Q. I wonder what open problems there are in bioinformatics/computational
biology? Which tasks are in need of an effective computer algorithm?

A. How to get biologists to write down their experimental procedures
before they begin an experiment.  This may be too hard to be
solved this century.

 | The study of tractability, and of universal systems, received its
 | impetus from an investigation of biological fractionation
 | procedures.  It would not have arisen from physics, which expects
 | its theories to be couched in forms of tractable systems rather
 | than statements of general interaction (the heart of intractability).
 | Indeed, it might not be amiss to consider biology as the physics of
 | intractable systems.  If this is so, then far from physics swallowing
 | up biology, the situation may well be the other way around.
 | Our analysis of the reductionist hypothesis has thus shown the
 | fertility of biology in generating important new insights in
 | mathematics in the sciences --though doubtless in a way different
 | from what was orignially intended.
Robert Rosen, "On Mathematics and Biology" in _The Sprit and the
Uses of the Mathematical Sciences_, Saaty & Weyl, editors, Mcgraw-
Hill, 1969 p. 209

20 years later:
 | One of the few physicists to recognize that the profound silence of
 | contemporary physics on matters biological was something *peculiar*
 | was Walter Elsasser.  To him, this silence was itself a physical
 | fact and one that required a physical explanation.  He found one by
 | carrying to the limit the tacit physical supposition that, because
 | organisms seem *numerically* rare in the physical universe, they
 | must therefore be too special to be of interest as material systems.
 | His argument was, roughly, that anything rare disappears completely
 | when one takes averages;  since physicists are always taking
 | averages in their quest for what is generally true, organisms sink
 | completely from physical sight.  His conclusion was that, in a
 | material sense, organisms are governed by their own laws ("biotonic
 | laws"), which do not contradict physical universals but are simply
 | not derivable from them.
 | Ironically, ideas like Elsasser's have not had much currency with
 | either physicists or biologists, although one might have thought
 | they would please both.   Indeed, in the case of the former,
 | Elsasser was only carrying one step further the physicists' tacit
 | supposition that "rare" implies "nonuniversal."
 | The possibility is, however, wide open that this supposition
 | itself is mistaken.  On the face of it, there is no reason at all
 | why "rare" should imply anything at all; it needs to be nothing
 | more than an expression on how we are sampling things, connoting
 | nothing at all about the things themselves.  Even in a humble and
 | familiar areas like arithmetic,  we find inbuilt biases.  We have,
 | for instance, a predilection for rational numbers, a predilection
 | that gives them a weight out of all proportion to their actual
 | abundance.  Yet in every mathematical sense, it is the rational
 | numbers that are rare and very special indeed.   Why should it
 | not be so with physics and biology?  Why could it not be that
 | "universals" of physics are only so on a small and special (if
 | inordinately prominent) class of material systems, a class to
 | which organisms are too *general* to belong? What if physics is
 | the particular, and biology the general, instead of the other way
 | around?
Robert Rosen, _Life Itself_, Columbia 1991, ISBN 978-0-231-07565-7,
pp. 12-13.

cf. http://en.wikipedia.org/wiki/Walter_M._Elsasser

 | Inferences of science and common sense differ from
 | those of deductive logic and mathematics in a very
 | important respect, namely, when the premises are 
 | true and the reasoning correct, the conclusion is
 | only probable.
Bertrand Russell,_Human Knowlege: Its Scope and Limits_, Routledge,
London, p. 353, 1948

I would interpret it this way:  within a formal system certain
conclusions are *syntactically* true because all semantics
have been stripped from the system and the production rules
move from axioms to theorems without interference.  Both
Science and Common Sense involve a mapping of relations
among external events to an internal representation.  Drawing
inferences based on our internal representation of our chronicles
of external phenomena *is* semantics and not only is it fuzzy,
it requires a leap of, well, ... okay, let's not go there
because it will blow your circuit breakers.

In the formal system 'truth' just means that you didn't screw
up the production rules [en attendant Godel].

 | Then the female embarks on the next part of her journey
 | - the search for a live cicada. Once locating her quarry,
 | the female captures the cicada in her long legs and
 | injects venom using her large stinger. The paralyzed
 | cicada is then transported back to the awaiting burrow.
 | The cicada is shoved into the hole and the female wasp
 | lays a single egg under one of the middle legs.
 | Within about two weeks the egg hatches into a larva and
 | has all the sustenance it needs to grow, supplied by the
 | paralyzed, still-living cicada. Growing to full size
 | within a week's time the larva will spin a silken and mud
 | cocoon where they remain protected underground throughout
 | the winter.

 | Some years later Szent-Gyorgyi wrote about the naming
 | of his newly found substance that "I called it 'ignose',
 | not knowing which carbohydrate it was.  This was turned
 | down by my editor.  'God-nose' was not more successful,
 | so in the end 'hexuronic acid' was agreed upon.  Today
 | the substance is called ascorbic acid"
Joseph S. Fruton, _Proteins, Enzymes, Genes_, p.280,
1999, Yale University Press

Fruton ends the section on Thermochemistry and Thermodynamics
in this manner: 
 | Some readers may deplore my omission of mention of the
 | contributions of Clerk Maxwell and Ludwig Boltzmann to
 | the statistical interpretation of Clausius's thermodynamics,
 | or those of the founders of quantum theory and quantum mechanics
 | in the furter development of thermodynamic theory.  The 
 | significance of these contributions to theoretical and
 | experimental physics is undeniable, but thus far their role
 | in the interplay of chemistry and biology has been rather 
 | limited, with more inpact in the realm of discourse than of
 | experimentaion.  In particular, much has been made in recent
 | decades of the relation of entropy (or "negentropy") to
 | "disorder" or of "information" to the question "what is life?"
J. Fruton, _Proteins, Enzymes, Genes_, p.254, Yale University, 1999

This is eerily reminiscent of Robert Rosen's quote posted here
a month or two ago, that Biology is the Physics of intractable

