Scientific realism

Scientific realism is a stance holding that scientific theory can reliably approximate true knowledge of reality independent of the human mind and not perhaps be, though appearing true, severely or even completely false.^[1]^{[clarification needed]} In philosophy of science, scientific realism crystallized around a 1975 publication by Hilary Putnam, fending off the two main scientific antirealist or nonrealist positions—logical positivism's operationalism and instrumentalism.^[2]

Scientific realism in brief

Scientific realism does not posit that all knowledge is scientific, but that scientific knowledge is one category of real knowledge.^[2] This position seems odd versus populist discussion of science, yet many philosophers of science maintain that scientific theory cannot offer verified true knowledge of reality.^[3] A naive scientific realist would regard scientific theory—even at unobservable aspects—to rival direct observation.^[4] Most pure scientists are fallibilist, however, acknowledging the conceptual and unverifiable nature of scientific theory.^[4]

Holding theory

Not indicating methodology, inference, and justification, scientific realism does not describe scientific epistemology—development of scientific knowledge—but holds that scientific theory, existing, itself offers justified knowledge of reality, thus general epistemology. (Selective variations of scientific realism may suggest how scientific theory is to be justified.) Though positing truth, scientific realism's focus is unobservable entities, relations underlying observations, and thorough explanation of observed events,^[5] and so is a metaphysic.^[5]

Questioning theory

Theory truth can be questioned particularly at existence of unobservable entities—invisible to unaided human senses—or at other unobservable aspects, such as principles.^[6] Explaining phenomena as interactions of multiple observable entities, two scientific theories might pose far differing unobservable aspects—entities, properties, processes, relations, principles, laws—to explain the same observations, and novel predictions deduced from both theories might be successful, thus raising the question of either theory's not merely explanatory value and predictive value'' but ultimate truth value.^[7]

Doubt at entities and aspects

An electron has not been directly observed—its existence is inferred. Yet by the data, electrons flit into and out of existence in a vacuum,^[8] appear in multiple places at once, react to human observation, and so some believe them as effects of human observation itself. Or the nature of a real entity might be doubted. Some regard a virus as an extremely simple microorganism hijacking cells, whereas others regard a virus as a complex molecule used by cells. Or a theory might contain an explanatory principle, perhaps a biochemical imperative of nucleic acid—RNA and DNA—to selfreplicate their own molecular sequences and so by chance develop molecular sequences encoding protein molecules, form cells—beginning life—and now control and direct all life. Some doubt that DNA is controlling the cell to begin with. Some maintain that we do not know what life is to begin with.^[9]

Scientific realism's summary

Scientific realism does not necessarily agree with prevaling theory, as a seemingly radical theory—such as theory of special relativity in 1905—is often premised upon offering greater scientific realism than orthodox theory. Yet a scientific realist at least roughly agrees with one of the following statements [Leplin, 1984, p 1]:

Scientific theories make genuine, existential claims.
The best current scientific theories are at least approximately true.
The central terms of the best current theories are genuinely referential to independent reality.
The predictive success of a theory is evidence of the referential success of its central terms.
A scientific theory may be approximately true even if referentially unsuccessful.
A scientific theory's predictive success is sufficiently explained as its approximate truth.
The (approximate) truth of a theory is the only explanation of its predictive success.
The theoretical claims of scientific theories should be read literally, and are definitively either true or false.
The history of at least the mature sciences shows progressive approximation to a true account of the physical world.
Science aims at a literally true account of the physical world, and its success is its progress toward achieving this.

Pure philosophy

Pure philosophy's major branch concerning the sources, nature, and limits of justified—not merely presumed—knowledge is epistemology, generally held to have two general forms: empiricism and rationalism. Empiricism presumes all justified knowledge rests on experience—direct sensory input—and sound inference thereupon. Pure philosophy's major branch logic concerns the inferences, either inductive or deductive. In induction, the truth of the premises proves tenable the conclusion, possible and perhaps seeming probable yet not entailed. In deduction, the truth of the premises proves the truth of the conclusion, entailed if all the premises are true. In any deduction, however, a premise somewhere—perhaps a background principle or a fundamental theory taken for granted—was induced. So neither induction nor deduction is foolproof. Knowledge eluding epistemology—justified knowledge—enters pure philosophy's major branch metaphysics, speculation on traits of reality beyond observation and logic. Rationalism appeals not to logic but to reason to identify a principle not introduced by one's experience yet perceived as selfevidently true—and perhaps inferring logically thereupon—thus justified knowledge in epistemology and recovered from metaphysics.

Logic: Theory of inference

When the general public uses the word logical, it tends to be synonym, rather, for reasonable, a conclusion or principle seeming likely or even obvious, not formally logical. Formal logic is uses mathematic equations revealing connections or disconnections between phenomena.

Induction

By an inductive inference, the truth of the premises proves tenable the truth of the conclusion. In induction's classic form, examination of specific instances premises inference of a general law covering unexamined instances. If one observes a lake and sees only white swans, one might induce that all swans are white, conclusion proved tenable, yet not entailed.

Deduction

In a deductive inference, the truth of the premises proves the conclusion entailed. The deduction's classic form, a general law is applied to determine the nature of an examined instance. The law is the major premise, and the observed fact is the minor premise. If both premises are true, the conclusion is true. If all swans are white, then a black bird observed is not a swan.

Deduction's fallibility

Any observation is embedded in a background of unknown factors. Either (a) the Sun revolves around Earth or (b) both the Sun and Earth are orbitless yet Earth rotates rapidly on its axis and we merely fail to detect our motion. Upon everyday observation of sky, unnecessary was that (c) Earth also hurtles around the Sun, a theory aspect appearing utterly improbable and grossly inelegant. Yet in 1543 that was the speculation seeming more elegant to Copernicus, a nakedeye astronomer. Galileo, who built a telescope, attained so many new observations of other celestial bodies that heliocentrism appeared more elegantly to Galileo too.

Yet logic did not entail selfevident elegance. Geocentrism seemed more elegant even to many nakedeye astronomers. Till the telescope it seemed logical, not merely reasonable, that the Earth—evidently motionless—was orbited in a loop by the Sun, whereas other celestial bodies tracked elaborate pathways around Earth. Upon the power of mathematics, inference, and reason—and perhaps a sense of elegance—a new Western society arose around heliocentrism. Till space flight in the 1960s, it was still theoretical, not empirical.

Epistemology: Theory of knowledge

Epistemology is pure philosophy's major branch concerning the sources, nature, and limits of justified—not merely presumed—knowledge.

Empiricism

Near 200 AD Sextus Empiricus explained that all knowledge rests on experience and sensory input.^[10] Premising knowledge on direct observation, and inferring other truths by connecting observations—logic—is empiricist. Science was developed to aid epistemology through test and observation—empiricism.

In 1731 Scotland's David Hume, a British empiricist, described the problem of induction—the mother of all problems in philosophy both pure and applied—as no methodology and inference can verify a natural law's absolute truth. Even if it could be proved absolutely true today, it is simply presumed that tomorrow will be like today—since today was observed alike yesterday, yesterday alike the day before, and so on—but this presumed uniformity of nature is neither verified by any observation nor entailed as logical necessity.

Yet even if reality always did and forever does conform to uniformitarianism—natural laws both absolutely true and universal—scientific methodology is observational, namely empirical, whereas a theory's conformity to the very fabric and fashions of reality cannot be directly observed and remains theoretical. Only predicted observations derived from theory—hypotheses—can be tested and confirmed. Empiricism cannot logically prove any theory true.

Rationalism

In 1781 Germany's Immanuel Kant distinguished between empiricism and rationalism.^[11] Though a stark division is elusive—anyone applies some degree of both—a rationalist is thoroughly skeptical of experience and appearances, and regards true knowledge as attained by rational reference to reasonable principles evident to the mind yet outside experience.^[11] Thomas Jefferson's 1776 assertion in the Declaration of Independence of the selfevident truth that All men are created equal exemplifies rationalism.

Metaphysics: Theory of reality

Metaphysics is pure philosophy's major branch concerning the nature and traits of reality beyond observation. Western metaphysics is often traced to Ancient Greece. Although Socrates is mysterious and left no writings, his students wrote about him, the prototype philosopher challenging students to ask questions, Socratic method, and to think for themselves, tried by Athenian democracy for corrupting the minds of the youth, and sentenced to death.^[12]

Realism

Naïve realism

The presumption that everyday impressions correspond to the true reality is naïve realism or commonsense realism, belief that the observed appearance—a woman's skin or the storm clouds or the ocean's waves or the grains of sand or the Sun's circular body or blue skies and pillowy clouds—are the real or true essence of the phenomena itself.

Platonic realism

Plato—student of Socrates and teacher of Aristotle—held that our world is real, existing and occurring, yet that there exists another realm, the truer reality, occupied by undying entities. Plato's "Allegory of the cave" illustrates that our observed particular forms are flawed and fleeting copies fashioned into visible matter by preexisting yet invisible ideal forms occupying a truer reality—outside space and time—yet interacting in space and time by arranging our visible matter temporarily into their own earthly likenesses and so yielding our observations, including our observations of ourselves as humans. And so Plato answered the problem of universals—where we derive our concepts of original traits and perfection.

Aristotelian realism

Aristotle disagreed with Platonic realism. Aristole posited that our visible world of material forms is reality's entirety, and that universal traits are simply shared traits borne by the material particulars themselves, and so if all particular instances of objects bearing that shared trait were destroyed from our visible existence—except perhaps in the memories of visible beings such as humans—that trait itself would vanish from all existence. Western society and science mostly developed upon and around Aristotelian realism.^[13]

Idealism

Some later pure philosophers, metaphysicians, maintained that observations themselves are constructed and cast by the mind, or at least resolved and arranged by the mind, or that all one can know about reality beyond immediate observation is ideas—either one's own or those of others.

Subjective idealism

Slightly ahead of Hume, fellow British empiricist George Berkeley offered subjective idealism. Berkeley maintained that the universe is God's thoughts occupied by other thoughts—all the thoughts projected as matter—and that if all beings including God suddenly and altogether stopped believing and thinking, all matter would vanish.

Transcendent idealism

In response to Hume's strong empiricism, Kant offered transcendent idealism. Kant indicated that although human knowledge is limited to human observations, by that very principle human perception is attuned to reality—human perception is human reality—and, since the human mind arranges human reality, the human mind contains an intuitive bridge mediating correct theory choice. Kant resolved metaphysical dilemma by discarding the quest for human knowledge of reality as knowledge of the thing in itself. The philosopher's task was no longer to observe noumena—true events seen by the enlightened philosopher—yet simply to organize the phenomena observed by everyone.

Absolute idealism

Soon Germany's Georg Friedrich Wilhelm Hegel offered absolute idealism. Hegel held that all a human knows of reality beyond immediate observation is one's own ideas, each idea initially so universal as to describe nothing existent, and that a human's knowledge of the world grows by conflicts among ideas. When one emits one's own idea, it gets marred in the conflict with other people's ideas, and gets denied and returned to sender, so to say, revealing the conflict among ideas. One reshapes the new idea, then, to conform to conflict signs, and emits the new idea into the pool of ideas, and the process repeats, refined one's idea. This occurs within the family, then in community, then in society, and then—among strong societies—among nations, and so the population of human ideas evolves globally. The organism attaining knowledge is humankind itself, a process mediated by interactions among ideas of individual humans who are constituents of the greater reality surpassing and outliving the individual while acting over the great expanse of history.

Ontology: Metaphysic of categories

To say that something is true is saying that it is—that it has some existence—and so occupies, then, a category of being. By ontology, one etablishes the categories, an endeavor occurring within pure philosophy's major branch metaphysics.

Language's basis

Upon these categories, derived through ontology, one can assign words meanings—perform semantics. Then one can arrange the words—encoding perspective, structure, relations, and motion for expression—namely syntax. Thus arrives language. Language structures brain operations.^[14]

Language's structure de facto is geometric, encoding structure and relations, while conclusions are arithmetic.^[15] The shapes and relations can be plotted and shifted into dynamics, described by calculus, or other forms of motion, yet remains mathematic. Yet the symbols, through ontology, can vanish or transform but reappear undercover, inserted elsewhere—implication or insinuation—by way of shifting semantics.

Words are polysemous—have multiple meanings in varying contexts. Ontology of scholars is not absolute truth along irrefutable lines, yet scholarship is distinguished by more consistent reference to particularly defined and standardly cited—not vaguely presumed, irrefutably asserted, or, where convenient, merely dodged—categories of reference. Thus discourse is steadier with scholarly ontology.

Correspondence

A correspondence theory of truth is usually posited in scientific realism, which regards theoretical terms—terms in a theory—as referential to entities and relations in a reality independent of the mind.^[16]

Coherence

A coherence theory of truth references elements of a statement to other statements. Truth can be attained logically, in principle up to tautology—a statement necessarily true by logic but uninformative outside itself—even if the statement's elements correspond to no objective reality. In idealism, one might seek a coherence theory of truth, as no independent reality—apart from categories in the mind—is found to affix the meaning of words.

Science

Theory structure

Populist ontology

In common conception, a fact is an obvious trait of reality, a hypothesis is guess, a theory is an informed estimate, and a natural law is a proved truth about the natural world.

Theorist ontology

In theoretical science, a fact is simply an observation, a hypothesis is a prediction, a theory explains and predicts an entire sphere of phenomena, and a natural law is simply one component of theory.

