Wednesday, June 21, 2017

Human genome only 90% sequenced

Were you under the impression that the human genome had been sequenced? That is was completed in 2003?

STAT reports:
“It’s very fair to say the human genome was never fully sequenced,” Craig Venter, another genomics luminary, told STAT.

“The human genome has not been completely sequenced and neither has any other mammalian genome as far as I’m aware,” said Harvard Medical School bioengineer George Church, who made key early advances in sequencing technology. ...

Perhaps nobody paid much attention because the missing sequences didn’t seem to matter. But now it appears they may play a role in conditions such as cancer and autism. ...

Church estimates 4 percent to 9 percent of the human genome hasn’t been sequenced. Miga thinks it’s 8 percent.
Why couldn't they announce that the genome was 90% sequenced? Did they think that the public was incapable of understanding that?

Of course the public can understand that. There was some sort of conspiracy to mislead the public.

I remember the original announcement making a big deal about finding all the genes, and then later learning that they did not even know how many genes there were.

I heard that there were gaps, but now I learn 4 to 9% is missing! That tells me that not only is a lot missing, but they don't even know how much is missing.

Tuesday, June 20, 2017

The continued failure to find SUSY

The NY Times reports on the ongoing hunt for SUSY:
Many theorists had also hoped that supersymmetrical particles would show up when the Large Hadron Collider was finally turned on in 2010. Indeed the mystery particles could have shown up even earlier, in the collider’s predecessors, according to some versions of the theory.

As a headline in The New York Times put it in 1993: “315 Physicists Report Failure in Search for Supersymmetry.”

So far they are still failing. In May, a new analysis by the 3,000 physicists monitoring the big Atlas detector (one of two main detectors in the CERN tunnel) reported no hints of superparticles up to a mass of almost 2 trillion electron volts. ...

Not everybody is ready to give up on supersymmetry or to pay off bets.

Gordon Kane, a superstring theorist at the University of Michigan who is well known in the community for his optimism about supersymmetry, ...

Another staunch supporter is John Ellis, ...

“It took 50 years to find the Higgs,” he said, standing beside his multistory detector, known as CMS, 300 feet underground one morning.

“Patience is clearly a virtue in physics,” he added.
SUSY requires dozens of new particles that have never been found. There are theorists who have a belief that it would make the theory nicer, but those ideas have never worked.

I don't see any end to this. In 20 more years, we could still have no SUSY particles, but still have most prominent theoretical physicists believing in them. The same could still be true in 50 or 100 years. Nothing will cause the advocates to give up, just as no one is going to give up on climate change.

Friday, June 16, 2017

Chinese send entangled photons

The LA Times reports:
Chinese scientists have just set a record in quantum physics.

For the first time, pairs of entangled photons have been beamed from a satellite in orbit to two receiving stations almost 1,500 miles away on on Earth.

At the same time, the researchers were able to deliberately separate the entangled photon pairs along a greater distance than has ever been recorded.

The experiment, described Thursday in the journal Science, represents the first measurable proof of an idea that has long been theorized but never tested, experts said.

“This is the first time you have a quantum channel between a satellite and the ground that you can actually use,”
No, this is not something useful.
Although the experiment was successful, the rate of sending and receiving entangled photons described in the paper was still quite low. Of nearly 6 million entangled photon pairs generated by Micius each second, only one pair was detected at stations here on Earth.

“The communication rates here are not yet sufficient for a practical application,” said Wenjamin Rosenfeld, a physicist at the Ludwig-Maximilians University in Munich.

However, he added that the mission represents a proof-of-principle demonstration of a quantum communication protocol that could be available in the near future.
So it sends one bit per second?!

The slowness is not the main problem. The security depends on accounting for all the photons. The system does not really stop eavesdropping, but alerts the parties if any photons are unaccounted for, as that might be a symptom of an attack.

But the Chinese can only account for one out of 6M photons anyway?!

Meanwhile, there are terabits of encrypted data being transmitted on satellites every second, and the method does not suffer the vulnerabilities of this quantum method.
That’s neat, but is this going to affect my life in anyway?

Not immediately, but eventually, it probably will.

For example, distributing entangled photons over large distances could be used to establish unhackable communications via what’s known as quantum cryptography.