<_Treasury of Philosophy_, Dagobert Runes, Editor,
Philosophical Library, 1955  has short excerpts from
hundreds of philosophers arranged in alphabetical order.
The Table of Contents gives the years of birth and death,
where known.  Here are those years for all of the A's and B's
arranged in chronological order by year of birth.  Third
column is the lifespan.  (- indicates B.C.)
-610	-547	63
-585	-525	60
-563	-483	80
-500	-428	72
-445	-365	80
-435	-366	69
-384	-322	62
-315	-240	75
121	180	59
354	430	76
475	524	49
735	804	69
870	950	80
979	1037	58
1033	1109	76
1059	1111	52
1079	1142	63
1091	1153	62
1126	1198	72
1193	1280	87
1214	1294	80
1221	1274	53
1225	1274	49
1380	1445	65
1437	1508	71
1460	1530	70
1548	1600	52
1561	1626	65
1575	1624	49
1590	1647	57
1685	1753	68
1700	1760	60
1729	1797	68
1735	1826	91
1738	1789	51
1748	1832	84
1765	1841	76
1781	1848	67
1799	1888	89
1807	1885	78
1813	1887	74
1814	1876	62
1815	1864	49
1818	1897	79
1828	1920	92
1835	1902	67
1837	1921	84
1838	1917	79
1843	1896	53
1845	1921	76
1846	1924	78
1847	1910	63
1848	1923	75
1850	1928	78
1851	1933	82
1856	1941	85
1859	1938	79
1859	1941	82
1869	1944	75
1870	1937	67
1872	1950	78
1874	1948	74

Stewart Brand interviews Margaret Mead and Gregory Bateson:
 | ...
 | B: No, structurally related, that there was a subject 
 | matter of inquiry defined by all these. You see the 
 | fantastic thing is that in 1856, before the publication of 
 | the Origin of Species, Wallace in Ternate, Indonesia, had a 
 | psychedelic spell following his malaria in which he 
 | invented the principle of natural selection. He wrote to 
 | Darwin and he said, 'Look, natural selection is just like 
 | a steam engine with a governor.' The first cybernetic 
 | model. But then he only thought he had an illustration, he 
 | didn't think he'd really said probably the most powerful 
 | thing that'd been said in the 19th Century.
 | M: Only nobody knew it.
 | B: Nobody knew it. And there it is, still in the text. 
 | Nobody picked it up. Well, there was the machinery, the 
 | governor itself. There was the mathematics of the machine 
 | with the governor, which was done by Clerk Maxwell in 1868, 
 | because nobody knew how to write a blueprint for these 
 | bloody things - they would go into oscillation. Then 
 | there's Claude Bernard about 1890 with the milieu interne - 
 | the internal matrix of the body, control of temperature, 
 | control of sugar, and all that.
 | SB: Which later became homeostasis?
 | B: Which later became homeostasis in Cannon. But nobody 
 | put the stuff together to say these are the formal 
 | relations which go for natural selection, which go for 
 | internal physiology, which go for purpose, which go for a 
 | cat trying to catch a mouse, which go for me picking up the 
 | salt cellar. This was really done by Wiener, and 
 | Rosenblueth and McCulloch and Bigelow. And who really put 
 | the truth through, I don't know, do you?
 | M: No. Wiener and McCulloch were first partners in this 
 | thinking, and then became rivals when McCulloch went to 
 | MIT. As long as McCulloch stayed at Illinois and Wiener at 
 | MIT they were working right together. With both of them at 
 | the MIT they became totally alienated, and then Walter 
 | Pitts got involved. He was the youngest member of the group.
 | B: Oh god, he was so clever. You'd set him a problem, you 
 | know, and he would reach up to his hair and take a couple 
 | of strands, and he would say, 'Well, now, if you say 
 | that, you see, um, no then, you see,' and he'd work it all 
 | out with his hair.
 | M: He was a very odd boy. Now, one of the important points 
 | at this stage was one that Gregory kept making, that a 
 | possible cross-disciplinary mathematical language was 
 | available. We never got very far with that because all you 
 | could ever get out of people like Wiener was, 'You need a 
 | longer run.' We used to drive them absolutely out of their 
 | minds because they were not willing to look at pattern, 
 | really. What they wanted was a terribly long run of data.
 | B: Of quantitative data, essentially.
 | M: Quantitative data, and we never got them really to look 
 | at the problem of pattern. Von Neumann came the closest to 
 | it.
 | ...

 | It is a characteristic of the design of scientific
 | research that exquisite attention is devoted to
 | methodological problems that can be solved, while
 | the pretense is made that the ones that cannot be
 | solved are really nothing to worry about.  On the
 | one hand, biologists will apply the most critical
 | and demanding canons of evidence in the design of
 | measuring instruments or in the procedure for taking
 | a unbiased sample of organisms to be tested, but
 | when asked whether the conditions in the laboratory
 | are likely to be relevant to the situation in nature,
 | they will provide a hand-waving intuitive argument
 | filled with unsubstantiated guesses and prejudices
 | because, in the end, that is all they can do.
Richard Lewontin, _It Ain't Necessarily So, The Dream of the
Human Genome and Other Illusions_, p.237, ISBN 0-940322-10-2

Vampyrella lateritia sucks chloroplasts from algal victim:

Don't worry, the following will all be clarified by UML
release 100000000.1 sometime around the entropic heat
death of the universe (nb. the filopodia/pseudopodia of
V. lateritia do *not* anastomose, unlike most(?) other
 | Vampyrella has a cell body which is often spherical. The 
 | taxonomy of the genus has been confused in the past, as 
 | early observers may have had mixed cultures and confused 
 | the life cycles of contaminant organisms with the amoeba 
 | being studied. Confusion exists concerning the taxonomy of 
 | V. lateritia (Fresenius) Leidy, 1879. According to Gobi in 
 | 1915, V. spirogyra Cienkowski, 1865 is identical to Amoeba 
 | lateritia Fresenius, 1856 and therefore should retain the 
 | species name. Leidy in 1879 described Vampyrella lateritia 
 | as an independent species,
 | which, in the view of Hoogenrad in 1907 was identical to V. 
 | spirogyrae of Cienkowski. However, Gobi considered that V. 
 | lateritia of Leidy and of Hoogenrad was not a Vampyrella at 
 | all but Gobiella borealis of Cienkowski (quoted by Gromov, 
 | 1976). Gobi also questions that validity of other 
 | Vampyrella species. This gives an idea of the confused 
 | state of the taxonomy of the genus as a whole. The feeding 
 | of Vampyrella has been observed to be either by ingestion 
 | of smaller algae or by penetration of filamentous algae. V. 
 | lateritia feeds by penetration of filamentous algae by 
 | filopodia (Cienkowski 1865; Leidy 1879; West 1901; Cash 
 | 1904). Other species of Vampyrella reported as feeding by 
 | penetration are: V. closterii Poisson & Mangenot, V. 
 | incolor Bruyne, V. intermis Klein, V. multiformis Zopf, V. 
 | pedata Klein, V. pedula Cienkowski, V. ulothricus 
 | Scherffel, V. variabilis Klein, and V. velata Gobi. Species 
 | reported as feeding by ingestion are: V. vorax Cienkowski,
 | V. flabellata Cash, V. gomphoneinatis Haeckel, V. 
 | polyblasta Sokokin, V. pallida Mobius, V. radiosa Penard, 
 | V. agilis Penard, V. atheyae Zyloff, and V. gromata Alen. 
 | If these feed by ingestion only, and not by penetration, 
 | they would appear not to belong to the genus Vampyrella but 
 | to one of the genera of Nucleariidae. Since penetration of 
 | food organisms has been observed to a large extent in 
 | Vampyrella it is not intended to include the genus in the 
 | new family Nucleariidae, but to retain a separate family 
 | Vampyrellidae for Aconchulinida feeding at least in part by 
 | penetration of algal cells. The filopodia of Vampyrella 
 | frequently start from a common basis, and may fork but do 
 | not anastomose (West 1903). The filopodia of V. lateritia 
 | may project from a small portion or from the entire surface 
 | of the body (Leidy 1879). It was not recorded however under 
 | what conditions the cells were being examined. The presence 
 | of what could have been external bacteria was noted by Leidy
 | in 1879. He described them being like "suctorial rays, 
 | pin-like, projecting from any part or the whole of the cell 
 | surface at once". However he went on to say that they were 
 | successively projected and withdrawn very quickly, whilst 
 | the longer rays (filopodia) were sometimes seen to vibrate. 
 | These observations are similar to those of Nucleosphaerium, 
 | but the bacteria did not move on their own accord, and were 
 | readily detached under the cover slip. The filopodia did 
 | not vibrate, but were slowly extended and withdrawn. 
 | Hyaline spheres were observed to run over the filose 
 | pseudopodia of Vampyrella (Penard, 1889). Spheres of the 
 | same sort were observed in Nucleosphaerium. (ref. ID; 4670)

 | The Chink in the Armor = the bacterial cell wall
 | The beta-lactams all work by interfering with the synthesis 
 | of the bacterial cell wall -- a structure that is not found 
 | in eukaryotes. The walls of bacteria are made of a complex 
 | polymeric material called peptidoglycan. It contains both 
 | amino acids and amino sugars. The amino sugars are of two 
 | kinds
 |     * N-acetylglucosamine (NAG) and its close relative
 |     * N-acetylmuramic acid (NAM).
 | These two form a linear polymer of NAG alternating with 
 | NAM. They are linked by a glycosidic bond between the #1 
 | and #4 carbons (this is the linkage attacked by lysozyme) 
 | and are oriented in the same way they are in cellulose. 
 | Side chains containing 4 or 5 amino acids are attached to 
 | each NAM. These form covalent bonds with amino acids in 
 | adjacent chains. The bonds may
 |     * be direct to the next chain or
 |     * include additional peptide cross bridges (e.g., 5 
 |       glycine residues) which
 |     * extend to chains in the same plane (shown here) as 
 |       well as to chains above and below. 
 | This elaborate, covalently cross-linked structure provides 
 | the great strength of the cell wall. It also leads to the 
 | remarkable conclusion that the bacterial cell wall meets 
 | the definition of a single molecule!
 | The beta-lactam antibiotics bind to and inhibit enzymes 
 | needed for the synthesis of the peptidoglycan wall. While 
 | they have little effect on resting bacteria, they are 
 | lethal to dividing bacteria as defective walls cannot 
 | protect the organism form bursting in hypotonic 
 | surroundings. 

 | The matter of copepods in the water supply, however, has raised a
 | peculiar problem for Jews who observe Kashrut in that copepods,
 | being crustaceans, are not kosher, and are not small enough to be
 | ignored as non-food microscopic organisms (since some specimens
 | can be seen with the naked eye). The discovery of copepods in the
 | New York water supply in the summer of 2004 in particular caused
 | significant debate in rabbinical circles and caused many observant
 | Jews to buy filters for their water.

 | What we can say, however, about the relation between
 | protozoa and neurons turns out to be far more important
 | than what we cannot.  The reciprocal comparison of the
 | two casts a unique light on each.  Neurons are protozoa
 | specialized with respect to their motile sensitivity to
 | a surround, as Binet first said.  The action potential
 | of the neuron is a protozoan movement, but one transferred
 | between now stationary neurons to generate pooled fields
 | of sentience and reactivity.  Graded depolarizations in
 | protozoa would constitute a readiness for movement, which,
 | in the full context of protozoan behaviors, can be a part 
 | either of approach or of avoidance patterns.
 | Hyperpolarizations are part of a "still" phase, showing
 | perhaps the beginnings of a separable capacity for
 | sentience, and one that is again potentially bivalent.
 | Receptor and compensatory hyperpolarization potentials
 | of protozoa would then be transducing gradients of
 | "outer" flow into an "inner" perceptual resonance and
 | proprioception.
Harry T. Hunt,_On the Nature of Consciousness: Cognitive,
Phenomenological, and Transpersonal Perspectives_, Yale
University Press, 1995, p.105 

 | Consider Sacculina which is a parasite of the blue crab and 
 | the green crab. The larval female enters the crab's body at 
 | a joint and then migrates to the genitalia under the 
 | genital flap and begins to grow, forming an orangish sac. 
 | It feeds by producing a network of root-like structures 
 | that eventually extend through the body and even into the 
 | eye stalks. Remarkably, it doesn't actually kill the crab, 
 | but it does neuter it so that it can no longer reproduce 
 | and it effectively turns the crab into a "zombie" allowing 
 | it to continue to feed and move so that the parasite can 
 | continue to survive. Here is a real-life instance of an 
 | Invasion of the Body Snatchers. This strange orange blob 
 | with an intricate network of feeding "rhizopodia" turns 
 | out, astonishingly, to be a barnacle.

 | Erythropsidinium (Gymnodiniales, Dinophyceae) in the Pacific Ocean,
 | a unique dinoflagellate with an ocelloid and a piston.
 | ...

Wait!  There's a movie!
Click "piston Erythropsidinium" at:
Safe for work, but just barely.

