Tuesday, December 31, 2013

Reflections on Dennett's Intuitions

Initial, cursory thoughts on Dennett's Intuition Pumps...

Intrigued by his conception of Design Space, seems to have some possibilities for being fleshed out.  Dennett is mostly about the intuitive and conceptual, hence the title, so it is in a (definitional) sense vague.

Dennett understands better than almost all the other materialists just how unlikely working designs are, and doesn't like that materialists shrink from calling well-engineered devices in biology "design."  How he seems to reconcile it that he imagines the solution space in metazoan architectures to be well-connected and smoothly connected -- to have significant structure.

This is something that I am thinking of as Speculative Darwinian Recursion:  If it is complicated, imagine it resulting from a plausible amount of tinkering on a slightly less complicated, slightly more plausible precursor. Dennett calls this "lifting" and, much as Darwin himself analogized natural selevtion from the deliberate process of artificial selection (i.e. breeding), analogizes with engineering efforts, with leveraging new technology form old.

In one of his hard AI arguments in the book he discusses a program for generating new compositions based on style samples from composers.  Give it enough Bach and it will create more -- well, more Bach-esque material.  Give it multiple composers' material and it will amalgamate the material.  I don't know that he is arguing necessarily (although it seem implicit) that this application is a trivial program, but he seems to suggest that there is nothing significant about programming into the application an insight into musical style itself, as opposed to simply writing a program that had enough Bach insights "hardcoded" in to generate Bach-esque material.

This appears in a context of "creation without comprehension" -- which for Dennett applies to both AI and biology -- and follows the example of the chess program that was able to beat the human chess-player Gary Kasparov.   Dennett asks us to ignore the brute-force approach of the application, as well as any path-pruning heuristics that were built into the program, and accept that in principle this is really not fundamentally different from comprehension and reasoning based on insight.

Are these intuition pumps or conceptual circularities?

Note: Revisit Roger Penrose's and Douglas S. Robertson's thoughts on insight.

Saturday, December 28, 2013

Course on Evolution Features Richard Dawkins's God Delusion


Ok, not the book by Dawkins, an article of the same name, but it makes you wonder what it's doing in a biology course.

I'm not against a biology teacher exercising some latitude in relevant articles.  In fact I think it is scary the way neo-Darwinists and evolutionary materialists oppose such academic freedom.  But this sort of thing provides insight into the prevailing double standard, as California materialists indoctrinate our young with no fear of violating the 1st Amendment.

Cal State Bakersfield has some provocative papers in its syllabus for its Upper Division biology course on "Evolution."  While most don't seem to weigh in on the controversy over the theoretical adequacy of neo-Darwinism, noteworthy are the articles by Dawkins, Gould, Dobzhansky, as well as an article about "the creationists' time scale."  (Does anyone else smell a strawman argument in the works?)  In the aforementioned article about atheism (and precisely what is a populist argument for atheism doing in an evolution course?) follows the predictable syllogism:

Further Reflections on Pig-Chimp

Some further reflections on the pig-chimp hypothesis:

(1) Reading P.Z. Myers' criticism of the "pig-chimp" hypothesis, it stood out to me again that there is a correlation between gradualist arguments against human-chimp comparisons and gradualist arguments against protein-protein comparisons. There is an argument that it is worthless to compare two closely related proteins because the plausibility of them both having developed from a common, less functional prototype is fundamentally different from the plausibility of changing one highly adapted protein into another. There is a similar argument about comparing humans and chimps, though I think Myers forgets this when he discusses what a chimp is likely to do with a monstrous hybrid rather than what a proto-chimp is likely to do.  If we were to imagine (within the neo-Darwinian construct) something with all the gentler nurturing primate instincts of humans, bonobos, and gorillas, say a homobo, maybe it would have a less Spartan attitude.

(2) One of the criticisms (there's a whole kitchen sink o' them) directed at ID is that it tells us too little about the sources of design:  nothing about their nature and number.  It would be natural for a theist to presume one designer, but as far as data is concerned I'm not sure there is anything gained by presuming exactly one agent or intelligence.  I would rather presume a group of engineering intelligences (or alternately, formal causes) who may be conferring or developing according to a common plan/goal.  

I was thinking about this in connection to the fact that ID proponents are not likely to talk much about the pig-chimp hypothesis.  One reason (maybe the biggest) reason is that it is doesn't have nearly the acceptance or interest that either symbiogenesis or self-organization has.  Dr. McCarty is more or less a side-show in the bio-theory marketplace.

But the other reason is that ID proponents tend to think, naturally, that the explananda are better explained by “a common designer, who re-used different components in the different designs that were made.”  And certainly, the idea of an engineered humanity is, I think, consonant with theism, but the idea of evolution as a history of engineering experiments may be too New Age for many who are attracted to ID.  However, as Dr. Behe has criticized Ken Miller, even if the idea of engineered predators and parasites are theologically problematic, that doesn't mean we stop following the data.  We are all, however, materialists and non-materialists alike, influenced by our philosophical commitments.

For me, the inference to intelligence as causal explanation is more fundamental than inferring a particular purpose. Not that the data is completely silent on the matter – I think it is a rational inference that the human brain is designed for abstract and self-reflective thinking, for creative insight.  Further inference (e.g. the why) likely goes beyond the biological facts into other areas of reason.  But inferring an application of deep knowledge to genetic information doesn’t necessarily preclude a role for chance in history.  Nor does thinking of the infusions of information at points of history (e.g. the Cambrian explosion) as “experiments” necessarily imply anything as capricious as Dr. Moreau’s horrors.

So the idea of engineers (extraterrestrial, interdimensional, or whatever) experimenting with biological diversity may well be an unpleasant characterization for ID proponents.
I suspect evidence of re-use is likely one of the most promising research activities. For me, “experiment” doesn’t exclude the teleological or purposeful, but it leaves as open issues what the design was meant to demonstrate and the degree to which chance co-exists causally with intelligence. It is a common ploy of the “science defenders” to demand that all evidence compel a sense of clear intention, perfection, and omniscience. As I understand the claims of ID, it doesn’t preclude (nor does it require) epochs of trial species coming about and going extinct. Whether each individual species were to play a perfectly anticipated/orchestrated role in history, is not essential to the validity of the general idea.

For me, the inference to intelligence as causal explanation is more fundamental than inferring a particular purpose. Not that the data is completely silent on the matter – I think it is a rational inference that the human brain is designed for abstract and self-reflective thinking, for creative insight. Further inference (e.g. the why) likely goes beyond the biological facts into other areas of reason. Inferring the application of deep knowledge to genetic information doesn’t necessarily preclude a role for chance. Nor does thinking of the infusions of information at points of history (Cambrian explosion?) as “experiments” necessarily imply anything as capricious as Dr. Moreau’s horrors.

Free will itself seems to me a kind of grand experiment (or adventure, as some might put it), whether or not a master plan can be perceived. Life is fraught with contingency.

