as on the structural configuration?  

David Berlinski, The Devil's Delusion, p. 191

Friday, December 12, 2014

Central but Superfluous: Physics Envy

From ID-hater Jerry Coyne's "Of Vice and Men":
In science's pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history's inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike "harder" scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture.
But wait, hasn't the academic priesthood community averred loudly and proudly that doubting "evolution" (presuming the equivocal term includes the historical narrative) is like doubting gravity?  (Look up discussions about whether or not evolution is "just a theory.")  Eugenie Scott, former head of the Darwinist lobby think-tank NCSE, would say so.

How much of physics could you do without at least the Newtonian concept of gravity?  There's a lot of experiment that can't be done without the Einsteinian conception of gravity.  Yet Coyne was implying that as far as he knew in 2000, his field was largely irrelevant to experimental biology.  Is the historical science of evolution central to biology in a very different way than gravity being central to physical theory?

Let's review Philip Skell's statement in "The Scientist":
"While the great majority of biologists would probably agree with Theodosius Dobzhansky's dictum that 'nothing in biology makes sense except in the light of evolution,' most can conduct their work quite happily without particular reference to evolutionary ideas," A.S. Wilkins, editor of the journal BioEssays, wrote in 2000. "Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one." I would tend to agree. Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No.
I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.
Re-read Coyne's "Vice" piece and Gould's famous Dr. Pangloss piece, and then think of what an "interesting narrative gloss" might mean.

Now, remember all those teachers in Texas who signed a petition because they were terrified that without a firm belief in the evolutionary narrative and the established power of selection, students would not be prepared for careers in biology.  These teachers apparently were privy to something Jerry Coyne didn't know in 2000.  I think Jerry has since doubted the superfluousness of evolution to medicine, but his supposed examples hinge on directed evolution and informational genetics.  Ask yourself how directed evolution is different from artificial selection, the technology that inspired and long preceded Darwin.  And Coyne wonders why biochemists and molecular biologists are turning on the evolutionary narrative?

I'm reminded of Jeffrey Shallit's comments (filed under "science stopper"?) that knowing that life is designed would turn out to be a completely uninteresting fact.  (Just think about that statement on its own terms, and then think about how hard textbook writers have tried to ingrain the "central" idea that lifeforms are engineered by processes that are undirected, nonteleological, and purposeless.)

I can think of a way in which Shallit's statement could be construed as true.  It could be true to the extent that modern biology already has a Designer.  To some extent biology already treats lifeforms as engineered by a "watchmaker," if a "blind" one.  But I can't rule out.  Currently, it would seem the main reason that Jonathan Wells has had trouble getting visibility on his centrosome hypothesis, is that journals are afraid of giving any credibility to someone who doubts the central tenets of the priesthood profession.

See more interesting quotes at "Darwinism Is Pseudo-Science."

Wednesday, December 10, 2014

It's complicated.

Some people equate complexity with randomness/disorder because of algorithmic information is also called complexity.

Small probabilities tend to represent a highly select, unusual chain of contingencies.  In the bean machine, the lefts vs. rights taken by the beans will have a more ordered structure at the tail ends.   This low algorithmic information in tail-end result represents a path whose description has low algorithmic information.

How many things must go just right (or just wrong) to get the unusual result?  It is highly contingent.  Maybe specified contingency is a better phrase?


Monday, December 8, 2014

The Complex Subject of Blowhards: Case Study in Crankiness

Has it not crossed Jeffrey Shallit's mind that Phillip Johnson is aware of those examples but doesn't find the case for the intermediate or transitional nature of those fossils very convincing?  -- Jonathan M. on Shallit's claim that Phillip Johnson lied about the fossil record 
Some notions of information are more closely tied to the Shannon notion of information (e.g. Thomas Schneider and Richard Dawkins) and tend not to wander much further. Much more closely related to some notion of meaning/function has been the Kolmogorov notion of information, also known as Kolmogorov complexity.  Complexity and information tend to be closely related notions; both are related to probability, and probability has a combinatorial nature.  The idea of mutual information is closely related to that of conditional probability.  A complex thing generally needs more information to describe it (or information and time, but that will have to wait), while a much simpler thing generally required much less information.  Highly improbable things tend to have many levels of contingencies, and convoluted  histories/developments. Optimal codes match less probable events to more bits of information.  An optimal code will tend to not only maximize the Shannon complexity of the messages but to also make the messages more compressed (maximizing K complexity per message length).

Jeffrey Shallit has become something of a public figure, not for math or computer science per se, but for being a "science defender" of the quixotic "anticreationist" variety. (Note: I have noticed Shallit also uses the term "anticreationist," though not in the ironic sense that I do.)  He has made a name for himself ridiculing ideas and the people who promote them.  He has complained in the past that 'specified complexity' would be better off called 'specified improbability.'  His and Elsberry's long critique of the idea of  'complex specified information' scoffs at the difficulty in reducing CSI neatly to one of the two kinds of information . (Everything else is "creationist information.") Winston Ewert's notion of algorithmic specified complexity is very closely related to Dembski's notions of CSI and is itself a specie of randomness deficiency, combining notions of K-complexity and probability.

