Replication Fall Offs

The replication of experimental results is a fundamental part of the scientific process. If you get some interesting results, someone else should try it too, to make sure what you got wasn't just a fluke. The Truth Wears Off: Is there something wrong with the scientific method? in the New Yorker documents many examples of scientific research in which there was an initial report of significance, followed by a sequence of replication attempts which yielded poor confirmation. Many of these cases were in medicine and psychology, fields in which experimental trials are extremely difficult and expensive.
This really isn't surprising at all. Scientific research is now a major industry. Thousands upon thousands of people are out there racking their brains to come up with new results. Each individual may try and discard dozens or hundreds of ideas before stumbling across something interesting and apparently significant. Now let's imagine a million people around the world are flipping coins every day. On some days, some of the flippers will get a very skewed outcome. A tiny number of people might even get a skewed result several days in a row. But if they keep trying to "replicate" their results, they will eventually find that the significance falls off due to a regression toward the mean. Alas, despite all the training and talent that goes into science, most of the novel ideas researchers try out will not end up being significant. But when thousands of insignificant ideas are tested, a small percentage will end up looking good - initially. Researchers are paid to get results, they will keep trying new ideas until they get a skewed result. But was that result truly significant, or was it just a statistical fluke? There are billions of circuit elements following Ohm's law in the computer I'm typing this with - that's not a statistical fluke. Some scientific results have been tested and replicated an astronomical number of times, especially when they prove useful in technology. But it shouldn't be surprising if difficult experiments - especially involving complicated living organisms - often prove to be disappointing despite some initial promise.
The Journal of Irreproducible Results collects science humor. Some of the examples in the New Yorker article aren't too funny however, especially in the medical field.

Human Activity and Fires

Humans cause fires, right? Only You Can Prevent Forest Fires! It might seem that in places and times with less human presence and activity there should be fewer fires. But there is now evidence to the contrary: The Burning Issue in Science reports that evidence from Antarctic ice cores shows declining levels of fire in the Southern Hemisphere until the 1600's, followed by a dramatic peak in the 1800's and now unprecedented low levels of burning.

Origins of Life at Higher Temperatures

Modern biology depends on an intricate web of chemical reactions, many of which are vastly accelerated by enzymes, which themselves are typically large molecules made by complicated machinery. How did this extraordinary network manage to evolve from a nonliving environment? This paper in PNAS, The Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes, points out in that many important biochemical reactions proceed much faster in higher temperature environments, which might have been typical in the early earth.

Sipidan

I've been scuba diving at Sipidan in Malaysia for five weeks now. Some of the highlights have included: swimming in the middle of school of 80 bumphead parrotfish, helping my dive guide Niger rescue a sea turtle which had a rope tied to its arms (today), watching two tiny (3 cm) cuttlefish apparently gobbling up even tinier shrimp by shooting out a long thin retractable tentacle out from the midst of their other tentacles (yesterday).
Allister Lee's blog Aquatastic has lots of nice pictures of Sipidan.

Money Spoils the Fun

People will do some things just for the fun of it. What happens if you provide a financial reward for the same task? The task in this case is to try to press a button exactly 5 seconds after a cue. This study shows that that the financial reward can undermine the appeal of a task people will do for fun: Neural basis of the undermining effect of monetary reward on intrinsic motivation and Removing financial incentives demotivates the brain

Entanglement at High Temperature

Entanglement is one of the most characteristic attributes of "quantum weirdness". Entangled systems are usually microscopic and low temperature. But when the system is not in thermal equilibrium, it should be possible to create entanglement at higher temperatures. Applications may include photosynthesis and perhaps even practical devices some day. See Quantum physics: Hot entanglement in Nature.

Is there a problem with Quantum Theory?

Jeremy Bernstein recounts the history of controversies in the interpretation of quantum theory in the preprint Dear Fellow Quantum Mechanics. In particular to we need to take a quantum/probabilistic view of past events as well as future ones? Creepy.

A New Kind of Robotic Gripper

Universal robotic gripper based on the jamming of granular material

How Cats Drink

I had always heard that the raspy hairs on the cat's tongue were what enabled it to lap up water so neatly. Not at all. The cat flicks the tip of its tongue into the water which shoots up a stream of water and the cat, with perfect timing, closes its jaws over the stream to capture it - four times a second! See For Cats, a Big Gulp With a Touch of the Tongue in The New York Times

Spidan Diving

I've been diving in Sipidan and Mabul in Malaysia for the past couple of days.  Two of the highlights were a purple hairy squat lobster (not a lobster but a tiny crab that lives on sponges and looks pretty much how it sounds) and a pair of sea moths or dragonfish, which at first glance look like a 3 cm long bit of scum sitting on the sand but are actually intricate little creatures under a cheap magnifying glass.

Atlantic Deep Water Reversal

Warm water sinks in the North Atlantic, forming a deep water current which flows southward at the bottom of the Atlantic all the way to Antarctica.  This has a profound effect on our climate - for example, contributing to the warm temperatures Europe enjoys despite its northernly latitude.  However, during the last Ice Age the deep Atlantic current may have actually been reversed, flowing instead from south to north.  See Reversed flow of Atlantic deep water during the Last Glacial Maximum in Nature.

Reionization Early Galaxies

According to the theory of the Big Bang, the cosmic microwave background was formed when then the temperature cooled so that that electrons and protons could combine to form atoms of neutral hydrogen. Currently however, the inter galactic medium consists mainly of ionized hydrogen gas.  When and how this gas became reionized is one of the biggest puzzles in current cosmology.    See Early star-forming galaxies and the reionization of the Universe in Nature.

