The Trenches of Discovery

Stem cells 2.0

2013-05-20T14:37:00.002-07:00

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.

TEDx CERN

2013-04-29T13:04:00.000-07:00

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.

Chris Lintott, one of the speakers. Chris will be talking about "how to discover a planet from your sofa". Chris works on Zooniverse, which is one of the coolest things that exists. It is a huge "citizen science" project that involves complete lay-people meaningfully contributing to science from their homes. Go, check out the website, maybe you could contribute to working out how galaxies form?

I think the reason for this is entirely down to marketing. Sports pushes itself into our consciousness and science doesn't. We are allowed to watch the sports take place, yet we can only see the science results. I love this video of Brady Haran discussing this topic and agree with him entirely. When I saw that video I almost invited Brady to come to Helsinki to give a seminar on this topic, despite him not actually being a research physicist. I might still invite him, though I'm not sure what the owner of the seminar purse strings would think of it. But, the point is that I think this is crucially important to fundamental research. The possible dividends from making science more popular are immense.

So, I love the fact that CERN is hosting this event. What's more, you can watch it live, because there will be a live webcast. And you should watch it live.

Another speaker, Hiranya Peiris. Hiranya is a cosmologist and will be talking about the universe as a detective story, which I think is a very apt analogy for cosmology. I will give a free glass of sparkling wine to anyone who can guess why Hiranya is holding that poorly-tuned television (collection of sparkling wine must be made at Helsinki physics department, this Friday).

You can take a look at the programme here. Interspersed with talks about fundamental physics (from cosmology, to particle physics, to marine physics) there will be a bunch of TED-ed CERN animations describing various science concepts and even a few live music performances. I'm honestly not too sure what to expect, but I'm sure it won't be boring. One of the issues I have with science documentaries is that they only show completed, packaged science. Or, at least, they portray it that way. This is fine and I'd rather those documentaries existed than that they didn't, but to follow the analogy it would be like only showing the grand final of a sports event, three months after the event had finished. There's no excitement or drama by then. We love sports because we know the characters involved and their hopes and dreams, because we've followed them through the season(s). We know their back-story, we know their styles, we know their strengths and their weaknesses. And we want to see them in their moment of triumph, or despair.

I don't think this TEDx-CERN event will reach the levels of the utopian future that Brady and I dream of, but it is a step. It is a scientific conference, aimed not at scientists, but at everyone. People will be presenting somewhat unpackaged (i.e. it hasn't been filmed in a studio) scientific thoughts and results to a public audience, live.

Whoever you are (scientist or non-scientist), you should watch the webcast. You should also tell all your friends about it, share it on facebook, tweet about it, write blogposts about it at your blog and tell your boss to give everyone the day off work on Friday. You should especially tell your friends about it if you're a scientist, or want science to be more popular. Help CERN to get people excited/interested in this sort of thing. And help create a demand for more things like this in the future.

Yet another speaker, John Searle. I've run out of speakers whose work I know (that's why we need more events like this), but apparently John is "one of the world’s great philosophers of mind and language" and "what he says about consciousness as a biological phenomenon will challenge you!"

Finally, anyone reading this and keen to watch the event with others should go to this link. If you look on the right hand side of the page you will see the locations of institutes around the world that will be hosting their own events to show the webcast. If you live nearby, you should go to one of them. At many of these events there will be informal discussions and physicists around to talk about the science with you. The Trenches of Discovery has a small but proportionately large Finnish audience (our fourth biggest). So, if you're lucky enough to be living in Helsinki, I can tell you that if you come to our live showing of the webcast you will also be provided with free pizza, wine, sparkling wine and enthusiastic physicists to harass over the course of the evening. You can find details about that event and sign up for it here.

I will probably write a summary of the event sometime after Friday. I also promise to eventually complete that post on anomalies in cosmology, in case anyone is particularly interested.

