Sunday, May 23, 2021

Noncoding “Junk” DNA Is Important for Limb Formation

 

Noncoding “Junk” DNA Is Important for Limb Formation

https://evolutionnews.org/2021/05/noncoding-junk-dna-is-important-for-limb-formation/
Casey Luskin

Image credit: Schäferle via Pixabay.

A 2021 article in Nature, “Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator,” reports important new functions for non-coding or “junk” DNA that underlie limb formation. Before we get to the paper itself, consider a description of it on the Proceedings of the National Academy of Sciences “Journal Club” blog. The latter describes the research in terms that sound like they could have come directly from an intelligent design source: 

Genes that code for proteins make up only about 2% of the human genome. Many researchers once dismissed the other 98% of the genome as “junk DNA,” but geneticists now know these noncoding regions help to regulate the activity of the 20,000 or so protein-coding genes identified.

A new study in Nature underscores just how important noncoding DNA can be for human development. The authors show that deletions in a noncoding region of DNA on chromosome 2 cause severe congenital limb abnormalities. This is the first time a human disease has been definitively linked to mutations in noncoding DNA, says lead author Stefan Mundlos, head of the development and disease research group at the Max Planck Institute for Molecular Genetics in Berlin, Germany.

“Severe Congenital Limb Malformation” 

The technical paper in Nature describes the research. The investigators examined the chromosomes of people who had naturally occurring limb malformation, and found that these people had deletions of DNA encoding long non-coding RNA sequences (lncRNAs) from human chromosome 2. They deleted corresponding DNA sequences in mice and found similar “severe congenital limb malformation,” suggesting these lncRNA sequences are functionally important:

Here we show that genetic ablation of a lncRNA locus on human chromosome 2 causes a severe congenital limb malformation. We identified homozygous 27–63-kilobase deletions located 300 kilobases upstream of the engrailed-1 gene (EN1) in patients with a complex limb malformation featuring mesomelic shortening, syndactyly and ventral nails (dorsal dimelia). Re-engineering of the human deletions in mice resulted in a complete loss of En1expression in the limb and a double dorsal-limb phenotype that recapitulates the human disease phenotype. Genome-wide transcriptome analysis in the developing mouse limb revealed a four-exon-long non-coding transcript within the deleted region, which we named Maenli. Functional dissection of the Maenli locus showed that its transcriptional activity is required for limb-specific En1 activation in cis, thereby fine-tuning the gene-regulatory networks controlling dorso-ventral polarity in the developing limb bud. 

In the discussion, the article explains how important it is that we seek to understand the key functions of non-coding DNA sequences that encode lncRNAs:

In the era of whole-genome sequencing, the findings described here underscore the need for a systematic annotation and functional characterization of lncRNA loci to interpret and classify non-coding genetic variants. They highlight the importance of elucidating the complex diversity of lncRNA modes of action to assess their role in organ development and disease.

Over 130,000 Functional “Junk DNA” Elements!

So just how are we progressing in the task of determining the functions of non-coding DNA elements? Some defenders of evolutionary orthodoxy would have us believe that we’ve only found a handful of non-coding DNA sequences that have function — exceptions to the rule that non-coding DNA is usually useless junk. Another 2021 article in Nature shows why it’s no longer tenable for evolutionists to hide behind such an argument from ignorance. The article explains that over 130,000 functional “genomic elements, previously called junk DNA” have now been discovered, highlighting how important these “junk” segments have turned out to be:

[I]t is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.

The article also observes that prior to the Human Genome Project, which was completed in 2003, there was “great debate” over whether it was “worth mapping the vast non-coding regions of genome that were called junk DNA, or the dark matter of the genome.” Under a paradigm informed by intelligent design, debates over whether to investigate junk DNA would have ended much sooner with an emphatic Yes!, furthering our knowledge of genetics and medicine. How much sooner would these 130,000+ “genomic elements, previously called junk DNA” have been uncovered if an ID paradigm had been governing biology research? 

Sunday, May 9, 2021

Human Origins

 

Review: Most human origins stories are not compatible with known fossils

by American Museum of Natural History

https://phys.org/news/2021-05-human-stories-compatible-fossils.html

 

The last common ancestor of chimpanzees and humans represents the starting point of human and chimpanzee evolution. Fossil apes play an essential role when it comes to reconstructing the nature of our ape ancestry. Credit: Printed with permission from © Christopher M. Smith

In the 150 years since Charles Darwin speculated that humans originated in Africa, the number of species in the human family tree has exploded, but so has the level of dispute concerning early human evolution. Fossil apes are often at the center of the debate, with some scientists dismissing their importance to the origins of the human lineage (the "hominins"), and others conferring them starring evolutionary roles. A new review out on May 7 in the journal Science looks at the major discoveries in hominin origins since Darwin's works and argues that fossil apes can inform us about essential aspects of ape and human evolution, including the nature of our last common ancestor.

Humans diverged from apes—specifically, the chimpanzee lineage—at some point between about 9.3 million and 6.5 million years ago, towards the end of the Miocene epoch. To understand hominin origins, paleoanthropologists aim to reconstruct the physical characteristics, behavior, and environment of the last common ancestor of humans and chimps.

"When you look at the narrative for hominin origins, it's just a big mess—there's no consensus whatsoever," said Sergio Almécija, a senior research scientist in the American Museum of Natural History's Division of Anthropology and the lead author of the review. "People are working under completely different paradigms, and that's something that I don't see happening in other fields of science."

There are two major approaches to resolving the human origins problem: "Top-down," which relies on analysis of living apes, especially chimpanzees; and "bottom-up," which puts importance on the larger tree of mostly extinct apes. For example, some scientists assume that hominins originated from a chimp-like knuckle-walking ancestor. Others argue that the human lineage originated from an ancestor more closely resembling, in some features, some of the strange Miocene apes.

