The human machine: non-standard components

The previous post in this series can be found here.

In a previous post I alluded to the origins of mitochondria, the tiny chemical power plants found within all our cells. These hard-working machines are responsible for aerobic respiration, which is the way in which the vast, vast majority of the energy you use is released from the chemical energy in the food you eat. The way in which they do this is very cool, involving currents of electrons and protons in a manner very similar to standard battery. If you're interested in this then I direct you to my earlier post on this topic here, but in this post I will be discussing a rather odd thing about mitochondria: they're not in fact human...

What do I mean by this? Well, obviously they are, kind of, human since they're inside all of us, they're born with us and die with us, they don't wander off on their own to live an independent life elsewhere. Nonetheless, mitochondria are different to the rest of the machinery in our cells - they have their own genomes, they regulate their own replication, they make proteins their own unique way - in fact they closely resemble lifeforms that we might consider to be evolutionary polar opposites of ourselves: bacteria. That sounds pretty odd, right, that there might be bacteria living inside our cells that somehow want to help us by churning out energy for us to use? Seems pretty implausible, but there is a mountain of evidence supporting it.

If it barks like a bacterium...

Firstly, mitochondria do, kind of, look like bacteria. They are about the right size to be bacteria (0.5-1 micron in length) and have internal structures similar to many bacteria. The main difference is that mitochondria possess two membranes and no cell wall, whereas most bacteria for one membrane and a robust cell wall. The inner membrane of mitochondria is also far more ruffled than most bacteria, creating a much larger surface area - this is highly important for reasons that I'll come to!

Spot the difference: mitochondria on top, bacteria on the bottom. 

The business of ignorance

Those of you who read this blog regularly may well be waiting on a post on the latest developments in stem cell therapy that I promised recently. I want to reassure you that this is coming, don't fret! However, a story has come to my attention of late that made me reconsider the topic of this post. The story has shocked, saddened, and angered me in equal measure and I felt that it needed sharing with you, dear reader, as it is a prime example of why the public engagement of science is a vitally important task. Given Shaun's heroic efforts last month to bring us the news from the latest  Cosmological Perturbations post-Planck conference, I thought it was fitting to exemplify just why this kind of science reporting is important.

I was first made aware of the story that shocked me so much by an excellent Panorama documentary that aired last month (UK readers can still watch the show online here). For those non-Brits amongst you, Panorama is a highly respected investigative documentary show produced by the BBC, not the kind of programme that bothers with unimportant issues. You can imagine, therefore, that my interest was piqued by the title "Cancer: hope for sale?". I had expected perhaps an exposé on some counterfeit medication ring, or maybe a look at a big pharmaceutical company pushing drugs through ahead of time in countries with lax regulation laws. I could not in my wildest dreams have imagined just how scandalous the actual story turned out to be, nor could I believe that this was the first I was hearing about it.

The main protagonist of this story is a Polish doctor called Stanislaw Burzynski - I had never heard of him before last week but he may be more familiar to those of you from the States. Dr Burzynski has been running a clinic out of Houston, Texas for over 30 years that offers treatment to cancer sufferers and has had thousands of patients through its doors. Burzynski's treatment is based on the notion that there exists a group of peptides (very short proteins) that exist within our bodies and have an immunoprotective effect against the development of cancer and other diseases, which he has given the reassuringly scientific-sounding name 'antineoplastons'. Cancer sufferers, it is claimed, can be treated by oral and intravenous administration of cocktails of various antineoplastons alongside a number of other components of the medication, such as steroids and anti-inflammatories. The antineoplastons used at the Burzynski clinic used to be purified from human urine but are now artificially synthesised from basic chemicals, and, it is claimed, are little short of a miracle weapon in the fight against cancer. The Burzynski clinic proudly asserts that not only do antineoplastons boost the immune response against cancer, but that the correct combination of antineoplastons can be used to generate therapies targeted against specific genes involved in different cancers and so allow for effective, personalised treatment.