BTW, dinoflagellates have only one cell (zero cells --acellular--
according to some).

 | One should tackle a problem only when its solution seems
 | trivially easy, it will then turn out to be just at the
 | limits of the manageable; when it appears more difficult,
 | trying to solve it is usually a hopeless undertaking.
Eugene Wigner to Walter M. Elsasser 

 | If we may be allowed to add another image to the many by which
 | Bergson's philosophy is illustrated, we may say that the universe
 | is a vast funicular railway, in which life is the train that goes
 | up, and matter is the train that goes down.  The intellect consists
 | in watching the descending train as it passes the ascending train 
 | in which we are.  The obviously nobler faculty which concentrates
 | its attention on our own train is instinct or intuition.  It is
 | possible to leap from one train to the other;  this happens when we
 | become the victims of automatic habit, and it the essence of the
 | comic.  Or we can divide ourselves into parts, one part going up
 | and one down;  then only the part going down is comic.   But
 | intellect is not itself a descending notion, it is merely an
 | observation for the descending motion by the ascending motion.
B. Russell, _A History of Western Philosophy_, Simon and Schuster,
1945, pp.794,795 

 | Recall now in what the Cartesian Method consists:  It claims that 
 | one should deal with complex systems by analyzing them into smaller
 | and simpler components and study these components individually,
 | putting them mentally together again at the end.  Clearly, the
 | Cartesian Method fails, and does so not by accident but because it
 | is inadequate, in the case of complementary relationships: It is
 | intrinsically impossible to apply the Cartesian Method successfully
 | to the case of quantum-mechanical complementarity.
Walter M. Elsasser, _Reflections on a Theory of Organisms_, 1987, p.101 

 | Objects Have Failed
 | (Opening remarks by Richard P. Gabriel, OOPSLA, November 6, 2002)
 | What can it mean for a programming paradigm to fail? A paradigm fails
 | when the narrative it embodies fails to speak truth or when its
 | proponents embrace it beyond reason. The failure to speak truth
 | centers around the changing needs of software in the 21st century
 | and around the so-called improvements on OO that have obliterated its
 | original benefits. Obsessive embrace has spawned a search for purity
 | that has become an ideological weapon, promoting an incremental
 | advance as the ultimate solution to our software problems. The effect
 | has been to brainwash people on the street. The statement "everything
 | is an object" says that OO is universal, and the statement "objects
 | model the real world" says that OO has a privileged position. These
 | are very seductive invitations to a totalizing viewpoint. The result
 | is to starve research and development on alternative paradigms.
 | ...

1859 Darwin: Origin of Species

1865 Mendel: Experiments on Plant Hybridization (Mechanism of heredity)

1891 Dubois: Discovery of Java Man (Descent of Man)

1896 Becquerel: Discovery of Radioactivity (Age of the Earth)

 | But the acrosomal process of Limulus, the horseshoe crab,
 | is premade and much more tightly bundled.  A bundle of 
 | actin filaments some 60 um long, and cross-linked by a 
 | distinctive bundling protein called scruin, lies coiled
 | up around the base of the head of the unreacted sperm.
 | Contact with the egg causes the actin filaments in the
 | bundle to change their relative packing, probably
 | triggered by a calcium-induced change in conformation
 | of scruin.  The bundle uncoils and extends, causing the
 | process literally to screw itself into the egg jelly.
Bray, Dennis. _Cell Movements: From Molecules to Motility_,
Garland, 2001, p.95 

 | On the 20th anniversary of the identification of the cystic
 | fibrosis gene, as new gene discoveries pile up weekly and
 | hype over the power of genes to transform medicine flows
 | fast, CF offers an object lesson in how difficult it is,
 | and how long it takes, to convert genetic knowledge into
 | treatments. Every CF expert agrees that the gene discovery
 | transformed their understanding of the disease's pathology.
 | But even after so much hard work, not a single therapy
 | based on the CF gene has reached the market. Some promising
 | treatments, especially gene therapy, have proven bitterly
 | disappointing.

 | These  questions are but a sample of possible ways in which
 | behavior on the cell level might be investigated in a form so
 | amenable to operation as Stentor.  Might the neurone itself, then
 | be capable of considerably more "behavior" than mere
 | "excitation", realizing as part of the nervous system something
 | of the potentialities which have been evolved in a different manner
 | but from the same cellular origins, in ciliates. 
Tartar, V., _The Biology of Stentor_, Pergammon, 1961, p. 27 

Bacteria range in size over three orders of magnitude but the
"average" bacterium is much smaller than the average eukaryotic
(human) cell.  Interestingly, mitochondria show only a single
order of magnitude variation across all cells.

 | My own scientific career was a descent from higher to lower
 | dimension, led by the desire to understand life.  I went
 | from animals to cells, from cells to bacteria, from bacteria
 | to molecules, from molecules to electrons.  The story had
 | its irony, for molecules and electrons have no life at all.
 | On my way life ran out between my fingers.
Nobel Laureate Albert Szent-Gyorgi, _The Living State, With
Observations on Cancer_ 

 "If you can't solve a problem, then there is an easier problem you
  can solve: find it."  -- George Pólya, Hungarian mathematician

 | Science is built on the premise that Nature answers
 | intelligent questions intelligently; so if no answer
 | exists, there must be something wrong with the question.
    --Albert Szent-Gyoergyi, Hungarian Physiologist

 | In human beings, the commensal bacterial flora in the gut consists
 | of a diverse set of microorganisms (up to 500-1,000 species),
 | amounting to about 10^14 bacteria and weighing a total of 1.5 kg.

 | Overuse of CT scans will lead to new cancer deaths, a study shows
 | Each year that today's scanners are used, 14,500 deaths could result,
 | researchers say. When healthy people are exposed to the radiation,
 | the imaging may create more problems than it solves.
 | ...

 | Dualist doubletalk
 | Dualism is often contrasted with physicalism. But modern
 | physics is rampantly dualist. An ice crystal is an
 | aggregate of fermions that exclude other fermions from
 | their space (have extension). It is also a force field of
 | bosons, which do not. To say that it is both (Descartes')
 | res extensa and res cogitans is not far off, (although
 | admittedly not quite how he saw it). Descartes included
 | bosons (light) in res cogitans if I remember. The
 | relationship between the fermions and the bosons is not
 | causal; they are two sides of a single state.
 | Physics is also dualist in that it requires us to consider
 | things as observers OR observables. Observers cannot be
 | described by the laws of observables. The trouble is that
 | physics has hardly got started with the description of
 | observers; except that they can only be in one place at a
 | time, as observers, or they would violate special
 | relativity. The physicists have left it to the biologists,
 | who think they are following the physicists' instructions! 

