## Monday, July 30, 2012

### The human machine: different models

The previous post in this series can be found here.

You may have noticed, but we're holding a little sporting shindig here in London over the next two weeks that's got everyone rather excited. I myself am going to be spending a lot of time shuttling back and forth between the Olympic park and my house in Oxford and most of the rest of the time glued to my laptop watching as many sports as is humanly possible! Thanks to this busy sporting schedule, this week's post will be somewhat shorter than some of my others in the past, but I hope you still find it interesting. You may think, dear reader, that I will be shirking my scientific duties by devoting myself so fully to the Olympic smorgasbord but my enthusiasm is born out of pure biochemical curiosity and the sporting element is, I can assure you, wholly secondary!

How does biochemistry fit into the greatest show on Earth, you may ask? How does it not, I would respond! All of the athletes competing in this year's games have spend years training to improve their body's biochemical response to stress and physical exertion in order to fulfil the Olympic ideal of 'faster, higher, stronger'. In my last post of this series I described the molecular processes that allow muscle contraction and in the preceding post I talked about how energy is processed within your cells to produce the 'energy currency' of your post: ATP.  In this post I will bring these two topics together and discuss how energy is regulated in different muscle types and how the biochemical situation varies hugely between the 100m and the marathon.

## Monday, July 23, 2012

### Worshipping the funding mountain

It was announced last week that an anonymous benefactor is to donate £20 million to be split between the University of Southampton and Cancer Research UK (CRUK), which will conduct its work in the new Francis Crick Institute, currently under construction in London. This money is going to be used primarily in the advancement of cancer immunotherapies, a branch of cancer treatments in which the patient's immune system is harnessed to fight cancerous cells. I wrote briefly about the use of the immune system in the fight against cancer in a post a few months ago, but since this field is now in the spotlight (in the UK, at least!) I thought I'd give you a short update on the kind of work that's being done and why £20 million is significant.

Targeting the traitors

Cancer, as you're probably aware, is the condition that arises when an individual cell or subpopulation of cells accumulates sufficient mutations in the genes that control cell division as to become rogue entities within the body - replicating indiscriminately and dangerously. As a species we are highly susceptible to cancer because we just live so damn long and generally don't die from the things that kill most other species (hunger, illness, predators etc.), and finding effective treatments remains one of the major goals of medical research. If  a cancer forms a tumour and stays like that then treatment is simple surgery to remove it and is highly effective. The killer scenarios are either when tumourous cells metastasise and circulate in the body as individual cells, establishing too many new tumours to be removed; or when the original cell is one that does not form a tumour, as is the case for leukaemia or lymphoma. In these cases, chemotherapy or radiotherapy is commonly used to attack the cancerous cells but often ineffectually and almost always with nasty side-effects. The idea behind cancer immunotherapy is to nudge the immune system into attacking these cancerous cells, thereby clearing the disease with minimal damage to other tissues.

## Tuesday, July 17, 2012

### Why don't more scientists enter politics?

Michelle is right in the middle of moving from the landmass somewhere west of Portugal to the medium sized set of islands lying somewhere in the southern Pacific Ocean. She begins this week a resident of the state that has this man in charge of science policy and ends it a resident of the state with this man in charge of science policy, so good luck to her on her travels and congratulations on the repatriation.

These travels mean she hasn't had time to write something for this week, so I shall fill the gap. I didn't have anything sitting in the hard-drive waiting to be posted. What follows instead is some thoughts on an issue that anyone who knows me in the real world will recognise as something I regularly rant about. One day I will write a more carefully worded (and thought out) post on this issue, but, for now, pseudo-stream of consciousness is what you get.

Why don't more scientists enter politics?

That's not meant to be a rhetorical question. If anyone knows the answer(s), please tell me in the comments.

Scientists (especially physicists) are highly opinionated. We like to tell people our opinions (hence all the blogs). Even more specifically, many scientists are highly opinionated about politics and we like to tell people our opinions on politics quite often. We lament particular policies the government of the day are implementing. We complain about the conditions set by government funded research agencies, claiming that we know how to do it better. Why don't more of us enter politics?

Apparently, in the current British House of Commons, there is one scientist, Julien Huppert, the Liberal Democrat MP for Cambridge. Margaret Thatcher was a scientist before she became a politician. So was Angela Merkel. However those two are exceptions to the rule. Why is this the case?

In many other fields, politics is a well known, accepted career path. Lawyers, journalists, writers, people from the business world and school teachers, just off the top of my head, are all fields where there is a clear path to politics (or at least, many people choose to take that path). However, science is an equally important part of politics. Climate change, nuclear power, the technology industry, tertiary education; all of these things are either a subset of science or are at least heavily dependent on scientists to exist, and all of them are important aspects of the modern political world. Why aren't there scientists in the parliaments around the world helping to make the decisions that impact upon those spheres?