This is close enough to real science to sound fairly convincing to the non-specialist. Some peptides are well known to have roles within the immune system (defensins, for example), and gene-targetted therapies represent a huge and promising area of oncology research. It all sounds pretty technical and reassuringly complex. That is enough for desperate individuals looking to cure themselves or loved ones when all else has failed; they're on the first plane to Texas.

The universe as seen by Planck - Days Three and Four II

[Continued from yesterday...]

In the first piece of this post I covered the implications of Planck for the paradigm of inflation. This piece covers the rest.

The anomalies

This is what the CMB would look like in an unphysical Bianchi universe. A worry for our physicality is that this unphysical Bianchi universe seems to fit the data better than a physical \(\Lambda\)CDM universe.

It would be impossible to provide an overview of this conference without mentioning the features and anomalies that Planck has chosen to draw significant attention to. I have a bunch of notes that I've written down that I might one day turn into a new blog post, but I'm not going to delve into them now.

These features and anomalies are clearly going to become a contentious issue in cosmology for the next few years. In fact, the words believer, atheist and agnostic were even being used by speakers during talks regarding whether the anomalies are real or statistical effects. Each time someone declared themselves an anomaly atheist or anomaly agnostic, someone in the audience inevitably spoke up and passionately defended the significance of the questioned anomaly.

The list of potential anomalies is long. There is the cold spot, the anomalously low quadrupole, the hemispherical asymmetry, the statistical difference between the odd and even multipoles at large scales, there is the dipole modulation, there is the general lack of power at large scales, there is the feature in the temperature power spectrum at small scales, the fact that the universe seems to be in an unphysical Bianchi model and there is the "axis of evil" (to name a few).

Pick your side. Atheist, believer or agnostic. The great anomaly wars of cosmology are about to begin (another inevitable consequence of an observational, rather than experimental science, I suppose - i.e. there is only a finite quantity of information available to us, so for some observables we can't just do the experiment again to check who is right).

What should we make of Planck vs SPT and Planck vs the local universe?

The universe as seen by Planck - Days Three and Four I

Sorry for the delay on this. I was pretty tired on Friday, travelling home on Saturday and doing physics on Sunday. I figured it would be better to write something with a little more care today.

Those who were following last week will know that on March 21 ESA finally released some cosmological results from the measurements they were taking with the Planck satellite. And, last week, they had their first scientific conference. I decided to blog about this. I had the initial ambition of one post for each day, but the conference dinner on Thursday beat me and all I got out was a brief teaser post. This post now will be comprised of a summary of what I found interesting on both Thursday and Friday, along with a summary of the whole conference at the end.

I hope you enjoy it (and thanks for the feedback during the week).

Highlights

• What has Planck told us about inflation?
• What should we make of Planck vs SPT and Planck vs the local universe?
• What is next for CMB science?

• Some final thoughts

What has Planck told us about inflation?

Slava Mukhanov. Cosmology can do what it wants, but Mukhanov's  predictions for inflation will remain unchanged. Somehow cosmology always seems to come back to him in the end. Will that last missing piece show up? Will primordial gravitational waves one day be detected? It's starting to look like a "no", but Mukhanov's heard that talk before. Time will tell...

The first talk on Thursday was about inflation, by another one of the scientists who helped found it. This was by Slava Mukhanov, another old-school Russian physicist. Mukhanov was one of the first to realise that inflation wouldn't just cause the universe to expand dramatically and to make it more homogeneous, it would also seed new fluctuations with a very small amplitude. These new, small, fluctuations arise from the stretching (and eventual amplification) of quantum fluctuations in the field driving inflation. This type of realisation was what took inflation from an interesting concept to a testable paradigm.

The universe as seen by Planck - Day Two

The cosmic microwave background (CMB) is the best probe we've yet found to study the early universe. The CMB's temperature is very nearly uniform. However this temperature does have very small anisotropies that can be used to study sound waves that existed in the primordial universe. The Planck satellite (an ESA funded experiment) has mapped these temperature anisotropies over the entire sky with the best resolution to date. Last month, Planck released its data and it immediately became the new benchmark for the testing of cosmological models and the measurement of cosmological parameters.

