WHAT IS YOUR FAVORITE DEEP, ELEGANT, OR BEAUTIFUL EXPLANATION? - Richard Dawkins

Evolutionary Biologist; Emeritus Professor of the Public Understanding of Science,...

Redundancy Reduction and Pattern Recognition

Deep, elegant, beautiful? Part of what makes a theory elegant is its power to explain much while assuming little. Here, Darwin's natural selection wins hands down. The ratio of the huge amount that it explains (everything about life: its complexity, diversity and illusion of crafted design) divided by the little that it needs to postulate (non-random survival of randomly varying genes through geological time) is gigantic. Never in the field of human comprehension were so many facts explained by assuming so few. Elegant then, and deep—its depths hidden from everybody until as late as the nineteenth century. On the other hand, for some tastes natural selection is too destructive, too wasteful, too cruel to count as beautiful. In any case, coming late to the party as ever, I can count on somebody else choosing Darwin. I'll take his great grandson instead, and come back to Darwin at the end.

Horace Barlow FRS is the youngest grandchild of Sir Horace Darwin, Charles Darwin's youngest child. Now a very active ninety, Barlow is a member of a distinguished lineage of Cambridge neurobiologists. I want to talk about an idea that he published in two papers in 1961, on redundancy reduction and pattern recognition. It is an idea whose ramifications and significance have inspired me throughout my career.

The folklore of neurobiology includes a mythical 'grandmother neurone', which fires only when a very particular image, the face of Jerry Lettvin's grandmother, falls on the retina (Lettvin was a distinguished American neurobiologist who, like Barlow, worked on the frog retina). The point is that Lettvin's grandmother is only one of countless images that a brain is capable of recognising. If there were a specific neurone for everything we can recognise—not just Lettvin's grandmother but lots of other faces, objects, letters of the alphabet, flowers, each one seen from many angles and distances, we would have a combinatorial explosion. If sensory recognition worked on the 'grandmother principle', the number of specific recognition neurones for all possible combinations of nerve impulses would exceed the number of atoms in the universe. Independently, the American psychologist Fred Attneave had calculated that the volume of the brain would have to be measured in cubic light years. Barlow and Attneave independently proposed redundancy reduction as the answer.

Claude Shannon, inventor of Information Theory, coined 'redundancy' as a kind of inverse of information. In English, 'q' is always followed by 'u', so the 'u' can be omitted without loss of information. It is redundant. Wherever redundancy occurs in a message (which is wherever there is nonrandomness), the message can be more economically recoded without loss of information (although with some loss in capacity to correct errors). Barlow suggested that, at every stage in sensory pathways, there are mechanisms tuned to eliminate massive redundancy.

The world at time t is not greatly different from the world at time t-1. Therefore it is not necessary for sensory systems continuously to report the state of the world. They need only signal changes, leaving the brain to assume that everything not reported remains the same. Sensory adaptation is a well-known feature of sensory systems, which does precisely as Barlow prescribed. If a neurone is signalling temperature, for example, the rate of firing is not, as one might naively suppose, proportional to the temperature. Instead, firing rate increases only when there is a change in temperature. It then dies away to a low resting frequency. The same is true of neurones signalling brightness, loudness, pressure and so on. Sensory adaptation achieves huge economies by exploiting the non-randomness in temporal sequence of states of the world.

What sensory adaptation achieves in the temporal domain, the well-established phenomenon of lateral inhibition does in the spatial domain. If a scene in the world falls on a pixellated screen, such as the back of a digital camera or the retina of an eye, most pixels see the same as their immediate neighbours. The exceptions are those pixels which lie on edges, boundaries. If every retinal cell faithfully reported its light value to the brain, the brain would be bombarded with a massively redundant message. Huge economies can be achieved if most of the impulses reaching the brain come from pixel cells lying along edges in the scene. The brain then assumes uniformity in the spaces between edges.

As Barlow pointed out, this is exactly what lateral inhibition achieves. In the frog retina, for example, every ganglion cell sends signals to the brain, reporting on the light intensity in its particular location on the surface of the retina. But it simultaneously sends inhibitory signals to its immediate neighbours. This means that the only ganglion cells to send strong signals to the brain are those that lie on an edge. Ganglion cells lying in uniform fields of colour (the majority) send few if any impulses to the brain because they, unlike cells on edges, are inhibited by all their neighbours. The spatial redundancy in the signal is eliminated.

The Barlow analysis can be extended to most of what is now known about sensory neurobiology, including Hubel and Wiesel's famous horizontal and vertical line detector neurones in cats (straight lines are redundant, reconstructable from their ends), and in the movement ('bug') detectors in the frog retina, discovered by the same Jerry Lettvin and his colleagues. Movement represents a non-redundant change in the frog's world. But even movement is redundant if it persists in the same direction at the same speed. Sure enough, Lettvin and colleagues discovered a 'strangeness' neurone in their frogs, which fires only when a moving object does something unexpected, such as speeding up, slowing down, or changing direction. The strangeness neurone is tuned to filter out redundancy of a very high order.

