Bending the light

One of the coolest (and most misunderstood) parts of science is the use of models.

A model is an artificially-created system that acts like a part of nature that might be inaccessible, difficult, or prohibitively expensive to study.  A great many of the models used by scientists today are sophisticated computer simulations -- these are ubiquitous in climate science, for example -- but they can be a great deal simpler than that.  Two of my students' favorite lab activities were models.  One of them was a "build-a-plant" exercise that turned into a class-wide competition for who could create the most successful species.  The other was a striking simulation of disease transmission where we started with one person who was "sick" (each student had a test tube; all of them were half full of water, but one of them had an odorless, colorless chemical added to it).  During the exercise, the students contacted each other by combining the contents of their tubes.  In any encounter, if both started out "healthy," they stayed that way; if one was "sick," now they both were.  They were allowed to contact as many or as few people as they wanted, and were to keep a list of who they traded with, in order.  Afterwards, we did a chemical test on the contents of the tube to see whose tubes were contaminated, then used the list of trades to see if we could figure out who the index case was.

It never failed to be an eye-opener.  In only five minutes of trades, often half the class got "infected."  The model showed how fast diseases can spread -- even if people were only contacting two or three others, the contaminant spread like wildfire.

In any case, models are powerful tools in science, used to study a wide variety of natural phenomena.  And because of a friend and fellow science aficionado, I now know about a really fascinating one -- a characteristic of certain crystals that is being used as a model to study, of all things, black holes.

[Image licensed under the Creative Commons Ra'ike (de:Benutzer:Ra'ike), Chalcanthite-cured, CC BY-SA 3.0]

The research, which appeared last month in Physical Review A, hinges on the effects that a substance called a photonic crystal has on light.  (We met photonic crystals here only a few weeks ago -- in a brilliant piece of unrelated research regarding why some Roman-era glass has a metallic sheen.)  All crystals have, by definition, a regular, grid-like lattice of atoms, and as light passes through the lattice, it slows down.  This slowing effect happens with all transparent crystals; for example, it's what causes the refraction and internal reflection that make diamonds sparkle.  A researcher named Kyoko Kitamura, of Tohoku University, realized that if light could be made to slow down within a crystal, it should be possible to arrange the molecules in the lattice to force light to bend. 

Well, bending light is exactly what happens near a black hole.  So Kitamura and her team made the intuitive leap that this property could be used to study not only the crystal's interactions with light, but indirectly, to discover more about how light behaves near massive objects.

At this point, it's important to clarify that light is not gravitationally attracted to the immense mass of a black hole -- this is impossible, as photons are massless, so they are immune to the force of gravity (just as particles lacking electrical charge are immune to the electromagnetic force).  What the black hole does is warp the fabric of space, just as a bowling ball on a trampoline warps the membrane downward.  A marble rolling on the trampoline's surface is deflected toward the bowling ball not because the bowling ball is somehow magically attracting the marble, but because the marble is following the shortest path through the curved two-dimensional space it's sitting on.  Light is deflected near a black hole because it's traversing curved space -- in this case, a three-dimensional space that has been warped by the black hole's mass.

[Nota bene: it doesn't take something as massive as a black hole to curve space; you're sitting in curved space right now, warped by the mass of the Earth.  If you throw a ball, its path curves toward the ground for exactly the same reason.  That we are in warped space, subject to the laws of the General Theory of Relativity, is proven every time you use a GPS.  The measurements taken by GPS have to take into account that the ground is nearer to the center of gravity of the Earth than the satellites are, so the warp is higher down here, not only curving space but changing any time measurements (clocks run slower near large masses -- remember Interstellar?).  If GPS didn't take this into account, its estimates of positions would be inaccurate.]

In any case, the fact that photonic crystals can be engineered to interact with light the way a black hole would means we can study the effects of black holes on light without getting near one.  Which is a good thing, considering the difficulty of visiting one, as well as nastiness like event horizons and spaghettification to deal with.

So that's our cool scientific research of the day.  Studies like this always bring to mind the false perception that science is some kind of dry, pedantic exercise.  The reality is that science is one of the most deeply creative of endeavors.  The best science links up realms most of us would never have thought of connecting -- like using crystals to simulate the behavior of black holes.

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Missives from the sixth dimension

Generally speaking, there are two things that rapidly identify a claim as the work of a crank: (1) saying that it explains everything; and (2) saying that it overturns all previous theories and models in one fell swoop.

Now, that's not to say there haven't been ideas that have blown away previous theories.  The heliocentric model of the Solar System, the germ theory of disease, Darwinian natural selection, genes and the role of DNA in heredity, Newtonian physics, quantum mechanics, James Clerk Maxwell's theories on electricity and magnetism, plate tectonics, relativity -- all of them were earthshattering, and each one caused a complete revision of what we thought we knew.

But you know what stands out about them?  How rare they are.  There might be a handful of others I've missed, but if you just count the ones I've named, from the earliest (the Copernican heliocentric model) in about 1520 to today, that's nine honest-to-goodness scientific revolutions in five hundred years.

Also, given the precision of our instruments and the rigor with which science is approached -- itself a relatively new thing -- the likelihood of our having missed something major that will "rewrite the textbooks" is pretty low.  (There may be one exception -- incorporating "dark matter" and "dark energy" into our model for physics.  There's a fair chance that when they're figured those out, we might see a revolution of no less magnitude than Einstein's General Theory of Relativity.  Of course, it's also possible that we'll account for them by physics we already know about.  Which it'll be, only time will tell.)

My point is, if there is an overturning of current scientific models, it's likely that the anomalous data and its explanation will come from within the realm of science, and not from a layperson waving his or her hands around.  And it will be a rare, headline-making event.