"All this has been said before--but since nobody listened,
it must be said again."  (Andre Gide?)

Morning Glories reach out and touch someone.
42 second stop-action video:

"The art of medicine consists in amusing the patient
while nature cures the disease." --Voltaire

Subject: Today's German Word "Schmutzdecke"

A slime layer that forms in the top of a sand filter-bed
without which the bacteria in water cannot be removed.
It is composed primarily of extensive colonies of
vorticellids, single-celled organisms which keep fresh
water fresh.

"One can best feel in dealing with living things
how primitive physics still is."

Ronald W. Clark, _Einstein: the life and times_, 1984, p. 34

 | To conclude, it must not be thought that a linear structure
 | is necessary for storing or transmitting information (or,
 | more precisely, significance); it is possible that a
 | language, a semantic model, conisting of topological forms
 | could have considerable advantages, from the point of view
 | of deduction, over the linear language that we use,
 | although this idea is unfamilar to us.  Topological forms
 | lend themselves to a much richer range of combinations,
 | using topological products, composition, and so on, than
 | the mere juxtaposition of two linear sequences.
Rene' Thom, _Structural Stability And Morphogenesis_, 1975, p.145 

 | Metaphors allow us to rephrase the new and puzzling in terms
 | of the homely and familiar, and so provide a staircase for
 | the mind to climb
Franklin M. Harold, _From morphogenes to morphogenesis_, 
Microbiology (1995), 141,2765-2778 

 | ... 
 | Reductionism versus Reductionism
 | We cannot proceed further without clarifying and discussing
 | what is meant by reductionism. The stakes here are high
 | because the concept is deeply woven into the fabric of
 | modern biology, and biology today has hit the wall of
 | biocomplexity, reductionism's nemesis. Thus, a topic that
 | previously had been left for the philosophers and
 | scientific dilettantes has suddenly become a very real and
 | global issue for the practicing biologist. "Reductionism"
 | is a confused and cathected issue at the moment, in large
 | measure because biologists use the term in two senses,
 | usually without distinguishing them. This we now have to
 | do. We need to distinguish what can be called "empirical
 | reductionism" from "fundamentalist reductionism." Empirical
 | reductionism is in essence methodological; it is simply a
 | mode of analysis, the dissection of a biological entity or
 | system into its constituent parts in order better to
 | understand it. Empirical reductionism makes no assumptions
 | about the fundamental nature, an ultimate understanding, of
 | living things. Fundamentalist reductionism (the
 | reductionism of 19th century classical physics), on the
 | other hand, is in essence metaphysical. It is ipso facto a
 | statement about the nature of the world: living systems
 | (like all else) can be completely understood in terms of
 | the properties of their constituent parts. This is a view
 | that flies in the face of what classically trained
 | biologists tended to take for granted, the notion of
 | emergent properties. Whereas emergence seems to be required
 | to explain numerous biological phenomena, fundamentalist
 | reductionism flatly denies its existence: in all cases the
 | whole is no more than the sum of its parts. Thus, biology
 | of the 20th century was in the strange position of having
 | to contort itself to conform to a world view
 | (fundamentalist reductionism) that 20th century physics was
 | simultaneously in the process of rejecting. In a
 | metaphysical sense, molecular biology was outdated from the
 | onset! What makes this curious period in biology's history
 | doubly bizarre is that a fundamentalist reductionist
 | perspective wasn't even needed in the first place in order
 | to study biology on the molecular level. The simple
 | empirical reductionist outlook would have done just fine,
 | and technology was moving us in that direction anyway! It
 | will be interesting to see what history has to say about
 | the biology of the 20th century.
 | ...
Carl R. Woese, "A New Biology for a New Century", _Microbiology
and Molecular Biology Reviews_, June 2004, p. 173-186, Vol. 68,
No. 2 

 | At the time of fertilisation, the size of a human egg
 | is about .1 mm in diameter and it weighs about one-millionth
 | of a gram.  After about seven weeks, it has become about
 | 17 mm long with a weight of one gram: an increase in 
 | weight of one million fold.  By the time an adult is
 | formed, the size will have increased by a further factor
 | of about one hundred in linear dimensions and one hundred
 | thousand in weight.
Enrico Coen, _The Art of Genes_, 1999 

 | Belief in afterlife would come very naturally to animals
 | undergoing complete metamorphosis, such as many insects:
 | they already have an afterlife of sorts. The caveat is that
 | insect's "afterlife," which is devoted to the celestial
 | joys of mating, is usually much shorter than their main,
 | larval, hardship-prone "life." They would notice this
 | brevity and their belief will be informed by this
 | observation. People expect their afterlife to be long or
 | eternal, probably by extrapolation, because our adulthood
 | is much longer than our childhood. The rational insects
 | would develop the belief in a succession of ever shortening
 | but ever more beautiful afterlives reaching the climax when
 | zero life span is attained and time itself stops, for this
 | moment of attaining perfection needs no duration. 
 | ...

 | BMC Med Genet. 2010 May 13;11:73.
 | Is Lamarckian evolution relevant to medicine?
 | Handel AE, Ramagopalan SV.
 | Wellcome Trust Centre for Human Genetics, University of
 | Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.
 | Abstract
 | BACKGROUND: 200 years have now passed since Darwin was born
 | and scientists around the world are celebrating this
 | important anniversary of the birth of an evolutionary
 | visionary. However, the theories of his colleague Lamarck
 | are treated with considerably less acclaim. These theories
 | centre on the tendency for complexity to increase in
 | organisms over time and the direct transmission of
 | phenotypic traits from parents to offspring. DISCUSSION:
 | Lamarckian concepts, long thought of no relevance to modern
 | evolutionary theory, are enjoying a quiet resurgence with
 | the increasing complexity of epigenetic theories of
 | inheritance. There is evidence that epigenetic alterations,
 | including DNA methylation and histone modifications, are
 | transmitted transgenerationally, thus providing a potential
 | mechanism for environmental influences to be passed from
 | parents to offspring: Lamarckian evolution. Furthermore,
 | evidence is accumulating that epigenetics plays an
 | important role in many common medical conditions. SUMMARY:
 | Epigenetics allows the peaceful co-existence of Darwinian
 | and Lamarckian evolution. Further efforts should be exerted
 | on studying the mechanisms by which this occurs so that
 | public health measures can be undertaken to reverse or
 | prevent epigenetic changes important in disease
 | susceptibility. Perhaps in 2059 we will be celebrating the
 | anniversary of both Darwin and Lamarck