Barlow pointed out that a survey of the sensory filters of a given animal could, in theory, give us a read-out of the redundancies present in the animal's world. They would constitute a kind of description of the statistical properties of that world. Which reminds me, I said I'd return to Darwin. In Unweaving the Rainbow, I suggested that the gene pool of a species is a 'Genetic Book of the Dead', a coded description of the ancestral worlds in which the genes of the species have survived through geological time. Natural selection is an averaging computer, detecting redundancies—repeat patterns—in successive worlds (successive through millions of generations) in which the species has survived (averaged over all members of the sexually reproducing species). Could we take what Barlow did for neurones in sensory systems, and do a parallel analysis for genes in naturally selected gene pools? Now that would be deep, elegant and beautiful.

http://www.edge.org/response-detail/2825/what-is-your-favorite-deep-elegant-or-beautiful-explanation

Конспекты

Оригинал взят у в Конспекты

Выложил слайды и конспекты лекций, прочтенных первокурсникам совместного бакалавриата ВШЭ и РЭШ. Здесь, по идее, нужны многословные оправдания: это полуфабрикат; редактировать времени нет; привести эти материалы в божеский вид - дело будущего; это не всегда точно соответствует тому, что реально было на лекциях; многие вещи вообще не отражены в тексте - в особенности это относится к темам, которые я был уверен, что внятно расскажу без шпаргалки; некоторые пространные куски, скопированные из-каких-то других моих книжек, статей и лекций, добавлялись в конспекты на всякий случай и в действительности не были оглашены. Несколько слайдов взято из лекций А.С.Кондрашова с его разрешения. Пара слайдов - из доклада А.Ю.Журавлева, любезно предоставившего свою презентацию. Львиная доля картинок взята из интернета с характерным для меня наплевательским отношением к копирайтам (плохо представляю, как еще можно сделать слайды для такого обзорного курса). Многое преднамеренно упрощено, даже примитивизировано, что для данного курса, по-моему, было правильно и необходимо - и уж чего мне совсем не хотелось, так это морочить студентам головы рассказами "о бессилии науки перед тайною Бермуд", поэтому некоторые гипотетические вещи поданы без достаточно пространных оговорок об их гипотетичности. Можно еще долго продолжать, но неохота. При всем при том надеюсь, что кому-то этот материал может пригодиться - для самообразования или при подготовке собственных курсов.
Слайды и конспекты курса "Введение в науки о жизни"

Lynn Margulis 1938-2011 "Gaia Is A Tough Bitch"

http://edge.org/conversation/lynn-margulis1938-2011

Jerry Coyne
Professor, Department of Ecology and Evolution, University of Chicago; author, Why Evolution is True

Lynn Margulis did indeed have a clever—and correct—idea that revolutionized our view of how life evolved, but later became a victim of the Big Idea Syndrome, thinking that because she was right about organelles, she was right about everything else. That led her to make repeated and completely unfounded attacks on evolutionary biology in the last decade, embarrassing herself with her pronouncements. Her legacy is a good one, but not unmixed.

Rereading her chapter "Gaia is a Tough Bitch" only reinforces my opinion about her misguided criticisms of neo-Darwinian evolution and her unwarranted antipathy toward population genetics. Not only did she fail to comprehend how population genetics has advanced our understanding of nature—the effects of inbreeding and of genetic drift are two such advances—but her views on speciation, a field in which I've worked for three decades, are simply wrong.

Margulis's idea that new species originate from symbiosis has no empirical support. When we try to understand the genetic underpinnings of new species, we find that, with the exception of polyploidy in plants, it always maps to changes in the DNA. That is, the splitting of lineages, like evolution within a lineage itself, is almost always the result of gradual, gene-by-gene change. We have no evidence that symbiosis has been responsible for even a single case of speciation.

All of us should honor Margulis's real contributions to biology: her recognition and working out of earlier suggestions that some cellular organelles were acquired by symbiosis, and that the ancestors of these organelles were bacteria. This was a tremendous advance, achieved in the teeth of substantial doubt. Sadly, Margulis's success in the face of such criticism seems to have made her stubborn and dogmatic about her other biological views. And, even sadder, those theories were often wrong. She strongly denied, for example, that AIDS was caused by the HIV virus, or that the HIV virus even existed. AIDS, she maintained, was simply syphilis, with the spirochete rendered undetectable because it formed a symbiosis with human cells. How does one balance her positive contributions against such a deadly form of denialism?

We should always honor those scientists who have advanced our understanding of nature in ways as profound as Margulis. But let us also remember that being right about one big matter does not render us immune to error in other matters, and that scientific fame does not give us a free pass for all of our ideas.


--------------------------------------------------------------------------------

LYNN MARGULIS was Distinguished University Professor in the Department of Geology at the University of Massachusetts, Amherst. She was the author of Symbiotic Planet, The Origin of Eukaryotic Cells, Early Life, and Symbiosis in Cell Evolution. She was also the coauthor, with Karlene V. Schwartz, of Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth and with Dorion Sagan of Acquiring Genomes, Microcosmos, Origins Of Sex, and Mystery Dance.


--------------------------------------------------------------------------------

Lynn Margulis 1938-2011

"Gaia Is A Tough Bitch"

From The Third Culture: Beyond the Scientific Revolution
Edge Online Edition
Amazon | B&N


Richard Dawkins: I greatly admire Lynn Margulis's sheer courage and stamina in sticking by the endosymbiosis theory, and carrying it through from being an unorthodoxy to an orthodoxy. I'm referring to the theory that the eukaryotic cell is a symbiotic union of primitive prokaryotic cells. This is one of the great achievements of twentieth-century evolutionary biology, and I greatly admire her for it.


[LYNN MARGULIS]: At any fine museum of natural history — say, in New York, Cleveland, or Paris — the visitor will find a hall of ancient life, a display of evolution that begins with the trilobite fossils and passes by giant nautiloids, dinosaurs, cave bears, and other extinct animals fascinating to children. Evolutionists have been preoccupied with the history of animal life in the last five hundred million years. But we now know that life itself evolved much earlier than that. The fossil record begins nearly four thousand million years ago! Until the 1960s, scientists ignored fossil evidence for the evolution of life, because it was uninterpretable.