Why aren't more of the ministers of science of the world scientists? One notable exception to this is the physicist and Nobel Laureate Steven Chu who happens to be Obama's secretary of energy. Looking back over past U.S. Secretaries of energy, Chu, and his predecessor Samuel Bodman, are also the exceptions to the rule. I appreciate that another requirement for a science minister is an understanding of law; however science is equally hard to pick up an understanding of as law. I'm not more comfortable with science ministers that are lawyers relying on advice about science than scientists who are receiving advice about law

All of the above makes me wonder. And it isn't like scientists are just choosing to engage with politics in other ways (well, to a small degree they do engage in other ways - but not nearly as much as other fields). Very few (although not zero) join political parties and those that do would very rarely try to take an active role in influencing a party's policy. But, there is another point here that causes this situation to really confuse me. Most people with doctorates in a science subject, don't end up as practising scientists. There just aren't that many jobs in science, especially in pure research jobs, but even in science based industrial jobs. Why isn't some proportion of the people who start out in science, but for one reason or another don't stick with it, not ending up in politics? All those other fields do it.

People I went through both undergraduate and postgraduate study with were well aware of finance and management consulting (etc.) as possible careers should the physics fall through or fail to inspire; why not politics?

If anyone has some thoughts and/or links on this, I'd love to read them. I will write a more thought out and detailed post on this before the end of the year, so any fodder you can give me now would be nice. In the meantime, if you're a scientist with political opinions of any persuasion, go join a party that matches that persuasion, attend their meetings and advocate policies that make scientific sense. And, convince your peers to do the same.

## Monday, July 9, 2012

### Why do galaxies rotate?

[Note from Shaun: The following is a guest post from cosmologist Bjoern Malte Schaefer, who works at the University of Heidelberg. He also writes at the blog, Cosmology Question of the Week, which, although aimed at undergraduate and postgraduate students of cosmology, is worth a look for everyone.]

 Image illustrating why there is a relationship between angular momentum direction and inclination angle (and hence  the apparent shape of a galaxy)

Why do galaxies rotate?

Galaxies rotate, every child knows that. Looking at the images of grand spiral galaxies it is quite suggestive to think how all the stars and gas that make up a galaxy all move in a more or less orderly fashion about the galaxy's centre. However, when we think about mechanisms through which galaxies can acquire angular momentum the matter seems very obscure: how do they start rotating in the first place?

The formation of cosmic structure, including galaxies and the larger clusters and superclusters in which they are embedded, is a fluid mechanical phenomenon, where gravity is the only force acting on the  distribution of matter on large scales. It is in fact gravity that amplified the tiny fluctuations present in the primordial distribution of matter that filled the early Universe (matter here means mostly cold dark matter) and caused them to evolve into the large-scale structure that we observe in the present Universe. These tiny fluctuations grew by self-gravity: a region in the matter distribution that is slightly denser than its surroundings generates a gravitational pull and accumulates more matter, hence its density increases with time.

At first sight it is very difficult to imagine how gravity could introduce rotation. After all, on the scales of cosmic structures, gravity is well approximated by the scalar Newtonian potential, which is parity invariant and does not possess any chirality: At which point would a galaxy in the forming decide whether it should rotate clockwise or counterclockwise? The answer to this lies in a process called tidal shearing, which consists in a misalignment between the tidal forces (the second derivatives of the gravitational field) and the moment of inertia of the protogalaxy (the second moments of the matter distribution). The meaning of these technical terms can be explained quite easily: Imagine a curling stone sliding along the sheet, where the ice surface on its left side is a bit smoother compared to the right side. The stone will be set into clockwise rotation by this difference in force. For a protogalaxy, it is the variation in gravitational force moving the galaxy along that introduces rotation, and is responsible for the galaxy's angular momentum.

## Wednesday, July 4, 2012

### A Higgs Hunter's story...

[Note from Shaun: Here is Higgs hunter Mikko Voutilainen's account of the recent search for the Higgs. You can find the teaser to this post here. And my own, partially cynical, but ultimately upbeat, account of Higgs-things, here.]

Here it is, finally

[I assume the readers of this blog are somewhat familiar with the Higgs boson; if not, there's a nice summary on the CMS pages here]

So, this is the follow-up to the teaser I wrote a week ago. Now that everybody knows we found a Higgs boson at $$125.3\pm 0.6$$ GeV, I'm free to talk about our finding, what it means and how we got there. Note the intentional use of 'a' Higgs there: although we, beyond reasonable doubt (less than one in a million chance of an error, to be precise), found a new particle, it's not 100% sure yet if it's *the* Higgs boson predicted by the standard model, or one of its many twins predicted by the hundreds of theories out there. There's even a tiny chance of it being an altogether different particle yet.