In reviewing the studies surrounding these diverging approaches, Almécija and colleagues with expertise ranging from paleontology to functional morphology and phylogenetics discuss the limitations of relying exclusively on one of these opposing approaches to the hominin origins problem. "Top-down" studies sometimes ignore the reality that living apes (humans, chimpanzees, gorillas, orangutans, and hylobatids) are just the survivors of a much larger, and now mostly extinct, group. On the other hand, studies based on the "bottom-up"approach are prone to giving individual fossil apes an important evolutionary role that fits a preexisting narrative.

The positional repertoire preceding human bipedalism is unknown (so it is still in some living apes). Credit: © Sergio Almécija

"In The Descent of Man in 1871, Darwin speculated that humans originated in Africa from an ancestor different from any living species. However, he remained cautious given the scarcity of fossils at the time," Almécija said. "One hundred fifty years later, possible hominins—approaching the time of the human-chimpanzee divergence—have been found in eastern and central Africa, and some claim even in Europe. In addition, more than 50 fossil ape genera are now documented across Africa and Eurasia. However, many of these fossils show mosaic combinations of features that do not match expectations for ancient representatives of the modern ape and human lineages. As a consequence, there is no scientific consensus on the evolutionary role played by these fossil apes."

Overall, the researchers found that most stories of human origins are not compatible with the fossils that we have today.

"Living ape species are specialized species, relicts of a much larger group of now extinct apes. When we consider all evidence—that is, both living and fossil apes and hominins—it is clear that a human evolutionary story based on the few ape species currently alive is missing much of the bigger picture," said study co-author Ashley Hammond, an assistant curator in the Museum's Division of Anthropology.

Kelsey Pugh, a Museum postdoctoral fellow and study co-author adds, "The unique and sometimes unexpected features and combinations of features observed among fossil apes, which often differ from those of living apes, are necessary to untangle which features hominins inherited from our ape ancestors and which are unique to our lineage."

Living apes alone, the authors conclude, offer insufficient evidence. "Current disparate theories regarding ape and human evolution would be much more informed if, together with early hominins and living apes, Miocene apes were also included in the equation," says Almécija. "In other words, fossil apes are essential to reconstruct the 'starting point' from which humans and chimpanzees evolved."

 


Wednesday, April 21, 2021

AI state of the artifice


The Myth of Artificial Intelligence by Eric Larson

 https://www.amazon.com/Myth-Artificial-Intelligence-Computers-Think/dp/0674983513

“If you want to know about AI, read this book…it shows how a supposedly futuristic reverence for Artificial Intelligence retards progress when it denigrates our most irreplaceable resource for any future progress: our own human intelligence.”―Peter Thiel

A cutting-edge AI researcher and tech entrepreneur debunks the fantasy that superintelligence is just a few clicks away―and argues that this myth is not just wrong, it’s actively blocking innovation and distorting our ability to make the crucial next leap.

Futurists insist that AI will soon eclipse the capacities of the most gifted human mind. What hope do we have against superintelligent machines? But we aren’t really on the path to developing intelligent machines. In fact, we don’t even know where that path might be.

A tech entrepreneur and pioneering research scientist working at the forefront of natural language processing, Erik Larson takes us on a tour of the landscape of AI to show how far we are from superintelligence, and what it would take to get there. Ever since Alan Turing, AI enthusiasts have equated artificial intelligence with human intelligence. This is a profound mistake. AI works on inductive reasoning, crunching data sets to predict outcomes. But humans don’t correlate data sets: we make conjectures informed by context and experience. Human intelligence is a web of best guesses, given what we know about the world. We haven’t a clue how to program this kind of intuitive reasoning, known as abduction. Yet it is the heart of common sense. That’s why Alexa can’t understand what you are asking, and why AI can only take us so far.

Larson argues that AI hype is both bad science and bad for science. A culture of invention thrives on exploring unknowns, not overselling existing methods. Inductive AI will continue to improve at narrow tasks, but if we want to make real progress, we will need to start by more fully appreciating the only true intelligence we know―our own.

Review

“If you want to know about AI, read this book. For several reasons―most of all because it shows how a supposedly futuristic reverence for Artificial Intelligence retards progress when it denigrates our most irreplaceable resource for any future progress: our own human intelligence.”Peter Thiel

“Artificial intelligence has always inspired outlandish visions, but now Elon Musk and other authorities assure us that those sci-fi visions are about to become reality. Artificial intelligence is going to destroy us, save us, or at the very least radically transform us. In The Myth of Artificial Intelligence, Erik Larson exposes the vast gap between the actual science underlying AI and the dramatic claims being made for it. This is a timely, important, and even essential book.”John Horgan, author of The End of Science

“Erik Larson offers an expansive look at the field of AI, from its early history to recent prophecies about the advent of superintelligent machines. Engaging, clear, and highly informed, The Myth of Artificial Intelligence is a terrific book.”Oren Etzioni, CEO of the Allen Institute for AI

“A fantastic tour of AI, at once deeply enlightening and eminently readable, that challenges the overwrought vision of a technology that revolutionizes everything and also threatens our existence. Larson, the thinking person’s tech entrepreneur, explores the philosophical and practical implications of AI as never before and reminds us that wishing for something is not the same as building it.”Todd C. Hughes, technology executive and former DARPA official

“A discussion of general human intelligence versus the current state of artificial intelligence, and how progress in a narrowly defined, specialized area (how to play chess) does not necessarily mean we are getting closer to human-like thinking machines. So, take a rain-check on the impending arrival of the robot overlords, that is going to have to wait a while.”Elizabeth ObeeTowards Data Science

About the Author

Erik J. Larson is a computer scientist and tech entrepreneur. The founder of two DARPA-funded AI startups, he is currently working on core issues in natural language processing and machine learning. He has written for The Atlantic and for professional journals and has tested the technical boundaries of artificial intelligence through his work with the IC2 tech incubator at the University of Texas at Austin.


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Tuesday, March 16, 2021

Tim Maudlin on knowledge and reality in physics

  This is Tim Maudlin’s review of two books in the Boston Review. It is the best essay that I have read in many years. I have been following Tim Maudlin’s writings on the philosophy of physics for many years and have been greatly instructed thereby. But this general review of the basic underlying philosophical issues I think is magnificent. Even if philosophy of physics does not interest you particularly there's a great deal to be learned from this essay.