I work in evolutionary biology, but with cells and microorganisms. Richard Dawkins, John Maynard Smith, George Williams, Richard Lewontin, Niles Eldredge, and Stephen Jay Gould all come out of the zoological tradition, which suggests to me that, in the words of our colleague Simon Robson, they deal with a data set some three billion years out of date. Eldredge and Gould and their many colleagues tend to codify an incredible ignorance of where the real action is in evolution, as they limit the domain of interest to animals — including, of course, people. All very interesting, but animals are very tardy on the evolutionary scene, and they give us little real insight into the major sources of evolution's creativity. It's as if you wrote a four-volume tome supposedly on world history but beginning in the year 1800 at Fort Dearborn and the founding of Chicago. You might be entirely correct about the nineteenth-century transformation of Fort Dearborn into a thriving lakeside metropolis, but it would hardly be world history.

"codifying ignorance" I refer in part to the fact that they miss four out of the five kingdoms of life. Animals are only one of these kingdoms. They miss bacteria, protoctista, fungi, and plants. They take a small and interesting chapter in the book of evolution and extrapolate it into the entire encyclopedia of life. Skewed and limited in their perspective, they are not wrong so much as grossly uninformed.
Of what are they ignorant? Chemistry, primarily, because the language of evolutionary biology is the language of chemistry, and most of them ignore chemistry. I don't want to lump them all together, because, first of all, Gould and Eldredge have found out very clearly that gradual evolutionary changes through time, expected by Darwin to be documented in the fossil record, are not the way it happened. Fossil morphologies persist for long periods of time, and after stasis, discontinuities are observed. I don't think these observations are even debatable. John Maynard Smith, an engineer by training, knows much of his biology secondhand. He seldom deals with live organisms. He computes and he reads. I suspect that it's very hard for him to have insight into any group of organisms when he does not deal with them directly. Biologists, especially, need direct sensory communication with the live beings they study and about which they write.
Reconstructing evolutionary history through fossils — paleontology — is a valid approach, in my opinion, but paleontologists must work simultaneously with modern-counterpart organisms and with "neontologists" — that is, biologists. Gould, Eldredge, and Lewontin have made very valuable contributions. But the Dawkins-Williams-Maynard Smith tradition emerges from a history that I doubt they see in its Anglophone social context. Darwin claimed that populations of organisms change gradually through time as their members are weeded out,...

"codifying ignorance" I refer in part to the fact that they miss four out of the five kingdoms of life. Animals are only one of these kingdoms. They miss bacteria, protoctista, fungi, and plants. They take a small and interesting chapter in the book of evolution and extrapolate it into the entire encyclopedia of life. Skewed and limited in their perspective, they are not wrong so much as grossly uninformed.

Of what are they ignorant? Chemistry, primarily, because the language of evolutionary biology is the language of chemistry, and most of them ignore chemistry. I don't want to lump them all together, because, first of all, Gould and Eldredge have found out very clearly that gradual evolutionary changes through time, expected by Darwin to be documented in the fossil record, are not the way it happened. Fossil morphologies persist for long periods of time, and after stasis, discontinuities are observed. I don't think these observations are even debatable. John Maynard Smith, an engineer by training, knows much of his biology secondhand. He seldom deals with live organisms. He computes and he reads. I suspect that it's very hard for him to have insight into any group of organisms when he does not deal with them directly. Biologists, especially, need direct sensory communication with the live beings they study and about which they write.

Reconstructing evolutionary history through fossils — paleontology — is a valid approach, in my opinion, but paleontologists must work simultaneously with modern-counterpart organisms and with "neontologists" — that is, biologists. Gould, Eldredge, and Lewontin have made very valuable contributions. But the Dawkins-Williams-Maynard Smith tradition emerges from a history that I doubt they see in its Anglophone social context. Darwin claimed that populations of organisms change gradually through time as their members are weeded out, which is his basic idea of evolution through natural selection. Mendel, who developed the rules for genetic traits passing from one generation to another, made it very clear that while those traits reassort, they don't change over time. A white flower mated to a red flower has pink offspring, and if that pink flower is crossed with another pink flower the offspring that result are just as red or just as white or just as pink as the original parent or grandparent. Species of organisms, Mendel insisted, don't change through time. The mixture or blending that produced the pink is superficial. The genes are simply shuffled around to come out in different combinations, but those same combinations generate exactly the same types. Mendel's observations are incontrovertible.

So J.B.S. Haldane, without a doubt a brilliant person, and R.A. Fisher, a mathematician, generated an entire school of English-speaking evolutionists, as they developed the neo- Darwinist population-genetic analysis to reconcile two unreconcilable views: Darwin's evolutionary view with Mendel's pragmatic, anti-evolutionary concept. They invented a language of population genetics in the 1920s to 1950s called neo-Darwinism, to rationalize these two fields. They mathematized their work and began to believe in it, spreading the word widely in Great Britain, the United States, and beyond. France and other countries resisted neo-Darwinism, but some Japanese and other investigators joined in the "explanation" activity.