This week ESA is hosting the first conference since Planck released its data. The conference is at ESTEC in the Dutch town of Noordwijk. I am attending this conference and will be doing my best to write updates about what was discussed during the week.You can read my introductory post where I give my motivation for doing this, here.

The CMB is not just useful for studying the primordial universe. As soon as the CMB forms, everywhere in the universe, it travels freely, in every direction, at the speed of light. This means that, in every direction, the CMB we measure here on Earth today has travelled to us from a point billions of light years away. In principle, this makes the CMB not just a really good probe of the state of the universe where and when it was emitted, but also of everything it passed on its way to us.

This secondary use for the CMB turns out to be very useful and many of the highlights from Planck relate to the way in which the CMB interacts on its way to us. The existence of matter in the universe affects the CMB gravitationally. This causes the CMB to bend towards regions of over-density and away from regions of under-density. It also causes the CMB's temperature to shift as it falls into and out of over and under-dense regions. This first effect is known as lensing and one of Planck's most impressive results is a map of the locations of matter in the universe through this lensing effect. The second effect is known as the Sachs-Wolfe effect, something I've written about in some detail.

There is a third way that the CMB is significantly affected by the intervening universe. Within clusters of galaxies there is a lot of hot gas. If the CMB passes through a cluster it can scatter off electrons in this hot gas. The effect of this scattering on the CMB is known as the Sunyaev-Zeldovich (SZ) effect. Therefore, we should be able to use the CMB to detect the lines of sight along which the most massive clusters lie.

We can. And Planck has.

The universe as seen by Planck - Day one

 I am currently attending the ESA run conference "The Universe as seen by Planck". I will be trying to write a summary each day of what I found interesting. To read about my motivation for this, please read yesterday's post. Below is the summary of the first day's talks. I apologise if the posts this week are overly technical. I don't have much time for writing these and this is the best I can do given the constraints. As always, if you don't understand, just ask questions in the comments.

Overall summary

Today was mostly about introducing the Planck experiment and its data. This is the first conference ESA has held since the data was released and in fact the first conference about Planck open to non-Planck scientists like myself at all. Therefore today was actually the first chance for the Planck collaboration to be honest about what their telescope has and has not been able to do. As a result, many of the talks that can lead to the most speculation will not come until tomorrow and Thursday. Still, there were some interesting things to come out of today. For example:

• The reasons why no polarisation data from the CMB were used in likelihood analyses this time
• (Not mentioned in a talk, but overheard from reliable sources) The reason no constraints on "\(g_\mathrm{NL}\)" were released this time
• The existence of two "features" in the temperature power spectrum and many "features" in the temperature bispectrum
• A few other curiosities

Here are, in no particular order, the things I found interesting today...

The missing data feature

People who watched the data release conference in March might have been a bit startled by the set of CMB maps that looked like the one below. I was. The particularly startling thing about these maps is the band slightly greyer in colour that persists right in the middle of the image and in the bottom left. The rest of the map looks quite similar to a typical map of the microwave radiation measured on the sky.

The universe as seen by Planck (conference)

The 47th ESLAB symposium. All the cool kids will either be there, or watching it live on the webcast. Are you one of the cool kids?

This week I will be at a scientific conference, organised by ESA. In ESA's words, this conference is "An international conference dedicated to an in-depth look at the initial scientific results from the Planck mission". The conference is taking place in the small Dutch down of Noordwijk. At this conference there will be many people from within the Planck collaboration, who I'm sure will be delighted to finally be able to talk about their work and many people like myself who have spent the last few years eagerly anticipating the Planck collaboration's results.

The conference will have a live webcast here, you should watch some of it.

I will also be blogging during the conference. My goal is to try to write a new post here each day summarising the most interesting talks and discussions from the conference that day.

Why am I doing this?