Methodology & inference

Inductivist

The precursor of Western science was inductivism. One observes regularly associated phenomena and then infers either cause and effect—a necessity of connection—or some other explanation, what itself encodes cause and effect embedded in the explanation, and regards it as general law. In natural science, a general law is a natural law, not merely a regularly occurring event but a mechanism explaining or encoding it.

A natural law is not that a turkey's food shows up every day. Rather, having observed for 200 consecutive days that food arrived after the light came on, a turkey induced that light made food appear—a natural law confirmed on many more days of observation—perhaps nullified on Thanksgiving Eve. Inductivism never quite vanished.

That the tide daily raises and falls is not a natural law. A natural law could be—and was—proposed, rather, that the phenomenon is due to the Moon's force called gravitation pulling by X strength, and so all the water in the oceans shifts to the side of Earth facing the Moon as Earth rotates.

Positivist

In scientific method, one induces a theory—explaining a regularly observed set of phenomena—containing laws encoding the regularly observed pattern. All possible observations by way of the theory placed in all possible situations are all its logical consequences, the theory content, either positive content (possible) or null content (impossible). One derives novel predictions by holding the theory's laws as major premises, couples them theoretically with observed and hypothetical facts, and so derives a new prediction: a positive hypothesis, which will be observed, or a null hypothesis, which will not be observed.

Testing positive hypotheses, one shows the theory tenable. Positivism seeks many confirmations of positive hypotheses, preferably of varying angles and in varying areas of prediction, in order to lay highly successful theory as foundation treated as true for all earthly purposes. Positivism tests positive hypotheses, as positivism effectively regards all science as useful—effectively applied science—the quest for metaphysical truth simply useless. So whether a theory is verified to metaphysical truth is simply not the matter, and instead one is seeking merely to confirm natural laws, not verify an explanation why such phenomena occur or what their meaning is.

Verificationist

Yet people shall seek truth—and wish to verify theory by observation. This is illogical, however, as any observation can host over one explanation: the success of any hypothesis can be explained by over one theory. Yet if one limits science to direct observation and merely encoding the observations, one can endeavor to deliver verificationist methodology and inference. That was the goal, in effect, of any positivism, yet complications came in the first three decades of the 20th century—delivered by physics as well as by society through culture and politics and economics and application of biology and medicine—that revealed the great susceptibility of positivist philosophy to seizure for just about any purpose.

Falsificationist

Only by testing null hypotheses can one test the theory's truth value—yet verify only theory falsity. Falsificationism values confirmations of positive hypotheses, yet does not so award theory verification, and instead awards theory corroboration—weak, moderate, or strong—and is always seeking confirmations of null hypotheses, too, so that a flaw in the theory can be revealed, and then a new theory, explaining prior theory's both successes and failures, imagined up.

Hypotheticodeductivist

In hypotheticodeduction one observes phenomena and imagines up a theory—no specific attempt being made to infer it rationally by inducing evident connections between events—that spans and explains all the data. Thereupon one deduces the theory's logical consequences to check the theory for compatibility with all observations indeed. If the theory then exhibits incompatibility either with theoretical data, particularly mathematic, or with empirical phenomena, the theory is deduced as faulty. Then a new theory is imagined up to explain the theory's both successes and failures, again spanning and explaining all the data and phenomena.

Types

Baconian model

Normal science

Thomas Kuhn found that science, as practiced, is puzzlesolving—in an area of the full canvas of reality.^[25] A scientific community gathers around an eminently successful theory that solved a problem puzzling the scientists, and so the theory becomes the exemplar, which scientists emulate by following an unwritten rulebook, normal science, encoded to the exemplar's interpretive lens, what becomes the paradigm of science held by science's ruling class. Through later researches and theories the scientists fill in the puzzle pieces around that exemplar's own interpretation of the world. The scientists reinterpret, frameshift, and reorient incoming ambiguous data to the paradigm. If the data remain incompatible, the scientists discard it as nonexistent or dismiss it as bizarre and omit it from theory.^[25]

Research programs

Imre Lakatos held that science is more flexible and occurs as research programs whereby each program competes with other, occurring or proposed research programs to yield the greatest successes.^[25]

Discovery science

K Popper

In The Logic of Scientific Discovery (Routledge, 1959), Karl Popper found that science grows by showing the previously thought impossible to be possible by falsification of existing theory. To Popper the main impediment upon science—and upon a society—is the psychologic and social preoccupation with feeling and appearing correct. Knowledge progresses by a method of conjecture and refutation, says Popper, by showing a prior conjecture's failures and then adding a conjecture to explain its explanatory failure.

T Kuhn

Kuhn found that scientific communities disregard Popper's model of science and ignore refutation unless it is overwhelming.^[25] Yet eventually new compatible data fall scarce, and a conceptual problem remains unanswered. Weakening faith in the paradigm appears, grows, and begins a crisis. If the society's general cultural climate permits thinking in a new way, a revolutionary scientific theory appears. Eminently successful—a solution to the scientist's conceptual problem—it is crowned the new exemplar. All the old data is seen through the new lens. The scientists' set out upon the enlarged vista to explain the world again. Linear accretion of facts and truths—with linear progression in understanding the world—is a myth, says Kuhn, for science grows by revolutions creating utterly new perceptions of the world.

L Thomas

Lewis Thomas, onetime president of Memorial Sloan-Kettering Cancer Center (MSKCC), has been considered a patron saint especially to biology, as in the late 1970s Thomas used his position to increase federal funding for biology basic research,^[26] and endeavored to maintain, or perhaps create, the freedom of civilian biologists to do such breakthrough research^[27] as had long been occurring in physics. There have been concerns, even in the 21st century, that U.S. federal funding of biology research is overplanned, approved by panels with their own expectations of what will be discovered.^[28] By Thomas's description, applied science occurs when the researcher is trying to attain an expected outcome, whereas basic science occurs when the researcher seeks an astonishing outcome.^[27]

Potential & purpose

These are not scientific epistemology—theory of creation of scientific knowledge—yet discuss the justified aims and potential of science.

Foundationalism vs non-

Foundationalism—any form of positivism—seeks to lay successful theory as an uncontested, unquestioned foundation for all later enquiry and inference and so build later theories upon that foundation, fundamental knowledge. In the 1960s Thomas Kuhn and Karl Popper brought in postpositivism whose nonfoundationalism does not discard fundamental theory spuriously yet welcomes justified refutation of fundamental theory.

Science had not grown by collection of facts arranged into truths for linear accretion of scientific knowledge, said Kuhn, yet by revolutions discarding fundamental theory for drastically different fundamental theory. Kuhn further explained that there is no algorithm—a formula where data input yields target output—to build new theory even upon a foundation.

Nonfoundationalists regard foundationalism as permitting science to stagnate while scientists work to justify their interpretations—not discover and explain—and science then becomes a cutural relic. Popper offered nonfoundationalism's methodology and inference—falsificationism—ever attempting to refute even fundamental theory.

Nonessentialism

Phenomenalism

Operationalism

Operationalism limits science only to what can be measured, as anything that cannot be measured must lack scientific meaning.

Instrumentalism

Instrumentalism regards scientific theory as simply a way that humans explain and predict phenomena—while we lack ability to determine even approximate truth of theory.^[29]

Essentialism

Scientific realism

Scientific realism holds that instrumentalism demotes all science, in effect, to applied science and misses the very point of science, which to scientific realism is attaining understanding of mindindependent reality.^[29]

Scientific realist commitment

Three dimensions

Metaphysical: there indeed exists a natural world whose reality is independent of the mind (mind-independence).^[30]

Semantic: the terms within scientific claims are referential to mind-independent reality and have objective truth value (true or false).^[30]

Epistemological: theoretical claims form true or approximately true knowledge of the natural world.^[30]

"Our best scientific theories"

Realist commitment is usually to "our best scientific theories".^[31] Such theories are usually attributed to a mature science, whose meaning is vague but generally is rooted in how established, longstanding, tested, or non-ad hoc is the field or are its theories.^[31] (An ad hoc clause or definition is supplied to save an earlier theory from shortcomings.^[31]) A realist regarding a particular science might not be realist regarding others, and might presume realism in a branch of physics but not in another branch of physics or in biology.

"Approximate truth"

A realist claim is that the terms in a mature science typically are referential to independent entities, and the laws within a theory are approximately true.^[32]

Selective variations

Explanationism

Explanationism espouses commitment to theory aspects both explaining the observed success of a theory's past predictions and called for to derive novel predictions—seemingly unexpected phenomena.^[31]^[33]

Entity realism

Entity realism espouses commitment to the reality of unobservable entities that can be manipulated, in causal relations, to yield intended outcomes.^[31]^[33]

Structural realism

Structural realism espouses commitment not to descriptions of the nature of entities yet to the theory's structure,^[31]^[33] the relations among and around its components, a mathematic structure even if it is encoded on words forming reference and relations. Ontic structural realism espouses the ontological priority of structures and relations—that structure is the existence and that there are no things.

Applied philosophy: Philosophy of science

Although laws of chemistry, a physical science, have developed rather straightforwardly,^[18] fundamental physics and biology have encountered great epistemologic questions, for instance determinism versus probabilism, causation and explanation, and the definitions of space and 'time—thus reality—and of life.^[18] It has been said that the success of modern science rests in part on its naïveté, as practicing scientists are often but vaguely familiar with philosophy of science, and believe that philosophy has little to do with their work.^[18]

Scientific epistemology

A total theory of creating and developing scientific knowledge, scientific epistemology is not identical with but somehow derived from general epistemology. It concerns the sources, nature, and limits of justified, not merely presumed, scientific knowledge, yet additionally describes methodology for obtaining science's observations, mode of inference to conclusion, and—if inference is not deductive—justification of theory choice, as well as reasons for or conditions of revising or abandoning of theory.

Demarcation

Karl Popper described the problem of demarcation, setting boundary of the domain of science—outside which endeavors or statements are unscientific. Popper maintained that science could not prove a theory true, and could prove only a theory's falsity, as scientific methodology has incapacity to test a theory's positive truth. Popper thus held that the demarcation of the domain of science is falsifiable, that any theory unfalsifiable is unscientific—is values, a matter of taste, outside science.

Pseudoscience

Popper held that application of scientific methodology to premise the truth of a theory either intrinsically unfalsifiable or methologically sheltered from refuation is pseudoscience. Popper's classic example was psychoanalysis, which none could refute. Psychoanalytic theory offered an explanation—in its own language—for failure of any psychoanalytic prediction. Not asserting that science equals truth, however, Popper indicated that psychoanalytic theory probably had some usefulness and even truth but merely was unscientific. Not necessarily false, its truth was simply unfalsifiable, thus the theory was outside science's observational reach—unscientific—but was dressed in science's methodologic wardrobe anyway, thus pseudoscience.

Determination

Scientific determination applies reasoning, not necessarily logical but preferably, to determine which hypothesis, entity, property, process, law, explanation, principle, or theory was confirmed, verified, corroborated, or justified—involving theory of confirmation—or instead was refuted, falsified, or underdetermined.

Underdetermination

Underdetermination occurs when scientific evidence fails to justify a particular theory choice. One solution is simply theory multiplicity—permitting multiple theories to coexist.

Confirmation holism

W V O Quine particularly explained that any observation is embedded in background of unknowns, and so any falsification may be explained by unobserved phenomena even if the theory itself informed accurate prediction.

Ladenness

Theoryladen

A fact is simply a specific observation. A direct observation—an empirical fact—is obtained with naked eyes. Yet science is not sought merely to collect direct observations. Science is sought to predict observations, explain observations, and discover unobservable or unobserved entitites, and explain them too. So some facts presumed in science are indirect observations, inferred by direct observation of a different entity or phenomenon plus preexisting theory. Not theoryneutral, facts in science are theoryladen.

Valueladen

Even a theory presuming only to track direct observations—not even explain them—can select and sort only what observations are noticed and seem relevant to the observer by the observer's preexisting theory. Nor can that preexisting theory be premised on all observations possibly relevant, "all the facts". Scientific theory is created by humans, and so embeds not only observations but human values, is valueladen.

Paradigm

Kuhn explained that scientific endeavor holds to a worldview—an interpretive lens—that theories are fit to, and this is science's prevailing paradigm, the ruling class in science, practicing normal science according to its presumed fundamental science.

Incommensurability

Kuhn explained that theories from differing paradigms are incommensurable—not directly comparable—and that trying to directly compare them mainly yields incoherence, not comparison. The terminology of a theory in one paradigm lacks direct correspondence to terms in a theory in another paradigm, as the theories own structure is encoded via the paradigm. To see which theory has more explanatory power, one must immerse onself into the culture, so to say, of the theory, and only then can one observe its compatibility with the data.

Modern philosophies of science

Positivism

Suggested by Francis Bacon, furthered greatly by Henri Saint-Simon, and influentially explicated by his student August Comte, modern philosophy of science began with positivism.^[34] Comte offered Course on Positive Philosophy.^[35] Positivism regards science as observation, prediction, confirmation, and statement of natural law, treated as positive knowledge, while regarding metaphysical knowledge as unobtainable—or at least unverifiable—and thus pointless.^[34]

Neopositivism

Logical positivism, like classical positivism, was a general epistemology that arose mid 1920s, yet it was strictly empiricist—calling for direct observation and deductive logic—in its scientific epistemology. Precluding metaphysical speculation even to form scientific theory, logical positivism regards scientific theory as aiming only to track patterns of experience, limited to the very data, namely facts.^[36] Thus a scientific theory must be verifiable—by rules of mathematic logic—as either false or true. Otherwise, violating the methodology verificationism, it is scientifically meaningless.^[36]

After World War II (1939–45), logical positivism became less urgent and, occurring the the UK and U.S., became what some might distinguish as logical empiricism, led in America by Carl Hempel who offered the deductive-nomological model (D-N model), nomology describing laws of fundamental physics and logic. Any variant of logical positivism—or logical empiricism—is neopositivism.