 

http://bostonreview.net/science-nature-philosophy-religion/tim-maudlin-defeat-reason

 

What Is Real?: The Unfinished Quest for the Meaning of Quantum Physics

Adam Becker

Basic Books, $32 (cloth)

The Ashtray: (Or the Man Who Denied Reality)

Errol Morris

University of Chicago Press, $30 (cloth)


People are gullible. Humans can be duped by liars and conned by frauds; manipulated by rhetoric and beguiled by self-regard; browbeaten, cajoled, seduced, intimidated, flattered, wheedled, inveigled, and ensnared. In this respect, humans are unique in the animal kingdom.

Aristotle emphasizes another characteristic. Humans alone, he tells us, have logos: reason. Man, according to the Stoics, is zoön logikon, the reasoning animal. But on reflection, the first set of characteristics arises from the second. It is only because we reason and think and use language that we can be hoodwinked.

Not only can people be led astray, most people are. If the devout Christian is right, then committed Hindus and Jews and Buddhists and atheists are wrong. When so many groups disagree, the majority must be mistaken. And if the majority is misguided on just this one topic, then almost everyone must be mistaken on some issues of great importance. This is a hard lesson to learn, because it is paradoxical to accept one’s own folly. You cannot at the same time believe something and recognize that you are a mug to believe it. If you sincerely judge that it is raining outside, you cannot at the same time be convinced that you are mistaken in your belief. A sucker may be born every minute, but somehow that sucker is never oneself.

A sucker may be born every minute, but somehow that sucker is never oneself.

The two books under consideration here bring the paradox home, each in its own way. Adam Becker’s What Is Real? chronicles the tragic side of a crowning achievement of reason, quantum physics. The documentarian Errol Morris gives us The Ashtray, a semi-autobiographical tale of the supremely influential The Structure of Scientific Revolutions (1962) by Thomas S. Kuhn. Both are spellbinding intellectual adventures into the limits, fragility, and infirmity of human reason. Becker covers the sweep of history, from the 1925 birth of the “new” quantum physics up through the present day. Morris’s tale is more picaresque. Anecdotes, cameos, interviews, historical digressions, sly sidenotes, and striking illustrations hang off a central spine that recounts critical episodes in the history of analytic philosophy.

Quantum theory first. Becker does not discuss the earliest signs that something was amiss in the theory of light and matter, but the fundamentals are well known. The first hints of particle-like behavior in electromagnetic waves were dropped by Max Planck in his treatment of blackbody radiation, the light given off as a body heats up. In 1905 Albert Einstein took a decisive step with his analysis of the photoelectric effect, the current that flows in certain metals exposed to light. Einstein postulated that the light wave delivers its energy to the metal in small packets or quanta. The energy per packet varies with the color (frequency) of the light, and the number of packets with the brightness (amplitude). Below a critical frequency, no current flows, no matter how bright the light. Above that frequency, some flows no matter how dim.

Light is not just absorbed by matter; it is also emitted. The emission from atoms occurs at only certain precise frequencies. These constitute atomic spectra, which permit us to determine how much of each element there is in a distant star.

In 1913 Niels Bohr devised the Bohr atom. Electrons orbit the nucleus just like planets orbiting the sun. Only certain orbits—which Bohr gave rules for—are available to the electron, and when an electron jumps from a higher orbit to a lower one, it emits light of a frequency determined by the energies of the orbits. The challenge was figuring out how these quantum jumps happen. Over the next decade, Bohr failed to find any precise electron motions. The spectra and intensities of emitted light never came out right. This is the period of the “old” quantum theory.

Becker’s main historical narrative begins dramatically at the October 1927 Fifth Solvay International Conference in Brussels. In 1925 Werner Heisenberg had invented matrix mechanics. Heisenberg’s mathematical formalism got the predictions that Bohr had been seeking. But the central mathematical objects used in his theory were matrices, rectangular arrays of numbers. The predictions came out with wonderful accuracy, but that still left the old puzzle in place: how does the electron get from one orbit to another? You can stare at a matrix from morning to night, but you will not get a clue.

Bohr took an unexpected approach to this question: instead of asking if the theory was too young to be fully understood, he declared that the theory was complete; you cannot visualize what the electron is doing because the microworld of the electron is not, in principle, visualizable (anschaulich). It is unvisualizable (unanschaulich). In other words, the fault lay not in the theory, it lay in us. Bohr took to calling any visualizable object classical. Quantum theory had passed beyond the bounds of classical physics: there is no further classical story to tell. This became a central tenet of the Copenhagen interpretation of quantum theory.

Imagine Bohr’s motivation to adopt this extreme conclusion. For over a decade, he had been seeking exact, visualizable electron trajectories and failed. He concluded that his failure was rooted in the impossibility of the task.

But in 1926 Erwin Schrödinger produced a mathematically different theory, wave mechanics. Schrödinger’s mathematics was essentially just the classical mathematics of waves. The atomic system was not designated by a matrix, it was described by a wavefunction. And waves may not be particles, but they are certainly visualizable objects from everyday life.

What is Real? and The Ashtray are spellbinding intellectual adventures into the limits, fragility, and infirmity of human reason.

Schrödinger’s theory proved easier to use than Heisenberg’s, in part because it is more intuitive. Furthermore, first Schrödinger and then Paul Dirac proved that the two theories are equivalent. In physics any two theories that make precisely the same observable predictions are observably equivalent. And one of the predominant philosophical views of the age—logical positivism—held that any two observably equivalent theories are really one and the same theory. That is, although the two theories may seem to be giving completely different accounts of the world, they are not. The total content of an empirical theory consists in the predictions it makes about the observable. No more and no less.

Logical positivism is a very attractive view for people who do not want to worry about what they cannot observe. It is ultimately a theory about meaning, about the content of a theory. According to the positivists, a theory says no more than its observable consequences.

Logical positivism has been killed many times over by philosophers. But no matter how many stakes are driven through its heart, it arises unbidden in the minds of scientists. For if the content of a theory goes beyond what you can observe, then you can never, in principle, be sure that any theory is right. And that means there can be interminable arguments about which theory is right that cannot be settled by observation.