So the fact that there are hundreds of websites that claim to outline some major flaw in a current scientific model, and propose a solution to it, means that most likely all of them are wrong.  (As a commenter put on one of them I saw a while back, "Here are your next steps: (1) Write this up as a formal academic paper.  (2) Submit to peer review.  (3) Collect Nobel Prize.  After you've done all that, come back and we'll talk.")

Most of these sites, therefore, are ringing the changes on the same crazy claims.  But every once in a while there'll be one that is so out there, so bizarre, that it has merit simply on the basis of how creative it is and how earnest its creator seems to be.  Which is why today I'm going to tell you about: Mosheh's Unifying Field Theory.  Which, as he points out right in the title, is not only a Unifying Field Theory, it's a God Theory.

Whatever that means.

I encourage you to visit the website, because there's no way I can excerpt enough here to give you the full experience, but here's one sentence so you can get the flavor:

There is the suggestion given by evidence, and if energy was removed from a 3D space, then rather than just shrinking, it could be reduced into a 2D plane, and if energy was removed from a 2D plane, then "it" would become 1 dimensional, and if more energy was removed, it would become a zero dimensional object, not being zero, as in not existing, but zero as in having no potential energy, a zero energy state.

Right!  Sure!  What?

And I just have to include one of the illustrations, which are amazing:

My favorite part is in the lower right corner, wherein we learn that dinosaurs evidently evolved not only into birds but into "Grey Aliens."

There are so many other delightful features of this website that I don't want to spoil them, so you'll just have to go there and take a look.  I think my favorite part is under the "General Theory Outline" page, where he draws four-, five-, and six-dimensional objects.  If only the mathematicians had realized years ago that it was this easy!

So Mosheh's "dimensional field theory" is so wacky as to be kind of charming.  He's a crank, yes; he's wrong, almost certainly; but you have to admire his creativity and chutzpah.  As for me, I'm going to go back and poke around some more, and see if I can figure out what he means by saying that "an object's four-dimensional spin is made up of time and something."

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Beauty, truth, and the Standard Model

A couple of days ago, I was talking with my son about the Standard Model of Particle Physics (as one does).

The Standard Model is a theoretical framework that explains what is known about the (extremely) submicroscopic world, including three of the four fundamental forces (electromagnetism, the weak nuclear force, and the strong nuclear force), and classifies all known subatomic particles.

Many particle physicists, however, are strongly of the opinion that the model is flawed.  One issue is that one of the four fundamental forces -- gravitation -- has never been successfully incorporated into the model, despite eighty years of the best minds in science trying to do that.  The discovery of dark matter and dark energy -- or at least the effects thereof -- is also unaccounted for by the model.  Neither does it explain baryon asymmetry, the fact that there is so much more matter than antimatter in the observable universe.  Worst of all is that it leaves a lot of the quantities involved -- such as particle masses, relative strengths of forces, and so on -- as empirically-determined rather than proceeding organically from the theoretical underpinnings.

This bothers the absolute hell out of a lot of particle physicists.  They have come up with modification after modification to try to introduce new symmetries that would make it seem not quite so... well, arbitrary.  It just seems like the most fundamental theory of everything should be a lot more elegant than it is, and that there should be some underlying beautiful mathematical logic to it all.  The truth is, the Standard Model is messy.

Every one of those efforts to create a more beautiful and elegant model has failed.  Physicist Sabine Hossenfelder, in a brilliant but stinging takedown of the current approach that you really should watch in its entirety, puts it this way: "If you follow news about particle physics, then you know that it comes in three types.  It's either that they haven't found that thing they were looking for, or they've come up with something new to look for which they'll later report not having found, or it's something so boring you don't even finish reading the headline."  Her opinion is that the entire driving force behind it -- research to try to find a theory based on beautiful mathematics -- is misguided.  Maybe the actual universe simply is messy.  Maybe a lot of the parameters of physics, such as particle masses and the values of constants, truly are arbitrary (i.e., they don't arise from any deeper theoretical reason; they simply are what they're measured to be, and that's that).  In her wonderful book Lost in Math: How Beauty Leads Physics Astray, she describes how this century-long quest to unify physics with some ultra-elegant model has generated very close to nothing in the way of results, and maybe we should accept that the untidy Standard Model is just the way things are.

Because there's one thing that's undeniable: the Standard Model works.  In fact, what generated this post (besides the conversation with my science-loving son) is a paper that appeared last week in Physical Review Letters about a set of experiments showing that the most recent tests of the Standard Model passed with a precision that beggars belief -- in this case, a measurement of the electron's magnetic moment which agreed with the predicted value to within 0.1 billionths of a percent.

This puts the Standard Model in the category of being one of the most thoroughly-tested and stunningly accurate models not only in all of physics, but in all of science.  As mind-blowingly bizarre as quantum mechanics is, there's no doubt that it has passed enough tests that in just about any other field, the experimenters and the theoreticians would be high-fiving each other and heading off to the pub for a celebratory pint of beer.  Instead, they keep at it, because so many of them feel that despite the unqualified successes of the Standard Model, there's something deeply unsatisfactory about it.  Hossenfelder explains that this is a completely wrong-headed approach; that real discoveries in the field were made when there was some necessary modification of the model that needed to be made, not just because you think the model isn't pretty enough:

If you look at past predictions in the foundations of physics which turned out to be correct, and which did not simply confirm an existing theory, you find it was those that made a necessary change to the theory.  The Higgs boson, for example, is necessary to make the Standard Model work.  Antiparticles, predicted by Dirac, are necessary to make quantum mechanics compatible with special relativity.  Neutrinos were necessary to explain observation [of beta radioactive decay].  Three generations of quarks were necessary to explain C-P violation.  And so on...  A good strategy is to focus on those changes that resolve an inconsistency with data, or an internal inconsistency.  

