## Monday, December 9, 2013

### Cubism. Realism. Sciencism.

 Post-impressionist carcinoma.

This week's post from me will be relatively brief as I am currently on honeymoon, and although Shaun somehow manages to find time on his travels to blog about his conference experiences I doubt my new wife would be too happy if I did likewise! So, in lieu of my intended Human Machine series post (which will be coming early in the new year), I wanted to bring your attention to something wonderful going on at the Cell Picture Show.

The Cell Picture Show has appeared in the Trenches before (here and here), but this recent instalment is to me even more original and interesting than anything they've had before. The image above has two halves, both of which are strikingly reminiscent of Van Gogh's famous and beautiful Starry Night. They look like the product of some brilliant mind with an extraordinary mastery of colour and texture. In fact, the image on the left is a cross section of mouse skin containing basal skin carcinoma, with various components stained different colours and imaged using a fluorescence microscope. The image on the right is an artist's rendering of the same image using different coloured fabrics stitched together. This is part of Cell's exhibition 'Art Under the Microscope', in which images of biological samples are recreated into works of art by professional artists. The image above is just one example, but there are many others of similar standard available in the exhibition. The technical prowess of the researchers who obtained the original images is impressive, as are the aesthetic abilities of the artists who recreated them.

 A fire-like network of neural stem cells in the human brain (left) and their artistic equivalent (right).
What I find so exciting about this exhibition is that it is redefining what can be the subject of art, and what can be the source of artistic inspiration. Nature has been inspiring artists for thousands of years, why should that be restricted to what we can see with our own eyes? We are now at a level of technology that we can begin to unveil many of the secrets that nature had previously been hiding from art. This should be exciting to both scientists and artists. Artists can be excited by the wealth of new subject matter that is beginning to open up to them, and scientists can be excited by the prospect of art adding to the ever-growing popularity and appreciation of science. Perhaps one day there will be great debates in artistic circles about new avant-garde artists who paint their proteins in a controversial way, much like the debates between the surrealists and romanticists on how to depict more macroscopic areas of nature.

Although 'Art Under the Microscope' is a small exhibition, it nonetheless marks a growing trend in the use of science as inspiration for art. I sincerely hope that this continues as it will enrich both science and art, and help to blur the boundaries between them. Art has been very successful in entering many concious aspects of our daily lives, and we are the better for it. Science is still catching up in many regards, although to be fair it hasn't had all that long to make up the difference. If science were as exposed in the public conciousness and as everyday as art is, then I believe we would benefit similarly as we have from the ubiquity of art. The fusion of the two is a match made in heaven that is finally beginning to take hold. I look forward to the days when parks are adorned with pieces of science-based public art, and the spectrum of human endeavour is appreciated as single entity rather than as the separated, delineated pigeon holes of 'art' and 'science' as discrete subjects.

## Monday, November 25, 2013

### How does one measure the mass of a neutrino, using cosmology?

I'm going to tell you how, soon, humanity might measure the masses of neutrinos just by observing past events in the universe. I like this topic because it is one of the few situations in fundamental physics where a measurement of the greater universe might detect something about fundamental particles and/or their interactions, before we manage to measure it in a lab. Another example is the existence of dark matter; however the mass of dark matter will almost certainly be first measured in a lab. Perhaps with neutrinos it will go in the other direction?

What is a neutrino?

I guess that before telling you how to measure a neutrino's mass, it might be pertinent to tell you what a neutrino is and how we can know it has mass before we've measured that mass. Well...

When an atomic nucleus decays, the decay products we see are other nuclei, electrons and/or positrons. These visible products always carry less energy and momentum than the amount that the initial nucleus had. This suggests strongly that some unknown other particle is also being created in the decay and that we just can't see it. This hypothetical particle was dubbed the neutrino and when theories were developed for the force responsible for nuclear decays, the neutrino became an important part of them. And, eventually, neutrinos were detected directly. It took a while because neutrinos interact incredibly weakly, which means you need either a lot of neutrinos or a lot of transparent stuff for the neutrino to interact with (or both) before you will see them.

Initially, it was assumed that neutrinos are massless. They don't need to be massless, but for a long time there was no evidence that they did have mass, so the simplest assumption was that they didn't. There are three types of neutrinos: those emitted in interactions with electrons, those emitted in interactions with muons and those emitted in interactions with tau particles. If neutrinos were massless, then a neutrino emitted as an electron neutrino would always remain an electron neutrino. Similarly, a muon neutrino would always remain a muon neutrino. However, if neutrinos do have mass, then a neutrino emitted in an interaction with an electron will actually travel as a superposition of an electron neutrino, muon neutrino and tau neutrino. The net result being that this neutrino could be detected as a different type of neutrino. Therefore, a smoking gun thing to look for when determining whether neutrinos have mass is this characteristic signal whereby one type of neutrino appears to oscillate into another type of neutrino.

This effect was then seen and seen and seen again. Neutrinos appear to have mass. From the perspective of particle physics this is a bit weird. Neutrinos must have really small masses and it is unclear why these masses are so small. Unfortunately, this mechanism of neutrino oscillations doesn't directly give the masses of the neutrinos. Although, it can be used to measure the differences of the masses of the neutrinos, thus setting lower bounds on the possible masses of the neutrinos.

What has this got to do with cosmology?

## Monday, October 28, 2013

### 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.

## Tuesday, October 8, 2013

### Being a foreigner in Finland (Intro)

The major goal of this blog has always been to try to make fundamental research accessible to interested non-specialists.

Another worthwhile thing to do, from the "Trenches of Discovery", is to describe what life is like in those trenches.

One of the most notable aspects of the postdoctoral research lifestyle is that you get to spend 2-3 years living in a series of places you might not otherwise have chosen to live. I've just finished three years living in Helsinki, the capital of Finland. I can say with pretty firm confidence that, prior to landing that job, I had never seriously considered the prospect that I might one day live in Finland. I had also never been there.

I've moved now. This is sad and exciting. I'm now employed by the University of Sussex. I've spent the six weeks between living in Finland and living in Britain, back in New Zealand on a kind of small time-frame sabbatical type thing, visiting Auckland University. I wish I could live in three places at once.

