Monday, April 29, 2013


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
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.

Twitter: @just_shaun

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).


  • 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.

Tuesday, April 2, 2013

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.

Monday, April 1, 2013

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.