Twitter: @just_shaun

The human machine: setting the dials

2013-04-10T14:32:00.001-07:00

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

Going up another level of scale now: these nucleosomes can be organised in different ways depending on the intended activity of the DNA therein. These complex organisations of nucleosomes are collectively known as chromatin, which can broadly be split into two forms: heterochromatin and euchromatin. The difference between hetero- and euchromatin is basically how tightly they are packaged. In euchromatin the nucleosomes are arranged much as in the image above - loosely packed and with short free segments of DNA in between. This is known as the 'beads on a string' form of DNA for hopefully obvious reasons. Heterochromatin, on the other hand, is far more tightly packed - nucleosomes are very closely associated and there is very little DNA between individual nucleosomes. This is called the '30nm fibre' because it is 30nm in diameter, and is quite similar to the kind of fibres that pack together the form the X-shaped chromosomes mentioned earlier.

DNA's many forms. Euchromatin corresponds to the 'beads on a string', whilst heterochromatin is the fibre of packed nucleosomes. Image from http://dellairelab.medicine.dal.ca/research.html.

These two types of DNA packing mean that all genes are not created equally! Heterochromatin and euchromatin have very different levels of activity - euchromatin's loose structure allows easy access to the machinery that relay DNA's instructions and so genes in this region are fairly active; whereas the inaccessible structure of heterochromatin means genes in these areas are pretty silent. Segregating areas of the genome into more and less active areas is important in the regulation of gene expression, as some genes simply need to be more or less active than others in order for the cell to function properly.

A classic example of this is X-inactivation. As you may be aware, 2 out of our 46 chromosomes are the sex chromosomes: women have XX and men have XY. The Y chromosome is entirely distinct from the X chromosome, which means that for every gene that exists on the X chromosome women will have twice as many copies per cell. This presents a problem because it just isn't feasible for male and female cells to have a two-fold difference in gene activity for the important genes on the X chromosome - it would require differences in the wiring of the cell that are just too extreme to exist between members of the same species. So, either males need to ramp up activity from their solitary X chromosome, or females need to halve activity from theirs. In the case of mammals (including us) each cell in a female randomly chooses one X to exist as euchromatin (and so have high activity) and one to become heterochromatin (and so have low activity), thereby redressing the balance between males and females. So, if you are a woman, half of the cells in your body are working off genes from the X chromosome you got from your mother, whereas the other half are working of those from your father. This is particularly apparent in certain types of cat known as tortoiseshell or calico cats, in which one of the genes responsible for coat colour is contained on the X chromosome. So, if a female cat inherited different copies of this gene from each parent, then the colour varies at different areas of the coat because in some it will be the colour from the father, and in others the colour from the mother, giving an attractive speckled effect. This is why the first cat to be cloned (called CC for 'Copy Cat'), which was a female calico, looked pretty much completely different to the cat from which she was cloned despite having 100% identical DNA.

X-inactivation is responsible for the attractive coats of calico cats. Image from Wikipaedia.

Reading the genetic code in many ways

The example of CC the cat touches upon a vitally important concept of genetics, that activity from genes is not fixed and is in fact quite malleable. Importantly, this is not limited to lifelong inherited traits such as cat coat colour, but is actually able to be influenced during the lifetime of an organism. Basically speaking, your genes can be switched on or off, or their activity decreased or increased by factors that occur during your lifetime, such as lifestyle, drugs, or hormonal changes. It is difficult to overstate just how ground-breaking an idea this was when it was first discovered: for the first time it seemed that we weren't limited by our pre-written genetic fate - we could be masters of our own destiny as long as we understood how to influence the system. The idea of nature and nurture being mutually exclusive was dismissed - we now knew that nature could be influenced by nurture.

The concept of a system of gene regulation by non-genetic means is called epigenetics. Segregating DNA into hetero- and euchromatin is a fairly rigid epigenetic mechanism that doesn't alter much throughout your lifetime. Instead, it is the behaviour of the associated histone proteins that can influence the activity of your DNA in a manner that alters according to environmental factors. This is possible because histones are able to undergo at least 60 different modifications to their amino acid building blocks whilst they are still bound to DNA. These modifications involve the addition or removal of chemical groups from the histone proteins, which acts as a code for how active any associated genes will be. Moreover, this is combined with chemical modifications made directly to the DNA itself that can further influence gene activity. Broadly speaking, each modification either promotes or inhibits activity from the DNA bound to that histone. For example, a methyl group is a chemical group comprised of one carbon atom attached to three hydrogen atoms - addition of three methyl groups on the lysine 4 or lysine 36 amino acids on histone protein 3 causes an increase in gene activity in that area, whereas adding three methyl groups to lysines 3 or 29 on the same protein causes a decrease in gene activity. The overall activity from any individual gene depends on the balance between pro- and anti-activatory histone modifications.

