Cosmic Apprentice: Dispatches from the Edges of Science (20 page)

NAMES ARE NOT THINGS, but they come mighty close.

“What’s in a name?” asks the star-crossed Juliet, feminine force of the play that bears her name. “Art thou not Romeo, and a Montague?”

“Neither, fair maid, if either thee dislike.”

Juliet is right to worry about her lover’s name, and the contentious family history it signifies cannot just be wished away. There is the love of Romeo and Juliet, and there is what society makes of that love, and however much society betrays the essence of that love with its fatal expectations, those expectations, reinforced by would-be arbitrary names, cast a real pall over the young lovers’ romance.

The name, if not quite a magic word making something that was not yet there jump into existence, creates a kind of field, organizing our expectations and creating real-world effects, for better or worse, according to a logic of self-fulfilling prophecy. Romeo should be against Juliet because she is a Capulet; Gondwana and Pangaea, with their proper names, must refer to real supercontinents that once existed.

HIV is another, highly problematic, example. Leave aside any medical protocols that were broken (and that HIV’s founder, Robert Gallo, was censured; and that the discovery of the putative virus was never made according to the Koch postulates hitherto considered crucial in virology; and that there are apparently no electron micrographs of the virus; and that tests identify antibodies that can be to a variety of proteins; and that Peter Duesberg, whose career was effectively ruined for questioning the HIV-AIDS connection, offered to inject himself with HIV to prove his deep doubt; and that Luc Montagnier, one of the Nobel Prize winners for the discovery of HIV, has become a target for derision because he does not espouse the HIV-AIDS party line),
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and just for the moment consider the acronym: Human Immunodeficiency Virus. At once subtly and blindingly obviously, the name contains the answer to the question we are supposed to be still asking. Like Molière’s “dormitive principle” that was a sufficient explanation for why we sleep, but in a tragic rather than comic register, the name simply restates the desired answer while foreclosing the question. Now no one in their right mind wants to wade into the vat of retroviral sludge and priestly accusations of denialism and conspiracy theory and weak minds that is this politically loaded issue. That’s why I’m not going to get into this here. I have smaller fish to fry.

IN HERNDON’S VIEW, our planet’s decompression comes about as a natural rebound from the crushing compression caused by the great overburdening weight of the gas giant stage. Earth’s surface area must increase to accommodate expanded planetary volume, and it does so by “rifting,” forming surface-splitting cracks. Cracks with underlying heat sources produce lava that forms the midocean ridges and paves the ocean basins before ultimately falling into and in-filling cold decompression cracks observed as oceanic trenches in a process that explains ocean floor geology without assuming mantle convection. Moreover, georeactor-produced heat, channeled to the surface, powers hot spots such as Iceland and Hawai‘i and aids in continent fragmentation, such as presently occurs at Afar in the East African Rift System.

This last Herndonian tenet is especially contentious (for those who even know about it), because plate tectonics was itself a hard-won, revolutionary geological idea, itself one of the poster children of scientific revolutions. Bold scientific thinking seems to be somewhat addictive, as if removing the chains of institutional decorum allowed one to run free through the Elysian fields. One book by Herndon, emboldened by the prize-winning journalist Guy Gugliotta’s accolade that he is a “Maverick Geophysicist,”
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is even named
Maverick’s Earth and Universe.
(If you are interested in looking at other mavericks and their claims, and attempts to judge them outside received opinion, in a contemplative noncommercial setting, I recommend the website Science Guardian: Paradigms and Power in Science and Society.)
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Obviously the tenability of Herndon’s connected suite of geological ideas won’t be settled here, but a couple of aspects of them are highly relevant to the whole question of scientific epistemology, of science-in-the-making and how the layperson, or indeed specialized scientists themselves, are supposed to adjudicate new possibilities of “how things really are” in the modern environment of institutionalized, governmentally supported, and fundamentally conservative science.