This application relies on another strange aspect of quantum mechanics — namely that the simple act of observing a photon disturbs it and causes it to change its orientation.
So if an evesdropping observers a photon, he changes it, and might get exposed.

But no, this has no practical value. Who wants a system that can be sabotaged by someone observing a photon?
“One measurement alone doesn’t tell you they are entangled, you need to repeat it many times,” he said. “With entangled photons no matter what you measure, or how many times you measure, or which side of the pair you measure, you always get perfect correlation.”

How is this possible?

Another great question. This one is more difficult to answer.

Scientists have not been able to explain why entanglement occurs. All they know is that it exists.

Einstein referred to the phenomena of entanglement as “spooky action at a distance.” Others have said it is kind of like the physics version of voodoo.
The correlations are perfect is the equipment is perfectly aligned and a perfectly parallel measurement is done.

In practice, these things are not perfect, and some photons are lost. And you can't really detect one photon being stolen, you can only make a statistical conclusion if a lot of your data has been stolen.

On the other hand, the non-quantum cryptographic technologies work just fine.

I would think that if the LA Times asked expert opinion from physicists and cryptographers, at least half of them would know that this whole field is a scam. Why don't any of them tell the LA Times?

Wednesday, June 14, 2017

Sapolsky says no free will, obviously

This interview is of a famous intellectual pushing his magnum opus:
It seems impossible to view the full range of influences on our behavior and conclude that there is anything like free will.

Sean Illing: That’s a bold claim…

Robert Sapolsky: You’re right. On the one hand, it seems obvious to me and to most scientists thinking about behavior that there is no free will. And yet it’s staggeringly difficult to try to begin to even imagine what a world is supposed to look like in which everybody recognizes this and accepts this.

The most obvious place to start is to approach this differently in terms of how we judge behavior. Even an extremely trivial decision like the shirt you choose to wear today, if dissected close enough, doesn’t really involve agency in the way we assume. There are millions of antecedent causes that led you to choose that shirt, and you had no control over them. So if I was to compliment you and say, “Hey, nice shirt,” that doesn’t really make any sense in that you aren’t really responsible for wearing it, at least not in the way that question implies.

Now, this is a very trivial thing and doesn’t appear to matter much, but this logic is also true for serious and consequential behaviors, and that’s where things get complicated.
Maybe he cannot freely choose his shirt, and if he says that he cannot, maybe I should believe him.

But when he says that it is obvious to most scientists that no one can exercise any choices, I have to wonder. Are there scientific papers saying this? How did it get to be obvious? Is it implied by some textbook knowledge?

Maybe this is more a philosophical question than a scientific one, but I object when someone declares some sort of scientific consensus, but it is just an opinion with no data to back it up.

Monday, June 12, 2017

Math Has No God Particle

The 538 blog writes:
“Mathematicians are extremely reluctant to publicize what they do,” Adams said. “The immediate reaction from 90 percent of mathematicians is, ‘It’s too hard, there’s no point in trying to write about this in the popular press.’” ...

This time around, however, there’s been no press release, no pretty picture, no city-size braggadocio, no New York Times story. Adams and his team haven’t trumpeted this latest accomplishment at all. When I reached him at his home, he summarized the milestone plainly, but proudly, in the jargon of his field: “We can now compute the Hermitian form on any irreducible representation.”

Raphaël Rouquier, a mathematician and Lie theorist at UCLA, echoed the ticklish relationship between mathematicians and the press. “There is a general feeling in the pure math community that popularizing mathematics is betraying mathematics,” Rouquier said.
There is some truth to this.

I have posted lately on the special relativity work of Poincare and Einstein, and the public reaction. My suspicion is that part of the difference can be accounted for by Poincare having the personality of a mathematician, and Einstein a physicist.

Poincare was concerned with applied science as much as Einstein, and also with theoretical physics, so it is not obvious that there should be a difference. But Poincare had the intellectual outlook of a mathematician, and Einstein did not.