And the truth is, when the model you already have is predicting with an accuracy of 0.1 billionths of a percent, there just aren't a lot of inconsistencies there to resolve.

I have to admit that I get the particle physicists' yearning for something deeper.  John Keats's famous line, "Beauty is truth, and truth beauty; that is all ye know on Earth, and all ye need to know" has a real resonance for me.  But at the same time, it's hard to argue Hossenfelder's logic.

Maybe the cosmos really is kind of a mess, with lots of arbitrary parameters and empirically-determined constants.  We may not like it, but as I've observed before, the universe is under no obligation to be structured in such a way as to make us comfortable.  Or, as my grandma put it -- more simply, but no less accurately -- "I've found that wishin' don't make it so."

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A black hole's warm glow

Once again I was sent a link by my buddy Andrew Butters, of the wonderful Potato Chip Math, who is not only a great writer but has a keen eye for a cool science article.

The link was to a story in Science Alert, and was titled, "Scientists Created a Black Hole in the Lab, and Then It Started To Glow," by Michelle Starr.  But before I tell you what the gist is, I have to bring up a peevish complaint about the headline (which may not have been Starr's fault; many times the headlines aren't written by the journalist herself, so I'm not jumping to blaming her for it).  The researchers, as you will see, did not "create a black hole;" what they did was create something that models some of the behavior of a black hole.  Which is cool enough, but doesn't have the cachet that black holes have, so Science Alert apparently thought they needed to jazz things up.  The headline is wildly misleading; no massive stars were destroyed in the course of this experiment.

Of course, this is not going to stop people from reading only the headline and then posting hysterical screeds about how those Mad Scientists Are Trying To Destroy Us All and undoubtedly tying in CERN, HAARP, the Illuminati, and Reptilian Aliens From Zeta Reticuli.

You know how it goes.

Anyhow, back to reality.  What the scientists really did was pretty amazing, and may give us some inroads into figuring out one of the biggest puzzles in physics; why theoretical physicists have been unable to reconcile the equations of quantum mechanics and those of relativity.  When they attempt to accommodate gravitational effects on the scale of the very small, the equations "blow up" -- they result in infinities -- usually a sign that something is very wrong about our understanding.

The reason black holes play into this question is that in the extraordinary gravitational field at the event horizon (the "point of no return," where the space is so strongly curved that even light can't escape), there is a quantum effect that becomes important on the macroscopic scale.  It's called Hawking radiation, after Stephen Hawking (who first proposed it), and deserves some closer attention.

 To start with, empty space isn't empty.  There is an inherent energy in space called zero-point energy or vacuum energy, and it is possible for this energy to be "borrowed" to produce particle-antiparticle pairs (such as an electron and a positron).  There's a catch, though; the pairs always recollide (in a minuscule amount of time, the upper limit of which is determined by the uncertainty principle).  So the pairs pop into existence and right out again, creating continuous tiny, extremely short-lived ripples in the fabric of space.  Not enough for anyone even to notice.

Well, unless you're near the event horizon of a black hole.

[Image is in the Public Domain]

The huge gravitational field at the event horizon means that vacuum energy is much higher, and pair production happens at a much greater rate.  And because of that boundary, sometimes one member of a pair falls into the event horizon, while the other one doesn't.  At that point, the survivor radiates out into space -- taking a little of the black hole's mass/energy along with it.

That's the Hawking radiation.  What it implies is that black holes don't last forever -- eventually they evaporate, finally exploding in a burst of gamma rays.

The problem has been that the Hawking radiation is impossible to study experimentally; we're (fortunately) not near any black holes, at least so far as we know, and the faint signature of the radiation would be lost in the general white noise of the universe.  But now -- and this is where we get to the current research -- a team led by Lotte Mertens of the University of Amsterdam has developed a model that simulates this behavior, and found that just like the real thing, it emits radiation exactly the way Hawking predicted (this is the "it started to glow" in the headline).

What they did was to lock together a chain of atoms that provided a path for electrons to move, and by fine-tuning the rate at which this happened, they created a simulated event horizon that caused some of the electrons' wave-like behavior to vanish completely.  The result was an increase in thermal radiation that matched the Hawking model precisely.

Why this is significant is that it could provide a way to study the quantum effects of gravity in the lab, something that has been impossible before now.  It's not like we can hop a spacecraft and fly to a black hole (which would be inadvisable anyhow).  So this fascinating experiment might be the first step toward one of the prime goals of physicists -- finding a way to unify the quantum and gravitational models.

So even if they didn't "create a black hole in the lab," the whole thing is still pretty freakin' cool.

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The celestial dance

It's interesting how the approach to science has changed in the last four centuries.

It's easy to have the (mistaken) impression that as long as we humans have been doing anything scientific, we've always done it the same way -- looked at the evidence and data, then tried to come up with an explanation.  But science in Europe before the eighteenth-century Enlightenment was largely done the other way around; you constructed your model from pure thought, based on a system of how you believed things should act, and once you had the model, you cast about for information supporting it.