An absolutely wonderful image showing how the various all sky images of the CMB anisotropies have improved each decade.

This won't be an easy task. The conference goes quite late each day and many topics will be covered, but I want to do this anyway. To understand why, first go watch my new favourite video on the internet. Brady Haran makes science videos and if you've never seen them, you should go check them out. I felt like Brady was taking the words out of my mind when I saw that video. One day the utopia that Brady and I envisage will exist and a Planck conference like this will be besieged by legions of fans. One auditorium will be fill of fans of non-Gaussianity and fans of Gaussianity, on opposite side, cheering their preference on. Another auditorium will be filled with fans of dark radiation, cheering their team on. Yet another will be filled with fans of the cosmological constant shouting their favourite chants at their mortal enemies, the quintessence crowd. But that day is not today.

Planck: All we need is six numbers to describe the universe

As I'm sure most of the readers of this blog are aware, the Planck data is now out. It turns out I was correct with two out of three of my rumours. I said that the "ISW mystery" was still present, it was. I said that Planck would present ~3\(\sigma\) evidence for non-zero neutrino masses, they did (though, as I suggested in my rumour, only after including information from galaxy clusters Planck has detected). Finally, I said that there would be 2-3\(\sigma\) evidence for some type of "non-Gaussianity", there wasn't. I will duly update my should-I-trust-that-rumour? algorithm in the following way: explicit remarks from Planck members, good rumour; wishful thinking from other theorists, bad rumour.

So what were those results? What big news is there?

The answer is that there isn't anything strikingly new or surprising. I've been trained by years as a theoretical physicist to to dread that sentence and, indeed, many of my colleagues have gone into various states of despair. But, for some reason, I spent the second half of last week in a state of excited wonder. Surprisingly, I loved what I saw on Thursday. It was both stunning and beautiful. This post will be me trying to explain why. (For more details of the actual results see Sesh's post and Peter Woit's list of other blog posts).

The model of cosmology that has been gaining traction over the last decade and a bit is called \(\Lambda\)CDM. This stands for \(\Lambda\) Cold Dark Matter, where the \(\Lambda\) represents the poorly named "dark energy". This model has a few theoretical issues, but it is incredibly simple. What Planck specifically found is that this model fits the CMB (Cosmic Microwave Background) very well and better than any alternative that they tested.

Why I found what Planck saw to be incredible

As I wrote above, Planck's results last Thursday had me in a state of impressed awe. On the day, I couldn't quite put my finger on why, until I read another cosmologist's tweets marvelling at how everything we were seeing could be described by just six parameters. Then it hit me. For once, cosmology had gotten it right. What Planck measured depends on a significant variety of physical phenomena. If the early universe had more matter, or more radiation than we expected, Planck would have seen it. If the primordial density perturbations had been shaped in a significantly different way to that in which we expected, Planck would have seen it.

Cosmology gets a lot of flak from some directions for the so-called "epicycles" of dark matter and dark energy. I can kind of understand this when people see images like this and are told that we "don't understand" 95% of the energy density of the universe. But what is often missed is that we include the effects of dark matter and dark energy in this \(\Lambda\)CDM model with one, single, parameter each. And once those parameters are fixed, the predictions of all of cosmology are too.

With this firmly in mind, take a look at Planck's most important, headline image below. This (sort of) shows the amplitude of the temperature fluctuations in the CMB as a function of their angular scale. Remember, it takes just six numbers to define what that entire curve should look like. Just six.

Following Planck's results today

For the people (new and old) who follow this blog and are interested in the Planck satellite's results, which are being announced today, here is a run-down of important things to know:

• Richard Easther will be live-blogging the data release at this location. If you can't watch the release yourself you should follow Richard's post.
• The first ESA event is a general-audience press conference, very soon, at 10:00 CET, which you can watch here.
• The second ESA event is a press conference aimed at scientists and science journalists, which will stream at the same location, i.e. here. You should watch that even if you aren't a scientist because it will be when all the interesting bits are revealed. If you're confused, you can follow Richard's live-blogging and/or ask questions of scientists on Twitter with the hashtag #askplanck.