So the situation in 1926 was rather confused. Matrix mechanics and wave mechanics were, in some sense, thought to be the same theory, differently expressed. But if you use the mathematics to derive a certain matrix yet have no notion of how the physical situation associated with the matrix would appear, how do you get a prediction about what you will observe? And wave mechanics is not much better off. Waves are certainly visualizable, but the world we live in, the world of laboratory experiments, does not present itself as made of waves. It presents itself, if anything, as made of particles. How do we get from waves to recognizable everyday stuff?

This, in a nutshell, is the central conundrum of quantum mechanics: how does the mathematical formalism used to represent a quantum system make contact with the world as given in experience? This is commonly called the measurement problem, although the name is misleading. It might better be called the where-in-the-theory-is-the-world-we-live-in problem.

For Bohr and Heisenberg, the measurement problem is how the unvisualizable can influence the observable (and hence visualizable). For Schrödinger it is how waves can constitute solid objects such as cats. In wave mechanics, the little planetary electron of the old quantum theory gets smeared out into a cloud surrounding the nucleus. If quantum mechanics provides a complete description of the electron—as Bohr insisted—this diffuseness is not merely a reflection of our ignorance about where the electron is, it is a characteristic of the electron itself. As Schrödinger memorably wrote to Albert Einstein, “There is a difference between a shaky or out-of-focus photograph and a snapshot of clouds and fog banks.” This unexpected (but perfectly visualizable) mistiness of the electron was fine by Schrödinger: after all, we have no direct experience of electrons to contradict it. But the dynamics of the theory could not confine the smeariness to microscopic scale. In certain experimental situations, the haziness of the electron would get amplified up to everyday scales. The electron that is nowhere-in-particular gives birth to a cat that is no-state-of-health-in-particular. Schrödinger found this result manifestly absurd: something must have gone wrong somewhere in the physics.

For his part, Bohr insisted—as he had to—that the description of an experimental procedure and its outcome be classical, which is to say visualizable. Otherwise, you could not tell what experiment was done and how it came out. But at some point, if we are probing the microscopic realm, we must reach the unvisualizable. And the interaction between the two must itself be unvisualizable, since one part is. So all one can ask for is a mathematical rule: if an interaction occurs, what are the probabilities of the various possible classical outcomes? There is no more to be sought from quantum theory than these numbers. And matrix mechanics typically does not provide a precise prediction but a set of probabilities for different outcomes. The deterministic world of classical physics has been lost.

Which is all well and good, so long as you know what counts as the point of interaction between a quantum system and a classical one. But this Bohr could never nail down. We are left with the question: under what conditions does such an interaction (a measurement of the quantum state) occur? Do we need a human observer? Some conscious detection device, even if not human? Will a mouse do? Some detection device, even if not conscious? The Copenhagen interpretation never answered.

For Schrödinger, we get a different problem. We can visualize the microworld: it is a wave. But at some point, waves must manage to appear as particles, things located at definite positions in space. And just as the Copenhagenists advert to measurement here, so too does Schrödinger. The sudden change from an electron wavefunction being spread all over space to being located at a point is called “the collapse of the wavefunction.” So for wave mechanics, the measurement problem becomes: When and how does the wavefunction collapse? And the tentative answer is, upon measurement.

By the time of the Fifth Solvay Conference, much of this doctrine had been worked out. And along with Bohr, Heisenberg, and Schrödinger, the conference attracted our other protagonist, Einstein.

Einstein demanded a clear account of what is going on in the physical world. Bohr thought that the key to quantum mechanics was the realization that there is no such thing.

Einstein was the great anti-positivist. His position is often called realism, but a better name is perhaps common sense. Einstein believed that there is a real, objective, mind-independent physical world, and that the goal of physics is to describe that world. Mere prediction, no matter how precise, is not enough: explanation is the goal. Further, he said, you do not start out knowing what you can observe and then building the theory to predict certain observations. Rather, it is the theory itself that tells you what you can observe.

So Einstein and Bohr were polar opposites in their approach to physics. Einstein demanded a clear and comprehensible account of what is going on in the physical world—at all scales—in space and time. Bohr thought that the key to quantum mechanics was the realization that no such thing could be had.

Becker sets up the Solvay showdown skillfully. In the conventional story, Einstein, once the radical, has aged into a conservative who cannot abide the idea that God plays dice. Desperate for determinism, he challenges Bohr with a thought experiment designed to show the untenability of Bohr’s contention that you cannot do better—even in principle—than probabilistic predictions. The necessity of probabilism was encoded in the Heisenberg uncertainty relations, which assert that the better one can predict one aspect of a system (e.g., its position), the worse one can predict another (e.g., its momentum). Einstein’s thought experiment comes as a shock, but after a tense night Bohr hits on the solution and refutes Einstein with his own brainchild: the general theory of relativity. A showdown for the ages. Einstein, defeated, drifts into crankhood, never more doing significant physics.

Here Becker begins his exposé. He shows that every single detail of the standard account of the Solvay Conference is untrue. Einstein was not concerned with saving determinism. His example was not designed to refute the uncertainty relation. And most critically, Bohr did not win, he lost.

Thus begins the great debunking. None of this is news to historians and philosophers of physics. The true account has been worked out by many people whom Becker cites. But he has done prodigious research and created a powerful narrative.

As we noted, Einstein was not centrally bothered by the indeterminism of quantum mechanics. What vexed him—as he said repeatedly—was the nonlocality, or, in his pungent phrase, the spooky action at a distance (spukhafte Fernwirkung) in quantum mechanics. Einstein put his finger on this right away and never took it off.

Consider the collapse of the wavefunction in Schrödinger’s wave mechanics. If an electron-wave is channeled through a very narrow hole, when it emerges it will spread out in all directions like a circular undulation in water. But a hemispheric screen constructed to catch the electron does not reveal anything spread out: there is a single bright flash, as of a particle hitting the screen. The transition from extended wave to localized particle requires the collapse of the wavefunction. What bothered Einstein was that the sudden appearance of the flash at one spot implied that there could not be a flash at any other spot, no matter how far away. Somehow, all the distant spread-out parts of the wavefunction instantaneously disappear. Faster than light. Spooky action at a distance.