While it is still fresh, I want to write here what life is like (for a foreigner) in Finland.

Nature, culture, day-length, work-day-length, an individual's mental state, whether some of Jesus' achievements can be considered to be miraculous or not, just about everything about life in Finland, is dictated by the seasons. So, I've decided to serialise this thing into four pieces, about life in each season, starting, in the next post, with winter. The rest of this post will be a more general introduction.

What is Finland?

 The Finnish coat of arms. The Nordic countries' coats of arms kind of satisfy their stereotypes. Here, the Finnish lion, drunk, and drooling, in a field of summer flowers, has unfortunately stabbed itself in the eye with a rather randomly human fourth limb.

Finland is a pretty remote place (though some others are more remote) and it doesn't try hard to be noticed on the world stage. Unless you approach Finland, it probably won't approach you. Therefore, for many people, the extent of their knowledge about Finland is that it is that cold, dark, place between Russia and Sweden. This is more or less what my knowledge of Finland was in 2009.

Finland is indeed the cold, dark place between Russia and Sweden. This is actually quite a good description of Finland in a historical context as well (on a couple of levels). It is only very recently (1917) that Finland became an independent nation, it previously having been a part of either Russia or Sweden, depending on the year. The national identity is, thus, very new compared to most of the rest of Europe. The Finnish language is, also, not a part of the Indo-European language family and as such has no close relative in all of Europe, except Estonian (a very close relative) and Hungarian (only recognisably related if you're a linguist). It's like a small pocket of something else, kind of European, but a little bit different, sitting up in the corner there on the map. Of course, people are people wherever they are, so the individual people of Finland are themselves no different to individual people in France, Fiji or the Falkland Islands, but the collective culture can differ.

Finland is very far North. Helsinki, the capital, despite being on the south coast of Finland, is still further north than the tip of mainland Britain. For those elsewhere than Europe, Finland has a similar latitude to Alaska, which is further north than all other U.S. states and most of the places that Canadian people live. For people from the better hemisphere, no permanent settlements exist as far south as Finland is north. Some bits of Finland are as far north as some bits of Antactica are south. This means that the longest nights in Helsinki are long (about 21 hours or so) and the longest day is even longer (about two months or so). I'll try to let that sink in later. The summer is nice and warm, without (normally) getting uncomfortably hot. And the winter is cold, though no colder in its extremes than a city in the U.S midwest. It's hard to express how much this significant difference in season affects everything in Finland, but hopefully I can get a bit of it across in the next few posts.

Finland is quite big (bigger than Britain and New Zealand, for example), but relatively unpopulated (just 5 million people in the whole country). This means there is a lot of space. Finland is also the nation that has the greatest proportion of its surface covered by water. This means that a huge chunk of Finland is lake, with most of the rest being forest. This sounds a bit like pointless trivia, but this large quantity of open space, and preponderance of lake and forest does have a strong influence on culture and frame of mind. There are no mountains, although I wouldn't quite compare Finland to Denmark or The Netherlands; there definitely are hills.

Finally, despite being somewhat remote geographically, and not a particularly boisterous nation, modern Finland is far from remote from the rest of the world, culturally. I didn't learn to speak Finnish. I found by far that the most difficult part about trying to learn Finnish was not the language itself, but the fact that almost every single Finn speaks English fluently. I used to joke that the second most spoken language in Finland is Finnish. It didn't really go down that well.

What's to come...

 In Finland, when someone is awarded a doctorate, they customarily buy a top-hat and a sword. That is a real sword. Hopefully  Finnish PhD graduates do a little better than that lion.

Experiencing Finland needs to be done (at least) twice for each season. You can appreciate moments more when you know what has lead to that moment and what that moment is leading to. I've found this particularly true for autumn, typically the most bittersweet of seasons anywhere. A Finnish autumn, in the moment, is delightful. There is a charge in the air, that, if you arrive for the first time in autumn, you notice right away. I didn't understand its origin the first time, but I came to associate it with an atmosphere left over from the vibrancy of a Finnish summer. And, the true poignancy of a Finnish autumn can only be experienced when you fully understood what the beginning of winter is like in Finland.

The darkness brought by the beginning of winter in Finland is oppressive. There is no point in hiding that. The second half of winter in Finland is wonderful, and easily one of my favourite things I've experienced, anywhere. But the beginning of winter can only be described as profoundly oppressive. This isn't necessarily an entirely bad thing. Witnessing anything extreme adds a sense of thrill and perspective. A Finnish winter definitely aids in quiet reflection. But it is only thrilling because it is extreme. Once the darkness breaks, however, winter turns into an almost literal wonderland, at least for a kiwi. You can walk on the sea. You can commute to work on skis (and some colleagues did). In one Finnish winter you see snow take thousands of forms and... apologies for geeking out... through these forms mimic many different kinds of rock, be they sedimentary, volcanic, granite, sand, or otherwise.

"Spring", in Finland, doesn't exist. Or, at least, it does, but what the rest of the world calls spring, happens for about fifteen minutes, at around 4pm, sometime late in May. Instead of spring, there is a long, ordinary length season, that would be more appropriately labelled "the thaw". This season is bleak and barren. Whatever got buried, under the snow, at the beginning of winter, be it leaves, grass, dog poo, bikes, cars, or even people, will emerge five months later, in April. The sterility of the cold and the snow passes, but what it leaves behind is the dead husk of the previous summer. None of any part of nature (plant, animal or human) will believe winter is over until it can be absolutely sure, so the city sits and it waits, continuing to wait long after the last snow has melted, and the tension builds.

Until summer arrives explosively. I'm only a little bit joking; you can see the grass grow in Finland in June if you sit and watch it. I've never been anywhere that feels more vibrant and full of life than Finland in the summer. August, in Helsinki, is my favourite thing in the world. I spent a significant chunk of each of my three Finnish Augusts wishing I'd had the chance to experience a Finnish August as a barefoot, lakeside, tree-climbing, berry-picking, lake-swimming, night-time book reading, eight year old. As it stands, I just got to be a sandal-wearing, seaside, tree-appreciating, berry-eating, sea-swimming, night-time book reading, 28 year old, which is still pretty good.