The Murders in the Rue Morgue

At the moment I'm in Kota Kinabula, Malaysia on the island of Borneo.  Earlier this afternoon I wandered into a little bookstore near my hotel, browsed through the classics section and idly picked up a copy of  The Murders in the Rue Morgue by Edgar Allan Poe, which is often credited as one of the earliest detective stories.  I just read it.  If you, dear detective, browse back a few posts in this blog, you may be able to perceive a tiny bit of a correlation between that story and my own recent activities.  The correlation was not premeditated:   I'm not sure if I've actually read Poe's story before, - but if I did, it was long ago and I definitely didn't remember the pertinent coincidence, because I was amusing myself by trying to figure out the mystery as the story went along. 

Unintuitive Mathematics

Some mathematical methods can seem rather unintuitive in practice and worse, sometimes yield startling and uninintuive results - for example Goedel's incompleteness theorem and Cantorian set theory.  Terence Tao continues his discussion of mathematical techniques in The “no self-defeating object” argument, and the vagueness paradox.

Why Medical Studies are Often Wrong

Lies, Damned Lies, and Medical Science in the Atlantic Magazine.
Much of what medical researchers conclude in their studies is misleading, exaggerated, or flat-out wrong. So why are doctors—to a striking extent—still drawing upon misinformation in their everyday practice? Dr. John Ioannidis has spent his career challenging his peers by exposing their bad science.

A Clever Auto Security Attack

An electronic car lock jammer (inexpensive and readily available) can be used by thieves to prevent a car owner from locking their car.  After the owner leaves the vicinity of their  unlockable car, the robbers collect any valuables left inside.  See Thieves jam key-fob lock signals in mystery car thefts:  Tech-savvy blaggers lift swag leaving windows intact

Problem Solving Strategies in Real Analysis

Fields medallist Terence Tao let's us in on his problem solving strategies - many of which are specific to the subject he was teaching, Real Analysis, but some of them are more generic. 

Orangutans

I just spent a week at an Orangutan sanctuary in Malaysia. Unsurprisingly, they have a great sense of balance - Harry was standing on my arms waving his hands in the air with the greatest of ease, somewhere in between these frames alas.

Dunster House at Sunset

Gravitational Lensing

One of the most intriguing predictions of Einstein's theory of gravity, General Relativity, is that light rays are bent by massive objects.  For example, if two galaxies are closely lined up from our point of view, the foreground galaxy can magnify the image of the background galaxy or create multiple images, etc.   The source for the gravity of the foreground object could even be the mysterious substance "Dark matter".  Hence gravitational lensing is a tool that can tell us something about the distribution of Dark matter - see the preprint Gravitational Lensing

Quantum Theory and Relativity

There are subtle issues with the compatability of the two workhorse theories of contemporary physics:  special relativity and quantum mechanics.  The EPR paradox from the 1930's (the E stands for Einstein)  and Bell's Theorem from the 1960's are two of the classic examples.  The weight of suspicion often tends to fall on the quantum side.  Einstein, notably unenthusiastic about the fundamental role of probability in quantum mechanics,  believed that "God does not throw dice".  John Bell, when asked if quantum mechanics could be wrong replied, "I hesitated to think it might be wrong;  but I knew it was rotten".  Nonetheless quantum mechanics has turned out to be fantastically accurate and the basis for much our current understanding of matter and radiation - likewise for special relativity.  The preprint Can quantum theory and special relativity peacefully coexist? discusses the issues.

Sunrise Mystic River Bridge

Moonrise Over East Cambridge

UFO Over Harvard

UFO Over Harvard, October 11, 2010, 6:52pm

Taken from my place looking west.  I might have been shooting through a closed window, not sure.  I didn't notice the "UFO" at the time and it didn't appear in the previous or the next frames, taken at the same place and direction with minutes.  The crescent moon was also near the horizon just outside the frame to the left.  What was it?

Counterfactual Reasoning in Mathematics

In mathematics, we often assume something (not P), show that it leads to a logical contradiction, and then conclude that P is in fact true.  Mathematician Terence Tao has an interesting discussion of proof by contradiction and related techniques in The “no self-defeating object” argument, revisited.

Void Models of Cosmic Acceleration

Spatial and temporal tuning in void models for acceleration is another preprint that makes the Void model appear rather contrived.  Here a couple of my previous posts on the topic:  A Vote for the Copernican Principle and The Copernican Principle.

À rebours

I recently stumbled upon the "decadent" 1884 novel À rebours by Joris-Karl Huysmans - a character in the book collects Redon paintings (see also my previous post). 

The illustrations by Arthur Zaidenberg are scanned from the 1931 Illustrated Editions issue of A Rebours.

The protagonist has gemstones set in the back of a tortoise, which causes its death.

Odilon Redon





Ophelia among the flowers

   

My whole originality, therefore,

consists in having made improbable beings live humanly

according to the laws of the probable,

by as far as possible putting the logic of the visible

at the service of the invisible.

-ODILON REDON (1898)

Crying Spider - Smiling Spider.

The Cosmic Distance Ladder

How do we know the distance to objects that are really, really far away, like planets, stars and galaxies?  Astronomers use a cosmic distance ladder to correlate different kinds of evidence about distances.  Mathematician Terence Tao explains the cosmic distance ladder in a set of slides with plenty of nice graphics.

The Kuiper Belt

More and more objects are being found in the Kuiper Belt, out beyond the planet Neptune.  Some of them are quite large -  over 2,000 kms in diameter.  Paired objects are also quite common, some of the pairs are only loosely bound by gravity.  Some of these observation pose difficulties for the standard theories of Solar System formation.  See Kuiper Belt may be born of collisions  at Nature.

The Accelerating Universe

The Accelerating Universe preprint.

In this article we review the discovery of the accelerating universe using type Ia supernovae. We then outline ways in which dark energy - component that causes the acceleration - is phenomenologically described. We finally describe principal cosmological techniques to measure large-scale properties of dark energy.

