I will use the results of the MAGIC experiment as an example to show the difference between fair and rational reasoning on one side and irrational bigotic propaganda, represented by Peter Woit, on the other side.
Lorentz violation: basic facts
Einstein's special relativity published in 1905 became one of the key pillars of modern physics. It unifies space and time and includes the Lorentz symmetry, an invariance under transformations mixing space and time, that severely constrains allowed laws of physics. Indeed, special relativity is a meta-theory that tells us that certain classes of laws of physics don't even have to be considered.
Since 1905, good "fundamental" physicists have only considered Lorentz-invariant theories. That's the reason why Schrödinger needed some more time to find his equation: he found the relativistic Klein-Gordon equation first. He saw that it didn't describe the Hydrogen atom correctly. So he didn't publish the equation - guess who published it first - and decided to solve an easier task and find the non-relativistic approximation of the right equation that is named after him. Dirac soon realized what is the right relativistic equation anyway. Soon after Dirac, quantum field theory was born and it was always relativistic i.e. Lorentz-invariant. String theory didn't break the symmetry either.
Is special relativity true? According to all observations we have, it is true and exact. The effect of all hypothetical violations of special relativity on any phenomena that can be realistically observed may be summarized by Lorentz-breaking terms in the effective action. Experiments show that these terms are zero or at least extremely tiny: the bounds are very stringent.
Can we imagine that special relativity is not exactly true? Even though it looks like returning before 1905, the answer is: Yes, of course, we can. Just add the small symmetry-breaking corrections. Can these hypothetical corrections be associated with other physical phenomena? Maybe. If they're associated e.g. with the quantum gravity scale, you may obtain an order-of-magnitude estimate how large these violations should be.
This violation is an assumption that has been made by many people such as Nanopoulos, Mavromatos, Sarkar, Amelino-Camelia, Mitsou, Farakos, Ellis, Kostelecky, Samuel, Pospelov, Myers, Alfaro, Morales-Tecotl, Urrutia, and others. Quite many people for this non-result, frankly speaking. ;-) It's been repeated by many other people. Later, the same scalings were argued to be compatible with loop quantum gravity but no rational justification of this assertion is available. The people who gave this interpretation just wanted to be parasiting on the work of others. For example, Smolin's implicit assertion that he has done something important in the context of Lorentz violation is a lie.
Also, the statement that "doubly special relativity" can give some constraints on physical theories that are somewhere in between broken and unbroken Lorentz invariance is mathematically flawed. There doesn't exist any set of conditions restricting a theory that would be somewhere in between. A theory is either Lorentz-invariant or not. Everything else that you can read in the media is a result of sloppy maths or an attempt to confuse the public (and sometimes the authors themselves).
An order-of-magnitude estimate leads to a specific prediction of the magnitude of these Lorentz-violating effects. But do these effects actually exist? Are they nonzero?
According to string theory, the only consistent theory of quantum gravity we know, these effects don't exist. That's a consequence of the equations of string theory as I understand them. Even in general quantum gravity, the local Lorentz symmetry is a crucial ingredient in the whole framework. Needless to say, most string theorists agree. If we're right, these Lorentz violations can't be used to test quantum gravity. Testing quantum gravity is as hard as the normal dimensional analysis applied to proper distances suggests - it is extremely hard. Every sane person who has been doing quantum gravity for years knows that it is probably hard to test it experimentally and theoretical work is inevitably dominant in this field. But it is a theoretical research about questions that obviously make sense in principle.
Even though some people haven't yet noticed, mathematically heavy work has been the most important part of theoretical physics for more than 350 years.
But whether most string theorists agree or not is scientifically irrelevant. We don't have the full answer to everything and we might be very well wrong and the list of people above who have written vague, mathematically loose papers may be right. If experiments show that the Lorentz invariance is violated exactly in the Nanopoulos-like way and if a more complete theory emerges or if it is even reconciled with the detailed rules of string theory, then we will have to shut up. We will be proved wrong. Prof Nanopoulos is surely not among the most respected string theorists even though he is in the top 5 of most cited particle physicists. But that doesn't mean he can't be right.