It's why Aristotle's statement that the rate of speed of a falling object is directly proportional to its mass stood essentially unchallenged for over a millennium and a half despite the fact that it's something any second grader could figure out was wrong simply by dropping two different-sized rocks from the same height and observing they hit the ground at exactly the same time.  As odd as it is to our twenty-first century scientific mindset, the idea of figuring out if your claim is correct by testing it really didn't catch on until the 1700s.  Which is why the church fathers got so hugely pissed off at Galileo; using a simple experiment he showed that Aristotle got it wrong, and then followed that up by figuring out how things up in the sky moved (such as the moons of Jupiter, first observed by Galileo through the telescope he made).  And this didn't result in the church fathers saying, "Whoa, okay, I guess we need to rethink this," but their putting Galileo on trial and ultimately under permanent house arrest.

That "think first, observe later" approach to science plagued our attempts to understand the universe for a long time after Galileo; people first came up with how they thought things should work, often based on completely non-scientific reasons, then looked for data to support their guess.  That we've come as far as we have is a tribute to scientists who were able to break out of the straitjacket of what the Fourth Doctor in Doctor Who called "not altering their views to fit the facts, but altering the facts to fit their views."

One of the best examples of this was the seventeenth-century astronomer Johannes Kepler.  He was a deeply religious man, and lived in a time when superstition ruled pretty much everything -- in fact, Kepler's mother, Katharina (Guldenmann) Kepler, narrowly escaped being hanged for witchcraft.  Kepler, and most other European astronomers from his time and earlier, were as much astrologers as scientists; they expected the heavens to operate by some kind of law of divine celestial perfection, where objects moved in circles (anything else was viewed as imperfect) and their movements had a direct effect on life down here on Earth.

At the beginning, Kepler tried to extend his conviction of the mathematical perfection of the cosmos to the distances at which the planets revolved around the Sun.  He became convinced that the spacing of the planets' orbits was determined by conforming to the five Platonic solids -- cube, dodecahedron, tetrahedron, icosahedron, and octahedron -- convex polyhedra whose sides are made up only of identical equal-sided polygons.  He tried nesting them one inside the other to see if the ratios of their spacing could be made to match the estimated spacing of the planets, and got close, but not close enough.  One thing Kepler had going for him was he was firmly committed to the truth, and self-aware enough to know when he was fudging things to make them fit.  So he gave up on the Platonic solids, and went back to "we don't know why they're spaced as they are, but they still travel in perfect circles" -- until careful analysis of planetary position data by the Danish observational astronomer Tycho Brahe showed him again that he was close, but not quite close enough.

This was the moment that set Kepler apart from his contemporaries; because instead of shrugging off the discrepancy and sticking to his model that the heavens had to move in perfect circles, he jettisoned the whole thing and went back to the data to figure out what sort of orbits did make sense of the observations.  After considerable work, he came up with what we now call Kepler's Laws of Planetary Motion, including that planets move in "imperfect" elliptical, not circular, orbits, with the Sun at one focus.

Start with the data, and see where it drives you.  It's the basis of all good science.

[Image licensed under the Creative Commons Gonfer, Kepler-second-law, CC BY-SA 3.0]

What got me thinking about Kepler and his abandonment of the Platonic-solid-spacing idea was a paper this week in Astronomy & Astrophysics showing that even though Kepler initially was on the wrong track, there are sometimes odd mathematical regularities that pop up in the natural world.  (A well-known one is how often the Fibonacci series shows up in the organization of things like flower petals and the scales of pine cones.)  The paper, entitled "Six Transiting Planets and a Chain of Laplace Resonances in TOI-178," by a team led by Adrien Leleu of the Université de Genève, showed that even though hard data dashed Kepler's hope of the motion of the heavens being driven by some concept of mathematical perfection, there is a weird pattern to the spacing of planets in certain situations.  The patterns, though, are driven not by some abstract philosophy, but by physics.

In physics, resonance occurs when the physical constraints of a system make them oscillate at a rate called the "natural frequency."  A simple example is the swing of a pendulum; a pendulum of a given length and mass distribution only will swing back and forth at one fixed rate, which is why they can be used in timekeeping.  The motion of planets (or moons) is also an oscillating system, and a given set of objects of particular masses and distances from their center of gravity will tend to fall into resonance, the same as if you try to swing a pendulum at a different rate than the rate at which it "wants to go," then let it be, it'll pretty much immediately revert to swinging at its natural frequency.

The three largest moons of Jupiter exhibit resonance; they've locked into orbits that are the most stable for the system, which turns out to be a 4:2:1 resonance, meaning that the innermost (Io) makes two full orbits in the time the next one (Europa) makes a single orbit, and four full orbits in the time it takes for the farthest (Ganymede).

This week's paper found a more complex resonance pattern in five of the planets around TOI-178, a star two hundred light years away in the constellation Sculptor.  It's a 18:9:6:4:3 resonance chain -- the nearest planet orbits eighteen times as the farthest orbits once, the next farthest nine times as the farthest orbits once, and so on.  This pattern was locked in despite the fact that the planets are all quite different from each other; some are small, rocky planets like Earth, others low-density gaseous planets like Neptune.

"This contrast between the rhythmic harmony of the orbital motion and the disorderly densities certainly challenges our understanding of the formation and evolution of planetary systems," said study lead author Adrien Leleu, in an interview with Science Daily.

So the dance of the celestial bodies is orderly, and shows some really peculiar regularities that you wouldn't have guessed.  But unlike Kepler's favored (but ultimately abandoned) idea that the perfect heavens had to be arranged by perfect mathematics, the Leleu et al. paper shows us that those patterns only emerge by analysis of the data itself, rather than the faulty top-down attempt to force the data to conform to the way you think things should be.  Once you open your mind up to going where the hard evidence leads, that's when the true wonders of the universe begin to emerge.