Steam Airships

Water vapor is actually significantly lighter than dry air.  Hence a steam balloon or airship would have characteristics in between those of helium and hot air balloons.  There are some issues, alas - condensation for example.  The Flying Kettle web page describes one such project.

Where do Cosmic Rays Come From?

Cosmic rays, high energy particles, mostly protons and alpha rays, are bombarding our atmosphere.  How are they accelerated and where do they come from?  We don't know.   It is thought that the cosmic rays originating within the Milky Way are generated by supernovas, though there are no direct observations.  However, there are good reasons to believe that extremely high energy cosmic rays originate outside our galaxy.  There's a review in the preprint The Search for the Sources of the Cosmic Rays One Century after their Discovery

A Quantum Tripwire

The quantum tripwire can detect an intruder with a very low probability of being noticed and low probabilities of false negatives and false positives.   It uses the quantum Zeno effect.  It is reported to work in realistic conditions.  Here's the preprint:  An Invisible Quantum Tripwire.

No hawks in church please

I'm reading The Wars of the Roses by Alison Weir.  King Henry VI of England was pious, even to the extent that he would not allow his courtiers to bring their hawks into church.  Apparently in the middle ages it was customary to bring your hawks and dogs to church and there were even cases when the right to do so was an express stipulation.

Strange radio pulses

In 2007 there was a report in Science of an intense radio burst which overloaded the detector at the Parkes radiotelescope in Australia. It was originally thought that the burst must be of extragalactic origin and of incredible power.  But in the meantime 16 additional similar pulses have been identified at Parkes - however they clearly originate on or near the Earth.  But the exact source is still unknown:  Radio Bursts with Extragalactic Spectral Characteristics Show Terrestrial Origins  .  The authors of that report whimsically refer to these odd bursts as "Perytons" after a winged deer which casts the shadow of a man in Borges'  Book of Imaginery Beings.


Parkes radio telescope



Post 666




The Number of the Beast is 666 - William Blake

   This is my 666th blog post.  In honor of this rather dubious milestone, here's a selection of 42 of the over one hundred articles I've edited on another website, Wikipedia.

Aerobic anoxygenic phototrophic bacteria:  very abundant marine plankton.

Big Bang nucleosynthesis:  there is an unexplained discrepancy for the element Lithium.

Linda B. Buck:  a Nobel prize winner in biology - recently retracted publications.

Lois McMaster Bujold:  award winning scifi and fantasy author.

Cartesian Coordinates:  French philosopher Oreseme anticipated Descartes by centuries.

Cassiopeia A:  a supernova remnant and a very strong radio source.

Clovis point:  beautiful spear points from ancient America.

Coherent perfect absorber:  a time-reversed laser.

 Dwarf galaxy problem:  there aren't as many as expected.

Geminga:  an unusual neutron star which generated the Local Bubble.

J. Richard Gott: Princeton professor of astrophysics with a Doomsday Theory.

GSI anomaly:  unexplained oscillations detected at a German laboratory.

Guzheng:  a classical Chinese musical instrument.

Haptophyte: tiny uncultured pico-prymnesiophytes are ecologically important.

Helical Dirac fermion:  behaves like a massless relativistic particle.

Helitron:  DNA which replicates by a rolling-circle mechanism.

 Inner Core:  the central core of the earth has an East-West asymmetry.

Richard J. Lipton:  computer scientist, Gödel's Lost Letter and P=NP is his blog.

Local Void:  a vast empty region of space near our Milky Way galaxy.

Mira B: the companion of the variable star Mira is now believed to be a white dwarf.

National Spatial Reference System: is a coordinate system managed by the US.

Pre-solar nebula:  a supernova shock wave may have triggered the formation of the Sun.

Puerto Plata:  is a resort town on the north coast of the Dominican Republic.

Ptychography:  allows X-ray microscopes without using lenses.

Quantum Gravity:  this theory has a Problem with Time.

The Rose of Versailles:  is a Japanese manga set during the French Revolution.

RX J0852.0-4622:  a nearby supernova which should have been visible around 1250.

SCP 06F6: an extremely luminous supernova. 

Second harmonic imaging microscopy:  useful in imaging in living tissues.

Segue 1:  a dwarf galaxy dominated by Dark Matter.

Three Tales:  the tale A Simple Heart by Flaubert inspired the novel Flaubert's Parrot.

Time dilation :  A surprising consequence of relativity.

Topological insulator:  an exotic material that has insulating and conducting regions.

Torquetum:  a medieval astronomical instrument.

Transit of Venus: Venus will cross the face of the Sun again in 2012.

Type IIn supernovae:  extremely energetic supernovae.

Type IIb supernovae:  a star with a mostly helium core explodes.

Venus: the planet was completely resurfaced 300-600 million years ago.

Water window: water is transparent to part of the X-ray spectrum.

Xenocarida:  the "strange shrimp" are a group of recently discovered Crustacea.

Shing-Tung Yau:  distinguished mathematician, Poincaire conjecture controversy.

 Zero Morphism: is a concept in the mathematical subject Category Theory.


Oxygen increase in the Devonian Period

There's new evidence of a substantial increase in ocean oxygen content during the Devonian period about 400 million years ago.  That was around the time that vascular plants arose, so perhaps that's what caused the increase.  At the same time more complicated animals such as predatory fish evolved  - so perhaps the higher level of oxygen is what made that possible.   See Plants set stage for evolutionary drama in Nature.

Shakespearean Titles

Many literary works derived their titles from passages in Shakespeare, e.g. Brave New World, The Sound and the Fury.
Another one of my favorites is the poem/novel Pale Fire by Vladimir Nabokov.