Both Dawkins and Lewontin, who consider themselves far apart from each other in many respects, belong to this tradition. Lewontin visited an economics class at the University of Massachusetts a few years ago to talk to the students. In a kind of neo-Darwinian jockeying, he said that evolutionary changes are due to the Fisher-Haldane mechanisms: mutation, emigration, immigration, and the like. At the end of the hour, he said that none of the consequences of the details of his analysis had been shown empirically. His elaborate cost-benefit mathematical treatment was devoid of chemistry and biology. I asked him why, if none of it could be shown experimentally or in the field, he was so wedded to presenting a cost-benefit explanation derived from phony human social-economic "theory." Why, when he himself was pointing to serious flaws related to the fundamental assumptions, did he want to teach this nonsense? His response was that there were two reasons: the first was "P.E." "P.E.?," I asked. "What is P.E.? Population explosion? Punctuated equilibrium? Physical education?" "No," he replied, "P.E. is `physics envy,'" which is a syndrome in which scientists in other disciplines yearn for the mathematically explicit models of physics. His second reason was even more insidious: if he didn't couch his studies in the neo- Darwinist thought style (archaic and totally inappropriate language, in my opinion), he wouldn't be able to obtain grant money that was set up to support this kind of work.

The neo-Darwinist population-genetics tradition is reminiscent of phrenology, I think, and is a kind of science that can expect exactly the same fate. It will look ridiculous in retrospect, because it is ridiculous. I've always felt that way, even as a more-than-adequate student of population genetics with a superb teacher — James F. Crow, at the University of Wisconsin, Madison. At the very end of the semester, the last week was spent on discussing the actual observational and experimental studies related to the models, but none of the outcomes of the experiments matched the theory.

I've been critical of mathematical neo-Darwinism for years; it never made much sense to me. We were all told that random mutations — most of which are known to be deleterious — are the main cause of evolutionary change. I remember waking up one day with an epiphanous revelation: I am not a neo-Darwinist! It recalled an earlier experience, when I realized that I wasn't a humanistic Jew.

Although I greatly admire Darwin's contributions and agree with most of his theoretical analysis and I am a Darwinist, I am not a neo-Darwinist. One of Darwin's major insights is the recognition that all organisms are related by common ancestry. Today direct evidence for common ancestry — genetic, chemical, and otherwise — is overwhelming. Populations of organisms grow and reproduce at rates that are not sustainable in the real world, and therefore many more die or fail to reproduce than actually complete their life histories. The fact that all the organisms that are born or hatched or budded off do not and cannot possibly survive is natural selection. Observable inherited variation appears in all organisms that are hatched, born, budded off, or produced by division, and some variants do outgrow and outreproduce others. These are the tenets of Darwinian evolution and natural selection. All thinking scientists are in complete agreement with these basic ideas, since they're supported by vast amounts of evidence.

Neo-Darwinism is an attempt to reconcile Mendelian genetics, which says that organisms do not change with time, with Darwinism, which claims they do. It's a rationalization that fuses two somewhat flawed traditions in a mathematical way, and that is the beginning of the end. Neo Darwinist formality uses an arithmetic and an algebra that is inappropriate for biology. The language of life is not ordinary arithmetic and algebra; the language of life is chemistry. The practicing neo-Darwinists lack relevant knowledge in, for example, microbiology, cell biology, biochemistry, molecular biology, and cytoplasmic genetics. They avoid biochemical cytology and microbial ecology. This is comparable to attempting a critical analysis of Shakespeare's Elizabethan phraseology and idiomatic expression in Chinese, while ignoring the relevance of the English language!

The neo-Darwinists say that variation originates from random mutation, defining mutation as any genetic change. By randomness they mean that characters appear randomly in offspring with respect to selection: if an animal needs a tail, it doesn't develop this tail because it needs it; rather, the animal randomly develops all sorts of changes and those with tails survive to produce more offspring. H.J. Muller, in the 1920s, discovered that not only do X rays increase the fruit-fly mutation rate, but even if fruit flies are isolated completely from X rays, solar radiation, and other environmental perturbation, a spontaneous mutation rate can be measured. Inherited variants do appear spontaneously; they have nothing to do with whether or not they're good for the organism in which they appear. Mutation was then touted as the source of variation- -that upon which natural selection acted — and the neo-Darwinian theory was declared complete. The science remaining required filling in the gaps in a "theory" with very few holes.

From many experiments, it is known that if mutagens like X rays or certain chemicals are presented to fruit flies, sick and dead flies result. No new species of fly appears — that is the real rub. Everyone agrees that such mutagens produce inherited variation. Everyone agrees that natural selection acts on this variation. The question is, From where comes the useful variation upon which selection acts? This problem has not yet been solved. But I claim that most significant inherited variation comes from mergers — from what the Russians, especially Konstantin S. Mereschkovsky, called symbiogenesis and the American Ivan Emanuel Wallin called symbionticism. Wallin meant by the term the incorporation of microbial genetic systems into progenitors of animal or plant cells. The new genetic system — a merger between microbe and animal cell or microbe and plant cell — is really different from the ancestral cell that lacks the microbe. Analogous to improvements in computer technology, instead of starting from scratch to make all new modules again, the symbiosis idea is an interfacing of preexisting modules. Mergers result in the emergence of new and more complex beings. I doubt new species form just from random mutation.

Symbiosis is a physical association between organisms, the living together of organisms of different species in the same place at the same time. My work in symbiosis comes out of cytoplasmic genetic systems. We were all taught that the genes were in the nucleus and that the nucleus is the central control of the cell. Early in my study of genetics, I became aware that other genetic systems with different inheritance patterns exist. From the beginning, I was curious about these unruly genes that weren't in the nucleus. The most famous of them was a cytoplasmic gene called "killer," which, in the protist Paramecium aurelia, followed certain rules of inheritance. The killer gene, after twenty years of intense work and shifting paradigmatic ideas, turns out to be in a virus inside a symbiotic bacterium. Nearly all extranuclear genes are derived from bacteria or other sorts of microbes. In the search for what genes outside the nucleus really are, I became more and more aware that they're cohabiting entities, live beings. Live small cells reside inside the larger cells. Understanding that led me and others to study modern symbioses.