I do appreciate your time, and also your wariness about both Eugene McCarthy and the connotations of the word “experiment.” I don’t think anyone is obligated to take Dr. McCarthy’s conclusions seriously even if he is an expert in backcrossing; as you point out, it’s a question of the meaning/interpretation of the evidence, not simply whether or not the evidence is significant. The bright side, I think, of the attention his theory is getting is that it draws attention to the uniqueness of the human body and to the inadequacy of selectionism to account for it. His data may be quite valid regardless of his conclusions. Then again, many people believe/assume that “all things are possible with” natural selection – so ‘absurd is as absurd does,’ as Mr. Gump might have said.

As bizarre a conclusion as it may be, the list of “not-so-primatish” traits in humanity seem remarkable, even if you don’t consider yourself cousin to bacon. I’m not advancing a theory that ancient alien astronauts engineered us to root for truffles, in case you were worried. J

 have almost as much interest in the sociology of science as in biological explanation. Sociologically speaking, I think it will be interesting whether or not the McCarthy hypothesis (as implausible as it is) does get taken more seriously, since it’s superficial/seeming plausibility owes a great deal to the implausibility of natural selection. That is, it appears to answer some questions well because people know intuitively that in Natural Selection’s ability to hindsight-predict any outcome it predicts nothing. (This is more a hyper-selectionist problem, but you know what I mean.) I suspect the infamous monkey-pig might haunt the hallowed halls of science even longer than the aquatic ape. Monkey-pig does suffer from being less vague than general hand-wavings of horizontal transfer, but has similar appeal (and some similar problems) to that of “acquired genomes.”

Whether it is desirable to have people mention the monkey-pig hypothesis in the same breath as ID is an understandable concern. Not all heterodox ideas are equal. But I find it curious that P.Z. Myers didn’t bother to mention them in the same breath, and I suspect that he doesn’t simply hate the monkey-pig hypothesis for its impossibility but rather for exposing just how little explanatory power neo-Darwinism has. This alone makes me smile, even if I do believe in something more like the Garden of Eden than the Island of Dr. Moreau.

http://www.aquaticape.org/wegener.html

Sunday, December 15, 2013

Rupert Sheldrake Banned TED Talk: Dogmatic Science

Rupert Sheldrake attempted to bring teleology back to biology with his hypotheses of morphic resonance and formative causation, years before the intelligent design program got real momentum in the late 1990s.  This is a great presentation on the questionable dogmas of materialist science.  Watch it before they pull it from Youtube again.  


_


Tuesday, December 3, 2013

Lysenkoism Part II: Collectivist Science

As I continue to ponder Elsberry and Perakh's denouncement of the comparison of  Darwinism to Lysenkoism, I find it funny that their attempt to "turn the tables" on ID proponents includes appeals to their alleged "self-aggrandizing puffery."  Apparently, they are offended by the effrontery of not exhibiting the proper humility and this, to them, makes them "Soviet-like" and Nazi-like. But this is (perhaps unintentionally) a red herring.

What is the most salient connection between the bullying and harrassment by the anticreationist coalition and the initimidation of totalitarian regimes is the urgency to suppress dissent and make sure that it has serious consequences.

Elsberry and Perakh try to steer the reader in the direction of seeing ID as kin of Lysenkoism.  ID and Lysenkoism are both against the neo-Darwinian Synthesis, for one.  Secondly, both are allegedly unproductive, whereas the Modern Synthesis supposedly can be credited with the great advances of modern biology.

In many ways, even though I think E and P's arguments on the matter are fallacious, I believe it is a red herring to argue at all based on which theory any one group's model of theory choice supports.  Fervent neo-Darwinist advocate (and contemptuous anticreationist) Jerry Coyne disagrees with E and P about the practical success of neo-Darwinism.  Many science defenders are aware of this inconvenient truth, but it is often considered impolitic to point it out.  But even if it could take credit as a productive heuristic, it is still not a good argument for suppressing alternative views or for excusing suppression.

The big problem with Lysenko's Michurinism was not really that it was unproductive or wrong.  The problem was that its shortcomings were foisted on people through intimidation and the use of state power to enforce a hegemony.  If dissent and controversy had been tolerated in the universities and if various firms and organizations had been free to pursue the erroneous theory of their choice, all of the public agriculture's eggs would not have been in the Michurinist basket -- maybe only a few government-sponsored experiments.   A free marketplace of ideas would have been ideal then as now.

Sunday, December 1, 2013

Is ID the New Lysenkoism?


"[I]mprovement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of 'like begets like'. 
[I]f truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say.
~ Jerry Coyne, fearless defender of neo-Darwinism, quoted here
Elsberry and Perakh, despite their obvious disdain for Darwin skeptics, make for interesting reading when they try to comment on the substance of ID approaches.  They completely jump the shark on the matter of ideological science in general and Lysenkoism in particular.

First of all, I'd like to comment on where I first heard Lysenkoism mentioned with respect to Darwin-skepticism.  The first was in some commentary by Eugenie Scott.  As I recall, it wasn't in response to anything by ID advocates, but simply an analogy based on her belief that all ID is driven by ideology, and since the Lamarckist approach under Stalin was favored because of Marxist ideology, ID and Lysenkoism are obvious soulmates.  Profound.  (It's possible she was inspired by the E&P paper, but I don't remember seeing any references to it.)

The second instance was in the book Corrupted Science, which was advertised as an unbiased look at the relationship between ideology and science, and ironically turned out to be completely political polemic.  This too wasn't a reaction to Lysenkoism comparisons by ID advocates.

My impression upon reading the Scott article was a sense of irony.  The lost jobs, lost tenures, lost promotions, etc. where professors and teachers go from being praised and celebrated to suddenly being denounced as third-rate hacks abound.  As neo-Darwinist zealots often remind us, skeptics of hyper-selectionism and neo-Darwinism are sorely outnumbered.  In spite of this, what you will hear from the "science defenders" are complaints as to how dangerous it is to question ID (you might lose the good opinion of all those cranks they make fun of).

Friday, November 29, 2013

Are Humans Long Pig? or Monkey-Fish-Frog?

Does the creature on the right look more like a primate?  It isn't.  It is a non-primate mammal with a severe developmental anomaly, a mammal that would not ordinarily have a very primate-like face.  I don't think anyone, as yet, knows what causes this syndrome.  I don't think the syndrome has ever been considered important enough to investigate.

I came across a very interesting series of articles at macroevolution.net by a Dr. Eugene McCarthy with a PhD in genetics. He specializes in cross-species hybridization (he has a book on avian examples), and he makes a thought-provoking argument that because humans share so many traits uncharacteristic of the great apes and that many of these traits are similar to those  of a particular non-primate mammal that the traits are best explained by an extremely unlikely hybridization event.  It sounds more than a little “monkey-fish-frog” (or man-bear-pig, if you get that reference), but even if the conclusion seems absurd, the evidence he brings up is compelling, the unlikelihood of a successful hybrid stabilization event notwithstanding.

There are many things about this theory (along with the reactions to it) that are engaging.  One is the following angle:  How well does Dr. McCarthy’s evidence support considering the human genome as a intentional incorporation of specific pieces of non-primate DNA into the basic ape architecture in a way  that required specific knowledge of the architecture?  That is, how much does it resemble a deliberate engineering effort?  (Aside: Some groups might be more supportive of pig-chimp theory if it declared that "all men are pigs" at the exclusion of the female gender.)