Postpositivism

Postpositivism's theory development, methodology, and inference is structured by Popper's scientific epistemology, critical rationalism, holding that a scientific statement can have meaning even if it is unverifiable—as verification is logically impossible—yet that no confirmations verify theory, simply corroborate theory, and that the goal of science is to develop theory simply of greatest appearance of truth, verisimilitude. The methodology is falsificationism, as a theory's falsity can in fact be deduced—not merely induced—once a predicated impossibility derived from the theory as a null hypothesis is nullified. Popper maintained that any scientific theory is imaginative—there is no logical way to construct or even induce new theory—and that any conjecture, even extremely improbable, perhaps more improbable the better, is scientific if it both explains all observations within the theory's sphere and permits operations that can potentially, by observation, nullify the theory.

Popper holds that the problem of induction is a myth within science, and that truly scientific methodology and inference, and then proper statement about the theory's status—at best strongly corroborated—removes induction from science.

Anarchy

Paul Feyerabend (Against Method, Verso, 1979) found that scientific theory choice had usually been determined by rhetoric, deception, and social flocking, and that new scientific theories—for instance molecular genetics replacing classical genetics—came from left field alike science fiction. Feyerabend held that, in science, anything goes—there was no scientific method—that the method of science is scientific anarchy.

Scientific realist vs antirealist arguments

It is generally held that an individual scientific realist argument is more compelling—and the scientific antirealist arguments more numerous.

Realist: No miracles

Hilary Putnam revived interest in realism by asserting the main realist argument, asserting that if scientific theories were not true, or approximately, then their empirical success would be a miracle.^[1]

Antirealist: Constructive empiricism

Bas van Fraassen has likened successful scientific theory to an empirical adaptation, since very many theories are developed, compete, and are tested, and so whichever theory offers empirical success is naturally selected.^[37]

Realist rebuttal: This empirical success itself attests to the truth of the theory since any increasing number of failed theories can be otherwise interpreted as the increasing improbability of developing a true theory by chance.^[37] Often it has been difficult to develop even one theory both explaining all the data and creating novel predictions that were confirmed, while constructive empiricism does not evidence but simply presumes theory falsity.^[37]

Antirealist: Pessimistic induction

Many theories once empirically successful are now thought severely false or unobservables are now believed wholly imaginary, for instance luminiferous ether.

Realist rebuttal: It was widely acknowledged that luminiferous ether was a speculation, and was never part of a mature theory.

Antirealist: Social constructivism

Kuhn found that a paradigm of science held by a community practicing normal science conformed to the society's worldview, which itself conformed, or was shaped by——the society's socioeconomic structure. Kuhn maintained that his thesis was skewed both by its opponents and by most of its putative proponents.^[38] In any case proponents of sociology, such as the strong programme, cited Kuhn's thesis to make their own argument that scientific theories are marred by cultural relativism.

Realist rebuttal: Although geocentrism appears utterly false, Ptolemaic theory predated modern science, which showed its selfcorrection even in the face of powerful cultural opposition. Molecular genetics explains the successes—and failures—of classical genetics, a theory developed in science itself. So the scientific realist stance tends to allege that social constructivism, rather, is the cultural relativism, and assert that science exhibits convergence.

Realist: Convergence

Putnam maintained that mature sciences show old laws to be but limiting cases of new mechanisms, as did Newton's universal gravitation became a limiting case of Einstein's general relativity.^[39]

Antirealist rubuttal: The idea that the theories converged, and therefore the old theory is approximately true, contained in the new, and still stands, is social constructivism, a Kuhnian rut. Kuhn explained that Newton's theory is utterly false and that calling it true is tantamount to instrumentalism, proof of truth by usefulness to humans applying its laws to engineer feats our level of everyday human observation.^[40] (Kuhn did not argue scientific antirealism, however, yet instead asserted nonfoundationalism. Kuhn maintained that presuming a fundamental theory true is the prime obstacle to discovery—and thereafter to wide acceptance by scientists—of greater truth through science.)

Antirealist: Truth's irrelevance

Paul Feyerabend explained that even if a scientific theory is true, its truth has little to do with it acceptance by a scientific community—a process socially determined and usually by rhetoric and deception.^[41] False or true, new scientific theories usually resemble science fiction versus the previous theory, such as heliocentricity replacing geocentricity or molecular genetics replacing classical genetics.^[41] And prior theory—geocentric universe or genetic determinism—was plied on the public, as is the current and yet previously shocking and bizarre theory being plied on the public, to resolve problems in the public identified by socioeconomic elite, not even by scientists.^[41] So the spirit of science—not faith—frees anyone in the public to dismiss a predominant theory and select his or her own theory, not necessarily false yet otherwise arriving late versus the scientific community's process, as seen with the success, long denied in the West, of acupuncture.^[41] Even if its theory is approximately true, a scientific community might be helping stymie science's progress toward a theory of greater truth, perhaps in bizarre theory—seeming obviously false—upon longstanding empirical data, already open to anyone's observation, just escaping the content horizon of theory.^[41]

Antirealist: Unconceived alternatives

P K Stanford has offered the problem of unconceived alternatives by explaining that scientists seldom have the imagination to assemble better theory already suggested in the field of reported data.^[42]

Natural science's unresolved aspects

In the introduction to The Origins of Life and the Universe (Columbia University Press, 2003), Lurquin PF explains,

The scientific method is a distant relative of the type of thinking that the ancient Greeks invented. Like them, modern scientists take a materialistic view of nature and do not rely on magical, mystical, mythological, and theistic principles. This is not to say that scientists are virulent atheists. Indeed, many have been and are religious. Simply, as the great French mathematician Laplace once told Napoléon Bonaparte,"Sire, God is a hypothesis I do not need". And indeed, science and religion should not be seen as antagonistic; they just do not need each other, as they ask questions and give answers within very different different modes of "knowing". Hence, my intentions are not polemical. Rather, I simply want to strictly adhere to principles of scientific discovery and interpretation of our world in my description of life and the universe.^[43]

Lurquin defines replication: "the mechanism by which DNA copies itself into two identical daughter double helices".^[44] The empirical aspect of molecular genetics explains that a plethora of different proteins copy the double helix—which does not copy itself—into two "daughters".^[45]

Disunity among sciences

The Lancet medical journal published an article by S Mitton (2006) on physics and cosmolgy.^[46] Learning that the vast space between cells and molecules—and within atoms—might be occupied by matter, energy, and events unto themselves, A Pasqualotto (2006) graciously pondered whether medical sciences, far from physics and philosophy, could still be related to a justified vision of reality.^[47] Most practices continue as if all of reality—including humans—must obey pre1920s physical sciences.^[48]

Not only the public is "scientificaly illiterate", but most scientists, too, are effectively illiterate in branches of science outside their own, as science is not a unified continent of knowledge, but alike a vast archipelago of islands often scattered farther from each other than from the mainland of general knowledge.^[49] Lurquin (2003 p 11), in any case, offers the explanation of ancient Greece's Democritus that "the universe consists of atoms and void and, moreover, everything existing in the universe is the fruit of chance and necessity. Presumably, Democritus meant that the universe never was a preordained thing (it thus came about by chance) and that its contents appeared as an inescapable followup to its creation (necessity). Many scientists think today that this is indeed the case. Democritus may well be the greatest visionary of all time".^[43]

Mathematics vs interpretation

In physics there is distinction of formalism versus interpretation.^[50] In formalism of scientific theory, if one performs an operation applying the theory's structure—which is mathematic—one shall observe such outcome.^[50] The interpretation in theory explains why.^[50] If one drops a feather and a bowling ball within a vacuum—omitting air resistance—both objects fall at equal measured speed, accurately by Newton's law of universal gravitation.^[51] It was Galileo who experimented and predicted this phenomena—later encoded by Newton—counterintuitive on context of daily observation.^[51]

Gowers T, mathematician, explains that if you are a doubter but witness the phenomenon in a vacuum, "your faith in science, and your admiration of Galieo, will be restored".^[51] Yet it is interpretation, embedded in human language, that this occurs because Earth's mass attracts all other mass by a constant force of gravitation, yet that the force must overcome less inertia of a feather's lesser mass and so pulls the feather at equal velocity.

In biology the distinction is termed empirical, which is confirmed by observation, versus metaphysical, which is speculation on unobservable aspects. If someone infects a cell with a virus in vitro, more virus particles are usually produced, the mathematic structure—by semantics and syntax of words—yet it is not selfevident why. It is simply data that the cell manufactures more virions—or else it was abortive infection and not productive infection—yet an interpretation why is metaphysical and thus unverifiable unless science finds in another dimension, perhaps outside spacetime, the phenomenon's physical meaning open to examination.

Science's unresolved foundation

Okasha (2002 p 8) explains, "Confidence in the Newtonian picture was shattered in the early years of the 20th century, thanks to two revolutionary new developments in physics: relativity theory and quantum mechanics".^[52] (Okasha p 8) closes, "Both relativity theory and quantum mechanics, especially the latter, are very strange and radical, making claims about the nature or reality that many people find hard to accept or even understand. Their emergence caused considerable conceptual upheaval in physics, which continues to this day".^[52]

Newton's explanation

In 1919 Newton's law of universal gravitation fell to Einstein's general theory of relativity (GR), what explains gravitation not as a force yet the effect of 4D spacetime warping in the vicinity of mass traveling along points in 3D space's curvature warping to the pace of 1D time. Earth's orbit of the Sun is the equivalent of a straight line—called worldline—tracing the warping geometry of 4D spacetime. It is though Newton, an accurate observer, encoded our everyday pattern of observation, including perceptual artifacts. The force constantly emitted by every object is unidentified, and it is unclear how it would instantly tug all other objects across the universe. Mass rearranging space's geometry in its vicinity could be called a force, perhaps, indirectly pulling the other objects, and yet Newton's law describes a force pulling other objects directly, as Newton's theory—premising the law's universality—was absolute space and time unalterable. Any scientific theory unbelieved appears bizarre, supernatural.

Relativity's explanation

Special theory of relativity (SR), offered in 1905, affixes not space and time yet the speed of light as the absolute constant.^[53] Einstein's insight was that, no matter one's speed, light arrives at a single speed—186 000 miles/second—and so speed must subtract from time's passage, slower for the moving object.^[53]

General theory of relativity (GR), offered in 1915, geometrically plots the positions of objects in 4D spacetime, a topology expanding in mass's vicinity—and contracting when it passes—within three absolute directions, and yet having no fixed shape. Spacetime warps at the speed of light, and so gravitation acts not instantly yet at the speed of light.^[54]

Relativity & quantum—disunity

GR describes only gravitation—classical mechanics. The other three fundamental forces occur in the sphere of quantum mechanics (QM): strong nuclear force, weak nuclear force, and electromagnetism. Subatomic wave/particles mediating these—photons through spacetime as light mediating electromagnetism—have been identified. Yet QM appears to falter outside its own range—subatomic realm of wave/particles—and since its 1920s development has conflicted with GR. Fundamental physics—the foundation of all other sciences—remains unresolved.^[55] All other sciences—like chemistry and biology—rest on resolved foundation. Ball (2008) explains,

Some physicists think that how quantum behaviour should be interpreted remains as unclear today as it was when Niels Bohr, Werner Heisenberg, Albert Einstein and others were developing (and arguing over) the theory. "This is an emotional issue", says quantum technologist Chris Monroe from the University of Maryland in College Park. "Some insist that there is no problem; others insist that there must be an infinity of universes, each with their own classical description of a definite quantum state".^[56]

Fundamental physics

Fundamental physics is fundamental science, the foundation of all other sciences—whether natural, social, behavioral, or cognitive—the special sciences, including the natural sciences chemistry and biology. Newton and Leibnitz developed new mathematics—calculus—encoding patterns of motion. In 1687 Newton set forth three laws of motion and universal graviation. In 1858 James Clark Maxwell unified electricity, magnetism, and light—electromagnetism. In 1899 Max Planck showed that light arrives in units—not infinitely divisible—and called these quanta. In 1905 Einstein described chemistry's Brownian motion with Newton's laws of motion, and it was widely accepted that atoms exist.

Some 20 years later Neils Bohr explained the spectral lines emitted by heated gases as quantum leaps, and resolved the atom's structure. Newton's equations had been replaced, however, by Einstein's general relativity, the updated classical mechanics. Electromagnetism, mediated by photons, became quantum mechanics, which in the 1920s developed quantum field theory. Later the strong force—enabling the atomic bomb undoing it—and then the weak force, mediating radioactive decay, as after an atomic bomb blast, were identified. QFT's standard model was developed accordingly.