The moon's an arrant thief,
And her pale fire she snatches from the sun.
       Timon of Athens

Once I got caught in a strange web created by Nabokov and another author which involved the following lines from Pale Fire:

Space is a swarming in the eyes,
and Time a singing in the ears

 I was reading the Nabokov novel Ada.  In Ada Nabokov mentioned the lines above as quoted by "the invented philosopher Martin Gardiner".  I thought I was hallucinating, since coincidentally I was also in the middle of reading a popular science book The Ambidextrous Universe with a nearly identical author -  Martin Gardner.  Fortunately it happened to be the second edition of the Ambidextrous Universe, which, when I read further, provided the explanation.  Nabokov's misspelling of Gardner's name was probably deliberate!

By the way, it probably wouldn't be too surprising if even a humble blog might have had the nerve to derive its title from a well-known passage in Shakespeare.

Two Plays by Tom Stoppard

I just reread The Real Inspector Hound and After Magritte, two plays by Tom Stoppard.  The Real Inspector Hound, a parody of the "murder at the stately English country home" genre, is much the better.  But my favorite exchange was in After Magritte:

THELMA:  ... All I can say is I'll be glad when it's all over and things are back to normal.  It's making you short-tempered and argumentative.  You contradict everything I say --
HARRIS: (heatedly)  That I deny --

What if, instead of contradicting her, Harris had agreed with Thelma and said "You're right"? 

Stoppard has worked on film scripts as well as theater.  The dystopian film Brazil, directed by Terry Gilliam, is one of my favorites.  I didn't realize that he also contributed much of the dialog for Indiana Jones and the Last Crusade, a Steven Spielberg film that I also enjoyed.

This (substantive) modification of Stoppard's dialog has bothered me:

ALICE:  You contradict everything I say.
BOB:  You're right.

I considered whether this might be some variant of the Liar Paradox similar to:

The next sentence is false.
The previous sentence is true.

That really is a logical paradox:  try to make the first sentence true - it doesn't work;  try to make the first sentence false - it doesn't work either.

But there's really no logical problem with Alice and Bob.  Alice's statement is false and so is Bob's.  Bob's response falsifies Alice's previous statement.  Bob proves Alice wrong by agreeing with her.  However since Bob proved Alice wrong, in a certain sense he actually did contradict her.   Which would seem to make Alice's statement true (or at least it could be true - assuming all of Bob's other statements also contradicted her).  But didn't I just say it was false?  Still it isn't really a paradox in pure logic.  Is it?

While we're at it, let's take a look at this stripped-down version of Stoppard's original Thelma and Harris exchange:

THELMA: You contradict everything I say.
HARRIS: That I deny.

Thelma's statement could be true (at least when Harris contradicts her in all other cases - let's go ahead assume that).  The Harris statement denies what Thelma just said, that denial counts as a contradiction (I suppose) and so the Harris statement is consistent with the meaning of Thelma's assertion.  Hence, the Harris statement supports Thelma's assertion.  Then given that we're assuming Harris otherwise contradicts Thelma, Thelma's statement must be true.  On the other hand, Thelma asserts that Harris contradicts everything she says and Harris' subsequent statement supports that.  If Harris' statement supports Thelma's statement, it can hardly be contradicting her.  So Thelma's statment must be false.  But didn't I just say Thelma's statement must be true?  Oops. 

What do you think?  But please, don't contradict everything I say.

 
"if it was so, it might be; and if it were so, it would be; but as it isn't, it ain't. That's logic."
--- Tweedledee in Through the Looking Glass by Lewis Carroll.

Time Will End

The preprint Eternal inflation predicts that time will end argues that cosmological theories which include "eternal inflation" will lead to the end of time - their estimate is 5 billion years for our galaxy.  It may seem like you still have plenty of time, but it's never too soon to panic.

Television Novels

Here are my choices for the best "Television Novels" a genre I might well have just made up, though it is presaged in this Lorrie Moore review of The Wire in the New York Review of Books.  It's a television series that transcends the genre and approaches or achieves the status of literature - not coincidentally a couple of the entries are adapted from excellent novels.  Unhappily very similar sounding, but on rather the opposite end of the spectrum, is the Telenovela, a Latin American soap opera, ordinarily devoid of literary aspirations. 

1. The Wire is the best thing ever made for television. This Baltimore of drug dealers and the po-lice perhaps may be how the early third millennium will be remembered in the centuries to come.
2. I Claudius:   Siân Phillips scheming depiction of Livia, the wife of Roman Emperor Augustus, is mesmerising. We are all rabbits and she is the snake.
3. Middlemarch the 1994 adaptation of the George Elliot novel. There's a film adaptation that's supposed to coming out soon, also by the screenwriter Andrew Davies.

Lost, Battlestar Galactica, Rome and Twin Peaks were all brilliant as well. I suppose The Sopranos should also be mentioned - James Gandolfini was tremendous but the pseudo-psychoanalytic intrusions put me off. Possibly the greatest work (after The Wire) made for television was The Decalogue made for Polish TV in 1988 by Krzysztof Kieślowski but it's a sequence of novellas as opposed to a single novel.

A couple of other of my favorite television series are rather more episodic than novelistic, so they don't quite fit the stated genre, but still excellent: a horse opera in outer space Firefly;  and the ferociously hilarious Australian comedy Summer Heights High.

Aristotle's wheel paradox

Embarrassingly I'm still slowly reading Galileo at Work: His Scientific Biography by Stillman Drake.  Aristotle's wheel paradox came up several times in the book so I finally looked it up at Wikipedia.

When the inner and outer attached wheels make a complete revolution, they trace out lines of equal length, yet their circumferences are different.
How can that be?

SCP 06F6

SCP 06F6 is a very unusual object discovered in 2006 by the Hubble Space Telescope.  Its spectrum and light curve are unlike any other known. Initial observations weren't able to identify any of the typical spectral lines. The Palomar Transient Factory was able to determine its redshift (z = 1.189) and that its luminosity is one of the highest currently known:  Mysterious transients unmasked as the bright blue death throes of massive stars.