With all the evidence that McCarthy trots out, it seems like a wonder that humans are considered so closely related to apes.  Think of the paleontological primacy of bone structure and how it is undermined by marsupial phylogeny.  Based on bone structure alone, it would be impossible to realize how different many marsupials are from their convergently evolved  placental counterparts.  Dr. McCarthy has begun to question the assumptions of paleontology (if it's really old it must be something like a lizard) and whether some dinosaurs should be considered to be much more like mammals than reptiles.  (And how long did it take for paleontology to accept the idea that some dinosaur creatures could be more avian than reptilian?)

Wednesday, November 27, 2013

Sun-Gazing: Tired Darwinist Arguments Against the 2nd Law of Thermodynamics

Who says Neo-Darwinists can't evolve?   The appearance of Intelligent Design has afforded them to add a new argument to the standard one of  "just add sunlight":  "Young Earth creationists have been pointing to the 2nd Law of Thermodynamics for years, so you can dismiss the argument out of hand."  If you don't believe me, look at how many articles start out with "guilt by association."   These same articles will purport to open your eyes to the (supposedly) mere rhetorical devices of all nonbelievers in Darwinism (collectively, and therefore misleadingly, called "creationists").
Accepting for the moment Sewell’s idiosyncratic terminology, we can say that if we take the Earth by itself as our system, then there is definitely something entering to make an increase in biological complexity more likely. The solar energy received by the Earth fuels the chemical reactions that allow living organisms to survive and reproduce. This cycle of survival and reproduction ultimately leads to natural selection, which can, in turn, lead to increases in biological complexity. Minus that energy living organisms would quickly go extinct and evolution would not occur. --Jason Rosenhouse  
The gas I put in my car certainly makes locomotion more likely.   How the gas makes an engine more likely is apparently unnecessary to explain.  Rosenhouse would almost certainly cry foul to this and fall back on the most common version of "I just point at the sun":  it is through an alchemical combination of chance and necessity as revealed in the Methinks It Is Like A Weasel experiments of the renowned atheism evangelist Richard Dawkins.  It is almost suggested that some precursor to natural selection acted on protometabolic processes, leading ultimately to natural selection in his words.  I say "almost" because I am giving the benefit of the doubt since it really does sound like the availability of energy to exploit directly leads to survival of complex cybernetic entities (i.e. "living organisms") which directly leads to complexity.   Keep this progression/cycle in mind.

Another argument that is almost always present either implicitly or explicitly is the bandwagon argument.  If you perceive a problem with the aforementioned progression, that means many people much more distinguished than you are wrong, and you don't want to appear foolish, do you?  Again, these articles proceed unabashedly in this manner even while warning you of the fallacious rhetoric of the enemy.

I want to revisit that last sentence there:
Minus that energy living organisms would quickly go extinct and evolution would not occur

Sunday, November 24, 2013

Stuart Newman: handwaving arguments undermine public trust

(about halfway through the Youtube video)

Stuart Newman speaks out on the negative effects of "entrenched old science":
Suzan Mazur: What is the danger in mediocre science being pushed on the public, aside from the wasting of public funds at a time of serious economic downturn in America?
Stuart Newman: It seems to me that if somebody is predisposed to be skeptical, perhaps because they are religious, and are told that the vertebrate column, for example, had to have evolved incrementally – they may not be persuaded by it because it’s not true, even though their motivation not to be persuaded might come from their religion. Then scientists who are working on this embryonic mechanism who have shown that there are non-incremental mechanisms that produce these things come along, and therefore everybody who’s been assuring this skeptic that it’s all incremental turns out to be wrong.
It really undermines confidence in science if people are always being subjected to what we call "handwaving arguments" that all complexity had to have had an incremental origin.
Suzan Mazur: Sam Smith of Progressive Review recently said the following: “[Scientists] are also subject to that most pernicious of academic temptations: the desires and biases of their funders.” He refers to the “distorting role of the Defense Department, agribusiness and pharmaceutical corporations in supposedly objective science.” Would you comment on that?
Stuart Newman: That’s true. I don’t know how pertinent it is to the evolution debate. I don’t think the pharmaceutical companies have a role in steering the field away from self-organization. In fact, if it’s true and you can patent it and make money on it, they’ll chase after that. So I don’t think the businesses, although they do have this grip on scientific development – I don’t believe they’re ideological in that way. The ideology really comes from entrenched old science – people who are educated in biology with no sense of physical sciences. The inertia and obduracy comes from the side of the scientific establishment rather than from industry.

Thursday, October 17, 2013

to add or not add; that is the question

The following does not seem to me an atypical statement in related topics:
CRCs are so called because the check (data verification) value is a redundancy (it expands the message without adding information) and the algorithm is based on cyclic codes.  [emphasis mine]
To the ones who talk about "adding information," this is not a meaningless distinction.  There are some functions of a collection of bits that may be considered strictly as functions of those bits and other functions that compute a function of  those bits with some other data built-in to the function itself.

So why, when it comes to biology, do some people pretend statements about conservation of information are meaningless?

Sunday, October 13, 2013

The Whistling Herring

 "He eteþ no ffyssh But heryng red."

The dialogue's not perfectly accurate but is more or less the MirrorMask version of an old Yiddish joke:
What’s green, hangs on a wall, and whistles?
Gryphon: I give up, I think, no wait, wait… Fine. What’s the answer?
Helena: Okay. It’s a herring.
Gryphon: But a herring isn’t green.
Helena: You can paint it green.
Gryphon: But a herring doesn’t hang on a wall.
Helena: You can nail it to a wall.
Gryphon: But a herring doesn’t whistle!
Helena: Oh, come on. I just put that in to stop it from being too obvious.
This puts me in mind of Dembski's tractability condition.  (In more recent developments of algorithmic specified complexity, the tractability condition is built in as a feature of randomness deficiency.)  Even if it's true that a herring can be green because of paint, and even if it can be made to hang on a wall, the effect is to include anything that can be painted green and hung on a wall.  These increase the specificational resources of the target space so that it's no longer specific.  I can paint a squirrel green and stick it on the wall.  Or a carrot.  Or a handkerchief.  Which is precisely the joke. Once I include things that aren't normally, typically green, as well as things that don't typically, normally hang on a wall, the riddle becomes intractable.   

Saturday, October 12, 2013

The Coexistence of Sound and Bad Adaptations

From Pierre-P. Grasse's Evolution of Living Organisms:
Rabaud's study of cases like Tipula led him to confuse finality with utility Had he referred to paleontology he would have realized that the two concepts do not [always] coincide.  An end may be useful, useless, or indifferent.  The evolutionary trend may be good, bad, or  neutral for the succeeding line.  Evolution is indifferent to the survival or demise of the species.  Faulty evolution is littered with the bones of its victims.  The coexistence of a sound adaptation and a bad one, of useful, indifferent, or harmful characteristics, is one of the facts that demonstrate that the last word does not lie with selection in the world of living things.
Do Grasse's examples reveal something about the noise threshold of natural selection?   Or do they more often than not reveal that we are too ignorant to recognize what features selection is responding to?