 | Jeffrey Pine
 | Uses
 | Ethnobotanic use. The turpentine obtained from the resin of
 | all pine trees is antiseptic, diuretic, rubefacient and
 | vermifuge.  It is a valuable remedy used internally in the
 | treatment of kidney and bladder complaints and is used both
 | internally and as a rub and steam bath in the treatment of
 | rheumatic affections.  It is also very beneficial to the
 | respiratory system and so is useful in treating diseases of
 | the mucous membranes and respiratory complaints such as
 | coughs, colds, influenza and externally it is a very
 | beneficial treatment for a variety of skin complaints,
 | wounds, sores, burns, boils etc and is used in the form of
 | liniment plasters, poultices, herbal steam baths and
 | inhalers.  
 | Commercial uses: The primary use for Jeffrey pine is for
 | lumber. The low-grade Jeffrey pine trees are processed into
 | dimensional lumber, as well as other construction products.
 | Some of the other construction products made from
 | high-grade lumber, as a raw material are molding, millwork,
 | cabinets, doors, and windows.  It is important to note that
 | for commercial use, no distinction is made between the wood
 | of Jeffrey pine and ponderosa pine.
 | Pure n-heptane is distilled from Jeffrey Pine resin.  It was
 | selected as the zero point on the petrol octane rating
 | scale.  Jeffrey Pine resin cannot be used to make
 | turpentine, as n-heptane is explosive when ignited.
 | Wildlife uses: The Jeffrey pine forests provide wildlife
 | cover for birds, small mammals and big game.  Its' seeds
 | are both disseminated and eaten by insects, birds, and
 | small mammals such as mice, chipmunks, and tree squirrels.
 | Description
 | General: The Jeffrey pine may live 400 to 500 years and can
 | attain immense size. It typically grows to 4 to 6 feet in
 | diameter, and 170 to 200 feet in height. To date, the
 | largest Jeffrey pine recorded in the western Sierra Nevada
 | had a diameter of 7.5 feet, and a height of 175 feet.
 | ...

I'll take "Wonders of Nature" for $500, Alex.

A. 100,000 RPM.

Q. What is the rotational speed of the polar flagella of the


 | Polar flagella of Vibrio species can rotate at speeds as high as
 | 100,000 rpm and effectively propel the bacteria in liquid as fast
 | as 60 micron/s. ...

Why a Duck is Superior To A Man

          |  Duck  |   Man |
|   Walk  |   Y    |   Y   |
|   Swim  |   Y    |   Y   |
|   Dive  |   Y    |   Y   |
|   Fly   |   Y    |   N   |

 | Birth of psychoneuroimmunology
 | In 1975 Robert Ader and Nicholas Cohen at the University of
 | Rochester advanced PNI with their demonstration of classic
 | conditioning of immune function, and coined the term
 | "psychoneuroimmunology".[7][8] Adler was investigating how
 | long conditioned responses (in the sense of Pavlov's
 | conditioning of dogs to drool when they heard a bell ring)
 | might last in laboratory rats. To condition the rats, he
 | used a combination of saccharin-laced water (the
 | conditioned stimulus) and the drug Cytoxan which
 | unconditionally induces nausea and taste aversion and
 | suppression of the immune system. Ader was surprised to
 | discover that after conditioning, just feeding the rats
 | saccharin-laced water was associated with the death of some
 | animals and he proposed that they had been immunosuppressed
 | after receiving the conditioned stimulus. Adler (a
 | psychologist) and Cohen (an immunologist) directly tested
 | this hypothesis by deliberately immunizing conditioned and
 | unconditioned animals, exposing these and other control
 | groups to the conditioned taste stimulus, and then
 | measuring the amount of antibody produced. The highly
 | reproducible results revealed that conditioned rats exposed
 | to the conditioned stimulus were indeed immunosuppressed.
 | In other words, a signal via the nervous system (taste) was
 | affecting immune function. This was one of the first
 | scientific experiments that demonstrated that the nervous
 | system can affect the immune system.
 | In 1981 David Felten, then working at the Indiana
 | University of Medicine, discovered a network of nerves
 | leading to blood vessels as well as cells of the immune
 | system. The researchers also found nerves in the thymus and
 | spleen terminating near clusters of lymphocytes,
 | macrophages and mast cells, all of which help control
 | immune function. This discovery provided one of the first
 | indications of how neuro-immune interaction occurs.
 | Adler, Cohen and Felten went on to edit the groundbreaking
 | book Psychoneuroimmunology in 1981, which laid out the
 | underlying premise that the brain and immune system
 | represent a single, integrated system of defense. An
 | updated fourth edition was released in 2006.
 | ...

 | Neural cytoskeleton capabilities for learning and memory
 | Abstract  This paper proposes a physical model involving
 | the key structures within the neural cytoskeleton as major
 | players in molecular-level processing of information
 | required for learning and memory storage. In particular,
 | actin filaments and microtubules are macromolecules having
 | highly charged surfaces that enable them to conduct
 | electric signals. The biophysical properties of these
 | filaments relevant to the conduction of ionic current
 | include a condensation of counterions on the filament
 | surface and a nonlinear complex physical structure
 | conducive to the generation of modulated waves.
 | Cytoskeletal filaments are often directly connected with
 | both ionotropic and metabotropic types of membrane-embedded
 | receptors, thereby linking synaptic inputs to intracellular
 | functions. Possible roles for cable-like, conductive
 | filaments in neurons include intracellular information
 | processing, regulating developmental plasticity, and
 | mediating transport. The cytoskeletal proteins form a
 | complex network capable of emergent information processing,
 | and they stand to intervene between inputs to and outputs
 | from neurons. In this manner, the cytoskeletal matrix is
 | proposed to work with neuronal membrane and its intrinsic
 | components (e.g., ion channels, scaffolding proteins, and
 | adaptor proteins), especially at sites of synaptic contacts
 | and spines. An information processing model based on
 | cytoskeletal networks is proposed that may underlie certain
 | types of learning and memory. 