The inertia of model making as opposed to fresh consideration of conflicting evidence is itself one of Herndon’s pet peeves. Although the division is no more ironclad than that between science and pseudoscience—Einstein initially dismissed quantum mechanics for its “spooky action at a distance” (a criticism that, when you think about it, might also be applied to Newtonian gravity!)—Herndon is keen to differentiate between model making and real science. And one signature of model making, with its emphasis on mathematical simulations, is the tendency for model makers to absorb would-be counterfactual evidence into their model by making ad hoc hypotheses to accommodate them. One of the more famous historical examples is from Ptolemaic astronomy. Observations of the outer planets from Mars to Neptune with Earth as the assumed solar system’s center must account for these planets appearing to move backward or “retrograde” (still familiar talk in astrology) for two to six months at a time.

This artifact of a “mistaken” or at least not as elegant frame of reference is reminiscent of the wagon or car wheels appearing to spin backward in films, because of a discrete number of frames per second in which the wheels fall short of a complete revolution before being caught on film. In Ptolemaic astronomy the backward movements were handled by the ad hoc hypothesis of epicycles—perfect circles that moved around off-centered points (equants) of a circle (deferent) around Earth, with each planet having a separate set of parameters and the center of the orbit never exactly Earth itself. A good example of a model that reproduced observations but wasn’t really true, the Ptolemaic epicycles (though Copernicus also used them, because it wasn’t yet realized that the planetary orbits were elliptical) might be compared with a description of your car going backward or “retrograding” when another car passes you on the way to work: descriptively accurate with regard to your chosen frame of reference, but not exactly true.

Strikingly similar, one might argue, is Herndon’s still-heretical view, based on Earth’s enstatite–chondrite composition, addressing the density anomaly in the standard model, accounting for the tendency of the geomagnetic field’s polarity to flip (much easier if generated by a georeactor), which was published and developed
before
the discovery of Jupiter-sized extrasolar planets close to their suns. The discovery of such giant near-to-sun planets has caused some scrambling amid the well-funded planetary model makers. Herndon’s view is comparable in its intellectual housecleaning way to Copernicus’s repositioning of the Sun to be at the center.

The relevance for modeling here is that Herndon’s “heretical” but more elegantly integrative view does not require ad hoc notions such as recently proposed “planetary migration” (of big outer planets to close-to-sun orbits) to account for the new evidence of Jovian-size extrasolar planets traveling in the range of one astronomical unit, or about the distance of Earth from our Sun, around their stars. Indeed, recently detected antineutrinos with a nuclear reactor spectrum coming from inside Earth suggest that as much as 26 percent of deep-Earth heat from uranium and thorium is produced by the georeactor (15 percent, according to Italian data).
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Herndon differs from the geophysicist’s tradition in that he rejects the assumption that our changing Earth has maintained a constant diameter. Continental drift and plate tectonics
assume
that Earth’s diameter has remained constant at today’s value through time. Herndon argues for a “continental cracking” of the originally continuous lithosphere as Earth decompresses. Hot cracks are forced to widen as the lithosphere breaks and spreads. Seafloor lava, pumice, and basalt spew out. Cold cracks, recognizable to geophysicists as their “subduction zones,” open to become the ultimate repositories for the basalt and the sediments that ride in on it.

Here, derived from Earth’s early origin as a Jupiter-like gas giant, is a new geoscience paradigm that explains myriad observations attributed to plate tectonics. Herndon’s explanation rejects “mantle-heat convection theory,” for which he claims there is very little evidence. Proposed by Alfred Wegener, John Tuzo-Wilson, Maurice Ewing, Frederick Vine, Drummond Matthews, William R. Dickinson, and others, the grand “continental drift–plate tectonics” paradigm plate-tectonics vision is itself a poster child for interdisciplinary scientific revolutions. Will future scientists look on in dismay at the rigid institutional structures Butler saw emerging, roadblocks that prevented Herndon’s connected suite of professional geophysical concepts of our “indivisible Earth” from being considered?