If an apparently better adapted snail is outpopulated by another snail in its own environment, are we too ignorant to be making meaningful speculations about the selectionist history of a prehistoric taxon? or are we mostly in the dark about what each organism brings to the table (again, generally in the dark about the features at selection's disposal)?

Many adaptationists would say, "But of course, we must be temporarily ignorant about the adaptations upon which selection is acting!"  And most of those who would heroically defend science from "Darwin deniers" would nod their heads vigorously at this, as a reasonable (and useful!) defense against the ever-present dangers of provincial antiscience.  In other (i.e. non-political) forums, they might just as well argue that Grasse is citing meaningful evidence for the prevalence of neutral mutations -- which has its own usefulness for protecting Darwinism.

Or they might argue there is really nothing significant about it either way since it could be evidence for either neutrality or for our ignorance or anything in between, underdetermined as it is.  That is, the meaning of these examples depends entirely on which pro-selection argument it seems to be good for in a given context.

Thursday, October 3, 2013

Lynn Margulis is a secular creationist too!

Jerry Coyne goes all anticreationist in branding Lynn Margulis as a secular creationist.

Coyne disapproves of Margulis's book Acquiring Genomes, to make an understaement, but what seems to have earned his disapproval is simply that Margulis' saw any need for any explanation.  In order for her to see any explanatory gap (Altenburg 16, anyone?), she had to be completely ignorant of all the advances in evolutionary speculation over the last 30 years.

You don't need to look any further, of course, than the title of the article:  By "dissing" neo-Darwinism, Margulis has dissed evolution.  Typical anticreationist fare.

Once again, macroevolution is a simple consequence of population genetics, not so simple that one has to be knowledgeable about a great many articles (the very many exciting scholarship to which Coyne alludes) in order to appreciate just how macroevolution has been explained to the satisfaction of neo-Darwinists.

Coyne seems to have missed (or "dissed") that Margulis' endosymbiotic theory ideas have caught on and become much more mainstream in evolutionary science.  If, as recent and sketchy jurisprudence has it, science is what scientists do, Margulis' "crazy" ideas, as he puts it, have wormed their way into science without his approval.  The explanatory gap is illusory, in Coyne's opinion.

Personally, I think there are some serious problems with Margulis' ideas with regard to the specific explanandum of generating novelty, but I believe she's very right about the explanatory gap:
This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.
After quoting the above, Coyne completely dances around Margulis' insight that selection is severely constrained and that natural selection is not omnipotent.

Coyne also defends his old friend Richard Lewontin. I think it may well be possible that Margulis remembers Lewontin's words in a more unflattering light than he said them (and I don't see a complete retraction there from Lewontin) but I think Lewontin more than likely said something akin to what Richard Feynman recounts in his Cargo Cult Science speech:
For example, I was a little surprised when I was talking to a friend who was going to go on the radio. He does work on cosmology and astronomy, and he wondered how he would explain what the applications of his work were. "Well," I said, "there aren't any." He said, "Yes, but then we won't get support for more research of this kind." I think that's kind of dishonest. If you're representing yourself as a scientist, then you should explain to the layman what you're doing-- and if they don't support you under those circumstances, then that's their decision.
Unlike Feynman's friend, Margulis did not claim that Lewontin mischaracterized his work but was honest about it.  Lewontin has since clarified that Margulis' recollection made it sound like Lewontin's work with disappointing formulas was so he could get grant money for himself where as it was to get money to “run an institution”: to “fund a group of creative people to do what they want.”  Once again the selfish gene has led to altruism.  I think maybe Coyne's overstated umbrage over Lewontin's alleged hucksterism disguises that he is reacting to Margulis getting dangerously close to the fact that there is big money in overflated claims of what has actually been explained, and neo-Darwinism has been a TROUGH.

Are all the papers on evolutionary biology written by hobbyists?  It takes money for people to spend their working life speculating on historical contingencies of how one organism changed into another during such and such an epoch and speculating on what natural selection may explain.  Whence cometh the money?   How might the money flow be affected by perceptions that evolutionary biology might be making popular evolutionary views more elaborate and more consistent with what it known about how organisms work, but not necessarily deepening our understanding of how organisms work?  Once you stop defining the deepening of knowledge in terms of refining "biology's unifying principle," it may be that our understanding is actually being stunted by so much number-crunching in the service of idle speculation.

I'll add here that Jerry Coyne also has a beef with secular creationist Mary Midgely, and anyone who undermines the popular credibility of the Modern Synthesis.  So if you want to know how the Modern Synthesis is falling apart, find out what Bilbo Baggins, er... I mean, Jerry Coyne hates.  Look up all the people he tries to discredit, and you will have an idea what's going on.   In tune with Thomas Nagel's "dangerous sympathy" for Darwin skeptics, Coyne thinks that Margulis may be "worse for science than creationists [Coyne probably has ID proponents in mind here], since her scientific credibility remains high." Actually, an anticreationist usually doesn't mind people doubting Darwinism as long as (a) they are in the minority (among tax-payers and grant-funders) and (b) they can all be denied "scientific credibility."  

Wednesday, October 2, 2013

The Cost of Combining the Results to Subproblems


Something to consider:  Recurrence relations must take into account the cost not only of solving subproblems but the combining the results.

One of the weaknesses in Elsberry and Shallit's essay is the short shrift they give to the arrangement of words within a sentence -- particularly in regard to the Weasel simulation.  In fact, it is so such a salient point that you wonder how anyone with a computer science background (namely Shallit) can be so blind to it.  E and S actually argue that, considering the random formation of separate words to a sentence as the solutions of the subproblems, the cost of getting them to link at precisely the right places into the correctly ordered sentences is trivial.  Of course, given their treatment of the problem mathematically, they are considering the spaces joining the words as no different from the characters in the words themselves.  Developing the "ks it" string is no different from developing the string "think", since the interrelationships between adjacent characters do not matter to the simulation at all.

If I have complete subassembly items of a jet plane, what is the information cost of  defining how they are put together -- or alternatively, what it is the computational cost of trial-and-error fitting together of components of the plane until it is assembled in a working fashion, in the absence of that information?

Even in "embarrassing parallel" problems, how much forethought or arranging needs to be put into how to put together the results of the distributed computation?   Considering natural selection as a computational problem, what is the cost of massively parallelizing?  Well, there is a definite cost to having too many mutations at one time.  This reduces the bandwidth and makes for an "embarrassing" amount of redundancy.  Now, a mutations themselves are distributed over a large population, and with a large population you can experiment here and there.   Mutational experiments can then combine without destabilizing the species.  However, this makes it very, very difficult for two mutations  needed to combine for a special result to combine in one special hybrid individual.  If the two mutations are not quite "neutral enough" they will likely never meet up.  Then, you say, small populations are often somewhat isolated.  Maybe it is this isolation, a "founder effect" and such that affords the complementary mutations a chance to find each other.  But then it is fortuitous for them both to occurred in the same small population.  Then, you say, it is some special combination of small populations occassionally.  This final retreat is rather like a shell game, I think.  In the end, if there is some ideal combination of ideal gene flow between ideally sized local populations, isn't this itself a deus machina?

But then, isn't that evolutionary science?  Speculating what remarkable conditions would be needed for natural selection to have done it, and then asserting then that this remarkable set of conditions is indeed what was the case, since we know that natural selection has brought it about?