• The release of the scientific papers is scheduled for 12:00 CET at the ESA website (I'm not sure of the precise url, maybe here?).

Although I won't be live-blogging the results, I will write a post later today summarising what we've learned and discussing the fall-out arising from all the new information.

Enjoy the day!

Edit: The papers will appear here at 12:00 CET: http://www.sciops.esa.int/index.php?project=planck&page=Planck_Legacy_Archive

Twitter: @just_shaun

Cinema verité - biology style

Animations of scientific principles are becoming more and more popular as a way of condensing complex data into an easily accessible format, particularly in the field of biology. Nonetheless, a recent article in Nature has raised a number of interesting points about how the visualisation of biological processes should not be taken lightly. Biology is unnervingly complex and there is still much that we don't understand - how are we to know how much of an animation is based on actual data and how much is just 'filling in the gaps'? This is not limited to the layperson - humans are very visual creatures and we are more easily swayed by pictures than words, experts are no exception. This is not new, journals have included idealised representations of biological processes for decades, but the advancement in computer animation has opened the door for more sophisticated animations that may imply a more thorough understanding where one does not exist. 

That said, I don't believe that researchers actively seek to mislead when presenting their findings in animated form, rather that they have to take the necessary steps to complete the movie - inherently requiring some artistic licence. And, for the most part, the bits being filled in are done so with reasonable scientific assumptions in mind and are not wild fantasy. The medium is an exciting one, and one that will hopefully play a significant role in not only disseminating scientific understanding, but also help to further research by highlighting gaps in our understanding. We must, however, always be vigilant when interpreting these animations as they are exactly that - animations - and not actual footage of molecular biology.

An excellent example of biological animation is the 'Inner Life of a Cell' video by a group in Harvard. I love this video, which depicts the events that occur upon the activation of T cell, and is pretty accurate in that almost everything show is backed up by real evidence. The 'motor protein' kinesin at 3:40 is particularly impressive because its mechanism of 'walking' along microtubules is backed up by extensive structural and biochemical studies, yet it just looks so much like a drunk guy who's been pulled over by the police and is trying to walk in a straight line! If you get the chance, I really recommend watching the video and reading the article mentioned above. Enjoy!

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.]

The Higgs: To be, or not to be?

[Note from Shaun: The following is a guest post from Higgs Hunter, Mikko Voutilainen. Mikko is a colleague of mine here in Helsinki. He is a postdoc working on the CMS experiment at the LHC in CERN. Below, he rhetorically asks the Higgs boson whether it exists or not. The irony of this is that Mikko asks this question, non-rhetorically, for a living and it is quite possible that he has already received an answer. He cannot (unfortunately) tell us this answer, yet. You should consider the following a teaser for what will follow next Wednesday when CERN unveils its latest results to the world. On that date, Mikko has promised to give us another guest post where he will reveal everything he knows about, The Higgs... (I've even heard rumours that this follow-up post has already been written)]

To be, or not to be?

That's a question for the Higgs boson to answer, and we might know soon enough. CERN just (well, three days ago really, but everybody here was out in the countryside celebrating Midsummer) published a press release about having a seminar on the new results on Wednesday 4th of July.

Coincidence that it's also Independence Day for the folks in the US? Probably yes, although my collaboration, the Compact Muon Solenoid (CMS) experiment at CERN, does have a strong representation from the States, including our spokesperson Joe Incandela.

The real reason, though, is that the 4th of July is also the eve of a major particle physics conference, ICHEP, starting in Melbourne. The ATLAS and CMS experiments will deliver the preliminary results of their 2012 data analysis there, and the seminar will be a kickoff for these presentations (you can see the live broadcast at webcast.cern.ch).

The experiments at the Large Hadron Collider stopped collecting data only on the 18th of June, and everybody is now busily analysing this dataset. We actually collected quite a nice bunch of data, just over 6/fb, which is a bit better than last year. The collision energy was also raised from 7 TeV to 8 TeV, which should increase the production rate of possible Higgs bosons by 20--30%.