And then autumnn comes again. Nature, and the rest of Finland, prepares for rest, and the intensity of the summer gradually dissipates into winter.

[More in later posts...]

## Monday, September 30, 2013

### Two doctorates, a wedding, a full-time job and a move overseas

Regular readers who knew we actually had a schedule here might have been wondering what's happened with the posts. If you're one of these people, then you might be happy to know that things will return to normal (well, 2013 normal) from next Monday.

Posts disappeared because all three of the contributors to the blog have had significant life events in August/September. James is now literally a couple of weeks away from submitting his doctoral thesis (see you on the other side, dude) after which he will be literally a couple of weeks away from getting married. Michelle has been balancing being a full-time PhD student with being a full-time museum curator all year. And I've just moved from Finland to the UK, via six weeks in New Zealand.

As my excuses are the weakest, I'll be the first back to blogging. This will be next Monday. Thanks for hanging around.

## Wednesday, August 14, 2013

### Working hard or hardly working?

"Life grants nothing to us mortals without hard work." So said Horace, the Roman lyric poet, over two millennia ago and little has changed since. I am currently one to attest to that sentiment as I am in the middle of writing up my PhD thesis and have accordingly developed the peculiar mania that grips many students at this stage in their degree where non-thesis pursuits become shamefully wasteful or even patently corrosive of your time! So, I'm afraid that this week's post from me is just a brief one, and the long-promised 'human machine' edition on stem cells is being pushed back yet again, apologies.

In light of this sudden idiopathic workaholism that overtaken me, it seems appropriate that my post this week be on the subject of how hard scientists work. Coming into science I knew that the pay is generally crap, and it's not particularly glamorous, and you have to look for a new job every three years until you settle down with your own cosy lab somewhere - but at least it's a fairly nice lifestyle, right? Well yes and no. I love the academic lifestyle - it's the right mix of individual freedom and motivating challenges, by which I mean that it isn't too stressful but isn't boring either. That has been my experience (present situation excluded), but a recent report from the University of Nottingham suggests that I may have been one of the lucky ones, or perhaps that things are going to worsen for me!

The report (available here) looked at the working hours of conservation scientists in several countries by analysing the time and day of 25,000 publication submissions to the journal Biological Conservation. It's true that this is not, perhaps, the most reliable indicator of general working patterns since people tend to put in extra hours in the run-up to publication, but the results are still intriguing nonetheless. The long and the short of their findings are that scientists, basically, work pretty damn hard (well, conservation biologists at least). They observed that 16% of manuscripts were submitted late at night, and 12% were submitted at weekends, and that the proportion of work submitted outside of normal hours has been increasing ~5% each year. This paints a fairly bleak picture for the future if working hours are going to stretch further and further into personal time.

Perhaps unsurprisingly, the study also found significant differences in working habits between different countries. The countries whose scientists seem to work the most unsociable hours are Japan and Mexico, who seem to work late (~30% manuscripts submitted out of hours on weekdays), as well as China and India, who work weekends a lot (up to 40% submitted at weekends). The most relaxed scientists were found in Belgium and Norway, who like their weekends off (~5% submitted on weekends), as well as South Africa and Finland, who go home at 5 (less than 10% submitted after hours on weekdays) - thus explaining Shaun's abrupt move to Helsinki three years ago! British and American scientists were about average in their working habits.

So what makes many scientists so busy, and why do they stick at it for often quite poor salaries? Well the combined research, teaching, reviewing, and administrative duties of senior scientists puts a big strain on their time. The authors of this investigation warn that this can may be having a negative impact on the quality of the science produced, as well as the happiness of the researchers themselves.  Dr Ahimsa Campos-Arceiz, who led the study, reflects:

"We call for academic institutions to remember that good science requires time to read and think and over-stressed scientists are likely to be less productive overall. We also recommend that peer-review activities are included as part of the academic job description and considered in staff performance evaluations. At the end of the day, working on this paper has been an opportunity to reflect about our own behaviour and priorities. Next time I go to Bali, I will spend more time swimming and talking with my wife and less working on manuscripts."
Why so many scientists are willing to put up with the current situation is perhaps the more informative question. People become scientists often because of a burning curiosity that they must fulfil, and the realisation of that goal is its own reward. In many ways, academic science is an indulgence that most other professions wouldn't tolerate. Researchers are, by and large, able to investigate whatever they're interested in, in whatever way they see fit. Clearly, dead-end research is eventually weeded out by funding bodies (*all hail the funding bodies*) but generally it's fairly flexible and if you're interested in something and stick in science then there's a good chance you'll end up working on it. As well as this, there is the feeling that you are contributing to something bigger than yourself. Research never disappears, it will outlive you and become your legacy once you're just a memory. This is the same sensation that artists must get when creating their masterpiece, or writers have as they pen their latest novel. Moreover, if your research is useful then it can have ramifications far beyond anything you could achieve in most other jobs, but even if it's not then you're still helping to take one more step along the path of human progress. This is why people chose to be scientists and work unreasonable hours for a lot less money than an investment banker, and it's why I would always encourage anyone who is interesting in entering science as a career.
So, Horace was right, life gives you nothing without hard work, but then if that work is intoxicating enough then life begins to mean nothing without it either.

## Monday, July 29, 2013

### Two years in The Trenches...

This Saturday (the 3rd of August) will be The Trenches of Discovery's 2nd birthday.

Ideally I should be writing a post on Saturday to celebrate this but for two reasons I've decided this year not to. The first is that this weekend I have some friends, one of whom is James, coincidentally enough, visiting me in Helsinki and so I probably won't have time to write anything. The second reason, is that I'm being sneaky/lazy. According to the schedule James and I have set each other I was meant to write a post last week and so far I haven't. The post I'd intended to write, on a paper I wrote recently with a PhD student here in Helsinki, is going to be a post where the line between "too technical" vs "not actually telling the truth" is incredibly fine (if not just completely non-existent).