Histone proteins and the potential modifications that can occur. Each type of modification (acetylation, methylation etc.) represents that addition of a specific chemical group to amino acids in the histone proteins.Figure adapted from http://www.integratedhealthcare.eu/1/en/histones_and_chromatin/1497/.

The ways in which these modifications influence gene activity are extremely complex but they all work by either increasing or decreasing interactions between the histones and either the DNA itself or the machinery involved in relaying its activity. The modifications themselves are made by histone-modifying enzymes that exist within the nucleus either chopping off or sticking on the modifications as required. It is the activity of these enzymes that is sensitive to external factors: for example, a cell may be under some form of stress that necessitates the activity of a specific repair gene, so signalling pathways within the cell cause the activation of histone modifiers and then target them to the target gene in order to turn it on and save the cell. The system is highly complex and highly dynamic, meaning that the instructions that make you you can be read in an infinite number of ways. This is why identical twins are never fully identical even though they are genetically equivalent. Importantly, though, it also means that if you are genetically predisposed to a certain medical condition, heart failure, hypertension, hereditary cancers etc., there is a chance that epigenetic alterations to your DNA may either spare you or condemn you by influencing how significant your genetic predisposition becomes. So, if we can understand and influence the code governing histone modifications then we may be able to change all of our genetic fates for the better.

This is very well exemplified by the link between epigenetics and cancer. Many cancers have been observed to rewrite the epigenetic coding within their DNA and so influence their growth. For example, a number of cancers have been found to block the activity of histone modifying enzymes responsible for adding activity-promoting acetyl groups to histone protein 3 bound to genes involved in suppressing cell growth, with the effect that these genes are now less active and so the cancer is freer to grow and multiply. Indeed, the projected outcome of patients diagnosed with some cancers is intimately linked the to epigenetic changes that have been found to occur in their cancerous cells. It is by no means limited to cancer, though, several developmental and immunological disorders have also been linked to epigenetic changes in the DNA of the affected patients. The more we learn about the code of histone modification, the more chance we have of being able to influence it in a clinical setting, both for therapeutic means such as in the treatment of cancer, but also as a prophylactic method of reducing the risk of some diseases in at-risk individuals. This is a big topic in molecular biology at the moment, and a huge amount of resources are being poured into unravelling its secrets.

Number of papers published with the keywords 'disease' and 'epigenetics' in the last 30 years - the exponential growth reflects the increased importance of epigenetic understanding to disease treatment. Source: http://www.sciencedirect.com/science/article/pii/S1357272508003889#.

Being master of your own destiny

I promised you at the outset that I was going to explain how you could take control of your own genetic fate and so give yourself the best chance of a long and healthy life. It may seem, so far, that the advances that I've mentioned will help those suffering from a number of terrible diseases, but will do little for us healthy folks whose genes haven't turned against us. Well it's certainly true that the majority of data collected is on the role of epigenetics in disease for the simple reasons that people with diseases need the most help and attention, and that they are easily classifiable into different groups (bowel cancer, lung cancer etc.) whilst healthy individuals can't be classified according to presented symptoms. Nonetheless, evidence is slowly building that some lifestyle changes can be beneficial to long-term health in part due to the epigenetic changes that they bring about. Not only that, but there are some indications that these changes may not be limited to your own lifespan but may also extend to those of your children by altering the epigenetics in the very first cell that grows into your bouncing bundle of joy!