Relativity

Space

In general relativity, light speed is contant, gravition is deterministic, and yet space and time are relativistic. From equal distances and angles, yet from different points of vantage, two observers of an object measure different lengths—at different times—according to the object's direction and speed of travel in relation to the observer. Mass yields gravitational redshift, the elongation of the peaks exhibited in the travel of the wave/particles photons—whose visible frequency range we call visible light—elongating as gravitation stretches space and expands the wavelength into lower frequency, lower energy, thus redder. Clocks aboard a moving object are confirmed to tick slower.^[53]

Theory

Any observation can host over one explanation, or simply derive from a certain power of observation, not all of existence, what might partly unobserved. Scientific realism demands essentialism—describing the essence of nature itself—whereas instrumentalism seeks success predicting observable phenomena. Any theoretician takes imaginative leaps, however. Einstein's equations presume a fact not verified by data, namely that light speed is the maximum in all reality. Instances were measured, Einstein presumed the data mindindependent, and reasoned the speed universal. Einstein's theory has been empirically successful. So was Newton's theory. The question remains how to explain the phenomena—and how real, independently of the mind, is the explanation?

Time

Time and space are, in effect, a sum equal to the speed of light (c).^[53] In Einstein's queations, one cannot exceed c and arrive at a location before spacetime even rippled to host one's arrival or electromagnetism arrived to shine light on it. Exceeding c is to arrive at a location in space before the arrival of the correlating time, or traveling backwards into a coming event's preceding events. Einstein explained observations without permitting travel into the past—after it occurred—or into the future before it arrives. Yet Einstein could not verify that it was impossible for any wave/particles anywhere in existence to accomplish the feat.

Quantum mechanics

On the 1927 formalization of quantum field theory (QFT), encoding QM's seemingly infinite probabilism, Einstein famously remarked, "God doesn't play dice". Bohr said, "Stop telling God what to do". For years the idea of unifying all four fundamental interactions was not sought. QM preceded in its own world—perhaps many worlds.

Superposition

When an electron or photon is a singlet, it leaves an imprint as does a particle. Yet if multiple holes are placed in front of one electron, it leaves a wave interference pattern on the detection board. It arrives in multiples—a field—of entities exhibiting wave/particle duality while donning the array of an infinite wave/particle field superpositioning into all available openings. Quantum superposition is like a photo double exposed, over and over.

Decoherence

As molecules are composed of these subatomic wave/particles it seems that they cannot coalesce into but a single object. It was simply presumed—not found compatible with data and mathematic inference—that as matter condenses into molecules, gravitation grows notable, and the wavefunction collapses down to negligible, decoherence of the wave/particle, leaving only the particle to build up matter.^[50] "Crudely speaking, decoherence is a sort of leaking away of quantum behaviour when a particle interacts with its surroundings—for example, when an atom or molecule collides with those around it, or when light bounces off it. All we are left with is a partial picture of the system: a picture in which only a well-defined subset of macroscopic properties, such as position, are apparent".^[56]

Uncertainty

An electron shows up only if the scene is unobserved. Yet when left to occur—unobserved—it deposits evidence of having filled every possible position. And yet it is not always in each position. The wave/particle field is probability wave manifesting a particle at each position only sometimes. Shining a light onto the event—spraying it with photons—ends the field and arranges the particles into a definite array, but until then it could have either been there or not there. Observation makes it commit to placing particles in positions. Reached in 1927, the Copenhagen interpretation is that unobserved quantum objects lack fixed properties, and that observation disturbs their quantum state, shifting them into classical reality.^[57]

The 1935 thought experiment of Erwin Schrödinger is Schrödinger's cat. If a cat is in a room with a quantum bomb—to explode if a single wave/particle touches it—and the room is unobserved, the cat is both alive and dead in all possible variations. it is observation of the room and cat—when the door is opened—that mediates selection of one position for observation. And yet now it seems that during that transition from the quantum field to classic observation, Schrödinger's cat can be rescued—drawn from the course toward classical observation and back into the quantum field.^[57]

Many worlds?

About 50 years ago Hugh Everett offered an explanation.^[50] Reminding us that our observable matter is composed of the subatomic wave/particles, even at observable scale all possible variations of reality—the entire quantum field—are simultaneously occuring and are real and yet the individual simply observes a single reality.^[50] By Everett's many worlds theory, then QM is deterministic, and only our observations are probabilistic.^[50] So everything might be both false and true.^[50] It might be unscientific to presume, by "scientific" faith, that if something exists, it will manifest from the quantum field both while we are trying to watch it and believing it fictitious.

Entanglement

Two wave/particles in near proximity vibrationally match and thereupon they are linked across vast gaps of space. Shifting one's orientation automatically reorients the other—across space.

Relativity conundrums

GR & speed of light

For GR to hold, the fastest possible speed must be of light (C). In September 2011 neutrinos were recorded exceeding C.^[58]^[59] It was presumed mismeasurement, though unexplained. Yet the data was repeated, even with extra precaution, in November 2011.^[60] Perhaps it still is mismeasurement and GR is deterministic.

Dark energy & dark matter

If GR is deterministic, then upon 1998 redshift data from Hubble Space Telescope observing distant supernovae, and then inference, about 96% of our universe's matter and energy are invisible and undetectable—dark energy and dark matter.^[61] NASA explains,

More is unknown than is known. We know how much dark energy there is because we know how it affects the Universe's expansion. Other than that, it is a complete mystery. But it is an important mystery. It turns out that roughly 70% of the Universe is dark energy. Dark matter makes up about 25%. The rest—everything on Earth, everything ever observed with all of our instruments, all normal matter—adds up to less than 5% of the Universe. Come to think of it, maybe it shouldn't be called "normal" matter at all, since it is such a small fraction of the Universe.^[61]

Einstein explained that space is not nothing—that it can hold its own energy and that more space can come into existence.^[61] In 1933 Swiss astronomer Fritz Zwicky predicted dark matter, said that without it, galaxies would fall apart, that additional matter, invisible, surrounds the regular matter.^[62]

Either like giant halos enveloping galaxies or "relatively small blobs", each millions of times heavier than the sun, dark matter seems to exhibit Brownian motion alike gas, and yet it is unclear what it is.^[63] Perhaps dark energy and dark matter are the same thing.^[62] Without dark energy to impel the universe's expansion, so much matter apparently would leave the universe to collapse in on itself.^[64]

Quantum field theory

Standard model

Elementary particles are either bosons that carry force—electromagnetism, strong force, weak force, and presumably gravitation—or fermions that compose matter. Weak force is mediated by the bosons called W and Z bosons. Strong nuclear force glues the atom's nucleus and is mediated by the bosons called gluons. The atom's nucleus, being matter, is composed of the fermions called quarks, themselves joined by strong force—mediated by the bosons called gluons—into the hadrons called protons and neutrons. Protons and neutrons, in turn, are held together—forming the atom's nucleus—by more of the bosons called gluons. The nucleus is orbited by the fermions called electrons. Electrons—unlike the fermions quarks that are joined to form protons and neutrons—are their own elementary particles. The bosons called photons carry electromagnetism, which travels over long distances as electromagnetic radiation—ranging from the low energy and long frequency radio waves to microwaves to infrared to visible light to ultraviolet light to X rays to gamma rays having high energy and short frequency—and photons are also absorbed and emitted by the fermions called electrons to orbit the atom's nucleus, itself composed of protons and neutrons, and thereby mediate chemical interactions among atoms and molecules.

Quantum gravity?

Newton's theory explained gravitation as mass attracting mass. Quantum field theory's standard model uses a hypothetical graviton to describe gravitation, predicted not to radiate through space between objects yet to mediate spacetime's local warpage. Particle physicists searches for gravitons to enable confirmations of predictions. Yet gravitation is extremely feeble versus the other three fundamental forces. Detection of even a single gravition is predicted as virtually impossible even if they exist.^[65]

Einstein's quest: GR & QM unification

Einstein's expressed view was not the quanturm theory was wrong, yet that it was incomplete. Einstein tried to unify gravitation with electromagnetism—trillions of times stronger than gravitation—and died in 1955 in Princeton, New Jersey, with a notebook nearby while still trying to.^[66] Along the way, at least as to physics theory, Einstein virtually ignored—or at least it seems—advancements in QM, such as the discoveries of the strong nuclear force and weak nuclear force. Einstein called entanglement, acting instantly over large distances, "spooky action at a distance", and refused to accept it—and yet it has withstood testing.^[67]

Electromagnetism and weak force were successfully united in a model—electroweak force—and some aspects of strong force can be joined with electroweak force.^[68] The standard model coheres well with special relativity, yet effects of gravitation is plotted in spacetime by general relativity.^[68] As prior predictions through QFT have been so successful upon mathematic predictions—like the prediction confirmed in the 1970s that protons and neutrons are composed of quarks—many theoretical physicists are confident with mathematic modeling. When QFT's standard model is placed into general relativity, however, it yields the output infinity—presumed mathematically senseless.^[68]

Quest renewed: Theory of everything (TOE)

With the unification of electromagnetism and weak force, and other discoveries, theoretical physicists focused on quantum field theory took up the quest to unify relativity theory and quantum theory with a theory of everything (TOE). Some posit a fifth force. Superstring theory presumes no other force per se needed, yet the existence of 10 or 11 dimensions of spacetime and parallel universes.^[69] Quantum loop theory, on the other hand, indicates that there is no background called spacetime, that space itself comes in quantum units that are the same phenomenon as energy/matter.

TOE: Superstring theory

In atomic theory, H₂O can be ice, water, or gas—still water. In Einstein's equations, matter coverts to energy and back. In M theory all matter is energy—vibrating into geometric configuration of a wave/particles—and this occurs within visible and invisible dimensions of space.^[70] In string theory all elementary particles are replaced with a fundamental unit—a string—that can be closed like a loop or open like a hair.^[68] Moving through time, an open string traces a sheet, whereas a closed string traces a tube.^[68] String vibration in different modes forms different elementary particles.^[68]

The original string theory was bosonic string theory, describing bosons but not fermions—thus force yet not matter.^[68] Adding supersymmetry to bosonic string theory—thus superstring theory—described matter too.^[68] Three different superstring theories made sense (yielded no mathematic inconsistencies).^[68] In two the strings were closed, in the third the strings were open, and then mixing the best features of bosonic string theory yielded two other mathematically consistent theories—heterotic string theories—although five TOEs could seem odd.^[68] All five theories described aspects of a greater theory—M theory.^[68]^[71]

The extra space dimensions are presumed to be tightly curled, treated in models as Calabi-Yau manifolds or orbifolds.^[68] The theory of added dimensions to unify theory is not new, yet offered by Kaluza and Klein.^[68] The charge of an electron, for instance, reflects a string's motion in a particular dimension.^[68] M theory predicts 11 dimensions—10 geometric with 1 of time—in other words 7 dimensions beyond the 4 of spacetime.^[71]

Gravitation

Perhaps when mass bends space, it presses on a parallel universe where gravitation is powerful—as are the other three fundamental forces in our universe—and gravitons leak into our universe, in part explaining electromagnetism's feebleness.

Multiverse

When a single wave/particle superpositions into an infinite array—the quantum field—the wave/particles, entangled, fills the open spaces with a probability wave condensing matter where observed. So parallel universes, each shifted slightly over from the other, a frameshift, could exist Movement of a wave/particle repositions entangled partners. Parallel universes might not touch. In one experiment, molecules of 430 atoms each exhibited wave/particle coherence.^[72] In 2010 an observable—a paddle about the width of a hair—was reported as detected in superposition, both moving and not moving at the same time.^[73]^[74] Perhaps the parallel universes are occupied other beings or versions of ourselves, and perhaps laws of nature unlike those in our universe.^[75] Superstring theorist M Tegmark (2007) has indicated that if quantum physics is universally true, it justifies the inference that parallel universes exist.^[76] If it is not universally true—or at least descriptive—then something is much confused.

Invisible dimensions

A superfinite dot extended to length is 1 dimension. Another one laid perpendicular is two 2 dimensions, a flat sheet. Some lines stood up is 3 dimensions, a box or a globe. Shifting some lines some more adds more dimensions—space inside of space. Yet if mass reshapes space, an individual cannot just walk around to space's other side to look behind it. Light—photons—travel through space. Trying to walk to the other side, one's mass reshapes spacetime, and one's observation—and perhaps thoughts—reconfigure the quantum field's manifestations offered to observation. Trying to perceive added dimensions would be like trying to walk around a corner that pivots away however many steps are taken toward it.

If we lived in a 2D world—a flat sheet—and a 3D globe passed through, we would observe a tiny dot grow into a big circle, the globe's circumference, and then observe the circle shrink to a tiny dot and vanish. The globe's third dimension—height—would be lost and its other two, as the globe passed through, would resemble a growing and shrinking circle. We might call it alive. If our observational media record data in 2D—width and height—added dimensions are omitted.

Humans' visual data arrives in 2D format—plus 1D of time by the collation of frame after frame—yet the brain must fill in each eye's blindspot where the optic nerve connects to the retina and the sensory rods and cones are lacking,^[77] flip the two images right side up after each eye lens had inverted the image upside down, and apply an algorithm to decode the difference in perspective between the two images' data, a stereo pair, to create 3D perception of depth beyond the recorded height and width. It would take a different algorithm in the brain to decode the 2D photon data to interpret added geometric dimensions of environmental objects shaping space beyond the decoded third dimension depth.^[78]

It it mathematically tenable that we are holograms cast from invisible dimensions.^[79] If energy/matter recedes to a dimension curled within spacetime's observable geometry—behind or within observable spacetime—perhaps it is still occurring yet not on our space and thus not in our time. If it crawls back onto our observable aspects of the geometry it would return to observation and back into our time—points of occurrence along space's warping geometry observable. Petr Horava hypotheses that at very small scales, time disconnects from space, perhaps explaining quantum uncertainty, as when unhinged from time, a wave/particle need not be—or cannot be—at any single position in spacetime's geometry.^[80] Perhaps Einstein's equations are true, and the neutrinos in the 2011 data did not exceed the speed of light, yet traveled in part along invisible geometric dimension—outside time—to arrive ahead of our prediction set to our observable geometry.