Symbiosis has nothing to do with cost or benefit. The benefit/cost people have perverted the science with invidious economic analogies. The contention is not over modern symbioses, simply the living together of unlike organisms, but over whether "symbiogenesis" — long-term symbioses that lead to new forms of life — has occurred and is still occurring. The importance of symbiogenesis as a major source of evolutionary change is what is debated. I contend that symbiogenesis is the result of long-term living together — staying together, especially involving microbes- -and that it's the major evolutionary innovator in all lineages of larger nonbacterial organisms.

In 1966, I wrote a paper on symbiogenesis called "The Origin of Mitosing [Eukaryotic] Cells," dealing with the origin of all cells except bacteria. (The origin of bacterial cells is the origin of life itself.) The paper was rejected by about fifteen scientific journals, because it was flawed; also, it was too new and nobody could evaluate it. Finally, James F. Danielli, the editor of The Journal of Theoretical Biology, accepted it and encouraged me. At the time, I was an absolute nobody, and, what was unheard of, this paper received eight hundred reprint requests. Later, at Boston University, it won an award for the year's best faculty publication. I was only an instructor at the time, so my Biology Department colleagues reacted to the commotion and threw a party. But it was more of "Isn't this cute," or "It's so abstruse that I don't understand it, but others think it worthy of attention." Even today most scientists still don't take symbiosis seriously as an evolutionary mechanism. If they were to take symbiogenesis seriously, they'd have to change their behavior. The only way behavior changes in science is that certain people die and differently behaving people take their places.

Next, expanding the journal article, after ten years of research and six weeks of intense writing, I produced a book called The Origin of Eukaryotic Cells. Even under contract, it was rejected by Academic Press. Finally, in 1970, the revised and improved work was published by Yale University Press. Now called Symbiosis in Cell Evolution, the most recent version of the statement is in a second — really a third — edition. Published by W.H. Freeman in 1993, that book is my life's work. It details the role of symbiosis in the evolution of cells, which leads directly to the origin of mitotic cell division and meiotic sexuality. My major thrust is how different bacteria form consortia that, under ecological pressures, associate and undergo metabolic and genetic change such that their tightly integrated communities result in individuality at a more complex level of organization. The case in point is the origin of nucleated (protoctist, animal, fungal, and plant) cells from bacteria.

While Gould and the others tend to believe that species only diverge from one another, I claim that — more important in generation of variation — species form new composite entities by fusion and merger. Symbiogenesis is an extremely important mechanism of evolution. Symbiogenesis analysis impacts on developmental biology, on taxonomy and systematics, and on cell biology; it hits some thirty subfields of biology, and even geology. Symbiogenesis has many implications, which is part of the reason it is controversial. Most people don't like to hear that what they have been doing all these years is barking up the wrong tree.

My argument is radical only to the extent that it inspires scientists to change their status quo about many issues. To take seriously our Five Kingdoms concept (the book by Karlene V. Schwartz and me is based on work by Robert H. Whittaker and Herbert F. Copeland) a school or a publisher would have to change its catalog. A supplier has to relabel all its drawers and cabinets. Departments must reorganize their budget items, and NASA, the National Science Foundation, and various museums have to change staff titles and program-planning committees. The change from "plants versus animals" to the five kingdoms (bacteria, protoctista, animals, fungi, and plants) has such a profound implication for every aspect of biology as a social activity that resistance to accept it abounds. Scientists and those who pay them have to dismiss or ignore this potential reorganization because accepting the shifting boundaries and new alliances is strange and costly. It is far easier to stay with obsolete intellectual categories.

For more than a billion years, the only life on this planet consisted of bacterial cells, which, lacking nuclei, are called prokaryotes, or prokaryotic cells. They looked very much alike, and from the human-centered vantage point seem boring. However, bacteria are the source of reproduction, photosynthesis, movement — indeed, all interesting features of life except perhaps speech! They're still with us in large diversity and numbers. They still rule Earth. At some point, a new more complex kind of cell appeared on the scene, the eukaryotic cell, of which plant and animal bodies are composed. These cells contain certain organelles, including nuclei. Eukaryotic cells with an individuated nucleus are the building blocks of all familiar large forms of life. How did that evolution revolution occur? How did the eukaryotic cell appear? Probably it was an invasion of predators, at the outset. It may have started when one sort of squirming bacterium invaded another — seeking food, of course. But certain invasions evolved into truces; associations once ferocious became benign. When swimming bacterial would-be invaders took up residence inside their sluggish hosts, this joining of forces created a new whole that was, in effect, far greater than the sum of its parts: faster swimmers capable of moving large numbers of genes evolved. Some of these newcomers were uniquely competent in the evolutionary struggle. Further bacterial associations were added on, as the modern cell evolved.

One kind of evidence in favor of symbiogenesis in cell origins is mitochondria, the organelles inside most eukaryotic cells, which have their own separate DNA. In addition to the nuclear DNA, which is the human genome, each of us also has mitochondrial DNA. Our mitochondria, a completely different lineage, are inherited only from our mothers. None of our mitochondrial DNA comes from our fathers. Thus, in every fungus, animal, or plant (and in most protoctists), at least two distinct genealogies exist side by side. That, in itself, is a clue that at some point these organelles were distinct microorganisms that joined forces.