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Just last week, I wrote about the internal voice most of us live with, babbling at us constantly -- sometimes with novel or creative ideas, but most of the time (at least in my experience) with inane nonsense.  The fact that this internal voice is nearly ubiquitous, and what purpose it may serve, is the subject of psychologist Ethan Kross's wonderful book Chatter: The Voice in our Head, Why it Matters, and How to Harness It, released this month and already winning accolades from all over.

Chatter not only analyzes the inner voice in general terms, but looks at specific case studies where the internal chatter brought spectacular insight -- or short-circuited the individual's ability to function entirely.  It's a brilliant analysis of something we all experience, and gives some guidance not only into how to quiet it when it gets out of hand, but to harness it for boosting our creativity and mental agility.

If you're a student of your own inner mental workings, Chatter is a must-read!

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

The power of models

I get that scientific terminology can be daunting.  Scientists, and therefore scientific papers, have become so specialized that unless you are an expert, the vocabulary by itself can be an overwhelming barrier to understanding.  That only gets worse in disciplines like physics and chemistry, where complex mathematics throws another spanner into the works.  I have a B.S. in physics, enough credits for a second major in biology, and a minor in math, and am reasonably articulate, but just about every academic paper I've ever seen loses me within a couple of paragraphs, except for the two areas I know best -- population genetics and evolutionary biology.

So I'm not expecting laypeople to become experts in scientific jargon.  But there are two words I really wish everyone would familiarize themselves with -- theory and model.

Confusion over the first one is what gives rise to the "it's only a theory" *shrug* reaction a lot of people have when discussing the theory of evolution.  Theory, in scientific discussions, does not mean "a wild guess that could as easily be wrong as right."  In scientific parlance, a theory is an explanation of a natural phenomenon that has passed repeated tests and makes predictions that are in good accordance with the data.  This is why intelligent design creationism isn't a theory; it makes no predictions.  If things get complex, it defaults to "God did it," and the conversation ends.

In science, a model is a representation of a natural object, system, or phenomenon, often idealized or simplified, that can then be manipulated -- once again, to see if the results are consistent with observed data from the real world.  As an example, the computerized three-dimensional maps of the climate are models, breaking up the atmosphere into thousands of cubical regions and the land and ocean into square blocks of area, with specifications for atmospheric composition, heat absorption capacity for land and water, solar radiation input, and so on.  The software can take the known input parameters and then run a simulation to see if what comes out matches what we actually know of the real climate data (and they have, to a startling degree of accuracy, something that is simultaneously impressive and terrifying).

The problem with the idea of modeling is that to an outside observer, it may look like the scientists are just messing around -- playing Sims with the world, with no particular expectation that what they're doing has anything in common with reality.  This, of course, is the opposite of the truth -- if a model doesn't align very well with the natural world, it's rightly abandoned for one that works better.

Even models that seem to be a little bit out there are only retained because they describe a known part of the universe sufficiently well that their predictions can be useful for describing something not yet understood.  Take, for example, the paper last week in Proceedings of the National Academy of Sciences that used what's known about biochemistry to make a stab at the configuration and composition of the earliest proteins, molecules that were around 3.5 billion years ago -- produced abiotically before there were any living things on Earth.

In "Small Protein Folds at the Root of an Ancient Metabolic Network," Hagai Raanan, Saroj Poudel, Douglas Pike, Vikas Nanda, and Paul Falkowski, of Rutgers University, describe a sophisticated computer simulation that took what we know about the chemistry that is common to all living organisms (such as using oxidation/reduction reactions to power metabolism) and combined it with what is surmised about the conditions on the early Earth, and used it to infer what the earliest energy-transfer proteins looked like.  The authors write:

Life on Earth is driven by electron transfer reactions catalyzed by a suite of enzymes that comprise the superfamily of oxidoreductases (Enzyme Classification EC1).  Most modern oxidoreductases are complex in their structure and chemistry and must have evolved from a small set of ancient folds.  Ancient oxidoreductases from the Archean Eon between ca. 3.5 and 2.5 billion years ago have been long extinct, making it challenging to retrace evolution by sequence-based phylogeny or ancestral sequence reconstruction.  However, three-dimensional topologies of proteins change more slowly than sequences.  Using comparative structure and sequence profile-profile alignments, we quantify the similarity between proximal cofactor-binding folds and show that they are derived from a common ancestor.  We discovered that two recurring folds were central to the origin of metabolism: ferredoxin and Rossmann-like folds.  In turn, these two folds likely shared a common ancestor that, through duplication, recruitment, and diversification, evolved to facilitate electron transfer and catalysis at a very early stage in the origin of metabolism.

Here's one of the ancestral proteins the model generated:

Now, maybe you see this as a bunch of hand-waving in an intellectual vacuum.  After all, we have no way of going back 3.5 million years and checking to see if the model is correct.  But the key thing is that this was created within parameters of how we know proteins work, and what we see in the energy-transfer proteins of current organisms.  This model was very much constrained by reality -- meaning that its results have a really good chance of being accurate.

Further, like any good model (or theory, for that matter), it generates predictions -- in this case, what we might look for as a signature of emerging life on other planets.  "In the realm of deep-time evolutionary inference," the authors write, "we are necessarily limited to deducing what could have happened, rather than proving what did happen...  Ultimately, our goal is for the proposed effort to inform future NASA missions about detection of life on planetary bodies in habitable zones.  Our effort provides a unique window to potential planetary-scale chemical characteristics that might arise from abiotic chemistry, which must be understood if we are to recognize unique biosignatures on other worlds."

So models and theories aren't guesses, they're real-world descriptions, and the best ones give us deep insight into the workings of the universe.  As such, they are part of the scientist's stock-in-trade -- and essential to understand for laypeople who would like to know what's happening on the cutting edge of research.