Nature as supernatural

The dustjacket of Is Nature Supernatural? A Philosophical Exploration of Science and Nature (Prometheus Books, 2002), by mathematical physicist S Altman, explains, "Mathematical truths are often so compelling that some mathematicians, scientists, and philosophers posit a nonmaterial realm of eternal truths accessible to the mind alone", and believe that Plato was correct.^[81] Goblins and dragons might have existed, got slain by heros, and simply never turned—into sight and time—once people stopped believing in them. When beliefs change, the world that manifests from the quantum field might alter. Though he claimed it was for rhetorical effect—to force science to answer and not presume—Feyerabend, a trained physicist, argued that astrology might be true and voodoo might work.^[82] Kuhn, a trained physicist, explained that when the paradigm of science changes, the world changes.^[83] Perhaps one can shifting along worlds—mechanistically—to an alternate course of history.

TOE: Loop theory

Loop theorist Lee Smolin asserts that superstring theory is not even theory but mere conjecture absorbing focus that would be better spent elsewhere.^[84] Smolin says that superstring theory is having trouble explaining dark energy, and calls the rise of superstring theory the fall of science.^[84] Loop theorists explain that there are no added dimensions, since spacetime itself is quantized—comes in particles—and that both energy/matter and spacetime are the same underlying phenomenon. Thus there would be no background shaped—an invisible dimension—called spacetime for energy/matter to vibrate in in to begin begin with.^[85] Loop theory explains gravitation as a property of spacetime itself, and that spacetime itself transform into energy/matter.

Objective taste?

In 2003 Brian Greeneexplained that superstring theory did not call for a new force per se, yet a theory of everything, such as M theory, "would provide the firmest foundation on which to build our understanding of the world. Its discovery would mark a beginning, not an end. The ultimate theory would provide an unshakable pillar of coherence forever assuring us that the universe is a comprehensible place".^[86] At 2006 some 90% of theoretical physicists were superstring theorists.^[85]

Some decry superstring theory as unscientific, purely speculative—literal science fiction—that it is "science set free from truth" and abandoning "objective truth".^[87] Some allege that a theory involving matter's being strings of energy offers no testable prediction, as it far exceeds human capacity to logically attempt the destruction of elementary particles.^[87] Around since 1986, looped theorists had gained ground on superstring theory, yet also lacked testable predictions.^[85]

Superstring theory might permit mass to condense in one universe and warp space so severely that it presses on a parallel universe—a big bang—and their two membranes of space bubble off into their own universe expanding.^[88] String theorists already so try to create a new universe.^[88] Loop theorists say that there was no big bang—that it was more like a big bounce.^[85]

Agreed is that much is unexplained. An electron flits into existence in a vacuum and then vanishs.^[8] Like the wave/particle duality of subatomic entities, evidently both matter and space—mediating time—are two aspects of the same reality, an underlying phenomenon, and the vacuum in cosmology's terminology is far from empty^[89]

Biology's fundamental science

Okasha (2002 p 56) explains that although living organisms are composed of molecules that are composed of atoms—physical particles—physics seems unlikely to soon explain either economics or even biology, which social science and natural science "largely seem autonomous of it".^[90] L Smolin (2007 p 19), physicist, opens a thesis on fundamental physics by well encapsulating general view by biologists:

Great unifications become the founding ideas on which whole new sciences are erected. Sometimes the consequences also threaten our worldview that surprise is quickly followed by disbelief. Before Darwin, each species was in its own eternal category. Each had been made, indvidually, by God. But evoution by natural selection means that all species have a common ancestor. They are unified into one great family. Biology before Darwin and biology afterward are hardly the same science.
Such powerful new insights lead quickly to new discoveries. If all living things have a common ancestory, they must be similarly made! Indeed, we are made of the same stuff, because all life turns out to be composed of cells. Plants, animals, fungi, and bacteria seem very different from one another, but they are all just groups of cells arranged in different ways. The chemical processes that construct and power these cells are the same, across the whole empire of life.
If proposals for unification are so shocking to our pevious ways of thinking, how is it that people come to believe them? This is in many ways the crux of our story, for it is a story of several proposed unifications, some of which have come to be strongly believed by some scientists. But none of them have achieved consensus among all scientists. As a consequence, we have lively controversy and, at times, emotional debate, the result of the attempted radical alteration of worldviews. So when someone proposes a new unification, how do we tell whether it is true or not?^[91]

Biochemistry

In biochemistry are three types of molecular bonds—hydrogen, ionic, and covalent.

Hydrogen bond structures a water droplet, as H₂O, is electrically polar, one region being electrically charged more greatly than the other, creating molecular attraction bridging (H
₂O) molecules. It also a molecule of a different chemical, or a region of a molecule, either hydrophobic (H₂O-repelling) or hydrophilic (H₂O-attracting). Lipids molecules are hydrophobic, and so do not mix with water.

Ionic bond transfers an electron from one to another atom, and the two associate by magnetic attraction, like the salt NaCl or the salt gluconate or lactate—gluconic acid or lactic acid associating with alkaline minerals like calcium or magnesium—yet the bond usually dissociates in fluid and the ions, carrying electric charge, roam free. Ionic calcium is key in many intracellular functions. Ionic potassium and sodium are manipulated by neurons forming electric current down neurons—some a meter long from spine to toes—as nerve signals.

Covalent bond permits atoms to share an electron, share its electric charge, the electric valence, as the new molecule absorbed electromagnetic energy—photons—maintaining this bond, such as a plant's photosynthesis of glucose. Only covalent bonding—absorption of electromagnetism—is considered particularly strong. A particularly strong covalent bond is disulfide bond, or disulfide bridge, whereby two cysteine amino acid positions, namely residues, in a protein molecule bridge at their thiol groups (SH).

The cell

Eukaryotic cells are 10–30 times longer, and 1000–10,000 times more voluminous, than a typical bacterium like E coli.^[92] Cytoplasm is the fluid inside a cell but ouside its nucleus—hosting eukaryotic genome—what holds its own nucleoplasm.^[92] Cytosol, however, is the fluid outside all organelles.^[92]

Cells' energy metabolism

In normal energy metabolism of the animal cell, covalent bonds in glucose or fatty acids are split. The freed electromagnetism is harvested by the cell and applied to covalently bond a third phosphate group (PO) onto the end of the previous two phosphate groups of adenosine diphosphate (ADP), yielding adenosine triphosphate (ATP). ATP is stored, transported, and expended—by breaking off the third PO group with the enzyme ATPase and so releasing that electromagnetism—wherever energy is called for in metabolism. ATP is expended in protein synthesis, cell function and tissue maintenance, cell division and growth, and contraction of cardiac muscle and skeletal muscle.

Animal cells share with most bacteria the primitive metabolic pathway glycolysis, which splits one glucose into two pyruvate and nets two ATP molecules. Yet animals—which have hearts and skeletal muscles—need far more ATP and have powerhouses, namely mitochondria, taking the two pyruvate molecules, applying oxygen, and, while forming carbon dioxide and water, netting 36 ATP from the one glucose molecule.

Physicochemical dynamics

Chemistry vocabularly omits electromagnetism's magnetic aspect and explains interactions between atoms and molecules by electric charge, valence. If the overall atom or molecule's charge is neutral, it has a neutral net charge and is considered, in chemistry, to have only chemical properties, the noticable or desired structural traits, for instance wood or plastic or doublestranded DNA's double helix. The bonds within the single standes are covalent—sharing electrons—and the two single strands join by hydrogen bonds, more electromagnetism. Further electromagnetic interactions—physicochemical dynamics—arrange the double helix. Electromagnetism's magnetic aspect pushes and pulls atoms and molcules.

On an audio speaker cone's rear is a magnet. An electric cable carries electric current at the frequency encoded on the recording. The signals peaks and valleys push and pull the speaker magnet at that frequency (distance between peaks) and amplitude (height of peaks), vibrating the cone and compressing air at that rate and degree. Air molecules hit the ear drum, and tiny ear bones strike and create electric signals carried along nerves to the brain. If the frequency of air compression is within the auditory range—from deep bass of 20 hertz to high treble of 20 000 hertz—the brain creates sound. Two ears—stereo pair—enable the brain algorithmic decoding of 3D placement of the air compression's source.

The double helix

Either RNA or DNA is nucleic acid, yet all cell's have genome's in DNA, whereas RNA is used in the cell not as genes as such. In prokaryotes the genomic DNA is a closed loop in the cytosol. In eukaryotes the DNA is an unclosed strand coiled around protein molcules called histones and then bunched up within the cell's nucleus. Locally, however, the genomic DNA is though to don a double helix—like a spiraling ladder or staircase. It is doublestranded DNA (dsDNA). Mentally laid flat, it is simpy two strands of singlestranded DNA (ssDNA). Hydrogen bonding draws and holds the two strands parallel, but genetically inert. The genetic code occurs functions on either, single strand—effectively flat. The single strands bonds are all covalent, requiring enzymes to break or make them.

The basic molecule of DNA has three subunits—a sugar, a base, and a phosphate. The sugar molecule in DNA deoxyribose. (In RNA it is ribose.) A base is either one of two purines—similar to caffeine—or one of two pyrimidines. Phosphate is oxidized phosphorus (PO).

Deoxyribose bonded to a base is a nucleoside. Nuclesosides are strung into a long strand by bonding the sugars end to end with phosphates, whereas the base is left free—perpendicular to the strand's length—alike half a step or rung of a staircase or ladder. The phosphate bonded to the nucleoside is a nucleotide (nt), which thus has three molecular subunits: sugar, phosphate, and base. Many nts strung together—from one nt's phosphate to the next nt's deoxyribose to the next nt's phosphate to the next nt's deoxyribose—forms a long strand, a DNA polymer, each base, projected inward, is one of the four letters in the genetic code.

The four bases: adenine (A), thymine (T), cytosine (C), guanine (G). (RNA replaces the sugar deoxyribose with ribose, and substitutes the base thymine (T) with uracil (U).) The sequence of bases—A, T, C, G—along the DNA polymer is arranged into syntax and punctuation. Three nts form a codon—a genetic word—specifying one of 20 possible alpha amino acids. Hydrogen bonding attracts complementary bases into base pairs (bps), complentary base pairing, A drawn to T, yet C drawn to G. Further physicochemical dynamics configures the double helix. Yet for physiology—either genome replication for cell division or transcription for gene expression—the hydrogen bonds must be split down the middle, freeing a single strand, no more double helix.

"DNA selfreplication"

It once appeared plausible, waching cells under a microscope, that chromosomes selfreplicated. They do not.^[45] For DNA replication—before cell division—the enzyme helicase unzips the hydrogen bonds between base pairs (bps). Topoisomerase clips and holds the dsDNA downstream, however, preventing overwinding by helicase.

DNA's replicative enzyme—DNA polymerase—copies the DNA strand. DNA polymerase cannot initiate replication, however, can only continue one. Primase initiates the DNA replication. DNA polymerase continues it. Yet primase blocks the sequences at the DNA polymer's end—the end replication problem. This is resolved by telomeres—repeating sequences at the chromosome's end—which, blocked by primase, shorten with each cell replication. Eventually the telomere, like a fuse, is gone and the cell can no longer divide. It has reached the Hayflick limit, then, about 50 divisions—observed, at least, in laboratory cell culture.

DNA polyermase replicates only short fragments—Okazaki fragments—later joined by DNA ligase into the full DNA strand. DNA polymerase has a proofreading function. If it inserts an incorrect nt, it backs up one nt, exhibits exonuclease activity, excising the incorrect nt, and resumes DNA polymerase activity, inserting the correct nt. This enhances replicative fidelity from cell generation to generation

Gene expression

Transcription

During gene expression, rather, the DNA sequence—the target gene—is copied to an RNA transcript by RNA polymerase (RNAP). It exhibits its own primase activity—initiating a strand de novo and thus losing no genetic information—and exhibiting its own helicase activity. The RNA polymerase binds the gene at its promoter, hosting attachment by RNA polymerase, what travels along the DNA strand until it reaches a stop codon terminating transcription. Making but temporary copies of a gene, RNA polymerase lacks proofreading.

Splicing

In the animal cell, which has a nucleus, the mRNA transcript is exported out the nucleus and the mRNA transcript must be spliced to remove introns from exons. Sometimes the transcript is alternatively spliced, yielding multiple protein species—physiologically functional—from the same DNA species, the gene.

Translation

The mRNA must be translated into a peptide—a chain of amino acids alike a pearl necklace—by nanomachines, in the cell's cytosol, called ribosomes. Lacking their own membranes, ribosomes are not organelles as such. Ribosomes are composed of ribosomal RNA (rRNA) and protein, altogether ribonucleoprotein (RNP), itself encoded in the cell's genome. The cell's genome also encodes RNA a set of RNA species, each three sequences, called transfer RNA (tRNA). Each tRNA molecule binds a specific, free amino acid in the cell's cytoplasm arrives in the ribosome as does the mRNA gene transcript. A ribosomal region of apparently pure RNA, no protein, acts alike an enzyme—thus called ribozyme—holding mRNA steady while and another ribozymal region grips a corresponding tRNA sequence and by physicochemical dynamics clamps the tRNA anticodon to the mRNA codon. The amino acid borne by the tRNA is covalently bonding, thereby, to the previous amino acid clamped likewise. The amino chain grows into a peptide, whose sequence of amino acids is its primary structure.