Herndon is not the only victim of rigid thought-styles. Another may be the thirty-year rejection of the “heretical” science of the marine zoologist Donald I. Williamson, working out of the Port Erin Marine Station on the Isle of Man. The English historian of biology and medicine Frank P. Ryan tells Williamson’s story of “saltatory evolution” in his recent works on metamorphosis, and the work is also documented in a 2011 film
Hopeful Monsters
by Robert Sternberg of Imperial College London.
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Animal larvae may evolve by hybridization: fertile crosses between members of different animal phyla may account for extraordinary metamorphoses in the sea. Despite intriguing evidence for these claims,
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there is extreme reticence among professional evolutionary biologists to even print Williamson’s ideas. In detailing evidence for evolution by hybridization, Williamson explicitly disputes Darwin’s central tenet that “descent with modification” (as he termed evolution) occurs slowly by gradual accumulation of naturally selected variations.

Darwin’s view was made in contrast to Christian views of special creation. Darwin, in
The Origin of Species,
acknowledges Aristotle’s knowledge of natural selection but dismisses the philosopher and early biologist’s views. Ironically, however, Aristotle dismissed natural selection because he in turn associated it with Empedocles’s pre-Socratic myth that organs once roamed Earth on their own, occasionally joining up and fusing as they were naturally selected into new forms. Aristotle seems to have thrown “the baby out with the bathwater,” and Darwin to have rejected rapid evolutionary change because it smacked of special creation. In both cases we can see these brilliant minds overreacting to protect against the excesses of their ancestors: in Aristotle’s case, against mythic accounts of chimeric unions among men, animals, and gods that violated observations of nature; and in Darwin’s case against the notion of simultaneous creation of species, the monotheistic explanation. Not even the greatest scientists, aware of the need for evidence, are immune from a tendency toward dogma. Ideology inhibits inquiry. New myths are created as people overshoot in their zeal to refute old myths. Everybody needs something to believe in, even nonbelievers.

Gazing into the spiral of the history of science is a fascinating spectacle: not only do “truths” become “myths,” but, as the spiral of evidence unwinds, some of what formerly was dismissed as myth, with new observations and new methods by new investigators under changed social conditions, sometimes is resuscitated as scientifically valid, with qualification, after all. Science nurtures endless curiosity and further investigation, exploration, and description. Really new scientific truths have come from kooks who need criticism and suffer failures. Beyond the battles of cranks and dogmatists dug deep in their holes are the alliances of skeptics and the curious, able, if evidence warrants, to change their minds. Reexamination, reinterpretation, reevaluation, and reinvestigation are intrinsic. The progress of knowledge through a combination of critical inquiry and open-mindedness is science itself.

CODA

After my mother died, her longtime companion, the highly respected Spanish microbiologist Ricardo Guerrero, when I asked him about the character of her rebellious views, mentioned that, though she’s an intellectual heroine in Spain, there were three things about her he refused to discuss there: (1) 9/11, (2) the
PNAS
affair (in which she, availing herself of her privilege as a member of the National Academy of Sciences, had Williamson’s paper on fertile cross-species unions published in the
Proceedings of the National Academy of Sciences,
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and (3) AIDS (where she questioned the canonical HIV-AIDS connection). When I asked him what he thought of her advocacy of Gaia theory, however, he quickly answered that it was one of the greatest scientific theories of the twentieth century. This contrast between Guerrero and the neo-Darwinists (whom Gould called “Darwinian fundamentalists”) exemplifies the existence of the kook–critic continuum of my subtitle: the very progress of science depends on tireless questioning of received opinions, especially when they are both supported by evidence and threaten entrenched assumptions, money flows, and careers. Truth, or its asymptotic representatives, may be stymied but in the long run “will out,” as Shakespeare put it.

CHAPTER 12

METAMETAZOA

LIKE A GRAY GEODE CRACKED OPEN
to reveal coruscating crystals of amethyst, the history of science sometimes surprises. Empedocles imagined an ancient world of organs mating and merging with one another to create bizarre half-hewn beasts, the most favorable matches surviving. Aristotle, schooled in Platonic typology and sick of unlikely stories of cross-species mating, metamorphosed mortals, and shape-shifting gods, rejected Empedocles out of hand.