Perhaps unsurprisingly, the best lifestyle choices that you can make to help improve your genetic lot are broadly the same ones that you should be making to improve your health in general anyway: i.e. exercise regularly, eat well, don't smoke etc. It seems that the beneficial outcomes of these behavioural choices are not limited to physiological effects such as strengthening the heart, but also influence long-term gene expression that may help to make you a healthier person throughout your entire life, as well as helping to stave off conditions such as cancer. For example, a report in Cell Metabolism has revealed that acute exercise has epigenetic effects on the expression of several genes involved with sugar metabolism that may help to prevent diabetes or improve the prognosis of diabetic patients. Current thinking is that the transient changes in gene expression brought about by lifestyle factors such as exercise may over time cause a stable reorganisation of epigenetic regulation that affords long-term health benefits that may well outweigh any genetic disadvantage that an individual may have. So the next time you consider slacking off training, remember that the effects may stay with you for the rest of your life!

As far as your children go, well it had been thought for some time that epigenetic markers were erased in primordial gene cells (which eventually develop into sperm and eggs) so that each individual would get a clean slate, and it is certainly true that this is the case for the majority of epigenetic modifications. However, recent research has indicated that about 1% of genes manage to hang onto their modifications in the form of methyl groups directly added to the DNA itself. It's not yet clear whether its always the same genes that get through unchanged or whether the process is just not fully successful, but the possibility is there that epigenetic changes that occur in your lifetime could influence the health of your future children.

Where next?

Most efforts at present are focussed on fully understanding the interplay between different epigenetic mechanisms and the effects that environmental factors have on them. Once that is further advanced there is the possibility to tailor treatments and lifestyle recommendations to individuals based on both their genetic and epigenetic profiles. This is a step beyond the current efforts to promote genomics-based medicine, in which patients are treated on the basis of their genetic profiles alone, most notably in cancer therapeutics.

Aside from that, uncovering the mechanisms of epigenetics is a worthy goal in and of itself as we will be one step closer to understanding the human machine in full. This is why I got into biochemistry in the first place - a love of the beautiful complexity of nature - and I hope that this, and not just the translational potential, drives future research in this and all areas of medical science.

Citations:

Barrès, R., Yan, J., Egan, B., Treebak, J., Rasmussen, M., Fritz, T., Caidahl, K., Krook, A., O'Gorman, D., & Zierath, J. (2012). Acute Exercise Remodels Promoter Methylation in Human Skeletal Muscle Cell Metabolism, 15 (3), 405-411 DOI: 10.1016/j.cmet.2012.01.001
Hackett, J., Sengupta, R., Zylicz, J., Murakami, K., Lee, C., Down, T., & Surani, M. (2012). Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine Science, 339 (6118), 448-452 DOI: 10.1126/science.1229277

The Trenches of Discovery

2013-04-09T19:18:00.000-07:00

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

2013-04-09T06:30:00.000-07:00

[Continued from yesterday...]

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

The anomalies

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

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

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

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

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

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

The cosmological results Planck has obtained for quantities like the expansion rate of the universe and the overall density of matter in the universe seem to be slightly discrepant with some other measurements of these quantities.

I've already discussed in some detail the nature of, and possible resolutions to, the discrepancy between Planck's CMB measurements and the abundance of galaxy clusters detected by Planck.

There is also a discrepancy between Planck and local measurements of the expansion rate of the universe. The value for the expansion rate inferred from Planck appears to be smaller than what was measured locally using supernovae and Cepheids. Unfortunately no real insight was gained regarding these discrepancies during the conference. One interesting, and mildly concerning, result was that already two of the local measurements of this expansion rate have been "corrected" to produce a smaller value. Although, thankfully, both of the groups claim that these corrections were in the pipeline before Planck released its results.

Finally there is a more curious discrepancy. This is the apparent discrepancy between Planck and the South Pole Telescope (SPT). This is curious because it is a discrepancy between two CMB measurements. In principle SPT should be measuring a sub-set of the same sky that Planck measures. Therefore any discrepancies are harder to understand or put down to misunderstanding the theory (and thus more interesting).

I overheard an interesting conversation during the conference. It was between a senior figure in SPT, a senior figure in WMAP and a senior figure in Planck. They were discussing this discrepancy. What I overheard was that, when Planck's data is examined on the same patch of sky that SPT can see, the data points from SPT and from Planck lie on top of each other. This is very interesting because it suggests that the source of this discrepancy is not coming from either Planck or SPT making a mistake. It is either just sample variance (i.e. a rare fluke), or something more interesting.