A Vote for the Copernican Principle

The preprint Confirmation of the Copernican principle at Gpc radial scale and above from the kinetic Sunyaev Zel'dovich effect power spectrum provides evidence against the void model of dark energy/cosmic acceleration.

AntiNeutrino surprise at MINOS

One of the fundamental principles of particle physics is that particles and their anti-particles should have the same mass.  So it was a big surprise when Fermilab MINOS collaboration found that the muon neutrino and muon antineutrino appear to have different masses.  Neutrino experiments are extraordinarily difficult because neutrinos are so hard to detect.  This result is still very preliminary.  But if it does hold up, the impact on theoretical physics will be earthshaking.
See Neutrino surprise emerges from MINOS at PhysicsWorld .

The Sky in Boston tonight

was spectacular. Venus just after sunset in the West and a nearly full moon and a gigantic Jupiter in East, one of its closest approaches to Earth. All four of the major satellites of Jupiter were lined up and nearby was Uranus - actually the first time I believe I've ever seen it, with binoculars.
Unfortunately I couldn't see the following sight (Carina Nebula) with my binoculars, it is in the Southern Hemisphere, but the Hubble Space Telescope did.

Dimensionality of the Universe

One of the most mysterious facts about our universe is that, for most purposes, it can be modelled as four-dimensional: with one dimension for time and three dimensions for space. Why four, why not three, why not 42? There have long been proposals that add more dimensions, especially extra spatial dimensions, which are curled up so tightly that we don't normally perceive them.
The following preprint proposes something different. At very small scales (subatomic) there are effectively fewer than three spatial dimensions while at very large scales (cosmological) there are effectively more than three spatial dimensions!
Vanishing Dimensions and Planar Events at the LHC

We propose that the effective dimensionality of the space we live in depends on the length scale we are probing. As the length scale increases, new dimensions open up. At short scales the space is lower dimensional; at the intermediate scales the space is three-dimensional; and at large scales, the space is effectively higher dimensional. This setup allows for some fundamental problems in cosmology, gravity, and particle physics to be attacked from a new perspective. The proposed framework, among the other things, offers a new approach to the cosmological constant problem and results in striking collider phenomenology and may explain elongated jets observed in cosmic-ray data.

Event honoring Feynman.

TEDxCaltech, an exciting one-day event to honor Richard Feynman.

Codons matter

DNA codes for amino acids with triplets of bases (codons). There are four different bases and hence 64 different triplets. There are typically twenty different amino acids (plus start and stop signals) which need to be coded, so there is some redundancy - a single amino acid can have multiple codons which are all translated the same way. However, there is now evidence that the actual codon may make a difference. New Roles for Codon Usage in Science reports that two very similar but distinct proteins are modified differently, depending on the original codon.

Quadrocopter Flys Through Hoop

Bowerbirds use an optical illusion to trick their mates

Bowerbirds trick mates with optical illusions at Nature News. Male bowerbirds construct their bowers to create an optical illusion called forced perspective which makes them appear bigger than they really are.

The Problem of Time

The Problem of Time in Quantum Gravity

The problem of time in quantum gravity occurs because `time' is taken to have a different meaning in each of general relativity and ordinary quantum theory. This incompatibility creates serious problems with trying to replace these two branches of physics with a single framework in regimes in which neither quantum theory nor general relativity can be neglected, such as in black holes or in the very early universe.

The heliospheric current sheet

"The Sun with the heliosheet is like a bashful ballerina who is repeatedly trying to push her excessively high flaring skirt downward".

Universality

A first draft of a non-technical article on universality by Fields medallist Terence Tao. Talks about universality: when important attributes of a large-scale system can be independent of how the system works at smaller scales.

Solar Neutrinos

The preprint Solar neutrinos, helioseismology and the solar internal dynamics begins with an interesting history of the "solar neutrino problem".

The Mafia Game

The mafia game (or werewolf or assassin game) is a party game in which the organiser divides the players into two groups: the citizens and the mafia. The mafia are told who the other mafia are, but the citizens don't know. The game alternates between the "day" when all the players decide who to "lynch" and the "night" when just the mafia decide who to eliminate. The game ends when either all the citizens or all the mafia are eliminated.
The preprint A mathematical model of the Mafia game provides an analysis of strategy.

Testing the Universality of Free Fall

There's an interesting debate in Nature about atom interferometry tests of gravitational redshifts and what they imply about the university of free fall and the Einstein equivalence principle. See the preprint Atom gravimeters and gravitational redshift and the reply. See also the preprint Gravitational Redshift, Equivalence Principle, and Matter Waves. One of the authors in this controversy is Nobel prize winner and Department of Energy secretary Steven Chu.

The Copernican Principle

The Copernican Principle posits that the Earth is not in any particularly special location in the universe. Prior to Copernicus, the Earth had been placed in the center of the universe and historically there was much resistance to moving it - early in his career even Galileo had a fanciful rationale for putting the earth at the center.
The Standard Model of Cosmology pretty much enshrines the Copernican Principle. It has had some success explaining phenomenon like the extragalactic redshifts, microwave background radiation and the abundances of light elements.
However there are some difficulties with this model, especially the observed acceleration of the redshifts (Dark Energy) and the abundance of lithium 7.
The preprint Do primordial Lithium abundances imply there's no Dark Energy? explains these observations by heretically suggesting that the Earth might be in a rather special place after all: near the center of a gigantic void. See also The Cosmic Microwave Background in an Inhomogeneous Universe - why void models of dark energy are only weakly constrained by the CMB by the same authors.

A Light Sucker

Laser science: Suckers for light in Nature.