We actually already know a fair deal about this new particle besides the rather impressively precise estimate of its mass: it seems to be produced at a rate that matches the standard model prediction within about 20% uncertainty, it decays into bosons (W, Z and photon) and fermions (b-quarks and tau-leptons) roughly in the ratios predicted by the standard model, and in particular it decays into W and Z bosons in the ratio predicted by the standard model. The last point is rather important, because the Higgs mechanism, and the Higgs boson along with it, was invented to give mass to the W and Z bosons, and leave the photon massless. This also fixes the ratio of the decay rates to W and Z. If the new particle didn't decay into Z's and W's in just the right ratio, it couldn't be the Higgs boson we predicted.

We've also had a stab at determining the more abstract properties of the particle such as a quantum number called parity, but the statistics are low and the results still inconclusive. Predictions say we should be able to tell by the end of the current run, when we've collected 2--3 times the amount of data we have now. At this point we should also have more precise determination of the particle's decay rates in all the different channels, in order to gain more confidence in calling the particle a Higgs boson or something else.

So, is this the end, or the beginning of something new? I'm really hoping for the latter. If the new particle turns out to be 'just' the standard model Higgs boson and there's nothing new to be found, that would be fairly boring. If instead it's a Higgs twin, we may have just opened a window into a new landscape of particles.

At the moment it's too early to tell for sure, but there are a few interesting features to the way the new particle decays. It seems to decay into photons more often than expected, and to tau-leptons less often than expected. Taking all the decays to fermions together, they only seem to add up to about half of the rate predicted by the standard model, albeit with an error of about 50% as well. That coincidence is causing a bit of excitement nevertheless.

It might not be too bad for the standard model, though, it could just indicate that it's 'non-minimal'. While the Higgs coupling to W and Z is pretty tightly constrained, all the other particle masses are more of an ad-hoc addition to the theory, and there's some freedom to adjust how these particles couple to the Higgs boson without breaking everything else. Another good example of something that would require a 'non-minimal' standard model are the neutrino masses, which in the simplest expectation are exactly zero. We now know they are not zero, although we've still to nail down exactly how much they weigh (it's very very little in any case).

What for me was most interesting in this was to see first-hand how things have evolved towards a big discovery. Things started rolling about six months ago, when the first results from LHC Higgs boson searches were presented last December. Back then both ATLAS and CMS saw a hint of a Higgs at 125 GeV, with about 2-2.5 sigma statistical confidence. If you were a Higgs-believer, you could have given the signal more than 95% chance of being true.

After December it was decided that we wouldn't look at the 2012 data in the signal region before we had enough to confirm or refute the hint seen in 2011. This process is called blinding, and its important for making sure the analyzers are not unconciously affected by their prior expectations. Blinding is also one of the reasons we've tried to keep a lid on the results until today's seminar so that the experiments would not affect each other's findings between opening their signal box opening and presenting the final results. I think we were fairly successful in the end, although rumors started circulating on the blogs within days, and by yesterday almost every major newspaper (including Nature) had run a story on Higgs.

Between opening the signal box and seeing the first evidence of a new particle there was a whole lot of work going on for 2--3 weeks to prepare for ICHEP. The analyses added around 50% more data, the particle properties were studied in more detail, the CMS management had regular meetings with both ATLAS and CERN directors, people were working day and night to scrutinize the results, prepare documentation, etc. The final days were spent polishing plots, rehearsing presentations and fine-tuning press releases. Although I didn't happen to be at CERN during that period (I did attend the signal box opening in the beginning, though), I could at least participate through the almost daily video meetings and by keeping my own small piece of CMS running (I'm responsible for a team calibrating jets).

Just two days prior to the seminar there was also a presentation of the Tevatron Higgs results at Fermilab. The Tevatron people had done a superb job in squeezing every last bit of sensitivity out of their data and fell just a hair's width short of claiming evidence for the Higgs (they got 2.94 sigma by the most optimistic count, and needed 3.0). The Tevatron experiments collected data for ten years before shutting down last summer, and have the same amount of data (10 fb-1) available for analysis as the LHC experiments now. The lower collision energy of the Tevatron, 2 TeV versus 8 TeV at LHC, means roughly ten times less Higgs bosons are produced, but they still have better sensitivity in one single channel, the Higgs decaying into two b-quarks. I was watching that live on video, too, cheering for my old colleagues (I did my PhD on D0, one of the two experiments at the Tevatron).