But the chronological vortex of knowledge’s wayward march turns on itself like a DNA molecule: Now we know that Aristotle, first biologist though he may be, was wrong on both counts. Empedocles’s intuition of natural selection and symbiosis was on the mark. Nothing as ghoulish as crawling pancreas and self-pumping hearts getting it on in the primordial mud, but today’s textbooks teach that our organelles, parts of the cell outside the nucleus, once swam as beings on their own. These are the mitochondria, and they give you the genetic intracellular infrastructure to breathe oxygen, a toxic waste gas first released in massive quantities into the atmosphere by cyanobacteria, which came up with the clever idea of using water to grab their hydrogen atoms. The archaea victimized by bacterial air pollution were saved by bacterial infection. We now celebrate their double victimhood with every breath we take, as their infection evolved into mitochondria at the heart of all animal metabolism and energy use. In retrospect, Empedocles was right. Although there’s no evidence of his “man-faced ox-progeny” that “perished and continue to perish,”
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there are, we could say, “bacteria-bodied archaea-progeny” that “survived and continue to survive.” You are one of them!

A similar story could be told of the scientific disproof of spontaneous generation. Lazzaro Spallanzani and Louis Pasteur with curved glass flasks protecting inoculation proved that life doesn’t arise from nonlife—meat doesn’t beget maggots, mice don’t defrag from rags. Yet, flash forward once more, to the origins-of-life experiments showing that amino acids naturally form when ammonia and other hydrogen-rich compounds are exposed to an energy source, and the possibility arises that life
can
occur from nonlife and not just be seeded by spores from the air (or space; see
chapter 4
). As in the T. S. Eliot poem, we return to a different floor of the expanding vortex, the Escherian staircase of science. Another example is the great Sphinx at Giza, whose chimeric mancat body is made of stone, yellowish calcium carbonate studded with nummulites, “coin stones” that Herodotus thought were fossilized lentils but are actually the remains of foraminifera. Live forams fill the oceans, their tiny spiked carbonate bodies usually no bigger than a pinhead but sometimes growing to inches without giving up their status as single cells. Cut transversely, they show spirals. And many of their species, whose variety tracks the hidden treasure of fossil fuels, are symbiotic: Again the baroque vortex turns, the mythological blend that is the Sphinx is a creature of the imagination, is made up, but its real body is made up of the fossil remains of real chimeras, as are the Great Pyramids themselves, 40 percent of whose yellow limestone consists of fossil forams, many of them symbiotic with specific species of diatoms and dinomastigote algae that floated in the Tethys Sea, during the Eocene, more than thirty million years ago.

The oldest known sphinxes are from Anatolia, Turkey, and are over nine thousand years old. The oldest fossils of possibly chimeric beings, such as acritarchs, are over three billion years old. More recently, in attempting an untested sleight with a piece of Dominican amber, I dropped it on the floor of my mother’s lab at the Morrill Science Center at the University of Massachusetts. This missed trick with the fossilized tree sap on loan from David Grimaldi of the American Museum of Natural History paved the way for thin-section electron microscopy. The cracked amber revealed a twenty-million-year-old termite whose hindgut was full of petrified swimmers--spirochetes, cellulose-digesting protists, and the spore-forming filamentous bacterium,
Arthromitus
—equivalent to
Bacillus cereus,
identical except for two or three plasmids, which are DNA coiled into tight rings, to
Bacillus anthracis,
the causative agent of anthrax.
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Life’s tenure on this planet has been so long, and its grip so tight, that many things that seem to be singular organisms reveal themselves—like the Sphinx or that tawny piece of Miocene butterscotch cracked open like Humpty Dumpty to reveal the termite
Mastotermes electrodominicus,
now known only as a living fossil from northern Australia, or the fossil itself, containing a miniature Pompeii in its swollen hindgut—to be constructed of other life-forms. As the helix of history turns, we descend deeper along this escalator into life’s ancient forms, its ghostly archive and living tombs. It slipped out of my hand, but that magical piece of amber made the cover of
Science News,
one of science’s leading magazines.
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HOW WILL THE BODY AND ITS LIFE come to have been construed by the future of biology? And more important, how will these be construed by a mythopoiesis and popular mythology whose social birthright now, through the midwife of contemporary biology, may create the “facts” from which a common future understanding will come? Transformations of classical models are already under way in contemporary biology, and here I look at three of them: Gaia theory (geophysiology or Earth system science), symbiotic evolution (symbiogenetics), and bacterial omnisexuality (hypersexuality).