So, partially to get something written for my scheduled post and partially because I really want to know, I'm going to canvass our audience's opinion (again).

Our initial aim, when we set up this blog, was to write about fundamental research, as it is happening, to an audience of the general public. This is obviously a very difficult task. The general public has no obligation to be interested in fundamental research, so in order to get you interested, we need to tell you the interesting stuff. The problem is that "the most interesting stuff" is not always the simplest stuff. We can really, really simplify things so that it all sounds understandable but if we do that, it is highly likely we will actually be telling you untruths (because it really isn't that simple) and also leaving out some of the coolest stuff (because the coolest stuff can be complicated at times). Alternatively, we can really get down in the trenches and fill in all the details, but then you need to also invest time trying to process what we write.

So, here are some questions for you, the reader:

• Who are you?

That is, what's your background? Sometimes I fear that all our readers are just cosmologists, reading my posts, and biochemists reading James' posts. Most of my feedback definitely comes from other cosmologists, and while it's nice to hear from them that they read the blog and find it interesting, and I hope they continue to read it, it's also kind of annoying, because they aren't meant to be the target audience. I can't help but think that if I was writing posts that appealed to the target audience, cosmologists would tell me that my posts were a little boring. I love reading James' posts, they make me want to quit research and start a career writing allegorical novels about the human immune system, but I do have to sit down and read them carefully in order to get something out of them.

• How did you discover the blog?

We can see from the stats what the various major sources of traffic to the blog are (google, facebook, reddit, other blogs, etc); however what we can't see is what types of readers these sources are bringing. Is google only bringing other cosmologists who will search for "mukhanov inflation planck" and biochemists who will type "central dogma of molecular biology" or do some of the people who type "cheats for jigsaw puzzles" actually end up sticking around?

• Are we achieving our goal?

Are our posts too technical? Is a blog the right medium to use in order to achieve the goal of making fundamental research more understandable to the general public, or are YouTube channels such as Veritasium, Periodic Videos, etc, a much more effective method? We've been toying with the idea of starting a podcast, because it would allow one (or two) of us to sort of interview the other(s) and would really help with the interdisciplinary ambitions of Trenches. It wouldn't replace the blog, but it might free the blog up to be a little bit more technical without fear of alienating the target audience.

Is there a different niche, that I would imagine we're actually filling quite well, which is a niche for people who were already really interested in the stuff we write about and who probably even have science degrees, but might not be involved in research any more and don't have the time to sift through the primary literature and who really like having us digest this stuff in advance? You guys are also somewhat the target audience. If you exist and are reading the blog and liking it, let us know. If we changed to be less technical, would you be disappointed? If you came for the cosmology, do you read and enjoy the biochemistry? If you came for the biochemistry, do you read and enjoy the cosmology?

I would be interested in any opinions that any readers might have.

Finally, we've also been pretty keen right from the start to add a social science-ish-type-person to the blog to (sort of) allow it to cover the entire spectrum (physical science, life science, social science and arts). If you are such a person, or know of one, please get in touch with us. Those who are new to the blog might not be aware of the mysterious third blogger, Michelle, who is currently on sabbatical as she finishes thesis (at least, we hope it is only a sabbatical), who is also a critic, creator and now curator of art.

That's all from me. No competition to guess the most viewed post this year. It's the same one as last year.

## Monday, July 1, 2013

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.

## Wednesday, June 12, 2013

### Cosmological perturbations post-Planck - wrap up

 Helsinki at midnight. OK, that's not Helsinki, and the photo wasn't taken at midnight. But it is in Finland (Kemiö) and was taken after 11:30pm. Image credit either Chris Byrnes or Michaela D'Onofrio, I'm not sure, although because I got it off facebook, I guess it belongs to Mark Zuckerberg now.

I'm very sorry. As I wrote last week, we just hosted a conference here in Helsinki. I wanted to cover it as the conference happened and I just didn't have the combination of time and mental energy to do so. I won't be covering it in any detail retrospectively either because I need to get on with research. Nevertheless, this blog is slightly more than a hobby for me, it is also slightly ideological, so I will try to work out how to do it all better next time and try again then (this will be the annual theoretical cosmology conference "COSMO" in early September).

Here's a summary of some of the more interesting aspects that I'll quickly write up, starting with some closure concerning the topic I was halfway through in my last post...

David Lyth, the curvaton and the power asymmetry

 David Lyth receiving the Hoyle Medal. David's the one in the photo who doesn't already have two medals. From this photo it seems that the guy on the left is graciously donating one of his many medals to David. I got this image from Lancaster University.

Where I left my last post I was describing David Lyth's talk about explaining the possible asymmetry in the amplitude of fluctuations on the sky (as seen through the temperature of the CMB). It's a small effect, the sky is almost symmetric; but it could be a real effect, the sky might be slightly asymmetric.

The possible asymmetry was seen before Planck and one candidate explanation involves quite large super-horizon fluctuations in some of the properties of the universe. "Super-horizon" here means fluctuations whose characteristic scale is bigger than the currently observable universe, i.e they are outside of our observable horizon. Such a fluctuation would be seen by us, within the observable universe as a smooth gradient in the fluctuating observable. Put simply, the idea is to have a smooth gradient in the amplitude of the measured temperature anisotropies. This would quite naturally result in a bigger amplitude in one direction, than another.

It seems that simple inflation can't achieve this without making the fluctuations in the universe significantly non-Gaussian. However, the curvaton can do it (according to David and a paper he is working on). Quite nicely, there is a relationship that David discussed that occurs between the amplitude of the asymmetry and the amount of deviation from a Gaussian distribution one would expect in both an inflation model and a curvaton model. For inflation, the deviation is too big, but for the curvaton it is small but not insignificant. This is nice because, according to David, if this asymmetry is real and the curvaton is responsible for it, then the fluctuations will be measurably non-Gaussian.

This means we can either rule this mechanism out as the cause of the apparent asymmetry, or even better, get evidence supporting it and thus supporting both the curvaton model and the real-ness of the asymmetry. So, watch this space...