Something that is ubiquitous among complexity theorists and attempts to quantify 'biological information' is notably absent from Shallit's writings on the topic of complexity.  It's what Jim Crutchfield calls 'humpology'.  Most of the attempts over the last 20 years have tried to distinguish 'useful' information/complexity from both highly ordered and highly disordered configurations.  Kolmogorov information considers highly disordered configurations to be provide more information, but most complexity theory tries to distinguish between useful information (what engineers typically mean by 'information': semantically "rich" information that carries some deep patterns) and the information maximized by total randomness.  This fundamental concern in complexity theory doesn't seem to concern Shallit at all (which is odd given reasons that we'll get to).

Sunday, December 7, 2014


Has it not crossed Jeffrey Shallit's mind that Phillip Johnson is aware of those examples but doesn't find the case for the intermediate or transitional nature of those fossils very convincing?  -- Jonathan M. on Shallit's claim that Phillip Johnson lied about the fossil record 

Saturday, December 6, 2014

the magic ratio

"Does it take more or less genetic information to grow forelimbs into functional wings, than into manipulatory appendages?"

This was going around on PT for a while and I was tinkering with it a bit. What I think is being asked is: "Is there a magic ratio of functionality to the number of bits required to implement it?"

Friday, December 5, 2014

list of complexity measures

From William Dembski's post about Jeffrey Shallit's nitpicks about information--the relationship between information and complexity is a lengthier subject--Seth Lloyd's non-exhaustive list of complexity measures:  

Wednesday, December 3, 2014

Is "Darwinism" a made-up term?

One of the many double messages one gets about evolution:
  1. Evolution is so much bigger (and more robust!) than Darwinism.  Dawkins is a Darwinist but I'm not.  
  2. By Darwinism, you mean "Biology." "Darwinism" is a propaganda term invented by creationists.
It's possible that (2) is more likely to be espoused by educators and lobbyists than researchers.  Richard Dawkins and Paul Gross probably exemplify (2).  Off the top of my head, Larry Moran (Sandwalk), James Shapiro, Lynn Margulis, Rudolf Raff, and the Alternberg 16 scientists own to (1), although for some of them (1) might simply mean that there is more than one mechanism even though adaptation through selection is still the primary explanation for functional information (since selection depends far less on serendipity).   

But the problem is exemplified in the recent Nature article in which biologists disagree about whether evolutionary biology is in great need of re-conception.  

Depending on which biologist you ask, attacking selection is either attacking a straw man or attacking an unassailable, unquestionable foundation of biology.  Point out this contradiction and the various factions will rally and point out that they all believe in evolution (cue "Book of Mormon" song "I Believe") and they all believe selection is important.  Just in case the "non-existent" controversy "gives aid and comfort" to the Enemy.   

I'll end with this bit of think-of-the-children-ism from secular evangelist Bill Nye:
And I say to the grownups, if you want to deny evolution and live in your world that's completely inconsistent with everything we observe in the universe, that's fine.  But don't make your kids do it because we need them.  We need scientifically literate voters and taxpayers for the future. We need engineers that can build stuff, solve problems.
We need your kids to think like us.  Because engineers can't build stuff without the narrative speculations of evolutionary biology. (See Salem hypothesis)

Monday, December 1, 2014

The Shallit Affair: Defeated at Waterloo

Filed under "responses so juvenile that only very learned men will attempt them":

Why, I'll decide which ideas get heard!
     I arrived at the university [Waterloo] to give my talk on 2013 November 28. I had never met Shallit, but I recognized him from the picture beside his blog. Just before starting my talk, I said “I'm surprised to see you here.”, to which he replied “I could use a laugh.”. I got no further than halfway down my first slide, having made one definition, when Shallit spoke up. He said that I had already gone wrong, and that there's no point in continuing. I replied that I am just starting to present the standard incomputability argument, and I haven't yet begun to talk about the problems with it. Shallit said that my version of the Halting Problem is nonstandard and faulty, and repeated that there's no point in continuing. I tried to continue, but Shallit would not allow me to. Other members of the audience joined the fight, all arguing against Shallit, saying that he should let me continue, and save his objections to the end. After that shaky start, having lost valuable time, I completed most of my talk and asked for questions. Shallit left.
     On 2013 December 3, Shallit sent me an email saying that he had figured out where I went wrong, and how to set me straight.
  - Eric Hehner, "The Shallit Affair"
Dr. Shallit was hoping to give new meaning to "Halting Problem," it seems.  

Comprehension and pattern vs. exception

signal/noise, program/data, regularities/randomness, pattern/exception...

From "Beyond the Turing Test" (page 8)

General zip utilities tend to overlook real pattern as well.  Is it possible that sophistication overlooks real structure because there aren't enough examples?  Effective complexity is simply an approximation for what would be the real pattern in the data.