This reminds me of the "fortuitous tree"...

Tuesday, October 1, 2013

Anticreationism from Stephen Jay Gould

In his Non-Overlapping Magisteria (I can't help but think of this phrase when watching The Golden Compass) Stephen Jay Gould claims "creationism" -- and one naturally thinks he has in mind specifically what he heroically opposed in McLean vs. Arkansas -- "a splinter movement (unfortunately rather more of a beam these days) of Protestant fundamentalists who believe that every word of the Bible must be literally true."

Phillip Johnson considered this proposed treaty between "magisteria" as disingenuous.  While I won't speculate here about Gould's motives, I do think most of the reasoning behind the idea of non-overlapping magisteria (which despite Gould's framing of the problem surely wasn't first thought of by him) does seem a little disingenuous to me.

More importantly though, you'll notice that whomever the initial supporters/advocates were in this land where Protestant fundamentalism is more than a mere footnote in its history, ID advocates (including those that advocate against this outlawing of ID) include more than Protestant fundamentalists.  As far as I know, neither Michael Behe nor Jonathan Wells nor David Berlinski nor David Klinghoffer nor Richard Sternberg are Protestant fundamentalists.

It's important to realize, however, that anticreationists believe that if the intelligent design movement evolved out of the creation science movement to any significant degree (Of Pandas and People is the important missing link fossil for the Barbara Forrests) then it has to classified as the same movement with the same pros and cons, the same limitations and problems, with all the same ideological grounds.   All one has to do is look into Eugenie Scott's treatment of Richard Sternberg to see this.  Or to look into the latest edition of Why People Believe Weird Things to see how Michael Shermer has updated his section on creationism to mention "intelligent design" as a new form of creationism and most of his criticisms of creationism have no bearing at all on intelligent design.  (I believe the ones that do have some sort of bearing are --as stated--strawman arguments or weakly applied to ID, but they could at least be developed in some way; the others are complete non sequiturs.)  But it's important to take evolutionist Michael Behe and pin a Duane Gish nametag to his chest and continue the debate from there.

Otherwise, what is the point of trying to discredit intelligent design with the guilt by association argument.  Association with Protestant fundamentalism.  If most people who find the courage to speak out against a sketchy scientific program -- in the face of great risk to their careers -- happen to do so because of a matter of faith, why does that become legal grounds for invalidating a cause?
Justice Scalia has a reputation for throwing attorneys off-balance with elaborate hypothetical questions. True to form, he posed for Topkis a long hypothetical question—for the purpose, presumably, of demonstrating that a law could have a religious motivation and yet be constitutional. “Let’s assume,” he began, “that there is an ancient history professor…who has been teaching that the Roman Empire did not extend to the southern shore of the Mediterranean in the first century A.D. And let’s assume a group of Protestants who are concerned about that fact, inasmuch as it makes it seem that the Biblical story of the crucifixion has [the] thing a bit wrong.” Concluding his story, Scalia tells Topkis that the upset students march “to the principal of the school, and say, ‘This history teacher is teaching what is just falsehood.’ And the principal says, ‘Gee, you’re right.’ And he goes and directs the teacher to teach that Rome was on the southern shore of the Mediterranean in the first century A.D.” The principal’s order was “clearly” religiously motivated, Scalia asserted, but wouldn’t it also, he asked, be constitutional?
Sometimes the only ones that will put up much of a fight are those who have a big stake in the outcome.  In spite of our First Amendment (and ironically, using an odd interpretation of it), those who have such a stake are often denied a voice precisely because of that stake.  Hmmm.

I think skepticism against Darwinism is nonetheless gaining momentum outside the Protestant faithful.  Thomas Nagel, a leading atheist philosopher, has joined the ranks of the secular creationists:
I realize that such doubts [about Darwinian naturalism] will strike many people as outrageous, but that is because almost everyone in our secular culture has been browbeaten into regarding the reductive research program as sacrosanct, on the ground that anything else would not be science.
No kidding.  In his Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False, Nagel has joined this mystical splinter cult of Protestant fundamentalism. He's even made given a "pernicious" and "dangerous" commendation to some of the intelligent design advocates at Discovery Institute.  One of the many who pretend to not be a Protestant fundamentalist in order to "mainstream" a thinly disguised form of Biblical literalism.

Can you say "bugaboo," kids?  I knew you could.  

PS:
Coyne also bizarrely characterizes Berlinski as a “creationist,” and a “defender” of Intelligent Design theory. In fact, he is neither. The notion that Berlinski is a “creationist” is nothing short of laughable and while “sympathetic” to ID, he is by no means an advocate of the theory, much to the chagrin of his colleagues at the Discovery Institute. 
Moshe Averick



Monday, September 30, 2013

new arrangements and the flash of genius


Came across this nugget from Wittgenstein's Philosophical Investigations:
The problems are solved, not by giving new information, but by arranging what we have long since known.
Another way of stating this in terms of information theory, I think, is to say that new information consists now of applying past knowledge into new arrangements.  Consider this interesting exchange from the movie Flash of Genius:
You have a Ph.D in electronic engineering, is that correct?
Uh, that's correct. I've taught for the past several years...
No, that's fine, sir. Your credentials are already part of the record. Now, when you said earlier that Mr. Kearns didn't create anything new, could you explain what you meant by that?
 Yes. As you can see, Dr. Kearns's basic unit consists of a capacitor a variable resistor and a transistor. Now, these are basic building blocks in electronics. You can find them in any catalog. All Mr. Kearns did was to arrange them in a new pattern, you might say. And that, that's not the same thing as inventing something new, however.
 Did Mr. Kearns invent the transistor?
 No, sir, he did not.
 Did Mr. Kearns invent the capacitor?
 Again, no, he did not.
 Did Mr. Kearns invent the variable resistor?
 No, he did not.
Thank you, Professor.
Or more amusingly, in an episode of the series "3rd Rock From the Sun," High Commander Dick Solomon tries to discredit a novelist by pointing out that he has used information that is accessible to anyone:
[to Jeff] You think you're pretty clever, don't you? I happen to know that every word in your book was published years ago! [to everyone in the room] Perhaps you've read...The Dictionary!
Jeff wrote his novel by merely recombining meaningful words, and Robert Kearns merely rearranged the previously discovered transistors, capacitors, and variable resistors into new parts.  In the first instance, plagiarism would consist of stealing Jeff's particular improbable combinations of words, and in the second instance, intellectual theft consisted of stealing Kearn's ingenious arrangement of standard components.

Consider now that Charles R. Marshall and other biologists have argued that the Cambrian Explosion might have resulted from "simply rewiring the existing genetic networks." To say that this solves the informational problem is like saying that all I need to do to create useful computer programs is to "tweak" how the procedures invoke one another and how data flows between them.

Pierre-Paul Grassé wrote, "If to determine the origin of information in a problem is not a false problem, why should the search for the information contained in cellular nuclei be one?"  Indeed.