## Wednesday, June 5, 2013

### CPPP II

This is a continuation of posts about the Cosmological Perturbations post-Planck conference being held in Helsinki this week. You can see my introduction post here and my first post from the conference here. If you're a member of the general public and want to understand more, please ask. If you're a cosmologist and want to add anything to what I've written, please add a comment.

The Curvaton

Yesterday I tried to introduce what the curvaton is. We had a few talks yesterday that related to this particular framework for generating the initial perturbations in the density of the universe (the curvaton is named the "curvaton" because, in this framework it is responsible for perturbations in the curvature of space-time). Prior to the Planck release, the curvaton had become quite a popular model because it would be capable of producing a distribution of density perturbations that was almost, but not quite Gaussian. This is quite a technical sounding term, non-Gaussian. To hopefully simplify it a little, I'll say that a Gaussian distribution is the familiar bell-shaped curve of a normal distribution. There is no a priori reason to expect that the distribution of the primordial density perturbations has to be Gaussian, but in many aspects of physics (and statistics in general) a Gaussian distribution does turn out to be the default.

However, even before Planck, we knew that the distribution of primordial density perturbations was close to Gaussian. Planck was going to be capable of measuring this distribution even more accurately and thus would be sensitive to even more subtle deviations from a Gaussian distribution. Ordinary inflation predicts a deviation from a perfect Gaussian distribution that would have been too small to detect with Planck. And, the WMAP satellite's measurements of the CMB provided a small amount of evidence that the perturbations did deviate from being Gaussian. This would have been fascinating to discover, and if WMAP's best-fit distribution had been true, Planck would have detected it beyond "all reasonable doubt".

Unfortunately, as we all know now, Planck found that WMAP's evidence was (probably) a statistical fluke (they do happen). So where, does that leave the curvaton?

David Wands gave a talk addressing precisely this question. I suppose the spirit of this talk (and a few others so far) could be summed up by one sentence on one of David's slides: "absence of evidence is not evidence of absence". This sounds like a cop-out, and of course to a certain degree it is. I'm certain David would have preferred to have been giving his talk in the context of a definitive detection of a slightly non-Gaussian distribution of density perturbations. He could tell us which specific curvaton models are favoured, which are ruled out, what needs done to tell the curvaton apart from other mechanisms that can generate non-Gaussianity, etc. On the other hand, the quoted sentence is also true. While the curvaton could generate detectably non-Gaussian perturbations, it could also generate perturbations that Planck wouldn't have distinguished from Gaussian ones.

However, the situation now is that there is no (strong) observational evidence that prefers a curvaton type mechanism to simple inflation. It is customary in this sort of situation to appeal to Occam's Razor and say that, in the absence of evidence that distinguishes between them, the simpler model should be preferred. In the case of the curvaton, I think this is probably going to be the community's consensus, for now (though if you're in the community and you disagree, speak up!).

The hemispherical power asymmetry

Having said that, David Lyth spoke yesterday about one of the infamous WMAP anomalies that Planck confirmed. David's choice of anomaly was the "hemispherical power asymmetry". This anomaly comes from the fact that the amplitude of the fluctuations in the temperature of the CMB along one particular line of sight seems to be systematically slightly larger than the amplitude in the opposite direction. I say "systematically" because this larger amplitude seems to persist when you average the CMB over a range of angular scales. Obviously, for any single angular scale there will be a direction of maximum asymmetry, but it wouldn't be expected that this direction of maximum asymmetry would be the same for other angular scales. The anomaly is then a combination of the fact the magnitude of this asymmetry is unlikely in the standard cosmology and the fact that all angular scales seem to have the same maximal direction of asymmetry.

I want to pause for just a moment to stress something for the people outside of the cosmology community who like to dwell on anomalies like this to claim that cosmology needs to be over-turned. This asymmetry is small (of the order of a few percent). The thing is though that Planck (and WMAP before it) has measured the CMB so incredibly accurately that even very small effects can now be noticed with quite strong statistical significance. Therefore, even if it turns out that this hemispherical asymmetry is more than a statistical fluke, this doesn't mean that the universe is very asymmetric. The universe would be almost symmetric, with a small perturbation away from perfect symmetry. It is certainly conceivably possible that some other, very different, model, will replace the current model (many cosmologists desperately hope for this); however whatever this model is it will still describe an almost perfectly symmetric universe, because that's not a theoretical prejudice, that's observed fact!

Back to David Lyth's talk. David started by making a somewhat over the top proclamation (mentioned in a comment in an earlier post about the conference) that the detection of this asymmetry was as important as the detection of the fluctuations in the CMB themselves (by COBE). I would probably back David up that if the asymmetry is not a statistical fluke and is primordial in origin, that it does rank as highly in importance; however, it is not unlikely enough to rule out the possibility that it is a fluke, yet. However, that wasn't the main point of David's talk. He's a theorist so he wanted to explain where the asymmetry might have come from (and in the process try to make a prediction for how to check whether this explanation is true).

Here, fans of the curvaton might have had their interest piqued, because David's explanation needs the curvaton to work. The method he described was originally proposed by Adrienne Erickcek, Mark Kamionkowski and Sean Carroll (EKC). Thankfully, Sean is also a blogger and has written a blogpost about this method. You should check it out.

I will try to give my own description later, but David did have a clear consistency relationship that would be satisfied if the curvaton and EKC method was responsible for the asymmetry...

The final post of the conference now appears here...

## Tuesday, June 4, 2013

### Cosmological perturbations post Planck (CPPP) I

This week Helsinki is hosting a conference on the theoretical implications of the recent results from the Planck satellite. The official theme of the conference is cosmological perturbations post Planck. This is alluding to the fact that on large distance scales and at early times, the universe is very homogeneous (it is almost the same everywhere) but has small perturbations in things like its temperature and its density. Planck measures the temperature of the cosmic microwave background (CMB) today, which is an almost direct measurement of the density of the universe soon after the big-bang. This is because the CMB that came from the more dense bits of the universe lost a bit of energy climbing away from that little bit of extra matter and vice versa, the CMB gained energy falling out of less dense regions. Therefore, Planck has made an accurate measurement of the perturbations of the density of the early universe.