Posttranslational modification

Posttranslational modification (PTM) occurs outside the ribosome. The peptide snaps to secondary structure, a geometric motif occurring along the peptide's length, as each molecule domain dons a configuration of either alpha helix (spiraling) or of beta sheet (pleated), a motif called secondary structure. Varying domains of the molecule, then, take greater geometric relations to each other—protein folding—shaping the molecule, alike origami, called tertiary structure, conferring the molecule's main physiologic function. Proteins called chaperone molecule—encoded in the DNA genome—can assist. Some proteins, for instance hemoglobin, also take quaternary structure via disulfide bridges between domains of two subunits—each with its own tertiary stucture—yielding quaternary structure, which then determines the molecule's physiologic functions. PTM also might add carbohydrates or lipid to the protein.

Molecular biology

Collagen molecules gets sugars and form cartilage—some of it mineralized into bone. Some protein gets lipids and, as lipoprotein, transport the cholesterol needed in every cell membrane and for steroid hormones, such as vitamin D, cortisol, and androgens (testosterone and estrogen precursors). Nuclear DNA encodes the RNA and protein sequences composing tRNA, ribosomes, cell receptors, extracellular matrix—collagen, bone, muscle, vessels, skin—enzymes, hormones, signaling molecules, and so on.

It is mainly the physicochemical dynamics of individual molecules, particularly proteins, by way of their 3D shapes and electromagnetic signatures, that determine the physiologic function of molecules.^[93] These are influenced by genes, but are not strictly set by genes, as a protein species' 3D structure—altogether secondary structure, tertiary structure, and sometimes quaternary structure, forming the protein species' native conformation—overrides most inherited variations in the molecule's primary structure, the structure level most resting on determination by gene variant.^[93] Each protein species has it native conformation, determined by levels of structure above structure, yet influenced by primary structure, as each amino acid has its unique electromagnetic traits.

^[94]

Human genome

In 1977 Sanger et al reported chain termination and Maxam and Gilbert reported chemical degradation methods of DNA sequencing, used to determine entire genomes.^[95] By 1990 the U.S. National Institutes of Health National Human Genome Research Institute had the Human Genome Project underway to sequence the human genome—3 billion sequences. It became a race between the NIH and a private company, known for applied research but subcontracted, to publish it first. Ahead of 2003 data, NIH's Francis Collins published a draft sequence in 2000.^[96]

Scherer SW explains that stories on science usually arrive far after its day—once the stories have been tidied up—missing the process of discovery, and yet this time a book was published in 2001, Cracking the Genome: Inside the Race to Unlock Human DNA (Free Press, 2001), though a nearsighted coverage.^[96] Reviewing the book, Jose AM explains, "It highlights the importance of knowing the sequence of the human genome in the light of the obvious usefulness to medicine as well as the imminent ethical issues that humanity has to deal with. The author sketches the important scientific breakthroughs since the discovery of DNA that have made it possible for man to decipher his own genetic makeup".^[97] Donna Maclean, a British waitress and poet, sought with patent application GB0000180.0 to patent "Myself".^[97]

Theory of genes

The prevalent view in biology is that the entire organism's anatomy and physiology is encoded somehow in its DNA genome—the organism's genotype—and that further researches by molecular biology's house molecular genetics will unravel the full code of the entire organism's form and function, namely anatomy and physiology, altogether called phenotype.^[19] This prediction generally presumes all biological phenomena are determined by an interplay of environmental and some molecular chaos acting on the genomic DNA molecules of the host organism.^[19]

DNA explains—in part—the amino acid sequence of protein molecules. An organism, however, is comprised of a vast population of protein molecules interacting with lipids, sugars, minerals, and vitamins, and cell types still being identified. As a genetic code encoding the entire organism's anatomy remains unreported, some philosophers are unconvinced that genomic DNA explains the anatomy of an organism to begin with. Walters K (The Stanford Encyclopedia of Philosophy, 2008) explains,

The modest answer to the question What do genes do? is that they "code for" or "determine" the linear sequences in RNA molecules and polypeptides synthesized in the cell. (Even this modest answer needs to be qualified because RNA molecules are often spliced and edited in ways that affect the linear sequence of amino acids in the eventual polypeptide product.) But biologists have offered a far less modest answer as well. The bolder answer is part of a sweeping, fundamental theory. According to this theory, genes are "fundamental" entities that "direct" the development and functioning of organisms by "producing" proteins that in turn regulate all the important cellular processes. It is often claimed that genes provide "the information", "the blueprint", or "the program" for an organism. It is useful to distinguish this sweeping, fundamental theory about the allegedly fundamental role of genes from the modest, basic theory about what genes do with respect to the synthesis of RNA and polypeptides.^[98]

A prime proponent of scientific realism, Hilary Putnam has expressed certainty that DNA is indisputably the determinant of an organism's physical traits. Potthast T (2009) similarly, discussing the term paradigm shift as mostly overused, says, "One could, for instance, indisputably describe the cracking of the genetic code as a revolutionary step forward for biology. Although it did not replace an existing paradigm, namely Darwin's theory of evolution, it did create completely new possibilities for practically using this knowledge and for thinking about the essence of life.^[99]

Darwin's theory

Darwins theory of evolution was pangenesis, whereby natural selection was but a component. Darwin's theory was discarded from biology in 1892—after Darwin's death—when August Weismann's theory was adopted as neodarwinism. In 1900 U.S. biologists took unearthed Austrian monk Gregor Mendel's 1864 reported on inheritance in snowpeas and developed the first genetics. Thomas Hunt Morgan's group researches in the 1910s on inheritance in fruit flies and revealed many aspects of chromosomal inheritance.^[100]

Genetic determinism

AR Cashmore (2010) opens a discussion in Proceedings of the National Academy of Sciences of the United States of America indicating that most biologists, although proudly believing that biology discarded vitalism long ago, are unacknowledged vitalists, clinging to the notion of free will, and that society's judicial system is based on this nonexistence, as all actions are explained by a human's genes, environmental influences, and molecular stochasticism.^[19] JP McEvoy (2010) explains that in 1894 this was discussed in an article in light of darwinism, and it concluded that without free will, the justice system lacks justice.^[101]

H Anckarsäter (2010) adds that although data shows that nerve impulse to a mind state or action precedes cognition of it by some fractions of a second, epidemologic data can attribute about half of criminality to genes—so about half is epidemiologically unaccounted for by genes—yet that at the gene level only 1 or 2% can be attributed to any single gene variant, and that claiming that science has disproved free will is "scientism, candidate to a worldview".^[102] K Hinsen (2010) says that a scientific model for free will is impossible, but that we ought to trust our perception and infer we have free will.^[103]

Cashmore (2010b) responds to Hinsen by explaining that "correlations tell us nothing about causality" and that "what little evidence there is addressing the causal relationship between conscious thought and behavior suggests that the former is simply the effect of neural activity, not its cause".^[104] Cashore (2010b) holds that all biological phenomena are due to GES (genes, environment, and stochasticism), whereas even Richard Dawkins, who argues vehemently for darwinism and against religion, propose these plus free will, whereas it is "appropriate to discard the belief in free will, at least until someone could provide an appropriate testable molecular model".^[104]

Cashmore (2010b) explains "that the evidence in favor of free will is based solely on a correlation between conscious thought and behavior", yet that "the properties of free will are those normally associated with vitalism: they are unpredictable; they do not seem to obey the physical laws as we understand them; there is no hint of any molecular or cellular model; they are totally independent of any relationship to our genetic and environmental history; and they are not simply explained by stochastic processes. Now, if we apply the rule of Occam’s razor, or the law of parsimony, to this comparison, which of the two models are we going to accept? Surely there is no contest".^[104]

Cashmore (2010b) closes, "The reality is that in this instance, the process of evolution has conned us into believing in free will. I urge biologists to give this topic more thought than they seem to have been willing to do in the past".^[104] Cashmore (2010b) reminds us, however, "As scientists, we know that correlations tell us nothing about causality".^[104]

Genetic epidemiology

Anckarsäter (2010) cites a meta-analysis by SA Burt (2009), which found that aggressive rulebreaking appeared highly heritable, as genetic factors explained 65% of the variance—with little role due to shared or common environment especially after childhood—whereas genetic factors expained 48% of nonaggressive rulebreaking while another 18% was attributable to shared environmental effects.^[105]

Such epidemiologic methodology and inference upon twin studies has been criticized as pseudoscience.^[106] It starts from the presumption that behavior is fully explained by DNA genotype and postnatal environment, applies statistical methods to control for environment, and then concludes that any remaining behavior is due to DNA genotype. This begs the question, however, of the validity of the initial presumption—that all behaviors are due to postnatal environment and genotype.

Besides whether factors besides genotype and environment operate, at the very least gestational environment and very early prenatal experience greatly affect later psychologic and behavioral phenotype—sometimes, as with schizophrenia, manifesting after delay.

Elementary unit of life

Cell theory

In 1838 Schwann and Schleiden offered cell theory. In 1857, to cell theory, pathologist Rudolf Virchow added Omnis cellula é cellula (Every cell arises from a cell).

Microzymian theory

In 1858 Béchamp reported microzymas and extended microzymian theory to all organisms and described microzymas as immortal entities whose origin defied explanation by newtonian mechanism.

Microbian theory

Pasteur refuted microzmian theory by extending cell theory to microbiology with Pasteur's microbian theory describing microorganisms as the elemental unit of their own anatomy (not arising from precursor entities).

Hypothetical units

Couch (1922) explains

Reflection made it clear that the evidence demands the existence of a unit of living matter smaller than the cell but larger than the physicist's molecule. This was first suggested by Henle in 1841, and has been accepted by most cytologists. A number of names for a hypothetical ultramicroscopical vital unit have been proposed: physiological units (Spenser), gemmules (Darwin), pangens (De Vries), Plasomes (Weisner), micellæ (Nägeli), plastidules [Häckel and Elssberg), inotagmata (Englemann), biophores (Weismann), bioplasts (Beale), somacules (Foster), idioblasts (Hertwig), idiosomes (Whitman), biogens (Verworn), microzymas (Béchamp and Ester), and gemmæ (Haacke). Of the terms listed above, one is of especial interest to students of chemical terminology. The term 'micellæ' proposed by Nageli in 1877 has been employed by the botanists. Today it holds an important place in colloid chemistry as the name for the ultimate colloidal particle. It is destined to even greater importance for it is being used as a base upon which is constructed the newer theories of life and death, of disease, immunity, and anaphlaxis, of development, growth, and inheritance. The 'micella' is not only the ultimate particle of colloidal matter—it is the ultimate living thing.^[107]

Virus

Moreria and López-García (2009) offer ten reasons to exlude viruses from the tree of life.^[108] Forterre (2010), however, defines life as an organism, and that as an "ensemble of integrated organs (molecular or cellular) producing individuals evolving through natural selection", and that the origin of life corresponds to "the first organism corresponding to this definition".^[109] Forterre calls life "an historical process" or a "mode of existence" either of cells, whose genomes encode, among other proteins, the cell's ribosomes—the cell's nanomachines that manufacture protein molecules—or of viruses, whose genomes encode the subunits of the viral protein crystal, namely the viral capsid.^[109] And this definition includes their "ancestors".^[109] Forterre explains, "Viruses are no more confused with their virions [the capsid containing an infectious genome], but can be viewed as complex living entities that transform the infected cell into a novel organism—the virus—producing virions".^[109]

Theory of virus

Bad news

Sherris Medical Microbiology, 10th edition, 2010, an esteemed textbook of medical microbiology, opens chapter 6, "The nature of viruses", with a banner: (A virus is) "a piece of bad news wrapped in a protein coat"—Peter Medwar.^[110] Calisher (2007) scans the history of DNA molecular discoveries and then comments,

All this is remarkable. Remarkable that the mechanisms occur as they do, remarkable that we understand as much as we do, and remarkable how much more there is for us to learn and understand. But how does cellular DNA and cellular RNA relate to viral DNA and viral RNA?
In general, viruses comprise a genome within a protective protein coat or shell, a capsid. Viruses do not multiply, they replicate. More correctly, they are replicated by the cell mechanisms, which are subverted by the infecting virus and under the direction of that virus. By themselves, viruses do nothing, except to exist as packages of nucleic acid and protein. [...]
Using viruses as an example (although the same analogy could be made for mammals, birds, fish, plants, and politicians, all of which have genomes), the sequence of the virus genome is the specifier, the conductor of the cellular orchestra, the anti-democratic, authoritarian, and despotic tyrant that subverts the cellular proclivities, the dictator of the replication cycle. Strong words, indeed, but true ones.^[111]

Just there

Introduction to Modern Virology, 6th edition, 2007, an introductory textbook of pure virology, explains, "Some viruses impact on the health of theirs hosts, although probably most have no impact, or very little impact". The effect on the host species can be made harsh by external factors, like nutritional status.^[112] In one report Ebolavirus was inoculated into its apparent native host and the fruit bats exhibited disease only if they had not adapted to the laboratory diet.^[113] The virology textbook's chapter 1 "Towards a definition of a virus" explains that we do not know whether a host of a virus accrues benefits from hosting its viruses and summarizes, "At the moment all that is possible is to list some of the ways that viruses impact upon their hosts".^[114] The authors say that asking what a virus is doing there is like asking what a lion is doing there—it is just there.^[114]

Useful

Some virologists have maintained for many years that viruses exist because they offer the host species an evolutionary edge.^[115] Viruses of a species of parasitic wasp inject their fertilized eggs into caterpillars, which carry the wasp's eggs to term only if the wasp's virus is injected with the eggs.^[115] It is possible to turn the usual perspective on its head and instead search for advantages of virus infection, which might be shown to be good for you.^[115] The human genome is about 8% retroviruses, human endogenous retroviruses (HERVs), and about 50% is pieces of viruses or sequences indistinguishable from retroviruses but for lack of genes encoding envelope proteins (env).^[116] One group of HERV appears to mediate mammalian pregnancy by encoding fusogenic proteins fusing syncytiotrophoblast cells mediating placenta formation.