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Any guesses as to what was the deadliest natural disaster in United States history?

I'd speculate that if a poll was taken on the street, the odds-on favorites would be Hurricane Katrina, Hurricane Camille, and the Great San Francisco Earthquake.  None of these are correct, though -- the answer is the 1900 Galveston hurricane, that killed an estimated nine thousand people and basically wiped the city of Galveston off the map.  (Galveston was on its way to becoming the busiest and fastest-growing city in Texas; the hurricane was instrumental in switching this hub to Houston, a move that was never undone.)

In the wonderful book Isaac's Storm, we read about Galveston Weather Bureau director Isaac Cline, who tried unsuccessfully to warn people about the approaching hurricane -- a failure which led to a massive overhaul of how weather information was distributed around the United States, and also spurred an effort toward more accurate forecasting.  But author Erik Larson doesn't make this simply about meteorology; it's a story about people, and brings into sharp focus how personalities can play a huge role in determining the outcome of natural events.

It's a gripping read, about a catastrophe that remarkably few people know about.  If you have any interest in weather, climate, or history, read Isaac's Storm -- you won't be able to put it down.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Missives from the sixth dimension

Generally speaking, there are two things that rapidly identify a claim as the work of a crank: (1) saying that it explains everything; and (2) saying that it overturns all previous theories and models in one fell swoop.

Now, that's not to say there haven't been ideas that have blown away previous theories.  The heliocentric model of the Solar System, the germ theory of disease, Darwinian natural selection, genes and the role of DNA in heredity, Newtonian physics, quantum mechanics, James Clerk Maxwell's theories on electricity and magnetism, plate tectonics, relativity -- all of them were earthshattering, and caused a complete revision of what we thought we knew.

But you know what stands out about them?  How rare they are.  There might be a handful of others I've missed, but if you just count the ones I've named, from the earliest (the Copernican heliocentric model) in about 1520 to today, that's nine honest-to-goodness scientific revolutions in five hundred years.

Also, given the precision of our instruments and the rigor with which science is approached -- itself a relatively new thing -- the likelihood of our having missed something major that will "rewrite the textbooks" is pretty low.  (There may be one exception -- incorporating "dark matter" and "dark energy" into our model for physics.  There's a fair chance that when they're figured out -- or, as I speculated in a recent post, are the impetus for a revision of our current model -- we might see a revolution of no less magnitude than Einstein's General Theory of Relativity.  Of course, it's also possible that we'll account for them by physics we already know about.  Which it'll be, only time will tell.)

My point is, if there is an overturning of current scientific models, it's likely the anomalous data and its explanation will come from within the realm of science, not from a layperson waving his or her hands around.  And it will be a rare, headline-making event.

So the fact that there are hundreds of websites that claim to outline some major flaw in a current scientific model, and propose a solution to it, means that most likely all of them are wrong.  (As a commenter put on one of them I saw a while back, "Here are your next steps: (1) Write this up as a formal academic paper.  (2) Submit to peer review.  (3) Collect Nobel Prize.  After you've done all that, come back and we'll talk.")

Most of these sites, therefore, are ringing the changes on the same crazy claims.  But every once in a while there'll be one that is so out there, so bizarre, that it has merit simply on the basis of how creative it is and how earnest its creator seems to be.  Which is why today I'm going to tell you about:  Mosheh's Unifying Field Theory.  Which, as he points out right in the title, is not only a Unifying Field Theory, it's a God Theory.

Whatever that means.

I encourage you to visit the website, because there's no way I can excerpt enough here to give you the full experience, but here's one sentence so you can get the flavor:

There is the suggestion given by evidence, and if energy was removed from a 3D space, then rather than just shrinking, it could be reduced into a 2D plane, and if energy was removed from a 2D plane, then "it" would become 1 dimensional, and if more energy was removed, it would become a zero dimensional object, not being zero, as in not existing, but zero as in having no potential energy, a zero energy state.

Right!  Sure!  What?

And I just have to include one of the illustrations, which are amazing:

My favorite part is in the lower right corner, wherein we learn that dinosaurs evidently evolved not only into birds but into "Grey Aliens."

There are so many other delightful features of this website that I don't want to spoil them, so you'll just have to go there and take a look.  I think my favorite part is under the "General Theory Outline" page, wherein he draws four-, five-, and six-dimensional objects.  If only the mathematicians had realized years ago that it was this easy!

So Mosheh's "dimensional field theory" is so wacky as to be kind of charming.  He's a crank, yes; he's wrong, almost certainly; but you have to admire his creativity and chutzpah.  As for me, I'm going to go back and poke around some more, and see if I can figure out what he means by saying that "an object's four-dimensional spin is made up of time and something."

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This week's Skeptophilia book recommendation is for any of my readers who, like me, grew up on Star Trek in any of its iterations -- The Physics of Star Trek by Lawrence Krauss.  In this delightful book, Krauss, a physicist at Arizona State University, looks into the feasibility of the canonical Star Trek technology, from the possible (the holodeck, phasers, cloaking devices) to the much less feasible (photon torpedoes, tricorders) to the probably impossible (transporters, replicators, and -- sadly -- warp drive).

Along the way you'll learn some physics, and have a lot of fun revisiting some of your favorite tropes from one of the most successful science fiction franchises ever invented, one that went far beyond the dreams of its creator, Gene Roddenberry -- one that truly went places where no one had gone before.

The Gaia Hypothesis and the danger of models

Scientists use models -- partial representations of reality, often expressed mathematically -- to explain the universe.  Both working scientists and science teachers often explain those models using analogies.