It is necessary, first of all, to distinguish the tenor of a “new biology,” whose theoretical sources are Gaia, symbiosis, and gene-trading bacteria, from the tenor of the more traditional biology for which the paradigm of individuality is the animal body. Modern biology, informed by cellular ultrastructure through electron microscopy and detailed knowledge of gene sequences, has supplemented or even negated the long-standing division between plant and animal kingdoms.
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Although vying for acceptance and mutually inconsistent, the two most favored current phylogenies split life into either three domains or five kingdoms. The five-kingdom classification system still reserves a place for the kingdoms Plantae and Animalia (both subsumed within the superkingdom Eukarya).

Carl R. Woese’s three-trunked tree of life, based on typical sequences of RNA in the ribosomes of cells, contains no separate kingdoms for plants or animals, for it lumps both within the eucarya (organisms composed of cells with nuclei), reserving two separate taxa (archaea, which Woese used to call archaebacteria, and bacteria, formerly eubacteria) for the rest of life. Molecular biology and microbiology have not only confirmed Charles Darwin’s paradigm-shifting argument that we are animals but have also provided evidence that the most fundamental fence in life lies not between plants and animals but between eukaryotes—cells with nuclei, mitochondria (and, in the case of algae and plants, plastids)—and prokaryotes, also known as monerans or bacteria.
Homo sapiens
clings to its crown as the walls of its kingdom come crumbling down. Moreover, each eukaryotic “animal” cell is, in fact, an uncanny assembly, the evolutionary merger of distinct prokaryotic metabolisms. Strictly speaking, there is no such thing as a one-celled plant or animal.

Easily recognizable life-forms appear only at the middle range. If we step back from, or come closer to, the living canvas, organisms blend into a pointillist landscape in which each dot of paint is also alive. In short, all previous biology has been grossly zoocentric.

Although psychoanalysis and phenomenology and their popular offshoots have disturbed a monolithic conception of mind, a monolithic notion of “the” body remains largely intact. In classical medicine, the body is considered a type of unity. Cancer, paradigmatically, but other diseases as well, are discussed with the rhetoric of war: the body is “attacked” and “invaded”; it puts up “defenses” and “fights back.” This medical model of the body-as-unity-to-be-preserved, though, of the body proper, is besieged by the new biology.

A radical rerendering of the body is under way in accordance with three models from the new biology, namely, symbiosis, Gaia, and prokaryotic sex. This reformulation augurs a breakdown of the medically proper animal body, which is simultaneously driven in at least two new directions, one post-structural and the other medieval-microcosmic in terms of extended selves within a living environment. Gaia refers to the biosphere understood not as environmental home but as body, as physiological process. Prokaryotic sex, or bacterial omnisexuality, refers to the fluid genetic transfers, by definition sexual, among continuously reproducing bacteria.

The consonance with certain post-structuralisms occurs in that the new biology parts company with the unitary self assumed in the zoocentric model. The expression “medieval-microcosmic” is inadequate but suggests the possibility of correspondences among prokaryotic, eukaryotic, zoological, and geophysiological (Gaian) levels. It now appears that a type of individuality has appeared at each of these levels. Both spatially and temporally more inclusive, Gaia and animals dwell within a holonomic continuum, superordinating the smaller beings of which they are made.