Microorganisms—or molecules?

A virus is now "any of a large group of submicroscopic infective agents that are regarded either as extremely simple microorganisms or as extremely complex molecules".^[117]

Venom

The word virus appeared in 1599 and meant "venom".^[117] When Pasteur developed rabies vaccine, virus meant merely "dreadful poison". It could have been an immunization to a toxin. A virus in the current sense was first identified in 1892 by Iwanowski—tobacco mosaic virus—who presumed it a toxin. In 1898 Beijerinck repeated Iwanowski's data but went further and passed it from plant to plant and found the action undiminished and so concluded it was infectious—replicating in the host—whereupon, alike germ theory, Beijerinck called it contagium vivum fluidum.^[118]

Filterable virus

Appearing in 1911 filterable virus referred to any pathogenic infectious entity passing a laboratory filter—Chamberland filter or Berkefeld filter having 0.22 micrometer pore size—entities now known to include both the current viruses and bacterial species, like mycoplasmas and rickettsias as well as filterable forms of classical bacterial, namely L forms.^[119]

Only in the mid the 1940s was a virus particle as a protein protein crystals sometimes encasing genes—encoding the crystal's subunits, envelop proteins (spike's binding cell receptors for entry into cells), and sometimes other proteins—recognized, as till then medical researchers were stuck in the paradigm of bacteriology..^[120] They presumed they were dealing with microorganisms alike bacteria but so small they unobservable.^[120]

Medical virology: Parasite

One individual, Thomas Rivers, launched virology as a field—independent of bacteriology—when virus particles were still unobservables. The Rockefeller Institute opened the Rockefeller Hospital—for clinical research—in 1910 with Rufus Cole as its first director. Cole met Rivers when they worked in a U.S. Army medical unit in World War I (1913-18). In 1922 Cole recommended Rivers as director of of the new virology laboratory at The Rockefeller Institute, whose director Simon Flexner ventured from New York City to Baltimore—to all three individuals' shared alma mater Johns Hopkins University where Rivers was working in pediatrics—to hire Rivers.^[121]

Rivers moved to New York in 1922 and later made an observation sharp within medical virology, a distinction in the modern definition of virus: it replicates only among cells.^[121] The Rockefeller Hospital (2011) explains,

In [December] 1926, Thomas M Rivers (1888-1962), director of The Rockefeller Hospital [though Rivers became its director in 1937], made a bold statement about the essential nature of viruses that set the course of virology for decades to come. He said, "Viruses appear to be obligate parasites in the sense that their reproduction is dependent on living cells".^[122]

Rivers reported two actions—cell proliferation and cell destruction—and wrote the definitive textbook, Filterable Viruses (Williams and Williams, 1928)..^[121] In 1937 Rufus Cole retired and Rivers replaced Cole as director of The Rockefeller Hospital.^[123] In 1937 Thomas Rivers modified "Koch's postulates" for viruses to make them simpler to implicate in diseases.^[124] (Koch never quite set forth the three steps of Koch's postulates—isolation, cultivation, inoculation—to identify an infectious entity as the cause of a disease.^[125] "Fulfilling Koch's postulates" is a mythical historical object to credential assertions in experimental medicine.)^[125]

Rivers once thought he had transmitted human herpesvirus to a rabbit by serial passage—inoculation from rabbit to rabbit—yet astutely recognized it was a latent rabbit herpesvirus raised.^[126] Richard Shope, a Rockefeller virologist trained by Rivers, noted in 1962 that this confusion—though noticed by Rivers—has continually dogged other virologists.^[126] Rivers was extremely observant and had astonishing memory, yet was authoritative, intolerant of disagreement, and extremely aggressive at it.^[126]^[121] Rivers trained a generation of virologists.^[121]

From 1937 till 1955—himself retiring at age 65—Rivers was director of the The Rockefeller Institute's bacteriology department as well.^[127] Rivers sat on New York City's board of Health.^[121] From 1922 till 1955 Rivers shaped The Rockefeller Institute into the globe's leader in virology.^[127] Rivers trained Thomas Francis Jr—America's first influenzaviruses A and B expert—who in turn trained Jonas Salk. Together they developed influenza vaccine for the U.S. military in 1943. In 1953 Salk developed the first polio vaccine, and Rivers led its introduction—against advice of the Nobelist virolgists who made it possible to culture poliovirus a couple of years earlier—and Francis Jr organized its nationwide field trial.^[128]

Chemistry: Ribonucleoprotein

In 1899 Albert Wood, an American, suggested TMV was an enzyme, questioned by Harry Hallard in 1915, but proposed again by several virologists.^[129] In 1926 Maurice Mulvania, an American, proposed TMV as a protein with autocatalytic traits.^[129] TMV was purified between 1927 and 1934 by Carl G Vinson, who in the early 1930s proposed it a protein but did not experimentally confirm it.^[129] In 1935 Wendell M Stanley, an American at The Rockefeller Institute, experimentally identified TMV as a protein.^[129] In late 1936 an English group led by Frederick C Bawden showed it was ribonucleoprotein: protein and ribonucleic acid (RNA).^[129] Aftera year refusing the data, Stanley took the RNP view but failed to credit the English group.^[129] In 1946 Stanley won the Nobel Prize in Chemistry and is generally considered to have established fundamental virology.^[129]

Electron microscopy: protein crystal

The electron microscope (EM) was developed in 1931.^[130] The first virus visualized with it was a plant virus, tobacco mosaic virus (TMV), in 1939.^[130] In 1948 the differences between smallpoxvirus and chickenpoxvirus was shown by EM. Poliovirus was first visualized in 1952, and research into the virus-host relationship began in the mid 1950s.^[130]

Virology/genetics: Mobile genetic elements

In the 1920s it was proposed by mulitple researchers that viruses either were genes or alike genes.^[100]

Nobelist Howard Temin, a discoverer of the retroviral enzyme reverse transcriptase, held that a retrovirus is a mobile genetic element.^[116] In August 1970 NATO sponsored an international summer school sponsored by called "Uptake of Informative Molecules by Living Cells",^[131] attended by Robert Gallo who soon joined virology's emergent subfield retrovirology.

The so-called dogma of molecular genetics is that physiologic information flows from DNA (gene) to RNA (transcription) to protein (translation). RNA does not turn into DNA, then. A retrovirus, however, is an RNA virus with a gene encoding an RNA-dependent DNA polymerase, namely reverse transcriptase (pol), that reverse transcribes the viral RNA into a complementary DNA (cDNA) copy. The viral enzyme integrase—encoded in the retrovirus—can integrate the DNA copy into the host cell's genome. Soluble viral proteins, virus particles, and infectious virions can be expressed from the integrated viral genome (provirus). Animal genomes contain retroelements (retrotransposons) that in effect are viruses but for lack of envelope genes (env), the proteins studding the virus particle's exterior and mediating entry of the full virion into a new host cell.

In 1977 it was observed that healthy gibbons can shed infectious retrovirus.^[132] Ebolavirus genes occur in the genomes of bats.^[133] Takemura (2001) proposed that the entire cell nucleus began as a poxvirus.^[134] Viral sequences in the animal encode proteins of immunity, cell structures, and viral sequences previously thought useless are now recognized to be key in gene regulation.^[135]

Immunology: Host immunity proteins

KV Suslov (2007) offers "Unified theory of immunity" whereby a virus is one of many proteins used by the body and shares "prion-like properties of the molecules in acquired immunity, complement, placental immunity, apoptosis, autoimmunity, cancer, and AIDS. Based on sequence homology, structural, and functional similarities between prions and viral proteins, virus-prion theory is proposed. According to virus-prion theory, virus is an aggregate of prion-like proteins with the nucleic acid encoding them".^[136]

Noninfectious human endogenous retrovirus (HERV) particles mediate placental function, and perhaps help suppress the mother's immunity at the fetus, explaining why pregnant women often test positive for HIVlike proteins.^[137] As the nuclear genome contains DNA genes from both parents, the fetus express's proteins from each parent, and the mother's body must tolerate the nonself antigens.

Electromagnetism

In 2009 Luc Montagnier, the Nobelist credited with discovery of HIV1 reported that he could detect HIV1 DNA seqeunces by electromagnetic signals even when viral RNA were absent.

Theory of microscopy

Theory of immunity

Adaptive vs innate

In the late 19th century Eli Metchnikoff identified immune cells, called phagocytes, that engulf targets.^[138] In 1890 Emil von Behring and Shibasaburō Kitasato identified that the blood sera of vaccinated individuals contained molecules binding to the target pathogen, and these molcules were named antibody.^[139] Metchnikoff identified an aspect of innate immunity. Behring and Kitasato identified an aspect of adaptive immunity.

Innate immunity, presumed to be ancestrally older, acts constitutively. It is mediated by soluble proteins (apparently encoded by viruses) and by phagocytes (alike carnivorous amoeba). The main phagocytes are neutrophils and monocytes in blood, yet macrophages in tissues. (Upon transmigrating through vessel walls into tissues, monocytes differentiate into macrophages.) Also in tissues also are the phagocytes dendritic cells (DCs), which in skin's layers have a specialized phenotype called Langerhans cells (LCs). DCs are the primary antigen presenting cells (APCs), what prime adaptive immunity.

Adaptive immunity, also called specific immunity, presumed a later innovation, is calls for lymphoid tissue. Central lymphoid tissues are the chicken's bursa sacs or the mammal's bone marrow and thymus gland. Yet ultimately lymphocytes reside in peripherial lymphoid tissues—lymphoid follicles and lymph nodes. Three forms of lymphocyte have been identified: natural killer cells (NK cells), T cells (mainly helper T cells and killer T cells), and B cells. Whereas NK cells act innately, T cells and B cells call for priming by an immunization event and then mediate specific immunity.

Autoimmunity

On whether the immune system could target host tissue, Paul Ehrlich predicated the phenomena would manifest as rapid demise of the host—a prediction not matching observations—and for many years autoimmunity was presumed to not normally occur. In the early 1930s, virologist Thomas Rivers was researching why smallpox vaccination or rabies vaccination sometimes triggers catastrophic, neurodegenerative disease, and found that by injecting nonhuman primates with brain tissue from other members of their species, they developed similar disease, yet it it took some 80 injections over a year. Other researchers added adjuvant, specifically Freund's complete adjuvant, and it took a single injection.

Later it was recognised that autoimmunity is a normal function, required to maintain health. Autoimmune disease occurs through immunization crossreacting with the host's self antigens and dysregulation of that immune response.

Infectious diseases

Lewis Thomas was among the biologists who in the 1950s made breakthrough discoveries such as the understanding that the immune system itself creates most of the pathology attributed to infectious diseases.^[140]

Symbiosis

In later epidemiologic data in wellnourished children, measles was found to improve longterm survival by over 3fold, and sublinical measlesvirus infection to correlated with improved survival over lack of measlesvirus infection.^[141]^[142] Measles was long known to reverse cancers, particularly Burkitt's lymphoma and Hodgkin's lymphoma, cancers of lymphatic tissue.^[143] The host's own innate immune cells—alveolar macrophages and dendritic cells—uptake measlesvirus from lungs and transport it to lymphatic structures.^[144] Such oncolytic viruses (lysing cancerous cells) help destroy tumors by interplay of virus, host cells, and immunity.^[145]^[146]

Theory of microbiology

19th century

In 1838 Schwann and Schleiden offered cell theory. In 1857, to cell theory, pathologist Rudolf Virchow added Omnis cellula é cellula (Every cell arises from a cell). In 1858 Béchamp reported that the two silkworm diseaess blighting France's silk industry were mediated by microorganisms arising from microzymas. Refuting cell theory, Béchamp extended microzymian theory to all organisms and described microzymas as immortal entities whose origin defied explanation by newtonian mechanism.

After three years of deriding the notion that microorganisms could mediate an animal's disease, Pasteur began writing prominent members of French society taking credit for the discovery, then developed pasteurization, applied at the problem of faulty batches of wine in France's wine industry. Pasteur's discovery in basic science was in chemistry by way of tartaric acid, showing that a chemical has a mirror-image form, a racemers, alike a left hand to a right hand. A trained chemist, Pasteur was an autodidact biologist and physician. Pasteur's three developments were in biomedcine: chicken cholera, cattle anthrax, and human rabies vaccines.