Friday, June 9, 2017

Einstein did not discover relativity

An anonymous commenter says that I under-credit Einstein for special relativity (SR), and has posted comments challenging me on these recent articles:

Einstein and Minkowski lied about Poincare
Poincare was the new Copernicus
Early work did not credit Einstein
Einstein did not find the group or covariance
Einstein was not the aether slayer
Calling the length contraction psychological

The history of special relativity is a fascinating episode in science. Much of the work was simple and profound, and it was all openly published, so it is clear what everyone did.

The main argument against crediting Einstein is that if you look at all the aspects, almost none of them were done by Einstein. Here is a timeline if the major concepts of special relativity.
length contraction (FitzGerald 1889, Lorentz 1892)
aether is just a convention (Poincare 1889)
first-order Lorentz transformations (Lorentz 1895)
relativistic time (Lorentz 1895)
relativity principle (Poincare 1895)
relativistic mass (Lorentz 1899, experimentally tested in 1902)
constant speed of light (Maxwell, Lorentz, Poincare pre-1900)
light synchronization of clocks (Poincare 1900)
E = mc(Poincare 1900)
full Lorentz transformations (Lorentz 1904)
4-dimensional spacetime geometry (Poincare 1905)
electromagnetic covariance (Poincare 1905)
The arguments in favor of Einstein are mainly that others credited him (with Germans slighting non-Germans), and that Einstein was responsible for some crucial step or insight that others were missing. This insight is never something Einstein actually said, but rather something that supposedly can be inferred from Einstein's famous paper. Or sometimes the credit is for obscure terminological issues.

Einstein was not particularly influential either, as the chain of development went from Lorentz to Poincare to Minkowski to a wide audience, with hardly anyone paying any attention to Einstein.

My biggest problem with crediting Einstein for SR is something else, tho. It is that he never had a modern geometric understanding of the subject.

Here are some interpretations of the Lorentz transformation (LT):
There were three historical formulations of SR, using Einstein's terminology:

Principle theory (FitzGerald 1889, Lorentz 1992, Einstein 1905) The LT is a logical consequence of an interpretation of Michelson-Morley, without much explanation of how it works.

Constructive theory (Lorentz 1995) The LT is explained by motion causing distortions in the electromagnetic fields that constitute our measuring instruments.

Geometric theory (Poincare 1905, Minkowski 1908) The LT reflects the mismatch between Euclidean and non-Euclidean coordinates.

The Michelson-Morley experiment could be interpreted as evidence for (1) a stationary Earth; (2) an emitter (non-wave) theory of light; (3) an aether drift theory; or (4) the relativity principle combined with a constant speed of light. FitzGerald and Lorentz reject the first 3 possibilities based on other experiments, and were led to option (4). They then deduced the LT as a logical consequence of those principles. ...

Einstein preferred the principle theory formulation that he got from Lorentz. The Einstein idolizers rave about how great this was, but geometric theory has been the dominant one among theoretical physicists since 1908.
I would call these interpretations top-down, bottom-up, and geometric.

The argument that the LT is a logical consequence of principles deduced from Michelson-Morley was first outlined in AAAS Science (the USA journal) by FitzGerald in 1889:
I would suggest that almost the only hypothesis that can reconcile this opposition is that the length of material bodies changes, according as they are moving through the ether or across it, by an amount depending on the square of the ratio of their velocity to that of light.
FitzGerald (and Lorentz) do use the archaic term "ether" (or aether), but Einstein similarly uses the term "stationary" dozens of times in his famous paper with similar epistemological problems.

FitzGerald wrote to Lorentz in 1994:
My dear sir,
I have been for years preaching and lecturing on the doctrine that Michelson's experiment proves, and is one of the only ways of proving, that the length of a body depends on how it is moving through the ether. ...

I am particularly delighted to hear that you agree with me, for I have been rather laughed at for my view over here. I could not ever persuade my own pupil Mr. Preston to introduce this criticism into his book on Light ... [as quoted in paper by Stephen G. Brush]
Einstein used a similar top-down argument in his famous 1905 paper, without mentioning Michelson-Morley, FitzGerald, or Lorentz explicitly. He later said that he was not rejecting the constructive (bottom-up) approach, but could not get it to work.

The essence of special relativity is that it puts physics on a 4D non-Euclidean geometry. That is what made the theory so important to XX century physics.