The amount of data collected in 2010, 2011 and 2012. One fb-1 amounts to almost 100 trillion proton-proton collisions.

People are really eager to see the new results, and for a reason. The data collected in 2011 showed some hints of a Higgs boson in the 124-126 GeV range. The amount of data collected this year is nearly equal to that collected last year so the results are directly comparable. We should be able to see whether the earlier trends are still there, or whether they've gone away. Either way, it should be pretty exciting.

The predictions made earlier indicate that a combination of the 2011 and 2012 datasets should get pretty close to five sigma, the traditional standard for a discovery in the field. Or, we should be able to rule the existence of the Higgs boson out at a 95% confidence level from the whole remaining mass window.

Predictions for the significance of a Higgs signal as a function of the boson mass. The combination of 2011 (5 fb-1, 7 TeV) and 2012 (5 fb-1, 8 TeV) data will correspond to roughly the average of the two red lines.

What happens in a week depends both on the hard work of the physicists, who are improving the sensitivity of their analysis, and, due to statistical fluctuations, pure luck. If we're unlucky, the existence of the Higgs boson may still remain a mystery, but if we're lucky, we might end the quest earlier than expected.

So, what if we find the Higgs or not? Is it the answer to Life, the Universe, and Everything? Or a piece in the puzzle of the origin of mass for the elementary particles? The latter, more likely.

If we find that the Higgs boson lacks existence, much of the theoretical work done in particle physics for the past few decades will end up in the dustbin. It's not all that bad, really, because it will allow the theorists to start from a clean slate, and that's often been a very fruitful thing. The experimentalists will continue to hunt for other particles that could replace the Higgs boson.

If the Higgs boson is found, it's properties will have to be scrutinized carefully. There are many theories out there besides the Standard Model of particle physics that predict the Higgs boson (or bosons) so determining it's precise identity might take a while. Many of the alternative theories also predict other particles, leaving plenty of work to be done for the experimentalists.

[Note: Mikko writes for a Finnish language blog, Higgs Hunters. This post is an English translation of his latest post at Higgs Hunters.]

Immunology under the microscope: knowing what is known

The previous post in this series can be found here.

As a passionate believer in science, I have had many debates over the dinner table or at the bar with those who consider scientific research either unimportant or ineffective. The argument often comes back to “Well, science doesn't know everything!” To say this inherently misunderstands science and scientific research. Firstly, science doesn’t know anything; science doesn’t think or know - it simply is. Science is just what exists, it is everything. Everything must be explicable otherwise it couldn’t exist, even if understanding it is beyond the capability of humanity or any other intelligence. If God exists, He presumably understands Himself and so is explicable, to Him at least. I suppose that when people make the claim that “science doesn’t know everything”, they really mean “scientists don’t know everything”.  This statement is obviously true, we don’t know everything, but it never fails to surprise me how little people often assume we do know. I don’t expect people to understand science in great detail, but it is a great shame that there is so much ignorance of the sheer amount of knowledge that we’ve gathered as a race. I have, in the past, been comprehensively informed that “we still don’t even know how genes work!”, which is very surprising news considering I thought I could explain in atomic detail how a gene is transcribed, translated and expressed as a protein – that is to say: how it works. An unfortunate mistake that many people often make is to confuse the statements “I don’t know this” and “nobody knows this”.

Perhaps this is to be expected; seen from the outside, science probably appears very sporadic: there are long periods where nothing is being discovered and then suddenly there’s a big finding and everyone gets very briefly excited before everything dies down again. This, however, is simply a product of the sensationalist way that it is often portrayed in the mainstream media, in which everything deemed too complicated or insignificant is not reported and things that do make the grade are often over-hyped. Following science in this way is a bit like following literature only by watching Hollywood adaptations of major novels. In fact, science progresses in tiny steps that can seem insignificant on their own but contribute to the field as a whole. Immunology is no different.