Einstein saw that the phenomena themselves—as distinct from Schrödinger’s theory with its wavefunctions—did not require anything spooky. All you had to believe is that the electron was always in some precise location, of which we are ignorant, and takes a humdrum path from the source to the screen, causing a flash. But because quantum mechanics does not specify the location, accepting this picture demands rejecting the completeness of quantum mechanics. The Copenhagen interpretation cannot be the final story.

Bohr never came to grips with this argument. Indeed, it is unclear whether he ever understood it.

But while Einstein won—and would continue to win—all the logical battles, Bohr was decisively winning the propaganda war. The Copenhagen doctrine of the completeness of quantum theory and the inescapability of fundamental chance spread, enforced by Bohr and Heisenberg and the rest of the Copenhagen school. Behind the scenes, the Copenhagenists did not agree with each other, but to the world they presented a unified front. Meanwhile, Einstein and Schrödinger both rejected Bohr, but they also bickered with each other.

Here is Einstein’s own description of Copenhagen: “The theory reminds me a little of the system of delusions of an exceedingly intelligent paranoiac.” Philosopher Imre Lakatos gave this later assessment:

In the new, post-1925 quantum theory the ‘anarchist’ position became dominant and modern quantum physics, in its ‘Copenhagen interpretation’, became one of the main standard bearers of philosophical obscurantism. In the new theory Bohr’s notorious ‘complementarity principle’ enthroned [weak] inconsistency as a basic ultimate feature of nature, and merged subjectivist positivism and antilogical dialectic and even ordinary language philosophy into one unholy alliance. After 1925 Bohr and his associates introduced a new and unprecedented lowering of critical standards for scientific theories. This led to a defeat of reason within modern physics and to an anarchist cult of incomprehensible chaos.

Strong words. It is Becker’s burden, and Becker’s triumph, to show that every word is true.

The story has twists and turns: John von Neumann’s purported mathematical proof (1932) that quantum mechanics is complete and one could not add anything more to it and retain its successful predictions; the philosopher Grete Hermann’s detection in 1935 of the fatal flaw in von Neumann’s proof—and the complete disregard of her work; the elaboration of Einstein’s reasoning into the famous Einstein-Podolsky-Rosen (EPR) argument; Bohr’s incomprehensible response to EPR; Schrödinger’s reaction, including his eponymous cat. Surely, one thinks, this mess must have been cleaned up eventually! But it never was. It persists to this day. And we are only through the first third of the book.

Robert Oppenheimer is reported to have said, ‘If we cannot disprove Bohm, then we must agree to ignore him.’

The middle third of Becker’s book adopts a somber tone in the stories of three renegades who bucked the system in the 1950s and ’60s, after the Copenhagen mysticism had congealed into an icy command: shut up and calculate! Work on the foundations of quantum theory was effectively forbidden, with one’s career and future at peril. The first renegade was David Bohm, a bright and dutiful Copenhagenist until he met the aging Einstein and recanted. Bohm rediscovered the pilot wave theory that Louis de Broglie had presented at Solvay in 1927. The theory slices through the enigma—wave or particle?—like Alexander’s sword through the Gordian knot: the answer is wave and particle. The wavefunction becomes a pilot wave that guides the particles along their paths. The theory is completely deterministic—no playing dice—and recovers all the predictions of standard quantum mechanics. One would think Einstein would love the theory, but he did not. The dreaded nonlocality had not been exorcized. Indeed, it was even more striking.

Bohm’s theory put the lie to von Neumann’s impossibility proof by direct counterexample. Contra Bohr, the particles are visualizable even at microscopic scale. In short, the theory demonstrates beyond all doubt that the Copenhagen interpretation is nonsense. But Bohm’s work was ignored and effectively suppressed.

A political leftist, Bohm had refused to testify at the House Un-American Activities Committee. He was dismissed from his job at Princeton and went into exile in Brazil. His U.S. passport was revoked. He eventually found his way to Birkbeck College in London, but never received the recognition that was his due. In a notorious episode, Robert Oppenheimer is reported to have said, “If we cannot disprove Bohm, then we must agree to ignore him.”

The second renegade was a graduate student at Princeton not long after Bohm left in 1952. Also rejecting Copenhagen, Hugh Everett took Schrödinger’s evolving wavefunction and removed the collapse. He argued that rather than an incomprehensible smear resulting, as Schrödinger’s neither-alive-nor-dead cat suggested, a multiplication of worlds results. Schrödinger’s cat ends up both dead and alive, as two cats in two equally real physical worlds. Today this approach is called the many-worlds interpretation.

Everett’s thesis advisor, John Wheeler, had great enthusiasm for Everett’s innovation. But he insisted that Everett get the nod of approval from Bohr. Bohr refused, and Wheeler required Everett to bowdlerize his thesis. Everett left academia and did not look back. His work lay in obscurity.

The last and greatest renegade was John Stewart Bell. Spurred by Bohm’s papers, Bell queried whether Einstein’s dreaded spooky action at a distance could be avoided. Copenhagen and the pilot wave theory had both failed this test. Bell proved that the nonlocality is unavoidable. No local theory—the type Einstein had sought—could recover the predictions of quantum mechanics. The predictions of all possible local theories must satisfy the condition called Bell’s inequality. Quantum theory predicts that Bell’s inequality can be violated. All that was left was to ask nature herself. In a series of sophisticated experiments, the answer has been established: Bell’s inequality is violated. The world is not local. No future innovation in physics can make it local again. The spookiness that Einstein spent decades deriding is here to stay.

How did the physics community react to this epochal discovery? With a shrug of incomprehension. For decades, discussion of the foundations of quantum theory had been suppressed. Physicists were unaware of the problems and unaware of the solutions. To this day, they commonly claim that Bell’s result proves Bohm’s theory to be impossible and indeterminism to be inevitable, while Bell himself was the staunchest advocate of Bohm’s deterministic theory. Even now, the average physicist has no understanding of what Einstein argued in the EPR paper and what Bell proved.