What Einstein fails to give is the geometric approach. He does not imply it either, as he always denied a geometric interpretation. In 1911 someone asserted that Lorentz and Einstein had different interpretations of the length contraction, and Einstein denied that there was any such difference. See Wikipedia. He even denied that general relativity geometrizes gravity in 1925.

While Einstein was writing that 1905 relativity paper, Poincare was submitting a paper that had everything Einstein had, and plus the geometric version of the theory. Poincare had the 4D spacetime, the non-Euclidean metric, the symmetry group, the electrodynamic covariance, and the broad vision of spacetime physics that was so important in the XX century.

While most physicists did not read or understand Poincare's paper, Minkowski read it, and spelled out the geometric version of SR in widely accessible terms. Then everyone got excited, and research papers on SR exploded. Some physicists may have thought that Einstein had something to do with progress in relativity, because Einstein and Minkowski refused to credit Poincare, and because Minkowski and Poincare soon died.

One reason the geometric version of SR was so exciting was that it solved the problem of how causality can be reconciled with mechanics. Physicists since Newton had been haunted by what appears to be action-to-distance. The Poincare-Minkowski geometric SR showed that non-Euclidean geometry is the key to understanding that causality takes place withing the light cone.

Poincare showed in 1905 that SR allows gravity theories where gravity propagates at the speed of light. This had been an unsolved problem for centuries. Poincare creates the non-Euclidean geometric view specifically for this purpose. Minkowski elaborated on this much more clearly, and this idea is the basis of all XX century notions of causality.

Einstein missed all of this. He wrote relativity review papers saying "union of Lorentz's theory and the relativity principle" in 1908 and "the essence of Lorentz's theory ... can be reconciled with the relativity principle" in 1909. That is, he affirmed his agreement with how Lorentz reconciled electromagnetism with the relativity principle. He made no mention of the causality or non-Euclidean geometry or covariance that Poincare and Minkowski had spelled out a couple of years earlier. While he always jealously tried to make sure that he got credit for his work, he made no attempt to argue that Poincare and Minkowski were using his ideas, or that he had independently discovered those ideas, or even that he understood or appreciated them. It is preposterous that he is often credited with those ideas today, because he had nothing to do with them.

Wednesday, June 7, 2017

Calling the length contraction psychological

I have been claiming that no one saw any difference between Lorentz's and Einstein's versions of special relativity, until differences were falsely invented many years later. Most papers referred to special relativity as "Lorentz-Einstein theory". Lorentz and Einstein just had slightly different ways of saying the same thing. As Lorentz explained, Einstein had a simpler presentation because he assumed as postulates what Lorentz and Poincare had deduced from accepted theory and experiment.

The first paper I found drawing a sharp difference is On Ehrenfest's paradox, by V. Varićak, 1911:
The occurrence of Ehrenfest's paradox is understandable, when one clings to the standpoint taken by Lorentz in the formulation of his contraction hypothesis, i.e., when one sees the contraction of moving rigid bodies in the direction of motion as a change which takes place in an objective way. Every element of the periphery will be changed independently of the observer according to Lorentz, while the elements of the radius remain non-contracted.

However, if one employs Einstein's standpoint, according to whom the mentioned contraction is only an apparent, subjective phenomenon, caused by the manner of our clock-regulation and length-measurement, then this contradiction doesn't appear to be justified.

That Ehrenfest took the Lorentzian standpoint in his argumentation is concluded by me from ...

I allude e.g. to the work of Lewis and Tolman[2], who especially emphasized the radical difference in the views of Lorentz and Einstein. There one can also see, by which considerations the stationary observer is forced to assume the contraction of the moving rod. But he remains conscious, that this contraction is so to speak only a psychological, not a physical fact, i.e., that the body experienced no change in reality.
He refers to this 1909 paper, which mostly treats Lorentz and Einstein as having the same theory but adds:
When Lorentz first advanced the idea that an electron, or in fact any moving body, is shortened in the line of its motion, he pictured a real distortion of the body in consequence of a real motion through a stationary ether, and his theory has aroused considerable discussion as to the nature of the forces which would be necessary to produce such a deformation. The point of view first advanced by Einstein, which we have here adopted, is radically different. Absolute motion has no significance. Imagine an electron and a number of observers moving in different directions with respect to it. To each observer, naïvely considering himself to be at rest, the electron will appear shortened in a different direction and by a different amount; but the physical condition of the electron obviously does not depend upon the state of mind of the observers.