What does the sound of the Big Bang look like?

Six weeks ago I wrote a post where I tried to explain how we know that the Big Bang definitely happened. There are of course other reasons why we know the Big Bang happened, but I decided to focus on one, relatively easily explained piece of evidence, which is the existence and frequency spectrum of the Cosmic Microwave Background (CMB).

Quickly summarising: The CMB is very cold radiation that permeates the entire universe. It was created when the expanding and cooling universe cooled to a point where it was cold enough for hydrogen atoms to form. Before this point, the electrons and protons in hydrogen had enough energy to be free from each other to form an opaque plasma. Once neutral hydrogen formed the universe became transparent and the CMB was formed and travelled (almost) freely forever after. We have detected and measured this CMB and its intensity as a function of its frequency (effectively, the brightness of each colour) is exactly what the Big Bang predicted. If there was no Big Bang there would be no reason to expect a CMB to exist, let alone for it to have this particular property. For more details please read my previous post and the links within.

When writing that post I had intended to say quite a bit more about the CMB and the Big Bang than I ended up having space for. It is not quite true that the mere existence (and spectrum) of the CMB is enough to conclusively determine that the Big Bang must have happened. However the existence of the CMB did build the metaphorical equivalent of a thousand big, bold and bright neon signs that all pointed aggressively towards the Big Bang being true.

When I began writing that earlier post and claimed that the CMB does conclusively prove that the Big Bang happened I had in my mind what I actually discuss in this post. This is the fact that we can see in the CMB the effects of sound waves that existed in the primordial hydrogen plasma. It is these sound waves and our measurements of them that puts the final nail in the coffin of all things not the Big Bang. They also represent what I claimed in that earlier post to be “jaw-droppingly stunning pieces of detective work”.

The glorious Planck satellite, measurer of all things CMB

The smoking CMB evidence of the Big Bang

The centre of the galaxy and a sliver of the CMB anisotropies

I was asked recently how I know that the Big Bang definitely happened. This post will be my attempt to answer that question. I will focus on something called the Cosmic Microwave Background (CMB for the rest of this post). The CMB is as close to smoking gun evidence of the Big Bang as you can get. In fact, it's such good evidence that it is better than a smoking gun. The figure of speech should no longer be “smoking gun evidence”. It should be “smoking CMB evidence”.

The other reason I am writing about the CMB is that humanity's prediction of its existence and our subsequent measurements of it and its properties are jaw-droppingly stunning pieces of detective work. If you are ever feeling down about human nature and our propensity to do kind of stupid things then just remember what you're about to read and reassure yourself that at times we can be incredible.

What is “The Big Bang”? (A very brief review)

Everywhere we look things are moving away from us and the further away we look the faster things are moving. This means that the distance between any two unbound objects in the observed universe is increasing. Or, in other words, the universe is expanding. As time goes on things will get further apart, the total density of the universe will decrease and the temperature of outer space will go down.

But what happens if we run the clock backwards? Well, naturally, things will get closer together, the total density of the universe will increase and the temperature of outer space will go up. This suggests that at one point far back in time the universe was in a very hot, very dense state that was rapidly expanding. This, and nothing else, is the essence of what the Big Bang model of the universe is.

Of course, we understand how the matter in the universe behaves at the current, low, temperatures. Also, thanks to results from particle accelerators and other experiments we even know how the matter in the universe behaves at quite high temperatures. This means that we can make very definite statements about what the universe should have looked like when it was below those temperatures. But, although we can and should speculate about what the universe might have looked like above these temperatures, we can't yet say anything about those times with certainty.

So, if you let me repeat myself for emphasis, at its heart the Big Bang model is nothing more and nothing less than the idea that the universe was at some point in the past very hot, very dense and rapidly expanding. To work out whether this is what the universe was actually like or not we need to know what the present day consequences of this might be. To answer that question we should take a closer look at what the universe we see now would actually look like at these higher temperatures.