This has a good result and a bad result.  The good result is that the use of model, analogy, and metaphor makes science accessible for non-scientists.  You don't have to understand piles of abstruse mathematics in order to get a glimpse at the weirdness of quantum theory; if you read last week's post on the Wigner's Friend Paradox, you've seen an example.  In my own teaching, I use analogy all the time.  Antibodies are like trash tags.  Transpiration in plants is like a very long chain attached to the underside of a trampoline.  The Krebs Cycle is like a merry-go-round in which two kids get on and two kids get off at every turn.

The downside, however, is twofold.  The first problem is that it's easy at times to think that the model is the reality.  The goofier the metaphor, the easier it is to avoid this pitfall; I've never had a student yet who thought that the Krebs Cycle really was a merry-go-round (although I did have a student of mine start her essay on antibodies on the AP exam, "So, antibodies are trash tags...").  But with sophisticated, complex models, it's tempting to think that the model is, down to the level of details, what is happening in the real world.

The second downside is that some people will grab the model and run right off the cliff with it.

All of this comes up because a friend of mine asked me what I thought about the Gaia Hypothesis.  I know that this friend to be a sharp, smart, and solid thinker, so I didn't wince, which is what I usually do when someone brings this subject up.  Because I can't think of an idea in science that has fallen so prey to the model vs. reality blur as this one has.

[Image is in the Public Domain, courtesy of NASA/JPL]

Gaia was dreamed up by two scientists of high repute -- James Lovelock and Lynn Margulis -- way back in the 1970s.  The central idea of Gaia is that the Earth's biosphere acts as an interlocking set of self-regulatory systems, and they work together to maintain the homeostasis of the whole in much the same way as organ systems do in an organism.  Lovelock and Margulis identified a number of features of the biosphere, including the carbon dioxide levels, nitrogen levels, oxygen levels, oceanic salinity, and average temperature, that all seem to work through a complex pattern of negative feedback to keep the Earth's systems within a range that is comfortable for living things.  Using computer simulations, Lovelock and Margulis showed that even with a simple model, they could create a "world" that remained stable, and for which the living things played a role in regulation.

All of this is well and good, and Lovelock and Margulis were completely clear about what their model did (and didn't) mean.  (If you're curious, here's the Gaia homepage, run by Lovelock and other scientists working in this field; Lynn Margulis, tragically, died in November of 2011.)

The problem is, lots of people think that the scientists who developed the Gaia Hypothesis meant way more than they actually did.  Part of it was Lovelock's rather inadvisable choice of a Greek goddess's name for christening his model, which brings up lots of images of personified deities, Mother Earth, and New Age nature spirits.  This particular twist really irritates fundamentalist Christians; take a look at the misleadingly named site Environment and Ecology, wherein we find that the Gaia model encourages "radical environmentalism and ecofeminism," because it runs counter to the biblical passage about god giving man "dominion" over the Earth.

Even ignoring the objections of the wacko biblical literalists, I suppose it's natural enough that people could misinterpret Gaia.  The whole thing is just so... suggestive.  And misinterpret it they did, first thinking that because Lovelock and Margulis said that the Earth was like an organism, that they were saying that it was one; and then grabbing the analogy and leaping into the void with it.  As an example of where this can lead, take a look at Truth and Reality: The Metaphysics of Gaia, wherein we find passages like the following:

The GaiaMind Project is dedicated to exploring the idea that we, humanity, are the Earth becoming aware of itself.  From this perspective, the next step in the evolution of consciousness would seem to be our collective recognition that through our technological and spiritual interconnectedness we represent the Earth growing an organ of self-reflexive consciousness.  While we believe that the Earth is alive, and we are part of it, we also affirm the Great Spirit of Oneness found at the heart of all the worlds great spiritual traditions.  What is most important may not be what we believe, but what we find we all share when we put our thoughts aside to go into meditation and prayer together.

I think I can say with some confidence that this is light years away from what Lovelock and Margulis had in mind.  Consider the chain of... I can't call it "logic," what is it? -- to get from Lovelock and Margulis to this stuff:

1. The Earth has interlocking systems that self-regulate, keeping conditions in homeostasis.
2. Organisms do, too.
3. So the Earth is like an organism.
4. Many organisms have organs that allow them to sense, and respond to, their environment.
5. This is called "awareness."
6. Some organisms have a second feature, rather poorly understood, of self-awareness, of the ability to see themselves, their interactions, and their internal mental states.
7. This is called "consciousness."
8. Consciousness is a feature of intelligence, a fairly recently-developed innovation amongst living things on Earth.

Ergo: The Earth is becoming conscious. It'd really be nice of you to pray about it, because that'd help the process right along.

It's all a matter of keeping your head screwed on when you read this stuff; where does the science end and the woo-woo start?  It's always best to go back to see what the scientists themselves said on the topic.  While being a scientist isn't always a guarantee against fuzzy thinking, I'd put more reliance on the ability of your typical scientist to tell fact from fiction than that of someone whose main contribution to the discussion is rambling on in some random blog on the topic.  (Irony intended.)

Still, the use of models is, on the whole, a good thing.  It gives us something to picture, a way to frame our understanding of what is going on in the real world.  You just have to know how far to push the model, and when to quit. It is, in other words, a starting point.  And if along the way it can piss off some creationists, it's all good.

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This week's Skeptophilia book recommendation is a look at one of the most peculiar historical mysteries known: the unsolved puzzle of Kaspar Hauser.

In 1828, a sixteen-year-old boy walked into a military station in the city of Ansbach, Germany.  He was largely unable to communicate, but had a piece of paper that said he was being sent to join the cavalry -- and that if that wasn't possible, whoever was in charge should simply have him hanged.