A Coherent perfect absorber is:

An optical device has been designed that performs a function exactly opposite to that of a laser. It perfectly absorbs incoming coherent radiation and turns it into thermal or electrical energy.

Backward lasing yields a perfect absorber

Just as a laser can emit coherent light from an amplifying medium, an absorbing medium can perfectly capture incoming radiation under the right conditions

CPA-based interferometers could thus have potential applications in the realization of transducers, modulators, or optical switches, for example, in on-chip integrated optical circuits based on Si waveguide/resonator technology.

The Sun's Elements

An Unsettled Debate About the Chemistry of the Sun in Science.
There's a debate about how much carbon, nitrogen, oxygen and neon the sun contains. NASA

Probability Puzzles

There's an intersting discussion of some confusing Probability Puzzles on John Baez's new blog.

“I have two children. One is a boy born on a Tuesday. What is the probability I have two boys?”

The "born on a Tuesday" information can't possibly make a difference, can it? So the answer should be same same as:

“I have two children. One is a boy. What is the probability I have two boys?”

Shoudn't it?

There's a thorough analysis at Some Thoughts on Tuesday's Child by Greg Egan.

Video Test

Take the video test and then see Seeing and Thinking in the Mist.

Collider Physics

There is currently much excitement in physics due to the LHC, the huge new European particle accelerator. This preprint explains the theoretical analysis of such experiments: Introduction to Collider Physics.

Insertion of the vacuum-tank of the CMS detector in the LHC

Fire Tornado

Fire Tornado in Wikipedia.

More Quantum Inequalities

Quantum mechanics: The usefulness of uselessness in Nature.
Bell pointed out that quantum mechanics violates certain inequalities that are true in classical physics. This article discusses other inequalities that even quantum mechanics respects but which distinguish it from "super quantum theories" that would be able to violate these inequalities.

How big is the Proton?

The proton shrinks in size: Tiny change in radius has huge implications - in Nature.

Problems with Quantum Mechanics

Might I say immediately … we always have had a great deal of difficulty in understanding the world view that quantum mechanics represents … I cannot define the real problem, therefore I suspect there’s no real problem, but I am not sure there’s no real problem.

Richard Feynman

Jeremy Bernstein in FAPP and Non-FAPP: A Pedagogical Essay discusses the foundations of quantum mechanics. Bernstein is a very good writer and he explains some aspects of this problematic field quite well. In the end, however, it still seems just as problematic as ever.

FAPP - For All Practical Purposes

Once Bernstein happened to visit physicist Erwin Schroedinger in his Vienna apartment.

There was no cat. He did not like cats.

Weak Lensing

Weak lensing, dark matter and dark energy preprint.

Weak gravitational lensing is rapidly becoming one of the principal probes of dark matter and dark energy in the universe. In this brief review we outline how weak lensing helps determine the structure of dark matter halos, measure the expansion rate of the universe, and distinguish between modified gravity and dark energy explanations for the acceleration of the universe. We also discuss requirements on the control of systematic errors so that the systematics do not appreciably degrade the power of weak lensing as a cosmological probe.

Nicole Oresme

Nicole Oresme was a sophisticated 14th century French philospher. He discussed and compared Earth-centered and Sun-centered models of the solar system and couldn't find any way to dismiss the Sun-centered model - though he personally didn't believe it. He also used techniques which were very close to Cartesian coordinate systems - over two hundred years before Descartes. See the Nicole Oresme article in the Stanford Encyclopedia of Philosophy.

RRAT's

Transient Radio Neutron Stars preprint.

Here I will review the high time resolution radio sky, focusing on millisecond scales. This is primarily occupied by neutron stars, the well-known radio pulsars and the recently identified group of transient sources known as Rotating RAdio Transients (RRATs). The RRATs appear to be abundant in the Galaxy, which at first glance may be difficult to reconcile with the observed supernova rate. However, as I will discuss, it seems that the RRATs can be explained as pulsars which are either extreme nullers, highly variable or weak/distant. I will re-cap some recent results including a re-analysis of the Parkes Multi-beam Pulsar Survey, which has identified several new sources, as well as the unusual timing behaviour of RRAT J1819-1458. This leads to an examination of where RRATs fit within the evolution of neutron stars post-supernova.

Measuring the mass of solar system planets using pulsar timing

Measuring the mass of solar system planets using pulsar timing
Apparently the pulse time of arrival from pulsars is so accurate it can help determine the masses of the planets of the solar system with accuracy comparable (or better) than data from spacecraft missions. That's because the motions of the other planets cause the Earth to wiggle in its orbit. The pulsar data allowed the researchers to determine the Earth's orbit so well, it could be used to determine the masses of the other planets!
See also Pulsar Signals Could Reveal Solar System Secrets at Science.

Hubble image of SN1987A

HST SN1987A
When I saw this Hubble Space Telescope image of Supernova 1987A on Wikipedia, it was so spectacular at first I thought it must have been just some artist's conception.

Picophytoplankton

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton in PNAS.

Small (2-3μm) uncultured photosynthetic eukaryotic plankton (picophytoplankton) are a substantial component of the biomass and primary production in the oceans. Pico-prymnesiophytes genomes seem to be a mosaic, with the chloroplast and nuclear genomes from different lineages.

The Pioneer Anomaly

The Pioneer Anomaly preprint.