But what, are (some of) the implications of this measurement..? Hopefully this conference will elucidate that a little.

I'm going to do my best to describe what is said as the conference proceeds...

Planck's results

The conference started this morning with Helsinki's Mr Planck, Hannu Kurki-Suonio giving an overview of specifically what Planck found in its measurements. If you want a more detailed summary of this you can read some of my posts from when the data was released. The essence is, however, that the standard cosmological model, which had been settled on by most of the community as the simplest model that fits all the pre-Planck data works very, very well in a post-Planck world. There are a number of things about this model that are uncomfortable from a theoretical perspective, but it fits the data we measure extremely well.

But, there are some anomalies (which Hannu ran out of time to cover), which means there are some aspects of the data that aren't predicted by this simplest cosmological model. The anomalies are anomalies because they aren't overwhelmingly statistically significant. This simplest cosmological model only predicts the statistical properties of the perturbations in the universe and all of these anomalies are technically possible, they're just somewhat unlikely. They also don't have obvious explanations from well-motivated new physical effects. They could be statistical flukes. If you have a big enough set of data and look at it in enough different ways you will find anomalies, that's just what noise is. There are two questions that need asked when considering these anomalies:

• Are there actually more anomalies than we would expect?
• For each anomaly, is there a well-motivated model that can generate the effect seen without changing all of the many other things that aren't anomalous (either by completely replacing this simplest cosmological model, or by tweaking it in some way)?

The first question is almost impossible to answer. There are too many ways of looking at a data set this big and it's just too hard to quantify all the ways in which is isn't anomalous. This leaves us with just the second question. The reason why these anomalies are called anomalies is that we weren't expecting things like this and the reason for that is that none of the things we thought were well-motivated deviations from the simplest cosmological model predicted these things.

That's the playing field at the beginning of the conference.

The Curvaton

Many of today's talks were on the topic of the curvaton.

It's going to be hard for me to describe to you what the curvaton is given that I haven't ever properly told you what the inflaton is, but I'll give you a quick whirlwind introduction of both. The inflaton is the field that drove something called inflation. Inflation is a (hypothetical) period early in the history of the observable universe when the universe's expansion accelerated. This period is thought to have happened because it would have smoothed out any pre-exisiting inhomogeneities in the universe (in its density, in the curvature of space-time, in the number density of exotic types of matter, etc). There are issues with this because inflation needs the universe to be somewhat homogeneous even to get started, but despite that inflation still definitely leaves the universe more homogeneous than it found it, so at the very least it helps.

But, the thing that is most interesting about this potential inflationary period is that it would also seed very small perturbations in the otherwise homogeneous universe it left behind. This doesn't sound like much of a gain. Without inflation the problem was that there might be too much inhomogeneity, why should we celebrate this small amount of inhomogeneity inflation leaves behind? The answer to that is that, for a given inflationary model we can actually predict the statistical distributions of these post-inflation perturbations. This gives us something to measure and then compare to theory. In other words, we can gain evidence for or against inflation through observation. There may have been inhomogeneities around in the universe before inflation but we have (almost) no way of predicting them. Inflation lets us make predictions and test them.

So, what is the curvaton in all of this? Well, in the simplest models of inflation there is only one thing other than space-time that is around during inflation. This is the inflaton, the field driving this accelerated expansion. In a curvaton model, there is still an inflaton driving this expansion, but there is also as least one other thing around, the curvaton. And, in these models, it is the curvaton that produces the perturbations that we observe today. The inflaton still produces perturbations, but they decay over-time and the curvaton's don't (as quickly).

Why is this interesting? Why should one study a curvaton model?

That's a very good question. The first, not-quite-completely-joking answer I can give is because you can. It is a possible reality for the universe. This is what theoretical physics is about, thinking about what is possible and exploring the observational consequences if the possible were real. So, from that perspective, why just assume that, if inflation occurred, that a curvaton field wouldn't be present? The counter to this perspective is that it adds complexity to inflationary models.

Unfortunately, it is now past midnight. More to come tomorrow...

## Saturday, June 1, 2013

### Cosmological perturbations post-Planck (conference)

 Helsinki, as it looked when the Planck data was released, less than three months ago. (Image credit: Samuel Flender's facbook photos)
Hello people reading this (present and distant future). Next week, we're hosting a conference here in Helsinki. On balance, I enjoyed covering the last conference I attended (it was demanding, but rewarding). So, I'll cover this one too. This means, each day I'll try to write a summary of what I found interesting during the day's talks.

The last conference was very observationally based. It was hosted by ESA and was the first scientific conference after ESA released data (measured by the Planck satellite) on the temperature fluctuations in the cosmic microwave background. The conference next week will be quite different. Next week, we'll mostly be theorists. Of course, there really isn't a cold, hard, dividing line between a "theorist" and an "observer", but nonetheless, this conference will be much more focussed on what the measurements from Planck (and other past and future experiments) mean for the universe and its laws. Whereas that last conference also focussed on what it is Planck actually measured (and how they measured it).

This is quite exciting. Planck's release was something of a bombshell, even if this was just because it seemed to strongly confirm the simplest cosmological model that was designed to fit all the previous data. People weren't (aren't?) so content with that model, and were hoping/expecting for something new that might show us where to look to replace it. However, even if theorists aren't, it seems that Planck is content with the model.

The theoretical cosmology community has now had three months, a quarter of a year, to digest these results. So this conference will be interesting, even just at the very least to see how the community is dealing with the shell-shock from March. However, it will be more interesting to see what models look good, which don't, and where people have adjusted their attentions from and to in this three month period. Should we still be interested in exotic particles potentially being present in the early universe? What about "monopoles" and "domain walls"? What inflationary models are still appealing and which are on their way out? Why is everyone suddenly talking about primordial magnetic fields? If the universe is a little asymmetric, what caused the asymmetry?

That's the sort of thing to be looking out for next week!