The last third of What Is Real? could hopefully be titled “Slow Convalescence.” Gradually the worst excesses of Bohr’s influence are mitigated as Bell’s work inspires a new generation to look into foundational issues. We meet a new cast of characters, and the overall atmosphere is mildly optimistic. But there is a long way to go, and this very book could prove to be a watershed moment for the physics community if it faces up to its own past and its present. Or, following the fate of Einstein, Bohm, and Everett, Becker could just be ignored. But if you have any interest in the implications of quantum theory, or in the suppression of scientific curiosity, What is Real? is required reading. There is no more reliable, careful, and readable account of the whole history of quantum theory in all its scandalous detail.

 

The subtitle of Errol Morris’s new book is, “Or the Man Who Denied Reality.” That might suggest a biography of Bohr, but the face on the cover is that of Thomas Kuhn. A renowned documentarian known for his dogged pursuit of truth that got one man off death row, Morris had a short-lived stint as Kuhn’s graduate student at Princeton. The cut-glass ashtray of the title was hurled at Morris’s head by Kuhn in a fit of pique. Morris has never forgiven Kuhn. And the ashtray is the least of it. Morris loathed Kuhn’s relativism and abandonment of reason and evidence, and Kuhn loathed Morris back.

Morris’s book is a settling of scores, both personal and philosophical. It is also delightful, digressive, unpredictable, engrossing, amusing, infuriating, and visually stunning.

The tale of The Ashtray is one of serendipity. Kuhn trained at Harvard as a physicist. There he started teaching classes in the history of science, and as a Harvard Junior Fellow decided to switch from physics to the history of science. His first book, The Copernican Revolution (1957), is a splendid work. Rejecting the usual physicist’s tendency to see past scientific work through the lens of present scientific theory, Kuhn brings the reader back into the debates of the time. There are no high theoretical pronouncements, just the patient historical work needed to make the assumptions and commitments of an earlier generation of scientists comprehensible to a modern audience. Had all of his work been of this character, Kuhn would be remembered as a talented historian of science, largely unknown by the general public.

Errol Morris’s clash with Thomas Kuhn was preordained: it is one thing to remark how hard truth can be to establish, and quite another to deny that there is any truth at all.

Through a series of random events, Kuhn was asked to write a monograph on the history of scientific revolutions for the Encyclopedia of Unified Science. That book became The Structure of Scientific Revolutions. Kuhn said that The Structure of Scientific Revolutions was just a sketch for a longer book which never got written. Instead it went on, as it was, to become the most widely read and influential work of philosophy in the last half of the twentieth century.

The first three quarters of The Structure of Scientific Revolutions give an insightful account of the everyday life of a scientist doing what Kuhn dubbed normal science. As a doctor of physics, Kuhn was on familiar ground and his account rang true. Normal science, according to Kuhn, is designed to solve puzzles. Both the nature of these puzzles and the acceptable means of resolving them are fixed by a set of rules, practices, and examples that Kuhn called a paradigm. Only by reference to the paradigm could a scientist defend the importance of the puzzle she is working on and the legitimacy of her solution. In particular, says Kuhn, it is not in the nature of normal science to question or challenge the paradigm: the paradigm provides the rules by which the game of a particular science is played. But of course, we are not playing the same scientific games as we did two hundred years ago. To get from there to here, various paradigms had to be overthrown and replaced. In Kuhn’s argot, there had to be paradigm shifts. And all of the excitement and controversy surrounding Kuhn turns on the nature and the outcome of these paradigm shifts. Exchanging one paradigm for another constitutes a scientific revolution.

We can ask three critical questions about scientific revolutions: how are they fought, why are they won (or lost), and what is the cumulative outcome of them. Kuhn’s answers to all of these questions could be read in an unsettling way.

Kuhn explicitly analogized scientific revolutions to political revolutions. The outcome of an attempted political revolution cannot be settled through political means since there is no institutional structure that both sides will submit to. “The parties to a political conflict,” writes Kuhn, “must finally resort to the techniques of mass persuasion, often including force.” Often elusive, Kuhn does not explicitly say that scientists engaged in a conflict over paradigms do the exact same thing, but he does not quite deny it either. (The fate of David Bohm cannot but spring to mind in this context.) The choice of a paradigm, he says, “can never be unequivocally settled by logic and experiment alone.” This repudiation of the rationality of scientific practice struck a chord in the zeitgeist. In the 1960s, it was chic to depict science as no more legitimate or authoritative than any other cultural practice. Instead, it is all a matter of propaganda and power moves.

But surely, one objects, these scientific revolutions lead to progress. Scientific theories, unlike fashion trends, do not merely change; they get closer to the truth. Here, too, Kuhn is adamant: he remarks near the end that the word truth has never once appeared in his text except in a quote by Francis Bacon. Then comes the coup de grace: truth is just what the winners of the conflict over paradigms say it is. And of course, according to the winners, their own paradigm is true.

To top it all off, Kuhn insists that the psychological effect of adopting a new paradigm is to change the very world you live in. Because different paradigms are incommensurable, the people who adopt them cannot communicate clearly with each other. They do not speak the same language and their very experience of the world is different. Hence there can be no neutral, objective, rational adjudication of their dispute.

So Errol Morris’s clash with Kuhn was preordained. After the ashtray incident, Morris did a stint as a philosophy graduate student at Berkeley, but he ultimately went on to be an investigative reporter and documentary filmmaker best known for The Thin Blue Line (1988). While shooting a movie about a prosecution psychiatrist in Texas known as Dr. Death, Morris came across a death row inmate convicted of a policeman’s murder. Morris became convinced the inmate’s claims of innocence were true. The Thin Blue Line examines the stories people tell, the explicit and implicit falsehoods, the distortions that can seal the fate of an innocent man. Although the film depicts several wildly different accounts of what happened the night of the murder, it is not, Morris insists, another Rashomon (Akira Kurosawa’s 1951 classic). Morris’s film is fact rather than fiction, and there is a unique truth about what happened. It occurred exactly one way. It is one thing to remark how hard truth can be to establish, and quite another to deny that there is any truth at all. Morris found the latter claim manifestly absurd. Indeed, by getting a confession from the real killer on tape, Morris solves the murder.