Although these changes in the units of space and time appear in a certain sense psychological, we adopt them rather than abandon completely the fundamental conceptions of space, time, and velocity, upon which the science of physics now rests. At present there appears no other alternative.
While this might seem like a deep insight on how Einstein had a superior understanding, Einstein denied that there was any such difference:
The author unjustifiably stated a difference of Lorentz's view and that of mine concerning the physical facts. The question as to whether length contraction really exists or not is misleading. It doesn't "really" exist, in so far as it doesn't exist for a comoving observer; though it "really" exists, i.e. in such a way that it could be demonstrated in principle by physical means by a non-comoving observer.[20]
Lewis, Tolman, and Varicak are making a legitimate point about how the FitzGerald length contraction can be interpreted, and how such an interpretation could be different from Lorentz's. But their interpretation cannot be attributed to Einstein, as you can see from his denial. Einstein's interpretation was the same as Lorentz's, and Einstein's papers never drew the distinction described in the above papers.

Calling the length contraction "psychological" is not the best term, but what these papers are saying is that the contraction is a property of the coordinates being used on spacetime, and not of the physical object. That view was presented by Poincare in 1905 and Minkowski in 1908, but Einstein still did not seem to understand or accept it in 1911.

Monday, June 5, 2017

Aaronson rejects reductionism

I submitted an essay to FQXi
Dissecting Human Social Purpose
Science is remarkably successful on many fronts, but has failed miserably on matters of freedom, consciousness, and purpose. ...

Reductionism cannot explain freedom ...
It was rejected without explanation, but presumably because I used some political examples that offended the folks at FQXi.

Now Scott Aaronson draws on current politics to post this:
Despite everything I said above, the real purpose of this post is to announce that I’ve changed my mind.  I now believe that, while Hoel’s argument might be unsatisfactory, the conclusion is fundamentally correct: scientific reductionism is false.  There is higher-level causation in our universe, and it’s 100% genuine, not just a verbal sleight-of-hand.  In particular, there are causal forces that can only be understood in terms of human desires and goals, and not in terms of subatomic particles blindly bouncing around.
Wow, I actually agree with him, altho his political examples are much different from mine.

My essay was based on me similarly changing my mind against scientific reductionism in favor of human causal forces.

Friday, June 2, 2017

Maudlin accepts the reality of time

Tim Maudlin says, in defense of the reality of time:
People often say, “I’m forced into believing in a block universe because of relativity.” The block universe, again, is some kind of rigid structure. The totality of concrete physical reality is specifying that four-dimensional structure and what happens everywhere in it. In Newtonian mechanics, this object is foliated by these planes of absolute simultaneity. And in relativity you don’t have that; you have this light-cone structure instead. So it has a different geometrical character. But I don’t see how that different geometrical character gets rid of time or gets rid of temporality.

The idea that the block universe is static drives me crazy. What is it to say that something is static? It’s to say that as time goes on, it doesn’t change. But it’s not that the block universe is in time; time is in it. When you say it’s static, it somehow suggests that there is no change, nothing really changes, change is an illusion. It blows your mind. Physics has discovered some really strange things about the world, but it has not discovered that change is an illusion.
I agree with him on this.

Here is an example of the block universe view:
For instance, Brad Skow adopts the “block universe” concept arising from Special Relativity and concludes that time doesn’t “pass” in the sense of flowing; rather, “time is part of the uniform larger fabric of the universe, not something moving around inside it.”
Here is another:
Relativity convinced most physicists that we live in a “block universe” in which past, present, and future are equally real. In that case, there’s no reason to suppose the past influences the future, but not vice-versa. Although their theories shout retrocausality, physicists haven’t fully grappled with the implications yet.
This is nonsense, of course. Relativity is all about how the past influences the future. A central premise is that all causality is within light cones.

It would be easier to deny the reality of time with pre-relativity physics. That allowed action-at-a-distance, and violated intuitions about causality. One could believe that planetary orbits were determined independently of time.

Bertrand Russell got this backwards in 1913. Many ppl still get it backwards. Glad to see Maudlin get it right.