What people will get up to if they don't have CSI:Miami and
Monday Night Football:

 | Owing to the probabilistic nature of most generalizations
 | in evolutionary biology it is impossible to apply Popper's
 | method of falsification for theory testing because a
 | particular case of a seeming refutation of a certain law
 | may not be anything but an exception, as are common in
 | biology.  Most theories in biology are based not on laws
 | but on concepts.  Examples of such concepts are, for
 | instance, selection, speciation, phylogeny, competition,
 | population, imprinting, adaptedness, biodiversity,
 | development, ecosystem and function.
Ernst Mayr, _What Makes Biology Unique_, 2004, p.28 

 | Curr Opin Microbiol. 2009 Dec;12(6):638-43. Epub 2009 Oct 31.
 | Epigenetic inheritance in ciliates.
 | Nowacki M, Landweber LF.
 | Department of Ecology and Evolutionary Biology, Princeton
 | University, Princeton, NJ 08544, USA.
 | Abstract
 | 2009 marks not only the 200th anniversary of Darwin's birth
 | but also publication of the first scientific evolutionary
 | theory, Lamarck's Philosophie Zoologique. While Lamarck
 | embraced the notion of the inheritance of acquired
 | characters, he did not invent it (Burkhardt, 1984). New
 | phenomena discovered recently offer molecular pathways for
 | the transmission of several acquired characters. Ciliates
 | have long provided model systems to study phenomena that
 | bypass traditional modes of inheritance. RNA, normally
 | thought of as a conduit in gene expression, displays a
 | novel mode of action in ciliated protozoa. For example,
 | maternal RNA templates provide both an organizing guide for
 | DNA rearrangements in Oxytricha and a template that can
 | transmit spontaneous mutations that may arise during
 | somatic growth to the next generation, providing two such
 | mechanisms of so-called Lamarckian inheritance. This
 | suggests that the somatic ciliate genome is really an
 | 'epigenome', formed through templates and signals arising
 | from the previous generation. This review will discuss
 | these new biological roles for RNA, including non-coding
 | 'template' RNA molecules. The evolutionary consequences of
 | viable mechanisms in ciliates to transmit acquired
 | characters may create an additional store of heritable
 | variation that contributes to the cosmopolitan success of
 | this diverse lineage of microbial eukaryotes.

Euplotes is a unicelluar organism:

 | ...
 | The demand for alum from countries to the north of the
 | Mediterranean was an ancient one; but from the 10th-12th
 | Cs. dyeing, and the consequent use of alum, had become
 | increasingly monopolized by Jewish communities who had
 | migrated to Italy and Provence from the Byzantine Empire
 | and to Spain from Tunis, and who had yet another stronghold
 | in Alexandria. The sources of supply were various. Some
 | European countries favoured supplies from Sicily and the
 | Aeolian islands; Spain had its own resources, with
 | especially high quality coming from Castile; but the best
 | qualities still came from the Middle East. The four
 | Crusades of the 12th C., however, interrupted many of the
 | established trade routes and aggravated the conflicts
 | between Saladin and the declining Byzantine Empire,
 | creating the embryonic elements of the dramatic changes
 | that were to come. For one thing, the last crusade helped
 | polarize the antagonism of the Roman and Eastern churches.
 | Meanwhile new agencies were affecting this situation. The
 | Mongols sacked Baghdad in 1258 shattering Arabian culture
 | at its source; the Turks were beginning to dominate the
 | middle eastern scene; and, equally important for the future
 | development of alum supplies, the City States of northern
 | Italy were transforming and widening the market. They
 | included, initially, the Venetian Republic, Genoa and Pisa.
 | Pisa, however, soon succumbed to the expanding power of
 | Florence. Genoa not only built up lasting trade links with
 | north-western Europe, e.g. with important centres such as
 | the Duchy of Burgundy and the extensive markets of the
 | Hanseatic League in the Baltic, but it acted as a
 | middleman, dyeing and finishing textiles imported from
 | these centres and selling them to Sicily, Egypt and the
 | Levant. Its sources of alum came via Alexandria; Bejaïa
 | (Algeria), brought there by caravan from Lake Chad; Castile
 | and Greece. Genoa was also to expand its sources of alum
 | and trade into the Black Sea and off the eastern coast of
 | Asia Minor, the latter especially vulnerable to embargoes
 | or attack from the Turks. 
 | ...

 | Anisotropic effects for an RPM-based compass
 | Behavioral studies conducted over several decades in many
 | laboratories show that animals from all five classes of
 | vertebrate and several invertebrates possess a magnetic
 | compass sense [114,115]. However, the physiological basis
 | of magnetoreception remains an enigma. In birds,
 | magnetoreception is known to require ambient light in the
 | higher-energy blue-green region of the spectrum.

 |  ...
 |  Sandy marine sediments are a rich source of protozoa,
 | especially the thin, ribbon-like forms that can squeeze
 | between sand particles. One such organism is a ciliate
 | called Kentrophoros. Most ciliates have a mouth, but
 | Kentrophoros does not and it never shows signs of having
 | ingested any microbes from the sediment. Another curious
 | feature is that Kentrophoros carries on its back a dense
 | coat of large bacteria with refractive inclusions.
 | The bacteria are rod-shaped, and lined up perpendicularly
 | to the surface of the protozoon. Bacteria in the process of
 | dividing into two are obvious, but rather than dividing in
 | the traditional way across the shorter axis, they divide
 | lengthwise, and the bacterial coat grows over the surface
 | of the protozoon. We never imagined that this bacterial
 | coat was incidental to the lifestyle of Kentrophoros, but
 | only recently did we discover its function: it is, in fact,
 | a microbial kitchen garden. The ciliate regularly
 | invaginates the surface of its cell, bringing with it the
 | attached bacteria. Inside the protozoon, the bacteria are
 | wrapped up in food vacuoles and digested. This is how the
 | mouthless ciliate obtains a meal: it simply harvests some
 | of the bacteria growing on its back.
 | But how do the bacteria manage to make a living? To find
 | out, we incubated the living consortium in the presence of
 | two radioactive isotopes (C14 bicarbonate and S35
 | sulphide). Later, we tracked down where the isotopes had
 | accumulated by covering them with a thin layer of
 | photographic emulsion and developing it. The bacteria can
 | oxidise hydrogen sulphide to elemental sulphur (the
 | refractive blobs inside the cells). They use the energy of
 | the reaction to convert carbon dioxide into cell material.
 | So the bacteria are autotrophs, that is, they manufacture
 | complex organic materials from simple inorganic ones. To do
 | this, they need three things: oxygen, hydrogen sulphide and
 | carbon dioxide. Oxygen and hydrogen sulphide are rarely
 | found together because the sulphide is easily oxidised. In
 | marine sediments, however, they do co-exist in one narrow
 | zone. The sulphide diffuses up from the anaerobic depths of
 | the sediment and oxygen diffuses down from the overlying
 | water. In the zone where they meet, low concentrations of
 | both persist. 
 | ...