David Luck and John Hall, research geneticists at Rockefeller University, recently made an astounding discovery that I more or less predicted twenty-five years ago. They demonstrated by well-developed techniques something they were not even seeking: a peculiar DNA — outside the nucleus of the cell, outside the chloroplast, and outside the mitochondria. This extranuclear DNA, these genes outside the nucleus, can be interpreted as remnants of ancient, invasive, squirming bacteria whose aggressive association presaged the merger.

If their discovery is correct — and at least three teams of researchers have disputed it — then the nonnuclear genetic system Hall and Luck revealed in green algae may represent the stripped-down remnants of bacteria inside all of us. The growth, reproduction, and communication of these moving, alliance-forming bacteria become isomorphic with our thought, with our happiness, our sensitivities and stimulations. If mine is a correct view, it organizes a great deal of knowledge. There are unambiguous ways of testing the main points. The implication is that we are literally inhabited by highly motile remnants of an ancient bacterial type that have become, in every sense, a part of ourselves. These thriving partial beings represent the physical basis of anima: soul, life, locomotion; an advocation of materialism in the crassest sense of the word. Put it this way: a purified chemical is prepared from brain and added to another purified chemical. These two chemicals — two different kinds of motile proteins — together crawl away, they locomote. They move all by themselves. Biochemists and cell biologists can show us the minimal common denominator of movement, locomotion. Anima. Soul. These moving proteins I interpret as the remains of the swimming bacteria incorporated by beings who became our ancestors as they became us.

The minimal-movement system is so physically and chemically characterizable that complete consensus exists that "motility proteins" are composed of typical carbon-hydrogen bonds, and so forth. All the details are agreed upon by cell biologists and biochemists. But I think an understanding of the extent to which the evolutionary origin involved symbiogenesis must be acknowledged. Such acknowledgment will lead to new awareness of the physical basis of thought. Thought and behavior in people are rendered far less mysterious when we realize that choice and sensitivity are already exquisitely developed in the microbial cells that became our ancestors. Even philosophers will be inspired to learn about motility proteins. Scientists and nonscientists will be motivated to learn enough chemistry, microbiology, evolutionary biology, and paleontology to understand the relevance of these fields to the deep questions they pose.

My primary work has always been in cell evolution, yet for a long time I've been associated with James Lovelock and his Gaia hypothesis. In the early seventies, I was trying to align bacteria by their metabolic pathways. I noticed that all kinds of bacteria produced gases. Oxygen, hydrogen sulfide, carbon dioxide, nitrogen, ammonia — more than thirty different gases are given off by the bacteria whose evolutionary history I was keen to reconstruct. Why did every scientist I asked believe that atmospheric oxygen was a biological product but the other atmospheric gases — nitrogen, methane, sulfur, and so on — were not? "Go talk to Lovelock," at least four different scientists suggested. Lovelock believed that the gases in the atmosphere were biological. He had, by this time, a very good idea of which live organisms were probably "breathing out" the gases in question. These gases were far too abundant in the atmosphere to be formed by chemical and physical processes alone. He argued that the atmosphere was a physiological and not just a chemical system.

The Gaia hypothesis states that the temperature of the planet, the oxidation state and other chemistry of all of the gases of the lower atmosphere (except helium, argon, and other nonreactive ones) are produced and maintained by the sum of life. We explored how this could be. How could the temperature of the planet be regulated by living beings? How could the atmospheric gas composition — the 20-percent oxygen and the one to two parts per million methane, for example — be actively maintained by living matter?

It took me days of conversation even to begin to understand Lovelock's thinking. My first response, just like that of the neo-Darwinists, was "business as usual." I would say, "Oh, you mean that organisms adapt to their environment." He would respond, very sweetly, "No, I don't mean that." Lovelock kept telling me what he really meant, and it was hard for me to listen. Since his was a new idea, he hadn't yet developed an appropriate vocabulary. Perhaps I helped him work out his explanations, but I did very little else.

The Gaia hypothesis is a biological idea, but it's not human-centered. Those who want Gaia to be an Earth goddess for a cuddly, furry human environment find no solace in it. They tend to be critical or to misunderstand. They can buy into the theory only by misinterpreting it. Some critics are worried that the Gaia hypothesis says the environment will respond to any insults done to it and the natural systems will take care of the problems. This, they maintain, gives industries a license to pollute. Yes, Gaia will take care of itself; yes, environmental excesses will be ameliorated, but it's likely that such restoration of the environment will occur in a world devoid of people.

Lovelock would say that Earth is an organism. I disagree with this phraseology. No organism eats its own waste. I prefer to say that Earth is an ecosystem, one continuous enormous ecosystem composed of many component ecosystems. Lovelock's position is to let the people believe that Earth is an organism, because if they think it is just a pile of rocks they kick it, ignore it, and mistreat it. If they think Earth is an organism, they'll tend to treat it with respect. To me, this is a helpful cop-out, not science. Yet I do agree with Lovelock when he claims that most of the things scientists do are not science either. And I realize that by taking the stance he does he is more effective than I am in communicating Gaian ideas.

If science doesn't fit in with the cultural milieu, people dismiss science, they never reject their cultural milieu! If we are involved in science of which some aspects are not commensurate with the cultural milieu, then we are told that our science is flawed. I suspect that all people have cultural concepts into which science must fit. Although I try to recognize these biases in myself, I'm sure I cannot entirely avoid them. I try to focus on the direct observational aspects of science.