In 1876 Germany's Robert Koch developed bacteriology and showed a that particular species, identified by Devaine, was indeed cattle anthrax's necessary cause. Pasteur's protegé Henri Toussaint identified a bacterial species and named its genus Pasteurella. Mainly Pasteur's colleague Emile Roux attenuated its pathogenicity in live culture, and Pasteur introduced it as chicken cholera vaccine in a 1879 public experiment. In 1881 Toussaint reported anthrax vaccine made by a different method—chemical modification—yet Pasteur derided it. In 1881 Pasteur performed a famed succesful public experiment using Toussaint's method, and used it commercially when producing vaccine for sale. Pasteur successes showed that vaccines could be created at will in the "scientific laboratory".

England's Joseph Lister, namesake of Listerine, introduced antisepsis—the killing of bacteria—to surgery. In 1882 Koch reported the tubercle bacillus, cemented germ theory, which Koch's 1876 report on anthrax first gave firm footing too. American physicians were inspired by Pasteur's feats that scientific medicine could deliver succesful interventions through applied science, specifically biomedicine, the application of biology to development of medical technology or technique, yet traveled to Germany for training in "Koch's bacteriology" as the basic science.

Béchamp had refuted spontaneous generation, yet Pasteur held to it and then later refuted it. Béchamp maintained, however, that bacteria arise from immortal entities called microzymas that build bacteria. Pasteur refuted microzymian theory by extending cell theory to microbiology with Pasteur's microbian theory describing microorganisms as the elemental unit of their own anatomy (not arising from precursor entities). Though microzymian theory did not propose spontaneous generation of bacteria, the principle's resemblance to spontaneous generation of bacteria helped give ground to Pasteur's microbian theory. Pasteur's vaccinology successes drew faith in "Pasteurian science". Paradoxically or not, however, held to vitalism.

20th century: Koch's followers

Monomorphism vs pleomorphism

Genomic era

Theory of life

Spontaneous generation

Vitalism

Like Germany's pure philosopher Immanuel Kant, "father of anthropology" Johann Friedrich Blumenbach, who in the 1790s developed the colorcoded classification of races—white, yellow, brown, red, black—was a vital mechanist, believing organisms to be animated by a vital force moving matter through conventional physics, yet like Kant shunned metaphysical excesses, embodied by earlier theories, notably religious, on its source or origin.^[147] Blumenbach held that the vital force, Bildungstrieb, operated through mechanism yet exercised teleology—ultimate goal or purpose—or teleomachanism arranging abiotic matter into organisms and mediating their biotransformations.

In 1847 Hermann von Helmholtz's paper "On the conservation of energy" largely purged biology of any vital force and reduced physiology to classical physics. Vitalism remained in philosophical circles into the first third of the 20th century, however, particularly in the intense scientific and philosophical atmosphere of Vienna, Austria.

Nanobacteria controversy

Greener (2008) explains that all we can do at the question of life is categorize our own observations, while for now we do not even know how life began—or, really, what life is.^[9]

On the origin

Darwin in his book On the Origin of Species speculated that life could have begun in a pond or such that hosts natural selection of fit molecular variants. In 1924 Alexander Oparin speculated abiotic Earth's reducing atmosphere—one whose chemicals offer electrons via covalent bondning and so reduces the electric charge of the host molecules—could have created the molecular building blocks of life. (Earth's current atmosphere, rich in oxygen, is oxidative, seeking electrons by covalent bonding and so, for instance, oxidizing iron to rust—crumbing into soil.) The Earth's atmosphere was mainly CO2 and N2—with some H2, H2S, and CO—with sunlight or electric discharge, organic molecules could have formed.^[148] In the 1950s the graduate student Stanley Miller showed that electric sparks into water holding H2, CH4, NH3—somewhat different from the abiotic Earth's but showing spontaneous synthesis plausible—could yield organic molecules, including several amino acids.^[148]

Quantum mechanics' cofounder Erwin Schroedinger speculatd in his book What is Life? that life had perhaps life had begun as an "aperiodic crystal".^[45] In a similar vein, James Watson and Francis Crick, who in 1953 identified DNA as a double helix, speculated that perhaps DNA could replicate itself without enzymes—and so began organisms and life.^[45] And yet Forterre P, Filée J, and Myllykallio H (2000) explain, "Times have changed, and several decades of experimental work have convinced us that DNA synthesis and replication actually require a plethora of proteins".^[45] The mystery became not how DNA selfreplicates but how DNA began "directing" and "controlling" the cell—fundamental theory of genes—in order to "selfreplicate".

Molecular darwinism

Molecular darwinism concludes that the transition occurred through stochastic chemistry. Molecular darwinism posits that life arose as a protocell via laws of chemistry amid molecular chaos, stochasticism, on an abiotic Earth by natural selection of random but incidentally fit mutations into a bacterial cell.^[149] The cell, in keeping with normal biology, is regarded as the elemental unit of life, and life is the orchestra of chemical reactions. By natural selection of random mutants and chance genetic recombinations, the present species diversity arose through an unbroken chain of direct inherence of DNA genomes. So evolution through inheritance can be mapped on an orderly phylogenetic tree back to a putative last universal common ancestor (LUCA), or a few LUCAlikes.

RNA world

In 1981 it was found that the region of ribosomes that synthesizes molecular bonds between individual amino acids apparent lacks portein and is pure RNA. The RNA sequences can both store information in their own molecular sequence and effect biocatalysis alike the proteins called enzymes—and so such RNA sequences are called ribozymes. It is now presumed that an RNA world must have predated our current DNA-RNA-protein world. In such theory, ribozymes selfreplicated while synthesizing proteins within selfreplicating liposomes—the equivalent of a cell membrane without membrane proteins such as receptors and channels—and eventually a protocell formed. To challenge is resolving how the RNA world switched to our DNA-RNA-protein world.

Koonin et al (2006) explains that upon this RNA-protein world, RNA viruses developed.^[150] Then a world of RNA and DNA retroelements developed.^[150] Then a DNA world arose—in addition to RNA and proteins—eventually yielding eubacteria and bacteria cells.^[150] In 2009 ribozymes were at last identified that apparently selfsynthesized, selfreplicate, and synthesize proteins.^[151]

Perhaps eventually a poxvirus—a large DNA virus that unlike most viruses is replicated not in the host cell's nucleus yet in its cytoplasm—began the cell nucleus.^[134] It seems that viruses encode the cell's cytoskeleton. Other viruses yet encoded the proteins of immunity: complement and antibody and major histocompatibility complex.^[135]

Mitochondrion mystery

Plant cells gained cynobacteria residing internally and becoming chloroplasts, whereas animal cells gained rickettsia residing internally and becoming mitochondria, and this is presumed to be endosymbiosis. Yet a mitochondrion has its own genome, mitochondrial DNA (mtDNA), what is inherited fully from the mother's egg, explaining use of mtDNA tracing lineage over many generations and thousands of years. A sperm is not a germ cell—it is made by a germ cell in the testis—and carries one set of chromosomes to the woman's germ cell, her egg. The fertilized egg secretes human chorionic gonadotropin (hCG) signaling the ruptured ovarian follice, namely corpus luteum, to continue secreting progesterone, which sustains the unterine lining, otherwise shed it for menstruation once both estrogen and progesterone levels fall if the egg is unfertilized. The dividing egg, implanted in the uterined lining, develops into a new organism.

As of 2009 the earliest eukaryotes in the fossil record are about 2 billion years old, yet paleontologists had reported no transitional forms.^[152] By examination of eukaryote genomes, insight into the emergence of eukaryotes has been inferred.^[152] A key step was the "acquisition of bacterial passengers, which eventually became the mitochrondria of eukaryote cells".^[152] Yet the "bacterial passengers" themselves helped develop other traits of the eukaryote cell—incuding its nucleus.^[152] It is unclear which came first—the mitochondrion or the rest of the cell. Mitochondria replicate independently within the cell—progeny cells apparently cannot form them from scratch—their escape from cells might help explain sterile inflammation.^[92]^[153]

^[154]

^[155]

Life's quanta?

Microzymas

Bird explains, "Even before Béchamp's time, other researchers had observed, but passed off as unexplainable, what they called 'scintillating corpuscles' or 'molecular granulations'. Béchamp, who was able to ascribe strong enzymatic (catalytic, change-causing) reactions to them, was led to coin a new word to describe them: microzymas (tiny ferments).^[156]

Bions

Wilhelm Reich, who trained under Sigmund Freud and later largely revised psychoanalytic theory, reported that he had identified the vital force, named orgone, pervading Earth's atmosphere, as well as the death force, destructive orgone (DOR), that tended to accumulate over desolate landscapes, such as deserts, yet could parasitize the cells of animals.^[157] The creative orgone condenses into "a mobile form consisting of mass-less pulsating vesicles", called orgonomes that pulsated as they accumulated more orgone and then entered vesicles, called bions, that formed cells and arranged them into plants and animals.^[157] Rycroft (1974) explains, "It would seem that Reich claimed both to have observed and to have induced experimentally the formation of orgones into organisms, i.e., to have created life in the laboratory".^[157]

Somatids

Christopher Bird, coauthor with Peter Tompkins of the Secret Life of Plants (1973), identified independent biologist, engineer, and pharmacist Gaston Naessens as "Galileo of the microscope" and held that Naeseens had in effect confirmed Reich's theory—there are units of life occurring as transforming particles associated with cells—as well as Jacques Pierre Antoine Bechamp's microzymian theory, though Naessens said that he had not known of the French biologist of the 19th century.^[158] Since at least the 1960s Gaston Naessen has offered somatidian orthobiology, which holds that somatids operate cells, yet that without somatids, cells stop dividing. In January 1964 when Naessens offered his cancer treatment Anablast to any government willing to test it,^[159] France's cancer institute, founded in 1926, Institut Gustave Roussy, took up the offer, said it would take a couple of years for clinical trails, but then reported in two weeks that Naessens was a fraud, that the reported entities were a type of debris of red blood cells called myelinic figures.^[159]

Nanovesicles

Soon after the identification of the putative nanobacteria, reports began of nanovesicles throughout Earth's entire atmosphere. Nanovesicles are reported to occur in all fluids of plants and animals and to pass out the body in urine, enter water, and so occur in all Earth's water—what is presumed to have arrived on Earth with a icy comet.

Theory of physiology

New science of "debris"

What is mind?

F Baluska and S Mancuso (2009) explain,

It is generally assumed, both in common-sense argumentations and scientific concepts, that brains and neurons represent late evolutionary achievements which are present only in more advanced animals. Here we overview recently published data clearly revealing that our understanding of bacteria, unicellular eukaryotic organisms, plants, brains and neurons—rooted in the Aristotelian philosophy—is flawed. Neural aspects of biological systems are obvious already in bacteria and unicellular biological units such as sexual gametes and diverse unicellular eukaryotic organisms. Altogether, processes and activities thought to represent evolutionary "recent" specializations of the nervous system emerge rather to represent ancient and fundamental cell survival processes.^[160]

Bacterial intelligence

A genome is encoded in a formal language, mathematic, and human language, although more plastic, is mathmematic.^[161] Bacteria exhibit linguistic communication and social intelligence.^[162] Bacteria continually monitor external and internal environments and exhibit cognitive, computational, and evolutionary capabilities "unimaginable in the first six decades of the twentieth century".^[163] Bacteria have widespread and multiple systems for mobilizing and engineering and DNA molecules, and bacteria cells collaborate, and can even commander the basic cell biology of plants and animals.^[163] Bacterial geneticist of some 40 years, Shapiro JA (2007) concludes, "This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings".^[163]

Bacteria actively resist antibiotics creating enzymes that cleave the antibiotic molecules, by actively pump the antibiotic molecules out the cell, by uptaking and installing fit genes loose in the environment (transformation), by installing the fit genes disseminated throughout the bacterial population by way of a bacterial virus (transduction), or by sharing the fit genes by constructing a tube, namely F pilus, encoded on an F plasmid, what tube mediates the fit genes' transport into the other bacterial cell that lacked the fit genes (conjugation).^[164]

Plants brains?

Vesicles in yeast cells at microtubules release proteins that seem to offer sensation as spacial cues and then proteins are secreted there, mediating growth of yeast cells.^[165] A similar process mediates the growth of a plant's root-tip hairs.^[165] Plant cells exhibit particlar similarities with neurons—otherwise exclusive to animals.^[166] In the second half of his life, Darwin turned focus to plants and wrote several books, including The Power of Movement in Plants, written with his son Francis.^[167] The two explain, "It is hardly an exaggeration to say that the tip of the radicle thus endowed [with sensitivity] and having the power of directing the movements of the adjoining parts, acts like the brain of one of the lower animals; the brain being seated within the anterior end of the body, receiving impressions from the sense-organs, and directing the several movements".^[167]

Notes

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^ Okasha S, Philosophy of Science: A Very Short Introduction (New York: Oxford University Press, 2000), ch 4 "Realism and anti-realism", p 58.
^ ^a ^b Niiniluoto I, "Scientific progress", sec 3 "Theories of scientific progress" sec 3.1 "Realism and instrumentalism", The Stanford Encyclopedia of Philosophy (Summer 2011 edn), Zalta EN, ed.
^ ^a ^b Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1177/0951692896008003003, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1177/0951692896008003003 instead.
^ Chakravartty A, sec 1 "What is scientific realism?", sec 1.1 "Epistemic achievements versus epistemic aims".
^ Leplin, "Introduction", in Scientific Realism (U C P, 1984), p 3.
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v t e Metaphysics
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