And then, finally, today we had a chance to see how our colleagues and rivals at ATLAS were doing with their Higgs search. According to blog rumors, newspaper leaks and sensitivity estimate just a tad behind CMS, but never far. As it turned out, both CMS and ATLAS came up with the same significance in the end, within 0.1 sigma precision. Both experiments have now just made it to the 5-sigma milestone, and it's pretty clear that the signal has been effectively confirmed by at least three experiments (counting D0 and CDF together as a single Tevatron experiment).

P.S. I wrote a lengthy story about the box opening the same evening when I was at CERN, and stored it on a time capsule on my e-mail account. I'm not sure if it's interesting anymore, but at least I shouldn't be breaking any confidentiality rules by releasing it. [Shaun speaking: I now have this item in my possession, so if anyone wants to see it please let me know and I will upload it in a few days.]

## Tuesday, July 3, 2012

### On its own, a Higgs discovery would be grim (II)

[...continued from yesterday]

This is like, instead of mapping the entire globe, the ocean explorers found that they had simply reached the edge of all navigable land, and, as far as any vessel could see, beyond that, there was just apparently endless ocean. The explorers would know, from measuring the curvature of the Earth, that Earth was a globe and had a finite extent, but the radius of the Earth would be so enormous that they would never be able to come close to traversing it by boat. It would also be as if, on the last few islands this civilisation discovered, there were all sorts of indications that there must be new land out there somewhere. Only there was no way of knowing where, or how far away, it was. The Higgs, for these explorers, would be one, last, island, discovered far into the wilderness of this ocean, farther from the mainland than anything else except the top quark (another island, alone in the wilderness). To reach either island would require the finest ship imaginable and would require a journey of decades.

 The Large Electron Positron Colllider (most accurate measurer of the precision electroweak parameters)

Such a civilisation would be left to wonder, 'what is it that is out there in that wilderness?' But, they would be unable to answer their question until the invention of the aeroplane hundreds of years later. The next land might be just over the horizon, or it could be on the other side of the globe. This world, is where particle physics will find itself if the LHC finds the Higgs and nothing else.

The LHC's great, great grandparent in this journey of exploration was Ernest Rutherford who fired alpha particles at gold and discovered the atomic nucleus. Where Rutherford was the first of this kind, the LHC (or ILC) might be the last. For just over 100 years, collision experiments have been one of the driving forces of fundamental physics. The photos interspersed throughout this post show a collection of some of the more famous colliders during this period. But, just as the days of the ocean explorer had to eventually come to an end and the romantic tales of discovery that came with them ceased to be written, so might we have to fare colliders well and accept that the Higgs is the last of its kind.

If such an event occurs, a thought should be spared for all the map-makers of this oceanic world (the theoretical physicsists of the last thirty years), who, for decades, have built ever more complicated maps showing that Higgs island would not be alone. They had fascinating and compelling arguments for why Higgs island should be surrounded by exotic new islands, completely different to anything we've encountered before, many maps even showed new continents. The map-makers will have built entire careers making those maps, but if the islands and continents turn out not to be next to Higgs island, they're simply not there; however much we thought they should be. Of course, these continents may very well still exist, somewhere out of HMS Large Hadron Collider's range, but the map makers themselves would never get the chance to know.

## Monday, July 2, 2012

### On its own, a Higgs discovery would be grim

 Rutherford, with the first ever particle collider

### Why the Higgs is cool

If rumours are to be believed, then, in two days time, CERN will announce the discovery of a new particle and it will be called Higgs. To the degree that the discovery of any new particle is a pretty big deal, this will be a pretty big deal.

To put things into perspective, not only will this be the discovery of an entirely new particle, if the standard model of particle physics is correct, this will also be the discovery of an entirely new fundamental particle. That is, it won't be made up of any constituent pieces. Also, the field that it will be excited from will not have been directly detected ever before. And that's not even it. Other aspects of the Higgs are also completely new. For example, the way it behaves when you rotate it will be unique amongst all the fundamental particles we've discovered so far, which is quite curious because its rotational properties will be the simplest (i.e. it has no spin at all).

So, irrespective of everything I'm about to write I want to first stress the following: the discovery of a Higgs-like particle is pretty damn cool and a great achievement of exploration for humanity.

### Beyond the hype

However, the Higgs is no God particle and it is not the origin of all the mass in the universe (or even a significant proportion of it). No great mysteries of the universe are about to be solved on Wednesday. The Higg's significance in our understanding of the universe is similar to the understanding gained when the last piece of a jigsaw is finally placed in a puzzle. Placing that last piece produces an enormous amount of cathartic pleasure (more so than any other individual piece). But, the image in the puzzle has become clear long before that final piece is placed. The role the Higgs plays in the standard model of particle physics is to break a certain symmetry in nature, the electroweak symmetry. All the other pieces of this broken symmetry have been found, some quite a long time ago.