The boy called himself Kaspar Hauser, and he was housed above the jail.  After months of coaxing and training, he became able to speak enough to tell a peculiar story.  He'd been kept captive, he said, in a small room where he was never allowed to see another human being.  He was fed by a man who sometimes talked to him through a slot in the door.  Sometimes, he said, the water he was given tasted bitter, and he would sleep soundly -- and wake up to find his hair and nails cut.

But locals began to question the story when it was found that Hauser was a pathological liar, and not to be trusted with anything.  No one was ever able to corroborate his story, and his death from a stab wound in 1833 in Ansbach was equally enigmatic -- he was found clutching a note that said he'd been killed so he couldn't identify his captor, who signed his name "M. L. O."  But from the angle of the wound, and the handwriting on the note, it seemed likely that both were the work of Hauser himself.

The mystery endures, and in the book Lost Prince: The Unsolved Mystery of Kaspar Hauser, author Jeffrey Moussaieff Masson looks at the various guesses that people have made to explain the boy's origins and bizarre death.  It makes for a fascinating read -- even if truthfully, we may never be certain of the actual explanation.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]

Hipster math

One of the guiding principles of teenagerhood is "I want to be unique, just like everyone else."

Not, mind you, that I'm criticizing efforts toward individuality.  We all have to find a way to express ourselves, be it how we dress, talk, or style our hair.  But what's always struck me as funny is how the drive to be different often pushes people toward the same solution, creating stereotypical pseudo-rebellious subcultures that are often parodied because they all on some level look and act alike.

This subject has been the focus of mathematician Jonathan Touboul, of Brandeis University, who looks at how information transfer through societies affects behavior.  And he's been studying something he calls the "hipster effect" -- that rejecting conformity simply drives people to conform to something else.  Even more interesting, he's found that these patterns of synchronization have parallels in how many other systems interact, in areas as different as neural firing patterns and reactions by investors to information about the stock market, and may well be describable by the same mathematical model.

[Image licensed under the Creative Commons Infrogmation of New Orleans, Redbeans15 Downtown Hipsters, CC BY-SA 2.5]

In his paper "The Hipster Effect: When Anticonformists All Look the Same," which appeared in the online journal arXiv, he has the following to say:

In such different domains as neurosciences, spin glasses, social science, economics and finance, large ensemble of interacting individuals following (mainstream) or opposing (hipsters) to the majority are ubiquitous.  In these systems, interactions generally occur after specific delays associated to transport, transmission or integration of information.  We investigate here the impact of anti-conformism combined to delays in the emergent dynamics of large populations of mainstreams and hipsters.  To this purpose, we introduce a class of simple statistical systems of interacting agents composed of (i) mainstreams and anti-conformists in the presence of (ii) delays, possibly heterogeneous, in the transmission of information.  In this simple model, each agent can be in one of two states, and can change state in continuous time with a rate depending on the state of others in the past...  [W]hen hipsters are too slow in detecting the trends, they will consistently make the same choice, and realizing this too late, they will switch, all together to another state where they remain alike.  Similar synchronizations arise when the impact of mainstreams on hipsters choices (and reciprocally) dominate the impact of other hipsters choices, and we show that these may emerge only when the randomness in the hipsters decisions is sufficiently large.  Beyond the choice of the best suit to wear this winter, this study may have important implications in understanding synchronization of nerve cells, investment strategies in finance, or emergent dynamics in social science, domains in which delays of communication and the geometry of information accessibility are prominent.

Which is kind of cool.  Although it's a little humbling to think that our choices about how to express who we are, which feel so important and deeply personal, can be emulated by a simple mathematical model that works equally well to describe how nerves fire and how investors make their stock trading decisions.

What's funniest is the outcome when Touboul tried to model a population with equal numbers of conformists and hipsters.  It resulted in a seesawing oscillation between different outcomes -- for a while the hipsters have beards and the conformists don't, but if you wait for a while, the reverse becomes true.

Of course, life is usually more complex than a bunch of binary choices.  But when this is the situation, the result is remarkably predictable.  "For example, if a majority of individuals shave their beard," Touboul said in an interview with Technology Review, "then most hipsters will want to grow a beard, and if this trend propagates to a majority of the population, it will lead to a new, synchronized, switch to shaving."

Touboul wants to expand his model to include choices where there are more than two options, and see if it continues to emulate observed trends in social dynamics.  My guess is it will, although I don't begin to understand how you'd manage the mathematics involved.  As for me, I've got to look around and count the number of guys with facial hair, and decide whether I should shave off my beard.  You know how it goes.

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This week's Skeptophilia book recommendation is not only a fantastic read, it's a cautionary note on the extent to which people have been able to alter the natural environment, and how difficult it can be to fix what we've trashed.

The Control of Nature by John McPhee is a lucid, gripping account of three times humans have attempted to alter the outcome of natural processes -- the nearly century-old work by the Army Corps of Engineers to keep the Mississippi River within its banks and stop it from altering its course down what is now the Atchafalaya River, the effort to mitigate the combined hazards of wildfires and mudslides in California, and the now-famous desperate attempt by Icelanders to stop a volcanic eruption from closing off their city's harbor.  McPhee interviews many of the people who were part of each of these efforts, so -- as is typical with his writing -- the focus is not only on the events, but on the human stories behind them.

And it's a bit of a chilling read in today's context, when politicians in the United States are one and all playing a game of "la la la la la, not listening" with respect to the looming specter of global climate change.  It's a must-read for anyone interested in the environment -- or in our rather feeble attempts to change its course.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]