Take a look at the programme for the conference. Whether you are a member of the general public or another cosmologist, if there is anything you see that you are interested in let me know and I'll make sure to pay particular attention to that talk and summarise it here afterwards. Absent from reader's suggestions I will write about the things I generally find interesting, anything that might have some sort of human interest value and things that get a lot of discussion (either during the talk, or afterwards). The more you interact (whether you are an expert or a member of the public), the closer to what you find interesting my blogging will be.

## Monday, May 20, 2013

### Stem cells 2.0

It's been a divisive issue for as long as it's existed, but the topic of human embryonic cloning has been thrust back into the spotlight this week with the news that researchers in the US have successfully produced human embryonic stem cells (hESCs) from adult cells for the first time. This is big news because hESCs have the potential, in theory, to become any type of adult cell - opening the possibility for repairing damaged tissues in previously unthinkable ways. Neatly, this was exemplified this month by the revelation that a blind patient has had his sight restored so significantly using hESC therapy that he is now legally able to drive. Such therapy could also be used in therapies for paralysis, myocardial damage, diabetes, and many other disorders.

This new method for generating hESCs relies on harvesting cells from an adult patient (typically from the skin) and then fusing them with oocyte (egg) cells that have been emptied of genetic material. This, in effect, generates a single-cell embryo with the genome of the original adult cell, which can then begin to develop into a multi-cellular body. The most recent work has identified the precise chemical signals that need to be applied to the cells, and at which stages, to generate hESCs. At present, it is illegal in most countries to allow such clones to develop beyond 14 days of age, yet it is still feasible that useful numbers of hESCs could be obtained from even such young embryos.

This promising development hopefully represents the start of an increased investment in the field of therapeutic human embryonic cloning, but is also very likely to reignite the fierce debate over the ethical issues linked to the generation of human clones. Such debate led to severe restrictions in funding and autonomy in hESC research in the United States during the Bush regime, which was subsequently overturned by the Obama administration in 2009. It is my sincere hope that the typically alarmist ways that this kind of work is often portrayed in the mainstream media (such as those that accompanied the cloning of Dolly the sheep) do not hamper scientific policy or public acceptance of such potentially ground-breaking advances.

This is, admittedly, a short post about something that you may already have read, but I am using this, dear reader, to whet your appetite for stem cells as I will be finding my way to writing a much more in depth and revealing post soon about what stem cells actually are and how the abstract 'treatments' that I mention above actually work. Watch this space for more soon.

## Monday, April 29, 2013

### TEDx CERN

 If you live in Helsinki come to our live webcast of the event. We will feed you.

I had intended to write today's post on anomalies in cosmology. Unfortunately, I have suffered a crisis of confidence and have decided to postpone such a post for the future. I now have both a bunch of notes on the topic, left over from the Planck conference and a half-written post, left over from the weekend. The topic is a bit controversial and when I publish some thoughts on it I want to be very careful and precise so as not to accidentally annoy anyone.

Instead, I will tell you quickly about a really cool event that is taking place this Friday.

CERN is hosting a TED-x event. What is that? Well, a TED-x event is similar to a TED event, except that it isn't organised by TED itself. It is only endorsed by TED. What is TED? OK, well, TED is an organisation that organises a set of conferences around the world. The theme of the conferences is "ideas worth spreading" and speakers are given quite short time slots (typically less then twenty minutes) to express these ideas. Consequently the talks are often very fascinating as the speakers are forced to only say what really matters, leaving all the superfluous details aside. At the main TED events the speakers are also almost universally very good at giving talks, so the quality is high.

 George Smoot, the host of the webcast/show. He has also been awarded one of the most illustrious honours any scientist can, a Nobel Prize guest appearance on The Big Bang Theory.

In fact, the TED realm of YouTube is one of the most dangerous black-holes of procrastination you can find. The shortness of the talks, combined with how interesting and intellectually stimulating they are is like the perfect storm of procrastination conditions. They don't last long enough for you to think that watching just one more is a problem. They are interesting, so you don't get bored. And they stimulate your mind so you don't even feel like you're using your time poorly (always my biggest procrastination danger). Then, half the day has gone.

Anyway, I have been making an analogy between science and sports in my mind for a long time now, and first wrote about it here more than a year ago. I really think that there is the potential for fundamental research to be as popular in today's society as sports is. Seriously! You might wonder why, if this is true, science isn't as popular as sports. Football matches fill out arenas and tennis players earn millions each year, entirely from the private sector throwing money at them to do nothing that is even remotely productive, yet even the highest profile fundamental research event of 2012, the discovery of the Higgs particle, was only front page news for a day.

## Wednesday, April 10, 2013

### The human machine: setting the dials

The previous post in this series can be found here.

It may seem sometimes that nature is a cruel mistress. We are all dealt our hand from the moment of  liaison between our lucky gold-medalist sperm and its egg companion. We are short or tall, broad or skinny, strong or weak because of the haphazard combination of genes that we wind up with, and that should be the end of the matter. Yet, as any seasoned card player will tell you, it is not the hand that matters, but how you play it! This, it turns out, also holds true when it comes to our genetic makeup - we can only play the cards we're dealt, but we don't have to play them all and can rely on some more heavily than others. In this post I'm going to discuss the ways in which DNA is organised and its activity regulated, and how this regulation is a dynamic, ever-changing process with cards moving in and out of play all the time. What's more, we'll explore the ways in which we can all consciously take control of our own DNA to help promote good health and long life!

Esoteric instructions laid bare

Most people are familiar with the concept of DNA - the instruction manual for every component that makes you you - but most are perhaps unaware of how DNA is actually organised within your cells. The importance of DNA has led to it achieving a somewhat mystical image in the public perception: a magical substance that sits inside you with omnipotent influence over every aspect of your construction. This perhaps might lead a layperson to think that we don't really understand how genes work, a perception that is encouraged by the abstract way in which the link between genetics and diseases is reported in the mainstream media. However, this impression is entirely false; we understand very well how genes work: DNA acts as a template for the generation of information-encoding molecules called RNA, which are in turn used as templates to make proteins, which then make everything else. This is called the 'central dogma' of molecular biology, which I'm not going to go into in detail now but have touched upon more thoroughly in a previous post: here.