Heuristics and Mechanical models



Following the tradition of the 19th century mathematical physics in Great Britain, James Clerk Maxwell extensively employed mechanical models in the study and representation of electromagnetic phenomena.
http://www.ifsc.usp.br/~cibelle/arquivos/SCED%202006.pdf

Sunday, September 29, 2013

Pierre-Paul Grassé, French biology, and mechanism

Pierre-Paul Grassé is the past President of the French Academie des Sciences and editor of the 35 volume "Traite de Zoologie" published by Masson, Paris. [+]
I think it was Berlinski that hypothesized that the French identification of Darwinism as an inherently Britannic idea allowed their biology to be free of the Darwinian stranglehold.  I almost love the avant-garde stubbornness of it.  Read here about Pierre-Paul Grassé.  He could make you become a Francophile.  
"The opportune appearance of mutations permitting animals and plants to meet their needs seems hard to believe. Yet the Darwinian theory is even more demanding: a single plant, a single animal would require thousands and thousands of lucky, appropriate events. Thus, miracles would become the rule: events with an infinitesimal probability could not fail to occur .... There is no law against day dreaming, but science must not indulge in it."
I would like to sit at a sidewalk cafe in Paris, sip some good coffee (okay, the French do that really well), and talk to Grassé.  Or listen, mostly. "Dr. Grassé, what do you think of the fact that most American biologists think that you can't actually do biology without a commitment to the truth of the Modern Synthesis?"  

Alas, it is too late to have such a conversation with Dr. Grassé. much as it is with Dr. Marcel Schutzenberger.  Though perhaps Dr. Schutzenberger may have said similar sorts of things.

This all reminds me of a Chinese researcher quoted by Dr. Jonathan Wells:
"In China we can criticize Darwin but not the government. In America you can criticize the government but not Darwin." [+]
Hey, something has to be sacred.

I just saw that there is a TalkOrigins article that tries to address the anti-Darwinism of the French, which they write off as mere cultural bias (and how much pro-Darwinism in England and America circa 1880-1920 was motivated by trends of atheism and scientism in university culture?) They clarify that it was Prof. Louis Bounoure who said:
That, by this, evolutionism would appear as a theory without value, is confirmed also pragmatically. A theory must not be required to be true, said Mr. H. Poincare, more or less, it must be required to be useable. Indeed, none of the progress made in biology depends even slightly on a theory, the principles of which are nevertheless filling every year volumes of books, periodicals, and congresses with their discussions and their disagreements.
while it was biologist (and atheist, for what it's worth) Jean Rostand of the Académie Française who said, "Evolution is a fairy tale for adults." French atheist and scientist Paul Lemoine who was director of the National Museum of Natural History, wrote in the Encyclopedie Francaise:
Evolution is a kind of dogma which its own priests no longer believe, but which they uphold for the people. It is necessary to have the courage to state this if only so that men of a future generation may orient their research into a different direction.
TalkOrigins explains that Paul Lemoine believed in descent with modification, and so, like Michael Behe presumably, was only referring to a theory about actual evolutionary mechanism, not to the theory that some sort of change over time occurred.  Of course, so rendered, such a theory devoid of mechanism doesn't fit with the umbrage taken over describing neo-Darwinism as "just a theory."

For the sole purpose of false economy of explanation, if there is some evidence of change over time, that is, a presumed relationship of organism A at time X and organism B at time Y, it is presumed that NaturalSelectionDidIt, and any diachronic difference between otherwise similar organisms becomes prima facie evidence of the power of natural selection.

Consider Dr. Paul Nelson's 1995 recollection of an exchange with ardent neo-Darwinist Kenneth Miller (the guy with the mouse-trap tie-clip).
The critical question is one of mechanism. Is it possible for mammals to vary sufficiently for - to take the case of whales - their skulls to be completely remodelled, so that the nostrils (nares) move all the way up to the top of the head? (Indeed, all the other cranial bones must change their size and shape as well.) If not, we're looking at an apparent, not actual, continuum. The designed forms are transformationally discrete, with independent histories. 
That's what I said to Ken, as he was putting away his slides. He replied, "Yeah, Paul, I know, with you it's always 'mechanism, mechanism, mechanism.' But there's more to it than that." 
What the "more" is ain't clear to me.
It isn't clear to a lot of us.  Especially after Eugenie Scott's highly publicized "theometer" comments and the desperate, desperate plea for a mechanism for intelligent design.  Tu quoque?

Back to Prof. James M. Tour:
Although most scientists leave few stones unturned in their quest to discern mechanisms before wholeheartedly accepting them, when it comes to the often gross extrapolations between observations and conclusions on macroevolution, scientists, it seems to me, permit unhealthy leeway. When hearing such extrapolations in the academy, when will we cry out, “The emperor has no clothes!”? 
…I simply do not understand, chemically, how macroevolution could have happened. Hence, am I not free to join the ranks of the skeptical and to sign such a statement without reprisals from those that disagree with me? … Does anyone understand the chemical details behind macroevolution? If so, I would like to sit with that person and be taught, so I invite them to meet with me.
How about Dr. Robert Hazen?  Dr. Hazen co-ao-authored an article with Dr. Jack Szostak on "Functional Information" which had a formula that reminds me wuite a bit of some of Dr. William Dembski's formulas.  Dr. Hazen states:
A fundamental law of nature, the law describing the emergence of complex ordered systems (including every living cell), is missing from our textbooks. 1
Why do Robert Hazen and Stuart Kaufman and so many others think we need to specify another fundamental law of nature when we have a perfectly adequate, fully specified mechanism in NaturalSelectionDidIt?

McCabe complexity of the polymerase machine

Most software engineers have probably heard of McCabe Complexity.  I can't help but wonder how Thomas McCabe would evaluate the complexity of DNA/RNA decoding and transcription process:

He [Thomas McCabe] is taking a much more achievable approach [than attempting to compute the complexity of the cell].  At the risk of oversimplifying his idea, we will say that instead of looking at all the metabolic processes in the cell, he is looking at just one. Specifically, there is a process in living cells that decodes the genetic information in the DNA molecule and builds biological structures accordingly. Conceptually, this process is not much different from the software program in a CD player that reads a compact disk and converts the information into music. Since we can compute the complexity of a program that reads a CD, one should also be able to compute the complexity of the biological process that reads and processes genetic information.
Sounds exciting.
 

Saturday, September 28, 2013

islands of functionality and the flash of genius

Hazen et al illustrate some alternative ideas of functional protein accessibility in protein space, where the plane represents the dimensionality of protein space (2 is much, much fewer than what would be needed) and the E axis represents the catalytic usefulness of the various points in protein space (in essence, a fitness landscape):
D has more of a needle-in-a-haystack problem than A, B, or C, due to its relatively small hypervolume (area in the figure) of protein space.  But it's not the only aspect that makes in inaccessible.  The relative distance from other islands of functionality.  Using the above figure a little out of its intended representation, we see that B and C are relatively close together, so that not as vast a distance of neutral mutation would have to be crossed to get from B to C as from A to D.

But vast oceans of neutral mutation to be crossed are not the only impediment to finding the points of especially high functionality ... There is also the fact that less optimal peaks might serve as attractors that divert computational resources away from the brass ring.  In this case, the good is the enemy of the best.