Radio-metric Doppler tracking data received from the Pioneer 10 and 11 spacecraft from heliocentric distances of 20-70 AU has consistently indicated the presence of a small, anomalous, blue-shifted frequency drift uniformly changing with a rate of ~6 x 10^{-9} Hz/s. Ultimately, the drift was interpreted as a constant sunward deceleration of each particular spacecraft at the level of a_P = (8.74 +/- 1.33) x 10^{-10} m/s^2. This apparent violation of the Newton's gravitational inverse-square law has become known as the Pioneer anomaly; the nature of this anomaly remains unexplained. In this review, we summarize the current knowledge of the physical properties of the anomaly and the conditions that led to its detection and characterization. We review various mechanisms proposed to explain the anomaly and discuss the current state of efforts to determine its nature. A comprehensive new investigation of the anomalous behavior of the two Pioneers has begun recently. The new efforts rely on the much-extended set of radio-metric Doppler data for both spacecraft in conjunction with the newly available complete record of their telemetry files and a large archive of original project documentation. As the new study is yet to report its findings, this review provides the necessary background for the new results to appear in the near future. In particular, we provide a significant amount of information on the design, operations and behavior of the two Pioneers during their entire missions, including descriptions of various data formats and techniques used for their navigation and radio-science data analysis. As most of this information was recovered relatively recently, it was not used in the previous studies of the Pioneer anomaly, but it is critical for the new investigation.

The Birthplace of the Sun

The Astrophysical Environment of the Solar Birthplace preprint.

Our Sun, like all stars, formed within a cold molecular cloud. Astronomical observations and theory provide considerable detail into this process. Yet cosmochemical observations of short lived radionuclides in primitive meteorites, in particular 60Fe, provide unequivocal evidence that the early solar system inherited fresh nucleosynthetic material from the core of a hot, massive star, almost certainly ejected in a supernova explosion. I give a short introduction to the fields of star formation and meteoritics and discuss how the reconciliation of their disparate clues to our origin places strong constraints on the environment of the Solar birthplace. Direct injection of supernova ejecta into a protoplanetary disk or a dense molecular core is unlikely since their small sizes require placement unusually close to the massive star. Lower density molecular cloud clumps can capture more ejecta but the radionuclides decay during the slow gravitational collapse. The most likely scenario is on the largest scales via the formation of enriched molecular clouds at the intersection of colliding supernova bubbles in spiral arms.

The Earth's Inner Core

Earth's Moving, Melting Core in Science.

Strange forces are at work 5000 kilometers below Earth's surface. The inner core is acting in ways that scientists can't explain. Theoretically, the core should be drawing iron from its molten surroundings and crystallizing it into solid metal. But that alone doesn't account for a number of odd observations—unless, as a few scientists speculate, the core is also melting.

P is not equal to NP?

Vinay Deolalikar a research scientist at HP labs, has a preprint (on his web page) which is a preliminary draft of a proof that P is not equal to NP. Claimed resolutions of P=NP are rife on the internet. However, this draft preprint is from a reputable researcher. The P=NP question is one of the most important research problems of our time. Any proof of this importance will have to be carefully checked by the research community. We shall see!

See how this process has been playing out as of August 16, 2010: Step 1: Post Elusive Proof. Step 2: Watch Fireworks. in the New York Times.

See also A Tale of A Serious Attempt At P≠NP by Computer Scientist Richard J. Lipton at CACM.

A Peculiar Moon in Lord of the Rings

Lord of the Rings, the fantasy trilogy by J.R.R. Tolkein, takes place in Middle Earth, which has a different geography than our Earth, some different humanoids (Elves, Dwarfs, Hobbits) walking/talking trees (Ents) etc. But the weather, the vegetation and the animal life are mostly similar to ours. In particular, the sun, the moon and the stars seem pretty much the same. The characters are often out and about by night, so the phase and position of the moon is often mentioned. In one scene, however, the moon behaves a bit strangely.

In The Two Towers, Book Four, Chapter 4, Of Herbs and Stewed Rabbits, in the first page of that chapter, "The moon was now three nights from the full, but it did not climb over the mountains until nearly midnight, and the early night was very dark." The mountains are to the east of their location, which would block the early rising moon. Does "three nights from the full" mean the moon is waxing and it is three days before it will be full - or does it mean the moon is waning and it is three days after the full moon? I intuitively interpreted that as the first case: the moon is waxing, it's before the full moon. In Moon Phases in The Lord of the Rings there's an impressively detailed accounting which agrees with that interpretation. But when the moon is waxing, it will typically reach its highest point in the sky before midnight. This really only depends on the fact that the moon is illuminated by light reflected from the sun. In much of the rest of Tolkein, the moon does behave quite normally, for example: "If the Moon gave enough light, we would use it, but alas he sets early and is yet young and pale".

Here's another loony scene however. In the chapter In the house of tom bombadil: "In the dead night, Frodo lay in a dream without light. Then he saw the young moon rising;". Dreams are notoriously full of nonsense, so I guess we can't hold Tolkein responsible for unfortunate lunar behaviour in the bad dream of a little guy with hairy toes.

In societies without widespread artificial lighting, most people were very conscious of the phases of the moon. Today however, this is far from true. Mention the easily observed fact that the full moon typically rises around the same time as the sunset and then sets around sunrise and the expression on people's faces will all too often plainly reveal that this is news to them.

The Darkest Galaxy

A Complete Spectroscopic Survey of the Milky Way Satellite Segue 1: The Darkest Galaxy arXiv preprint.