THE BODY AS CHIMERA

The body as seen by the new biology is chimerical. Instead of the tripartite division of that mythical creature of antiquity, the chimera, into lion, goat, and snake, the animal cell is seen to be a hybrid of bacterial species—although the word
species,
as seen below, is not that apt when applied to bacteria. Like that many-headed beast, the microbeast of the animal cell combines into one entity bacteria that were originally freely living, self-sufficient, and metabolically distinct. Mitochondria populate and energize virtually all eukaryotic cells. These specialized cell parts respire; they take up oxygen and produce carbon dioxide, making ATP (adenosine triphosphate), a kind of molecular capacitor storing energy within cells. It is now widely accepted among biologists that these tiny intracellular power stations were once autonomous respiring bacteria. Eukaryotic cells evolved over a billion years ago, probably when respirers entered and did not kill but
were incorporated by
larger anaerobic archaea. The archaea include sulfur-breathing, acid-resistant, and heat-tolerant extremophiles—an impressive range of resistances that may reflect an ancient ability to survive hot temperatures and meteoritic bombardments of the early Earth. Over time, the two distinct metabolisms merged, and the new incorporated cells produced more and hardier cells than either line of their unincorporated relatives.

Some intriguing signs recall the ancient free lives of mitochondria. Although they lie outside the cell’s nucleus, they have their own genetic apparatus, including their own DNA, messenger RNA, transfer RNA, and ribosomes enclosed in mitochondrial membranes. Unlike the DNA of the nucleus, but like bacterial DNA, mitochondrial DNA is not coated by histone protein. Mitochondria assemble proteins on ribosomes very similar to the ribosomes of bacteria. Both mitochondrial ribosomes and those of respiring bacteria tend to be sensitive to the same antibiotics, such as streptomycin. Perhaps most telling, mitochondria reproduce on their own timetable and in their own way, forgoing the complex mitosis of the nucleus for a simple bacterium-like division. They engage in the nonsystematic genetic transfer that characterizes bacterial sex. All in all, they behave like prokaryotic captives.

As early as 1893, the German biologist A. F. W. Schimper proposed that the photosynthetic parts of plant cells came from cyanobacteria (often still called blue-green algae, but the term is a misnomer, since they have no nuclei in their cells). The French biologist Paul Portier believed by 1918 that mitochondria are the descendants of bacteria that had become lodged within the cells of animals and plants. In the first quarter of this century, the American anatomist Ivan Wallin and the Russian scholar-biologist Konstantin S. Mereschovsky had independently come to the same conclusion. In 1910 Mereschovsky, who taught at the University of Kazan, published an essentially contemporary view of the origin of eukaryotic cells from various kinds of bacteria.
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Experiments at isolating the putative bacterial partners, however, have always failed; the evidence for cooperation rather than parasitism was overlooked and dismissed as “sentimentalism.” Herbert Spencer equated the necessary evils of competition with an eminently desirable social progress, and Thomas Huxley referred to the animal world as a “gladiator’s show”; Pyotr Kropotkin wrote
Mutual Aid,
and others implicitly linked evolutionary ideas of symbiosis to labor unions, mutualistic societies, and socialist ideas.

The animal cell, as well as the cells of plants, fungi, and protoctists (a miscellaneous eukaryotic kingdom composed mainly of algae and what were once called protozoa),
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combines oxygen-using mitochondria and a larger host cell. Despite its suggestive appearance, the nucleus was probably never autonomous but, rather, the result of interactions among members of cellular communities that evolved into cells. The same cannot be said of the chloroplasts of plants and the plastids of photosynthetic protoctists such as algae. The grass-green photosynthetic organelles of all plants may be the descendants of a single, wildly successful bacterium, now shackled, albeit gently, in its cytoplasmic prison.

A body of behavioral evidence similar to that for mitochondria supports a cyanobacterial origin for the pigmented bodies within algae and plants. The ancestors of all plants were probably cells with mitochondria that ate, but never digested, their live vegetarian dinner. The undigested photosynthetic organisms grew inside their hosts, offering a steady diet of metabolites in return for protective cover and continued life.

The red plastids of seaweeds also probably come from autonomous bacteria. If one compares the sequence of nucleotide bases in the ribosomal RNA of red plastids in the seaweed
Porphryridium
with that of RNA in the seaweed’s own cytoplasm, the resemblance is less than 15 percent. Making the same comparison with the ribosomal RNA of the cyanobacterium
Synechoccus
and the plastid of the swimming green protist
Euglena
yields similarities of 42 and 33 percent, respectively. Indeed, there have always been behavioral clues to the xenic origins of the eukaryotic cell.