In the same way, if experiments demonstate a marriage of loop quantum gravity and doubly special relativity controlling our Universe, we will also have to shut up. So far it is not even clear what the previous sentence could possibly mean. But someone may give it a meaning in the future and experiments could hypothetically confirm this meaning: it is just superextremely unlikely right now.
Some people just don't seem to be capable to understand this basic mechanism of science: evaluating hypothesis by looking at more detailed evidence.
The four-minute delay seen by the MAGIC collaboration is exactly of the right magnitude that could be derived from Lorentz-violating effects suppressed by the string scale (which is close to the Planck scale). So if Nanopoulos, Mavromatos, and Ellis really believe their scenario, they must be pretty excited. I am not that excited because I think that this effect will be explained by local dynamics of the source and their explanation will go away. The four-minute delay is also of the same magnitude as the duration of the flare itself which suggests a local explanation. Most likely, one of us is right and the other is wrong. More precisely, I am right and Nanopoulos is wrong but unless you copy the whole content of my brain into yours, you can't really know it for sure at this moment. ;-)
Improving MAGIC experiments
Is there a way to decide? Sure, there is. Repeat similar observations with other, more distant galaxies. Try to increase the delay relatively to the length of the flare. If their ratio can be increased and if the scalings quantitatively agree with a Nanopoulos-like theory, all of us will have to pay some attention to their so-far unusual and so-far unconvincing theories. If the delay is always comparable to the length of the flare, it means that the origin of the delay is local in character. The delay of the high-energy gamma rays has something to do with the source.
That either means that the high-energy gamma rays are emitted after the low-energy ones - for example because the electrons that emit them are slower at the beginning of the flare and gradually accelerate - or it means that the high-energy gamma rays arrive from a greater region because of some dispersion or scattering (this hypothesis predicts a wider spread of the high-energy gamma rays). At any rate, experimenters can converge towards the right answer in a finite amount of time. There is absolutely nothing untestable about this situation and only complete morons could suggest that the hypotheses here are untestable.
Pragmatic unions of theorists and experimenters
The only thing that I find morally problematic about the recent paper is that those 100+ experimenters were forced or convinced to believe and promote a particular theoretical explanation that is prominently featured in their paper. I don't believe that these 100+ experimenters universally started to believe that this explanation is correct or likely, especially because the same team of 100+ people has published a previous paper with a completely different explanation half a year ago.
That's why I think that the theorists should have written their interpretation of the MAGIC data separately from the experimenters. There has been no real collaboration here: there was just a pragmatic coalition in which the theorists were used to make the experimental results sexier than they are. The theorists' interpretation became more visible, too, because of the visibility of the large experimental team. I think that similar papers that are really composites of two unrelated research programs should be published separately.
If the paper were properly divided, I would find nothing morally bad about it. The only bad aspect of the theoretical paper is that it is probably wrong, I think - but in science, it is not a crime to be wrong. Being wrong for some time, or at least the right to be wrong, is a necessary step in the scientific approach to questions.
Peter Woit doesn't write a single sentence about the scientific topic itself. That's not hard to understand. The reason is that he has no idea about physics whatsoever. He doesn't have a clue whether string theory or loop quantum gravity predicts Lorentz violation and how large this violation is supposed to be. He doesn't know what string theory means. He has no idea about the alternative, conventional explanations of the observed delay either. He hasn't done a single calculation in his life that would be relevant for answering any of these questions.
Suddenly, he refers to the authority of string theorists including Jacques Distler and your humble correspondent who have said that string theory exactly implies local Lorentz symmetry. When did it happen that we became such authorities for Peter Woit so that our words can be used as reliable ingredients of Woit's "precious" conspiracy theories?