We present the results of a comprehensive Keck/DEIMOS spectroscopic survey of the ultra-faint Milky Way satellite galaxy Segue 1. We have obtained velocity measurements for 99.1% of the stars within 67 pc (2.3 half-light radii) of the center of Segue 1 that have colors and magnitudes consistent with membership, down to a magnitude limit of r=21.7. Based on photometric, kinematic, and metallicity information, we identify 71 stars as probable Segue 1 members, including some as far out as 87 pc. After correcting for the influence of binary stars using repeated velocity measurements, we determine a velocity dispersion of 3.7^{+1.4}_{-1.1} km/s, with a corresponding mass within the half-light radius of 5.8^{+8.2}_{-3.1} x 10^5 Msun. The stellar kinematics of Segue 1 require very high mass-to-light ratios unless it is far from dynamical equilibrium, even if the period distribution of unresolved binary stars is skewed toward implausibly short periods. With a total luminosity less than that of a single bright red giant and a V-band mass-to-light ratio of 3400 Msun/Lsun, Segue 1 is the darkest galaxy currently known. We critically re-examine recent claims that Segue 1 is a tidally disrupting star cluster and that kinematic samples are contaminated by the Sagittarius stream. The extremely low metallicities ([Fe/H] < -3) of two Segue 1 stars and the large metallicity spread among the members demonstrate conclusively that Segue 1 is a dwarf galaxy, and we find no evidence in favor of tidal effects. We also show that contamination by the Sagittarius stream has been overestimated. Segue 1 has the highest measured dark matter density of any known galaxy and will therefore be a prime testing ground for dark matter physics and galaxy formation on small scales

Quantum Interference

Pairs Rule Quantum Interference in Science.

Quantum interference is one of the most mysterious features of quantum mechanics. In fact, Feynman referred to the double-slit interference experiment for single particles as the "only" mystery in quantum mechanics (1). On page 418 of this issue, Sinha et al. (2) describe a recent experiment that shows that quantum interference from a single photon arises only from pairs of possible paths through an interferometer. There is no need to invoke additional interference terms that might arise from interactions of three or more paths.

The Cyberiad by Stanislaw Lem

I'm in the middle of rereading one of my favorite collections of tales, "The Cyberiad" by Stanislaw Lem, translation by Michael Kandel. Originally in Polish, the English version is filled with delightful word play and whimsy.
"He who has had, has been, but he who hasn't been, has been had"

A Film about East Timor

A Hero's Journey : A documentary film about forgiveness with Xanana Gusmao of East Timor (Timor-Leste) directed by Grace Phan.

FREE FALL: World champion freediver Guillaume Nery special dive at Dean's Blue Hole, the deepest blue hole in the world filmed entirely on breath hold by the french champion Julie Gautier. This video is a FICTION and an ARTISTIC PROJECT. Edited by BLUENERY (c).

Cosmic Acceleration

Cosmology forum: Is dark energy really a mystery? in Nature.

The Universe is expanding. And the expansion seems to be speeding up. To account for that acceleration, a mysterious factor, 'dark energy', is often invoked. A contrary opinion — that this factor isn't at all mysterious — is here given voice, along with counter-arguments against that view.

Topological Insulators

Topological insulators: Star material in Nature.
Topological insulators are a new kind of material which conduct electricity only on their surfaces. There are new, inexpensive compounds based on bismuth which have created a lot of excitement.
Solid-state physics: U-turns strictly prohibited also in Nature.

According to theory, electrons on the surface of a topological insulator are not allowed to make U-turns. This notion, and some of its main consequences, has now been tested experimentally.

North Pacific Deep Water Formation in the last ice age

When Still Waters Ran Deep in Science.

"Deep water" and "bottom water"—the waters that fill the deep parts of ocean basins—form when surface waters become dense and sink. Today, this occurs in the northern North Atlantic and around Antarctica, but not in the North Pacific. There, surface waters do not become dense enough to sink more than a few hundred meters. In the past, however, it seems things were different. Recently, Okazaki et al. offered new insight into the ancient history of the ocean from radiocarbon data and modeling analyses (1). They suggest that deep water formed in the North Pacific at the beginning of the transition out of the last ice age.

The Mystery of Sea-Floor Methane

The Ongoing Mystery of Sea-Floor Methane in Science.

Each year, ocean sediments produce a quantity of methane equivalent to about half of the methane emitted to the atmosphere from all natural sources (1). Very little of the methane produced below the sea floor, however, reaches the ocean or the atmosphere; most is consumed by anaerobic microorganisms as it diffuses up through oxygen-poor (anoxic) sediments. Researchers recognized this process, known as anaerobic methane oxidation (AMO), nearly 35 years ago (2), but it remains poorly understood. Investigators have not been able to firmly establish the reaction mechanism, fully understand the factors that control oxidation rates, or isolate the responsible organisms. This represents a gaping hole in our understanding of one of Earth's primary sinks for methane. Recent studies of a rare but intriguing sedimentary environment–sea-floor seeps of methane-rich fluids–have provided new insights into the microorganisms that inhabit methane-rich sediments, but raised new questions regarding reaction mechanisms.

A Low Luminosity Supernova

The Subluminous Supernova 2007qd: A Missing Link in a Family of Low-Luminosity Type Ia Supernovae preprint.

We present multi-band photometry and multi-epoch spectroscopy of the peculiar Type Ia supernova (SN Ia) 2007qd, discovered by the SDSS-II Supernova Survey. It possesses physical properties intermediate to those of the peculiar SN 2002cx and the extremely low-luminosity SN 2008ha. Optical photometry indicates that it had an extraordinarily fast rise time of <= 10 days and a peak absolute B magnitude of -15.4 +/- 0.2 at most, making it one of the most subluminous SN Ia ever observed. Follow-up spectroscopy of SN 2007qd near maximum brightness unambiguously shows the presence of intermediate-mass elements which are likely caused by carbon/oxygen nuclear burning. Near maximum brightness, SN 2007qd had a photospheric velocity of only 2800 km/s, similar to that of SN 2008ha but about 4000 and 7000 km/s less than that of SN 2002cx and normal SN Ia, respectively. We show that the peak luminosities of SN 2002cx-like objects are highly correlated with both their light-curve stretch and photospheric velocities. Its strong apparent connection to other SN 2002cx-like events suggests that SN 2007qd is also a pure deflagration of a white dwarf, although other mechanisms cannot be ruled out. It may be a critical link between SN~2008ha and the other members of the SN 2002cx-like class of objects.