 | This fire stolen from heaven, the torch of Prometheus, does
 | not only represent an ingenious and poetic idea, it is a
 | faithful picture of the operations of nature, at least for
 | animals that breathe; one may therefore say, with the
 | ancients, that the torch of life lights itself at the
 | moment the infant breathes for the first time, and it does
 | not extinguish itself except at death.
Antoine Lavoisier 

n.b. "...life, itself...",_The Oval Portrait _, E. A. Poe 

 |      Science stands today on something of a divide. For two
 | centuries it has been exploring systems that are either
 | intrinsically simple or that are capable of being analysed
 | into simple components. The fact that such a dogma as "vary
 | the factors one at a time" could be accepted for a century,
 | shows that scientists were largely concerned in
 | investigating such systems as allowed this method; for this
 | method is often fundamentally impossible in the complex
 | systems.  Not until Sir Donald Fisher's work in the '20s,
 | with experiments conducted on agricultural soils, did it
 | become clearly recognised that there are complex systems
 | that just do not allow the varying of only one factor at a
 | time--they are so dynamic and interconnected that the
 | alteration of one factor immediately acts as cause to evoke
 | alterations in others, perhaps in a great many others.
 | Until recently, science tended to evade the study of such
 | systems, focusing its attention on those that were simple
 | and, especially, reducible (S.4/14).
 |      In the study of some systems, however, the complexity
 | could not be wholly evaded. The cerebral cortex of the
 | free-living organism, the ant-hill as a functioning
 | society, and the human economic system were outstanding
 | both in their practical importance and in their
 | intractability by the older methods. So today we see
 | psychoses untreated, societies declining, and economic sys-
 | tems faltering, the scientist being able to do little more
 | than to appreciate the full complexity of the subject he is
 | studying. But science today is also taking the first steps
 | towards studying "complexity" as a subject in its own
 | right.
W. Ross Ashby, _An Introduction to Cybernetics_, 1956 

Full text (156 pages):

Why is it not okay for athletes to use performance-enhancing
drugs, but okay for actors to have plastic surgery?


 | Work is of two kinds: first, altering the position of matter
 | at or near the earth's surface relative to other matter;
 | second, telling other people to do so.
 |                 -- Bertrand Russell

 | Microbial growth at hyperaccelerations up to 403,627 x g.
 | Deguchi S, Shimoshige H, Tsudome M, Mukai SA, Corkery RW,
 | Ito S, Horikoshi K.
 | Source
 | Institute of Biogeosciences, Japan Agency for Marine-Earth
 | Science and Technology, Yokosuka 237-0061, Japan.
 | shigeru.deguchi@jamstec.go.jp
 | Abstract
 | It is well known that prokaryotic life can withstand
 | extremes of temperature, pH, pressure, and radiation.
 | Little is known about the proliferation of prokaryotic life
 | under conditions of hyperacceleration attributable to
 | extreme gravity, however. We found that living organisms
 | can be surprisingly proliferative during hyperacceleration.
 | In tests reported here, a variety of microorganisms,
 | including Gram-negative Escherichia coli, Paracoccus
 | denitrificans, and Shewanella amazonensis; Gram-positive
 | Lactobacillus delbrueckii; and eukaryotic Saccharomyces
 | cerevisiae, were cultured while being subjected to
 | hyperaccelerative conditions. We observed and quantified
 | robust cellular growth in these cultures across a wide
 | range of hyperacceleration values. Most notably, the
 | organisms P. denitrificans and E. coli were able to
 | proliferate even at 403,627 x g. Analysis shows that the
 | small size of prokaryotic cells is essential for their
 | proliferation under conditions of hyperacceleration. Our
 | results indicate that microorganisms cannot only survive
 | during hyperacceleration but can display such robust
 | proliferative behavior that the habitability of
 | extraterrestrial environments must not be limited by
 | gravity.

 | In 1879 Eduard Tangle discovered cytoplasmic connections
 | between cells in the cotyledons of Strychnos nuxvomica,
 | which he interpreted to be protoplasmic contacts. This led
 | him to hypothesize that 'the protoplasmic bodies . . . are
 | united by thin strands passing through connecting ducts in
 | the walls, which put the cells into connection with each
 | other and so unite them to an entity of higher order'

 |     I would like to add that there are so many claims about
 | the origin of life -- it has been "found" on hydrothermal
 | vents, on ice, on clay, on pyrite, at very high and very
 | low pressure ... and there are so many corresponding
 | "worlds" -- but, as we have seen, all these worlds stop at
 | the synthesis of low-molecular-weight compounds or at the
 | most short oligomers. Of course, for the "origin of life"
 | you need to start from low-molecular weight compounds, and
 | in this sense the synthesis of water from hydrogen and
 | oxygen can also be considered the origin of life. However,
 | as is mentioned throughout the book, you could have all the
 | low-molecular-weight compounds in any quantity --and you
 | would not be able to make life.
Luisi, P.L., The Emergence of Life, _From Chemical Origins to
Synthetic Biology_, Cambridge, 2006, p.268 

Danish theoretical physicist Per Bak reviews some OoL literature in 1998:
 |     I find hot primordial soups unappealing, whether on the
 | surface or beneath the sea. Hot, reactive systems tend
 | towards thermal equilibrium, with no possibility of the
 | unlikely events needed for the formation of complex
 | molecules. I would argue something like this: since
 | DNA-like molecules can be transported through space, they
 | were. The entire Universe is replete with so many
 | possibilities--so much more "phase space" is available than
 | on our tiny Earth that it is much more likely that the very
 | unlikely process of formation of DNA, or its precursors,
 | took place somewhere out there.

Ironic -->