Instead of looking at physics, Woit is irritated by a Slashdot headline that says that this anomaly could test string theory. The Slashdot headline is clearly correct. If this experiment really measured Lorentz-breaking terms in the effective action suppressed by the Planck scale, it would surely say a great deal about string theory to the string theorists and about quantum gravity to all researchers in the field of quantum gravity. We would immediately start to ask detailed questions - how these terms actually look like and what is their origin. We would suddenly consider these far-fetched vague papers by Nanopoulos et al. in a more serious light. Things would change. If this ambitious interpretation is refuted, we will learn something, too. It will only be less surprising. ;-)
Every sane person knows that testing quantum gravity is probably difficult but certainly possible in principle. And if there are effects that influence long-distance physics, such as these Lorentz-violating effects, then testing quantum gravity is not only doable in practice but it will be done in the near future.
Peter Woit has written about 591 nearly identical blog postings. In each of them, he repeats the same lie - the same idiocy - that string theory can't ever be tested. He relies on Goebbels' rule that if a lie is repeated 591 times, it becomes the truth. And indeed, there exist hundreds of ignorants and morons who keep on reading the junk that he keeps on producing. Woit is scared by any indication of progress in science because his goal is exactly the opposite. His goal is nothing else than the destruction of theoretical physics.
While I am happy that George Musser blogging for Scientific American has understood how Woit has been working in this case, I am always flabbergasted by the stupidity of the people who still haven't understood, after more than 3 years, that Woit's writings are 100% vitriolic junk that has nothing to do with science. They haven't understood that Woit has no idea about science whatsoever and the only thing that he is doing is to invent emotional and usually hateful fairy-tales about the sociology of every event in science, fairy-tales that are consistent with his primary idiotic opinion, namely his opinion that modern theoretical physics is no science. Every other drunk hateful high-school student would be able to do the same thing as Mr Woit.
Woit only repeats selected quotes of others and gives them an anti-string-theoretical flavor and spin. He never offers any meaningful idea himself. This is my theory how this primitive animal works. It is a falsifiable theory: show me a single text written by Woit that disagrees with my thesis if you want to falsify it.
It seems to me that you don't have to understand any physics if you just want to understand why Peter Woit's "work" is pure garbage. Just look at his postings: there is not a single physics-related idea, and if there is one, it is always copied from a convenient "authority". What he cares about is to transform people into fanaticized imbeciles - imbeciles who are never willing to learn the truth or understand details about any question. Imbeciles who can't listen and who only know how to attack and intimidate people whose IQ is roughly 40-60 points above the imbeciles' IQ.
I must tell you: these aggressive imbeciles have already intimidated a huge portion of smart people - scientists who are afraid to say what science has actually found because they would be instantly attacked by Woit and his trash fan club. Unless we do something about this scum, they will soon control the whole scientific community.
And that's the memo.
Update: Despite his proclamations, I am in no agreement with the critic of science about any essential question here. At the level of accessible experimental data, this experiment is compatible with the Lorentz-breaking explanations. Woit disagrees. I think that further observations can easily figure out which explanation is correct. He doesn't. I think that the Slashdot headline was fine. He doesn't.
I think that it is string theory that allows us to predict that the explanation will be conventional. He doesn't. I want to know the right answer as chosen by Nature regardless of our preconceptions. He doesn't. I think that minorities or individuals may be right. He doesn't. I am making a prediction based on my knowledge of physics. He doesn't. Instead, he chooses his "answers" to fit his dirty agenda. He chooses whom to agree with in such a way to maximize the hormones behind his jihad against theoretical physics.
You can't use the word "agreement" for any binary similarity between the man's assertions and science. Even a stopped clock tells the right time twice a day. He doesn't have any of the correct reasons or methods to find the answers. It is not my fault that my best judgement has a binary similarity with an anti-theoretical-physics agenda in individual questions. And frankly speaking, I don't care about it and I am not influenced by it. That's not how I use my brain to make decisions. I am not choosing answers to questions in order to agree or disagree with a particular irrelevant parody of a human being. I am choosing my opinions by rational arguments.