D of Hazen et al's figure above corresponds to this diagram from one of Douglas Axe's papers, where sequence/protein space is represented by only one dimension:
Here the white noise of suboptimal adaptations might be considered negligible, all of the being more or less neutral in that they don't change the survivability rate of the organisms enough to inhibit the traversal of sequence space.  It is possible that the neutral is filled with many little hills and valleys, a so-called rugged landscape.  In the Picasso-esque landscape below, it may be that the difficulty in finding the high peak of innovation is compunded, both by the volume of sequence/protein space to search but also by the attractive "force" of suboptimal solutions.
The size of the relevant space to be searched along with the distractive force of more accessible (more "obvious") solutions might contribute to the Non-Obviousness of the more optimal solution.

It would seem that both of these have relevance to Bennett's concept of "logical depth", as they both may drive up the necessary computational resources (or, the amount of brute force "tinkering") to realize the non-obvious solution -- where a flash of genius might render all that brute force tinkering unnecessary.  

In Shadows of the Mind, in which Roger Penrose argues for mathematical insight requiring something beyond computation, Penrose has a section on "Things that computers do well -- or badly":
Conscious understanding is a comparatively slow process, but it can cut down considerably the number of alternatives that need to be seriously consideredand thereby greatly increase the effective depth calculation.  
In other words, a flash of insight can cross large distances of "logical depth" a la Charles H. Bennett.  Insight is like a wormhole, a directed wormhole, through solution space.

The Land Bridges of Solution Space


Once upon a time, before the scientific community as a whole really started taking continental drift seriously, doctrine was that flora and fauna distribution was brought about by some sort of land bridge network that spanned the oceans.  There was no evidence for these land bridges other than the terrible need for them to have existed, the explanandum itself.


Now, in sequence space, there is also a terrible need for bridges.  To a certain extant bridges can be made through sequence space, "wormholes" that connect remote regions of the space, but it can be very tricky to make the ends of the wormhole open at useful locations.

One kind of such wormhole, maybe Kenneth Miller's favorite kind, is the frame shift mutation.  Where these wormholes open up is determined by the genetic code itself, but the chances of a useful mutation on one part of sequence space being bridged to a much more useful  (for a completely different purpose) mutation in a remote part of solution space does not seem like something that can be relied upon for a pervasive mechanism.

Crossover is another, more plausible source of wormholes through sequence space.  Again, there is a precipitous element of contingency about this, not about what is predetermined by the genetic code, but in the chances of a useful part of gene P being spliced onto a useful part of gene Q so that gene P'Q' does something that is of significant value to the organism.

As with the land bridges that were presumed ubiquitous (and explanatorily sufficient) before continental drift, the chance in a quintillion bridges between islands of measurable utility in sequence space are evidenced to occur in the right locations and frequency by whatever explanatory gap calls for them to exist.  It is not clear that hyperadaptationists necessarily depend on them (it's all smooth fitness functions like Methinks It Is Like A Weasel), but if they do, you can be sure that all sorts of enzymes can be produced as easily as "nylonase."

Friday, September 27, 2013

NaturalSelectionDidIt


NaturalSelectionDidIt is one of the masterstrokes and trump-cards that Darwinists or other neo-positivists have at their disposal when debating points with skeptics (who they call "deniers") and ID proponents.  It proposes that anything is and was possible because of the omnipotence of natural selection - specifically the ability to bend the laws of time, logic, and physics.  This means that arguments that focus on the feasibility of the de novo ability of microevolution to bring about macroevolution -- the development of complicated body plans or to change an artiodactyl ("no more amphibious than a tapir") into a highly adapted marine mammal -- can be swept away and ignored.

The concept of NaturalSelectionDidIt can be used to create unfalsifiable* theories. A neo-Darwinist need never doubt the creative power of chance and selection because Natural Selection could have made anything that was made.  (What is the proof that Natural Selection can do it? -- why, the fact that it was done!)  It may also be used as a euphemism to indicate something that cannot be explained in terms of natural laws, most likely due to having no idea how evolution works anyway.)


This was inspired by the Goddidit entry at RationalWiki.  :-)







antibiotic resistance: is evolution a fact?

Sometimes an ID proponent gets caught up in hyper-adaptationists' conflation of evolution with Darwinism, that he/she starts to borrow the use of "evolution" as a shorthand for neo-Darwinism.  Descent with modification, on one hand, has a compelling case that can be made for it, much more compelling than neo-Darwinism, and I'm not sure how much more compelling the case for DwM has been made since Darwin made it, but it is still compelling.  What it means is another story entirely, and there are many ways to get descent with modification.  For example, Michael Behe believes so many mainstream things about evolution that it seems utterly absurd to call him a creationist -- I'd say, it is absurd for any other reason than a political one, and I'm sure there are some obvious political reasons for Eugenie Scott and Barbara Forrest to call him a creationist.   However, Behe essentially believes in descent with modification and in some version of common ancestry.

So on the one hand, I would prefer ID proponents not get caught up in the game of "Duck Season, Rabbit Season" and use "evolution" as a shorthand for undirected evolution with complexity built via natural selection.  Evolution is so vague to be almost a useless word in biology except for the most general concept of apparent vast changes of ecosystems over the billenia.

Still, the vast awe-inspiring wisdom of Judge Jones the Third notwithstanding, those that are less than impressed with DwM often make good points themselves, and unlike Dawkins and others like him infected with The Smug, I think they often make good points.

On that note, from "Is Evolution A Fact":
Nobel laureate Sir Ernest Chain (credited with purifying penicillin in a way that made it possible to employ it as an antibiotic) wrote in agreement.  
To postulate that the development and survival of the fittest is entirely a consequence of chance mutations seems to me a hypothesis based on no evidence and irreconcilable with the facts. These classical evolutionary theories are a gross oversimplification of an immensely complex and intricate mass of facts, and it amazes me that they are swallowed so uncritically and readily, and for such a long time, by so many scientists without a murmur of protest” (1970, p. 1, emp. added).
Now consider Sir Chain's statement as you read this bit of Doonesbury satire:


I don't understand.  How did Sir Chain do any science with penicillin without true belief in natural selection?  He isn't a true believer like cartoonist Gary Trudeau.  Trudeau has the sense to believe in antibiotics.   Actually, exactly how do we treat resistant strains other than just trying different antibiotics until we find one to which the strain isn't resistant?  Exactly how did neo-Darwinism.  How does Fisher's mathematics guide my primary care physician's choice of antibiotics?  Trudeau seems to know.

Although Trudeau seems to actually believe the false dichotomy between neo-Darwinism and Biblical literalism, and he seems completely unaware of the difference between microevolution and macroevolution. (Once you have an idea of artificial selection--as any ancient animal breeder would--does antibiotic resistance really seem counter-intuitive?)   But he is a cartoonist, and he seems bursting with pride over his anti-religious sensibilities.  So believe like Trudeau.