Whereas Becker’s villain is Bohr and his heroes are Einstein and Bell, Morris has Kuhn get his comeuppance from philosophers Saul Kripke and Hilary Putnam. Morris’s cast of characters reads like a who’s who of modern analytic philosophy: Bertrand Russell, Karl Popper, Ludwig Wittgenstein, Norwood Russell Hanson, and John Earman. For the reader familiar with all these names, there is good sport in seeing them bouncing off each other in Morris’s historical pinball machine. If a few ring a bell, then with application one can learn some ins and outs of twentieth-century Anglophone philosophy. If none do, the book may be heavy going. And whereas Becker’s history is meticulous and his explanations careful and measured, Morris writes more impressionistically, with passion. His account of the philosophical issues is in the ballpark but not right on target.

The central philosophical issue that Morris discusses is the reference of terms: how does a noun such as mass or planet or Albert Einstein pick out or denote something in the world? Without an account of reference, we cannot construct a theory of truth. A true claim correctly describes the object or objects it denotes, so determining truth or falsity requires determining the object under discussion. Analysis of the reference of terms goes back to the very beginning of the strangest and most intellectually shocking philosophical view in the Western tradition. The pre-Socratic philosopher Parmenides defended the thesis that all change and motion is an illusion. Parmenides came to this conclusion by reflecting on claims about nonexistence or, in Greek, tō mē on, that which is not. We all accept as true the claim that Santa Claus does not exist, or, equivalently, Santa Claus is nonexistent. But what, exactly, is this supposedly true claim about? It cannot be about Santa Claus because if it is true, then there is no such thing. Parmenides asserted, “The same things exist for thinking as for being.” In other words, you can only think about existent items because there are no nonexistent items to be the objects of thought. It follows that a nonexistence claim such as “Santa Claus does not exist” cannot be true: if it were true, then Santa Claus would not refer to anything, so the sentence would be meaningless. Parmenides took this result to establish the incoherence of all nonexistence claims. And since to say that things have changed is to say that the nonexistent has come to be, and the nonexistent is meaningless, there can be no change.

Philosophers rose to Parmenides’s challenge by theorizing how a term such as “unicorn” can be meaningful even if it does not refer to anything. Unicorn is just shorthand for a description such as “horse-like animal with a horn growing from its forehead.” And “unicorns do not exist” is true just in case no animal fits that description. Bertrand Russell suggested a similar analysis of everyday proper names: “Santa Claus does not exist” just means there is no jolly, bearded, red-suited, toymaking individual who lives at the North Pole. John Mill accepted the descriptive account of unicorn but objected to the parallel theory of proper names: a name such as Heisenberg has no associated description or connotation. It is a mere tag that has only a denotation, the man Heisenberg himself. There is no description in virtue of which Werner Heisenberg denotes that very man. So Parmenides’s puzzle still remains for names of nonexistent items such as Santa Claus.

Kuhn believed that we can do no better than miscommunicate, misunderstand, and ultimately resort to raw institutional power to resolve our disputes.

One advantage of the descriptive view is that it works not only for talk of the actual world, but also for talk about mere possibilities. The descriptive view explains not just why it is true to say there are no unicorns, but how under certain conditions there would have been. All you need are conditions that would have produced horse-like animals with horns. So there are two quite different contexts in which the meaning and reference of terms has to be explicated: how they get (or fail to get) referents in the actual world, and how they work when considering merely possible (counterfactual) situations. The difference between indicative propositions about the actual world and counterfactual propositions about mere possibilities is illustrated by these two conditionals: if Lee Harvey Oswald did not shoot John F. Kennedy, then someone else did (indicative and true); and if Oswald had not shot Kennedy, then someone else would have (counterfactual and probably false).

Kuhn implicitly accepts the descriptive view. The meanings of theoretical terms such as “mass” are determined by the theories in which they are deployed. Mass as used by Newton means something different from mass as employed by Einstein because the theories they are embedded in are different. Therefore Newtonians cannot really communicate with Einsteinians, Ptolemaic astronomers cannot really communicate with Copernican astronomers, and so on. This is why, for Kuhn, scientific revolutions cannot be settled by rational means: the disputants necessarily speak different languages.

The descriptive view was demolished by Kripke and Putnam in a series of lectures and papers in the 1970s. Whereas Russell took the descriptive theory and applied it to both general terms like unicorn and proper names like Heisenberg, Kripke took Mill’s view that names have no connotation and applied it to general terms like unicorn and water. This left both Kripke and Putnam with the task of explaining both how scientific terms like mass manage to refer to anything in the actual world, and how they function when used to talk about merely possible situations. These two tasks were addressed in different ways: the first by the causal theory of names, and the second by the theory of rigid designation. Articulating these fine distinctions would be out of synch with the spirit of Morris’s boisterous book, but as a result, conceptually different issues get somewhat muddled together.

One page contains a picture of a pet rock, another a painting called Truth Coming from the Well Armed with Her Whip to Chastise Mankind. Here is a Glyptodon, there a map of bomb damage in London, and last of all a photograph of a school class that contains a young Adolf Hitler and, perhaps, a young Ludwig Wittgenstein. For Morris, Wittgenstein so effectively undermined the philosophical ideals of truth and reason that he seriously pauses to consider which of the two did more damage to mankind.

The question may seem extreme but it springs from the noble place of a firm commitment to the possibility of rationality and evidence. Our beliefs should not be whatever feels comforting but what is most likely to be true. As angry as Morris is about how Kuhn treated him personally, he is much more outraged at the widespread influence of Kuhn’s ideas. He must delve into philosophy to elucidate the refutation of Kuhn’s sophistry. For if, as Kuhn suggests, we all live in worlds of our own manufacture, worlds bent to conform to our beliefs rather than our beliefs being adjusted to conform to the world, then what becomes of truth? All of us living in this post-truth political culture must face that question.