Gaia is a tough bitch — a system that has worked for over three billion years without people. This planet's surface and its atmosphere and environment will continue to evolve long after people and prejudice are gone.

Остановившийся на полпути

Оригинал взят у в Остановившийся на полпути

Посмотрел замечательный фильм про знаменитого бонобо Канзи, который понимает человеческую речь и общается с людьми при помощи лексиграм (а не жестов). Множество документальных съемок, демонстрирующих интеллектуальные возможности обезьян. Вообще говоря, здесь как раз тот случай, когда лучше один раз увидеть. Фильм из четырех частей (три под катом). Понравилось, как бонобо играли в «страшное»: одна обезьяна надевает себе на голову маску злой обезьяны и начинает пугать другую. Когда с Канзи разговаривают по телефону – тоже впечатляет.




После просмотра не отпускает вопрос: если человекообразные настолько развиты, то отчего живут как [прочие] обезьяны. Если для выживания такие способности им не нужны, каким образом они появились в ходе эволюции? Тогда, получается, естественный отбор за это не в ответе. Вот в свежей статье Е.Кунин пишет, что у эволюции генома можно обнаружить некие законы, и что они обходятся без отбора. Может, с эволюцией интеллекта происходит похожая штука. Кроме того, способности врановых и попугаев очень высоки, почти на уровне шимпанзе – а эволюционная история совсем иная и мозгов совсем ничего.











Фильм давнишний, 1993 года. С тех пор Канзи возмужал, а исследователи заметно постарели… Канзи стал отцом. Зовут малыша Тико и 1-го июня сего года ему исполнился год. Ему уже дают играть с iPad. Чтобы привыкал – впереди много занятий.

В мозгу человека нашли "животную" зону

Мозг человека специально "заточен" распознавать в окружающих объектах животных. Такой вывод сделала группа ученых по итогам прямого сканирования активности мозга. Работа исследователей опубликована в журнале Nature Neuroscience, а коротко о ней пишет портал ABC Science.

Специалисты работали с добровольцами, страдающими эпилепсией, которым необходимо хирургическое лечение. Ученые имели возможность напрямую подсоединить электроды к мозгу испытуемых и измерять активность отдельных нейронов. Людям показывали изображения различных объектов и оценивали, как реагируют на них те или иные нервные клетки.

Оказалось, что определенные нейроны в правой части зоны, называемой миндалевидным телом, активно реагируют, когда человек видит изображения любых животных независимо от размера. У людей эта зона участвует в формировании положительных и отрицательных эмоций (например, страха и удовольствия).

Ученые полагают, что столь отчетливый ответ на изображения животных именно в нейронах миндалевидного тела сформировался в ходе эволюции, когда далеким предкам человека (и других животных) необходимо было быстро распознавать в окружающей природе как хищников, так и потенциальных жертв.

Ранее другой коллектив ученых обнаружил в мозгу человека особые нейроны, реагирующие на изображения конкретных персонажей или известных архитектурных памятников. Более того, исследователи выяснили, что за узнавание каждого такого объекта отвечает индивидуальная нервная клетка.

Ссылки по теме - Humans hardwired to tune into animals - ABC Science, 30.08.2011

Epigenetic 'Memory' Key to Nature Versus Nurture

 Added: Monday, 25 July 2011 at 2:15 AM

ScienceDaily (July 25, 2011) — Researchers at the John Innes Centre have made a discovery, reported this evening (24 July) in Nature, that explains how an organism can create a biological memory of some variable condition, such as quality of nutrition or temperature. The discovery explains the mechanism of this memory -- a sort of biological switch -- and how it can also be inherited by offspring.

 

 

The work was led by Professor Martin Howard and Professor Caroline Dean at the John Innes Centre.

Professor Dean said: "There are quite a few examples that we now know of where the activity of genes can be affected in the long term by environmental factors. And in some cases the environment of an individual can actually affect the biology or physiology of their offspring but there is no change to the genome sequence."

For example, some studies have shown that in families where there was a severe food shortage in the grandparents' generation, the children and grandchildren have a greater risk of cardiovascular disease and diabetes, which could be explained by epigenetic memory. But until now there hasn't been a clear mechanism to explain how individuals could develop a "memory" of a variable factor, such as nutrition.

The team used the example of how plants "remember" the length of the cold winter period in order to exquisitely time flowering so that pollination, development, seed dispersal and germination can all happen at the appropriate time.

Professor Howard said: "We already knew quite a lot about the genes involved in flowering and it was clear that something goes on in winter that affects the timing of flowering, according to the length of the cold period."

Using a combination of mathematical modelling and experimental analysis the team has uncovered the system by which a key gene called FLC is either completely off or completely on in any one cell and also later in its progeny. They found that the longer the cold period, the higher the proportion of cells that have FLC stably flipped to the off position. This delays flowering and is down to a phenomenon known as epigenetic memory.

Epigenetic memory comes in various guises, but one important form involves histones -- the proteins around which DNA is wrapped. Particular chemical modifications can be attached to histones and these modifications can then affect the expression of nearby genes, turning them on or off. These modifications can be inherited by daughter cells, when the cells divide, and if they occur in the cells that form gametes (e.g. sperm in mammals or pollen in plants) then they can also pass on to offspring.

Together with Dr Andrew Angel (also at the John Innes Centre), Professor Howard produced a mathematical model of the FLC system. The model predicted that inside each individual cell, the FLC gene should be either completely activated or completely silenced, with the fraction of cells switching to the silenced state increasing with longer periods of cold.