Dr. Sean D. Pitman in "Stepping Stones" offers a meaningful explanation:
In the case of de novo antibiotic resistance, such rapid evolution is made possible because there are so many beneficial "steppingstones" so close together, right beside what the bacterial colony already has. Success is only one or two mutational steps away in many different directions since a multitude of different single mutations will result in a beneficial increase in resistance. How is this possible? 
In short, this is made possible because of the way in which antibiotics work. All antibiotics attack rather specific target sequences inside certain bacteria. Many times all the colony under attack has to do is alter the target sequence in just one bacterium by one or two genetic "characters" and resistance will be gained since the offspring of this resistant bacterium, being more fit than their peers, will take over the colony in short order. A simple "spelling change" made the target less recognizable to the antibiotic, and so the antibiotic became less effective. In other words, the pre-established antibiotic- target interaction was damaged or destroyed by one or two monkey-wrench mutations. As with Humpty Dumpty and all the king's men, it is far easier to destroy or interfere with a pre-established function or interaction than it is to create a new one, since there are so many more ways to destroy than there are to create.

Here is an interesting statement as well by Prof. James M. Tour:
Let me tell you what goes on in the back rooms of science – with National Academy members, with Nobel Prize winners. I have sat with them, and when I get them alone, not in public – because it’s a scary thing, if you say what I just said – I say, “Do you understand all of this, where all of this came from, and how this happens?” Every time that I have sat with people who are synthetic chemists, who understand this, they go “Uh-uh. Nope.” These people are just so far off, on how to believe this stuff came together.  I’ve sat with National Academy members, with Nobel Prize winners. Sometimes I will say, “Do you understand this?”And if they’re afraid to say “Yes,” they say nothing. They just stare at me, because they can’t sincerely do it. 
I was once brought in by the Dean of the Department, many years ago, and he was a chemist. He was kind of concerned about some things. I said, “Let me ask you something. You’re a chemist. Do you understand this? How do you get DNA without a cell membrane? And how do you get a cell membrane without a DNA? And how does all this come together from this piece of jelly?” We have no idea, we have no idea. I said, “Isn’t it interesting that you, the Dean of science, and I, the chemistry professor, can talk about this quietly in your office, but we can’t go out there and talk about this?”
I don't understand.  I thought evolution was so simple that even a million monkeys sitting at typewriters could understand it...  !!!   Maybe Prof. Tour has a science-poor background.
Professor James M. Tour is one of the ten most cited chemists in the world. He is famous for his work on nanocars (pictured above, courtesy of Wikipedia), nanoelectronics, graphene nanostructures, carbon nanovectors in medicine, and green carbon research for enhanced oil recovery and environmentally friendly oil and gas extraction. He is currently a Professor of Chemistry, Professor of Computer Science, and Professor of Mechanical Engineering and Materials Science at Rice University. He has authored or co-authored 489 scientific publications and his name is on 36 patents. Although he does not regard himself as an Intelligent Design theorist, Professor Tour, along with over 700 other scientists, took the courageous step back in 2001 of signing the Discovery Institute’s “A Scientific Dissent from Darwinism”
What a dunce!  I don't know.  I think Prof. Tour just can't grasp a heady concept like macroevolution through natural selection.  No doubt explainable by the Salem Hypothesis.

Thursday, September 26, 2013

insights from directed evolution

Is their any reason for using the term "directed evolution" instead of the old "artificial selection"?  Well, "natural selection" was an analogy to "artificial selection" -- and the analogies in evolutionary computing continue.  The term "directed evolution" attempts to reverse this and treat "undirected evolution" as the original inspiration and merely be a speeding up of the natural process.

However, "directed evolution" of necessity must, to be effective in a large number of cases, involve a means of skipping between the islands of functionality in protein space:
Though mutation and screening is the essence of directed evolution, there are many factors that combine to turn the process into as much of an art as a science. These considerations include initial protein choice, mutant library construction, and method of screening.(here)
Initial protein choice: starting off the process at a point that is likely to get you what you want, a key location in what you hope is an archipelago of related functionality.  Mutant library construction: this is actually the method for not being bogged down by the typical Darwinian problems with searching nucleotide sequence space -- the sort Michael Behe discusses at length in The Edge of Evolution.  Method of screening:  In natural selection, nature is a terrible screener for the once-in-100-millenia innovation.  Just because an organism has a prize-winning genetic innovation, this doesn't mean that the noise in the innovation-detection system won't overwhelm it.  The survival/reproductive advantage may be washed out in the collective effect on survival, not the least of which is natural danger.  Walk by a tiger, and the innovation may be lost to bad luck, and there is no shortage of this sort of bad luck in the natural world.  So a protein engineer must have a better detection system, in order to ensure that he recognizes what he's looking for once it appears.

Wednesday, September 25, 2013

Colin Patterson questions biologists on evolution

Colin Patterson's question to biologists:
...I mentioned a question ('Can you tell me anything you know about evolution?') that I have put to various biologists, and an answer that had been given: 'I know that evolution generates hierarchy.' In the framework of phylogenetic reconstruction and our current problems with it, another answer comes to mind: 'I know that evolution generates homoplasy' [or "convergence," in the older jargon of systematics]. In both cases, the answer is not quite accurate. It would be truer to say, 'I know that evolution explains hierarchy' or 'I know that evolution explains homoplasy.' We must remember the distinction between the cart--the explanation--and the horse--the data. And where models are introduced in phylogenetic reconstruction, we should prefer models dictated by features of the data to models derived from explanatory theories.
Careful there, Patterson.  You are starting to sound like a secular creationist.

Saturday, September 21, 2013

not only unwelcome but unneeded

Berlinski:
My own view, repeated in virtually all of my essays, is that the sense of skepticism engendered by the sciences would be far more appropriately directed toward the sciences than toward anything else. It is not a view that has engendered wide-spread approval. The sciences require no criticism, many scientists say, because the sciences comprise a uniquely self-critical institution, with questionable theories and theoreticians passing constantly before stern appellate review. Judgment is unrelenting. And impartial. Individual scientists may make mistakes, but like the Communist Party under Lenin, science is infallible because its judgments are collective. Critics are not only unwelcome, they are unneeded. The biologist Paul Gross has made himself the master of this attitude and invokes it on every conceivable occasion. 
Now no one doubts that scientists are sometimes critical of themselves. Among astrophysicists, backbiting often leads to backstabbing. The bloodletting that ensues is on occasion salutary. But the process of peer review by which grants are funded and papers assigned to scientific journals, is, by its very nature, an undertaking in which a court reviews its own decisions and generally finds them good. It serves the useful purpose of settling various scores, but it does not -- and it cannot -- achieve the ends that criticism is intended to serve. 
If the scientific critic finds himself needed wherever he goes, like a hanging judge he finds himself unwelcome wherever he appears, all the more reason, it seems to me, that he really should get around as much as possible.
[Emphasis mine]  From The Deniable Darwin


Thursday, September 19, 2013

diffusion through conformational space?


http://link.springer.com/static-content/lookinside/371/art%253A10.1007%252FBF00163809/000.png

Protein evolution as diffusion through conformational space?

Shouldn't it be diffusion through typographical space?

Another thing:  If it is an easy thing to make a protein for any particular effect, why isn't it exceptionally easy to make a protein that really gums up the works?  either ties itself into a useless little knot or turns into something that binds with all sorts of things it shouldn't and kills its organism (slowly or quickly)?

But then again maybe it isn't that easy:
The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions1234. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: ~98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, ~3.5×109yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.