 

Accounts of human gullibility are generally retrospective. We laugh at tulip mania, and shake our heads at the Salem witch trials. But both Becker and Morris are after more dangerous game, delusions that are still in effect. One exposes the intellectual rot in the foundations of physics and the other decries the anti-rationalism sprouting from Kuhn. For Kuhn’s legacy lives on, not in philosophy (where he is widely derided for his excesses) but in other parts of academia and in popular culture.

Becker exposes how Bohr and company succeeded, in some cases by smash-mouth academic politics, including the shameful treatment of Bohm and the denigration of Einstein. But Kuhn wielded no such power. The Structure of Scientific Revolutions succeeded through its own allure. What is the attraction of Kuhn’s account of science? It has its roots far back in time, with the biggest self-deluder of all, Immanuel Kant.

The hand of Kant lies behind both Bohr and Kuhn. In his epic and epically incomprehensible masterpiece The Critique of Pure Reason (1781), Kant pulled off the grandest intellectual hocus-pocus in scholarly history. Kant called it his Copernican revolution in philosophy. According to Copernicus, phenomena that had been attributed to the motion of the stars and other heavenly bodies—the daily cycle of the sun and stars, the erratic motions of the planets—were really the product of the motion of Earth itself. These apparent motions had their source not in the observed but in the observer. Similarly, Kant argued that what have been taken to be features of a mind-independent reality—the structure of space and time, the existence of cause and effect, the law of conservation of energy—are actually imposed upon our experience by the mind itself. We have no justification for thinking that reality is intrinsically spatiotemporal or causally structured. But we are nonetheless eternally destined to experience the world in those terms because those are the intellectual and perceptive structures we must bring to our experience.

Our beliefs should not be whatever feels comforting but what is most likely to be true.

Kant’s argumentation for this Parmenidean thesis is famously obscure, and his writing forbiddingly impenetrable. But the moral he wanted to draw, which goes by the name of transcendental idealism, is easily summarized. I just did. And for whatever reason, this conclusion of Kant’s has been attracting people like a siren’s call ever since. Remarkably, many people just want Kant’s conclusion to be true.

Bohr grew up in an atmosphere of neo-Kantianism. And his most prized achievement, the doctrine of complementarity, is an insidious tweak on Kant. Kant had argued that in order to be comprehensible to us—in order to be anschaulich—the world of experience must be given in space and time and governed by deterministic laws of causation. Fundamental quantities must be conserved. Bohr adopted these as the essential properties of the classical world. The world of everyday experience, of lab experiments and their outcomes, must of necessity be classical, said Bohr.

The microphysical world, according to Bohr, is not visualizable, not classical. It does not, and could not, satisfy all of Kant’s requirements. But Bohr hit on his great revelation: although the microscopic world cannot be both pictured in space and time and regarded as governed by deterministic causal laws, it can be either pictured in space and time or treated by means of deterministic causal laws.

Furthermore, which of these two possibilities is realized is up to the observer. By setting up one sort of laboratory situation, the concepts of space and time can be applied to the microsystem, and by setting up an incompatible laboratory situation the concepts of causation and determinism, of energy and momentum, can be applied.

The conversion of a classical both/and into a quantum either/or became Bohr’s great mania. He started to see this complementarity everywhere. In biology, being alive is complementary to having a detailed account of the structure of cells: “Thus the existence of life itself would have to be regarded in biology, both as regards the possibilities of observation and of definition, as no more subject to analysis than the existence of the quantum of action in atomic physics,” Bohr wrote. There was complementarity between the practical and mystical understanding of human life. Complementarity would solve the mind-body problem.

Bohr showed as much obsessive attachment to his brainchild as Kant had to his. When granted the Danish Order of the Elephant in 1947, he chose as the motto on his coat of arms Contraria Sunt Complementa (opposites are complementary). He even appealed to complementarity to account for the obscurity of his own writings. According to Rudolf Peierls, Bohr would often say, “truth and clarity are complementary.” This sentiment is the death of Enlightenment rationality. Descartes, Locke, Berkeley, Spinoza, Leibniz, and Hume all strove for both clarity of expression and for truth. But according to Bohr, necessarily the more you have of one, the less you have of the other. Bohr triumphed through anti-rational aphorisms such as this. As the great physicist Murray Gell-Mann said, after conversations with Putnam, “Bohr brainwashed a generation of physicists.” A vivid illustration of Kuhn’s kinship to Bohr in this respect can be drawn from Morris: “What I hated most about Kuhn’s lectures was the combination of obscurantism and dogmatism. On one hand, he was extremely dogmatic. On the other, it was never really clear about what.” It is no stretch to apply this precise description to Bohr, and not much of one to apply it to The Critique of Pure Reason as well.

When the Copenhagen interpretation got imported to the pragmatic soil of the United States, Bohr’s incomprehensible nonsense was replaced by the more concise “shut up and calculate.” That is the philosophy that dominates physics to this day.

What of Kuhn? He was quite explicit about his relationship to Kant. Late in his life, Kuhn declared, “I am a Kantian with movable categories.” That is, he embraced Kant’s thesis that the mind imposes structure on the experienced world rather than discovering structure in it, but, contrary to Kant, the imposed structure can change. Such a change is a paradigm shift, the ultimately irrational replacement of one experienced reality with another incompatible one. Caught in our own little thought-worlds, deprived of access to objective truth (because there is no objective truth), we can do no better than miscommunicate, misunderstand, and ultimately resort to raw institutional power to resolve our disputes. As appropriated and mangled by Bohr and Kuhn, Kant—despite his own embrace of science and reason—becomes the agent of the anti-Enlightenment, the post-truth Age of Spin and Branding we live in.

Both Becker and Morris, each in his own way, is fighting an uphill battle against these trends. Each wants to reestablish the authority of reason and evidence. But it is the most difficult of all tasks. How do you convince a whole culture that it is deluded? How do you shine light into conceptual blind spots? Each of these books, as different as they are in style, is an attempt to provoke an epiphany and a revolution.

If works like these cannot succeed, then we ought to acknowledge the situation. We should shorten the dignified designation Homo sapiens to the pithier and more accurate Homo sap.