The mystification of genetics in the mainstream perception can encourage people to forget that DNA is just a molecule, with as much physical presence and chemical potential as any other molecule in your body. As such, its supreme influence over you is dependent on pure chemistry and physics. The most obvious consequence of its being a physical entity is that it needs, in some way, to be arranged and organised. DNA exists within the nuclei of your cells, but it doesn't just float around randomly and aimlessly - its organisation is tightly regulated. First of all, DNA exists as a number of different strands, each its own molecule. These are chromosomes, humans have 46 in each cell nucleus, 23 of which you inherit from your mother, and 23 from your father. The classic image of a chromosome is the tightly packed 'X' shape like those in the image below, but actually this is a comparatively rare structure in the life of DNA as this only forms as the cell is dividing.

 Chromosomes seen under an electron microscope. Image is from http://trynerdy.com/?p=145.
In non-dividing cells, DNA does not exist in the cosily familiar 'X' shapes, but instead spreads out to fill the whole nucleus. This is out of physical necessity - the DNA in compact chromosomes like those above is simply too tightly packed to do anything! Proteins and other molecules that need to interact with the DNA in order for its influence to be felt just can't get to it because there's no space. If the DNA spreads out to fill the nucleus, however, there's plenty of room for manoeuvre. Nonetheless, this organisation is not random and is still highly organised. DNA never exists on its own in a live cell - it is always bound to proteins called histones, which act as a scaffold around which DNA is able to wind, like a string around a ball. There is about 1.8m of DNA in each cell of your body, but once wound around histones it has a length of only around 0.09mm - a pretty significant space saving measure! Each little ball of DNA and histone is called a nucleosome; it is held together by attraction between the negatively charged backbone of the DNA and the positively charged side chains of the amino acids making up the histone proteins.

 DNA wrapped around histone proteins to form nucleosomes. Adapted from Muthurajan et al. (2004) EMBO J. 2004; 23(2):260-71

## Tuesday, April 9, 2013

### The Trenches of Discovery

Hello. Our audience here has grown a little over the Planck release period. Welcome to the blog. You might be surprised to learn that there are actually three of us here. The others are James, the biochemist and Michelle the English student/artist/museum curator. Michelle is on sabbatical as she finishes her doctoral thesis, but James is still very much active. In fact, a new post from him should be appearing later today.

I'm guessing that if you arrived over the last few weeks, your primary interest is physics/cosmology/astronomy. One of the main aims of this whole blog was to bring different communities together. So, please engage with all the themes of the blog. I promise you won't be disappointed. Even if you're mostly interested in physics, you should still read James' post later today. In fact, James' posts are still, despite Planck, our most viewed posts (and closest to award winning). I'm not a biochemist and I really enjoy reading them. If you don't understand something he writes, then just ask him to clarify.

In the meantime, feel free to follow the blog through rss, or to like us on facebook, or to follow Michelle or myself on Twitter. You should also check out the other blogs in Collective Marvelling and SciComm.

And, on that note, goodbye a bit from me for now. I'm not as prolific a blogger as it might have seemed these last few weeks. Blogging the Planck conference and results has helped my research by forcing me to concentrate and digest the results, but continuing at this rate any longer, would not. We have each committed to at least one new post every six weeks though, so I will be writing a new post on April 29 at the latest. If you have any preference for the topic of that post, then leave a suggestion in the comments.

And lastly, thanks for all the encouragement and sharing of my posts that has occurred during the conference. Constructive criticism and suggestions for improvement are also welcome. As are rumours and offers of guest-posts from other people involved in fundamental research.

### 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?

## Monday, April 8, 2013

### 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.

## Thursday, April 4, 2013

### The universe as seen by Planck - Day Three (two rumours)

The conference dinner here is about to start (has already started), so I don't have time for a proper post. However, there were some very interesting rumours/revelations today so I'll write them down super-quickly. In increasing order of potential interest (note this post might be a bit technical, I'll explain all of this before the end of the weekend):

The feature at l=1700

A senior Planck figure gave a talk today on the features in the Planck angular power spectrum. Much of his talk was devoted to the apparent feature at $$l\simeq 1700$$. In the 15 months worth of data that Planck has used to generate the cosmological results shown in their released papers, the statistical significance of this feature (when any feature is looked for) was $$\sim 3\sigma$$. This was with a look elsewhere effect that took into account the possibility of the feature occurring at another $$l$$ value.

What he let slip was that, when they analyse this same feature with the full temperature data set, the significance of the feature drops to $$\sim 2\sigma$$.

Of course, not too much should be read into this because the additional data isn't quite as well understood as that first 15 months; however, its the same telescope looking at the same sky and foregrounds, so there shouldn't be too many complications. Note that this feature is out of the resolution range of Planck's polarisation capabilities, so the new temperature data is the only additional data we will get in the next data release.

Planck's data analysed on the SPT sky

One of the curiosities of the Planck release was that it seems to give cosmological results that are slightly discrepant with what the South Pole Telescope was giving. If Planck disagrees with BAO or supernovae, or galaxy clusters this is all interesting, but potentially the result of Planck and/or one of those other analyses getting it wrong. However, SPT is another CMB experiment, the fact that Planck and SPT are a bit discrepant is very confusing.

Perhaps SPT made a mistake and the CMB they measured is not the correct CMB?

The obvious way to test this is to analyse the Planck data on the same part of the sky that SPT measured. I overheard a conversation between lead figures in Planck, WMAP and SPT and it seems this is exactly what SPT have done (in unpublished work).

The result is striking.

They found a cosmology that agrees with SPT.

If true, this means that it isn't just Planck and SPT that are slightly discrepant, but different regions of Planck's sky.

What this means cosmologically is unsure. I'll speculate a bit tomorrow.

Power asymmetry

There was quite a bit of excitement over a plot that showed power asymmetry in different directions of the sky. I was going to write about it, but upon reflection, the excitement seems confusing. I'll try to explain the excitement and background before the end of the week.

[The final summary is now available here]

## Wednesday, April 3, 2013

### 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.