To provide experimental evidence to back up the model, Dr Jie Song in Prof. Dean's group used a technique where any cell that had the FLC gene switched on, showed up blue under a microscope. From her observations, it was clear that cells were either completely switched or not switched at all, in agreement with the theory.

Dr Song also showed that the histone proteins near the FLC gene were modified during the cold period, in such a way that would account for the switching off of the gene.

Funding for the project came from BBSRC, the European Research Council, and The Royal Society.

Professor Douglas Kell, Chief Executive, BBSRC said: "This work not only gives us insight into a phenomenon that is crucial for future food security -- the timing of flowering according to climate variation -- but it uncovers an important mechanism that is at play right across biology. This is a great example of where the research that BBSRC funds can provide not only a focus on real life problems, but also a grounding in the fundamental tenets of biology that will underpin the future of the field. It also demonstrates the value of multidisciplinary working at the interface between biology, physics and mathematics."

Science News

 

Выжить — это убийственно дорого

Способен ли все-таки прогресс дать обещанное счастье всему человечеству? Когда был более прав философ Жан-Жак Руссо — веря в усовершенствование человека или выражая свой знаменитый скептицизм по этому же поводу? И возможна ли вообще справедливость, если удобное проживание на планете Земля становится все дороже и оказывается не по карману миллиардам людей и десяткам стран? Такие большие вопросы ставят перед нами крошечные бактерии, бросающие вызов могучим антибиотикам (Подробнее читай: «Микроб, который нас победит»).

 

В 1928 году Александром Флемингом был открыт и вскоре стал лекарством пенициллин. Им можно было вылечить болезни совершенно ясной этиологии, как говорят врачи, то есть с понятными причинами: заражение раны или воспаление легких от переохлаждения. То есть до появления антибиотика у человека был выбор, заниматься ли травмоопасным делом и пренебрегать ли шарфом зимой. Теперь, получается, выбора нет. Мы отправляем в рот обычный помидор, соблюдя правила гигиены, а он нас хорошо если не убивает. А ведь еще за полвека до антибиотиков Пас­тер и Мечников спасли людей от эпидемий, и тогда казалось, что прогресс действительно победил. Что же думать теперь?

Ясно одно: у человечества не хватает денег на созданную им цивилизацию. И мы в России в этом смысле еще далеко не самые бедные.

А у самых богатых, оказывается, свои проблемы. Медицина в США лучшая в мире, но при этом она настолько дорогая, что, похоже, не может быть распределена на всех. Многие там остаются без надлежащего медицинского обеспечения. Казалось бы, в Северной Европе эти проблемы решены, высокие налоги и социальные расходы обеспечивают ей первенство в мире по уровню качества доступной медицинской помощи. Но когда подобное смогут себе позволить бедные ныне страны? Не оплачено ли благосостояние одних нищетой других? Ведь поделиться благополучием, попытавшись усреднить его уровень на планете, никто в богатых странах не готов. Максимум эффекта от международных программ — это скудная благотворительность и «программы развития», лишь закрепляющие на мировом Юге отсталость и статус стран-должников.

Два самых популярных зрелища глобального телеэфира — футбол и «Формула-1». Эти два «ф» могут кому-то напомнить окончание в названии тоже очень популярного в мире российского напитка. Но тот помогает забыться, а эти выражают философию стремления во что бы то ни стало вырваться вперед. Вспомним еще пандемию самого страшного средства забвения — наркотиков. Забыться или мчаться вперед все быстрее и быстрее — похоже, у нас и вправду только такой выбор. Утопия всеобщего равенства, хотя бы только равенства возможностей, рушится. Только те люди и те страны, которые стремятся обойти других, могут пытаться поймать ускользающий хвост благополучия, для обеспечения которого нужно все больше денег, все больше налогов и все больше лекарств.

Но спасение ли это, не замкнутый ли круг? В иной богатейшей стране благополучнейший менеджер глотает дорогой овощ из элитной диеты, и этот овощ погружает его в состояние унизительного поноса — того способа справлять нужду, который так хорошо знаком бедным. Восставшая из клеточного ада колония бактерий бросается изнутри на его образцовый, весь в кубиках мышц живот и терзает, как какого-нибудь руандийца с тремя начальными классами за плечами. И выясняется, что закон страдания общий для всех. Может быть, справедливость только в этом? Мы-то ждали, что она сделает всех счастливыми, а она, оказывается, в том, что каждый, как и прежде, может оказаться несчастным.

Прогресс в целом начинает выглядеть как самый большой «пузырь», который надуло современное человечество. Он все дороже и требует все новых и новых расходов. Сего­дняшняя медицина надеется на искусственные органы, но какие новые проблемы и затраты они породят? Мы этого не знаем, как не знаем, лопнет ли этот «пузырь», как и когда. Известно лишь, что все они рано или поздно лопаются. Может быть, «пузырь» прогресса проткнут своими копьями сами всадники Апокалипсиса. А может быть, и после этого второго «Большого взрыва» еще поживем.

И все же отсидеться не удастся. Да, гонка порождает новую гонку, но выйти из игры нельзя. Глобальное соревнование стран, технологий и, в конечном счете, людей, начавшееся в XX веке, не признает просто зрителей — как бы ни были велики риски, не участвовать еще хуже. В сущности, мы в России сейчас и решаем вопрос, в какую разновидность инновационных игр и в какой команде играть. Как показывает наличие тех же бактериофагов, мы на это способны. А дисквалификация недопустима.