On Friday, John Carlstrom, from SPT was part of a discussion panel where he was asked to address this discrepancy. His explanation for the discrepancy suggested two sources (both of which probably combine to cause the change). One is that the power in the WMAP temperature anisotropies is systematically slightly larger than Planck's. SPT is a ground based telescope, which means that it cannot measure the whole sky. Therefore, to do cosmology, SPT needed to combine its small-scale measurements with WMAP's large-scale measurements. Therefore, WMAP's small, but non-zero surplus of power relative to Planck will affect SPT's cosmology. Note that the WMAP people at the conference were taking this small surplus very seriously. On the large scales Planck and WMAP should see exactly the same CMB. The fact that they don't indicates that one of the groups has missed some systematic effect in their telescope (my impression from the conference was that WMAP thought it was them).

The second effect that Carlstrom discussed is an extra "rounding of the small-scale peaks" in Planck as compared to SPT. The implication seemed to be that this could partially be due to the effects of lensing on the CMB by local structures. This lensing effect is real and expected and measured, but it will still vary from line of sight to line of sight. It is conceivable that there is simply less structure to provide lensing along SPT's line of sight, which would mean less rounding of the small-scale peaks, which would mean SPT would require less matter than Planck to describe its measurements.

Of course the probability of this happening is included in both SPT and Planck's error bars, so if there is an excess or shortage of lensing along any line of sight, it would require some sort of new physics in the local universe along that line of sight. Such a conclusion should certainly be approached cautiously, but it is worth observing that all of these discrepancies between Planck and other measurements seem to have potential explanations in modified late-universe physics (i.e. this SPT discrepancy, the cluster abundance discrepancy and the local measurements of the expansion rate).

The late-universe is nowhere near as tightly constrained as the early universe.

Time will tell...

What comes next for CMB science?

An artist's depiction of the Cosmic Origins Explorer (COrE). Hopefully one day COrE will do to CMB polarisation what Planck did to CMB temperature; suck it dry.

Planck has more or less exhausted the temperature anisotropies in the CMB as a useful probe of cosmology. In principle a new telescope could be made that could measure microwave radiation with even better resolution, but the primordial CMB has almost no fluctuations on scales smaller than Planck's best resolution and foregrounds are already dominant on Planck's smallest scales.

So what else is there? Do we give up on the CMB and find other sources of information about the early universe?

Not just yet. Firstly, Planck will not exhaust the polarisation of the CMB. Planck was not initially designed to be a polarisation sensitive telescope and so its polarisation resolution is well below its temperature resolution. There is scope for a future polarisation telescope that will be able to exhaust the polarisation the same way that Planck has exhausted the temperature. An example of such a telescope is the COrE (Cosmic Origins Explorer) telescope proposed to ESA by European collaborations.

In the meantime both the Atacama Cosmology Telescope and South Pole Telescope have attached polarisation detectors to their CMB telescopes and have begun taking high resolution measurements of the small-scale polarisation spectrum. There is also Planck's impending polarisation measurements. The future holds exciting prospects for constraining cosmology using the CMB's polarisation.

But there is another source of potential information lurking in the CMB that is often forgotten. The spectrum of Planck is equivalent to an almost perfect blackbody, but it can't be completely perfect. At some level, there must be some distortion. The best measurements to date of the blackbody spectrum of the CMB were made by COBE (by the FIRAS instrument) in the 1990's. These measurements were rightfully hailed as one of humanity's greatest achievements at the time. The famous plot produced by FIRAS where the theoretical blackbody curve and experimental data points fit so closely that you can't even see the error bars, truly is impressive. However, technology has come a long way in twenty years. Why should we not measure the frequency spectrum of the CMB to even better accuracy?

I can tell you why we should.

Firstly, there is a guaranteed signal. The same physics that takes the power spectrum of temperature anisotropies and reduces the power at small scales, will also introduce a spectral distortion to the blackbody spectrum. On Friday we had a talk from Rashid Sunyaev, another old-school Soviet cosmologist (though Sunyaev is more on the astrophysics side and less on the field theory side than the other two), who told us that this spectral distortion would be measurable by a proposed future telescope called PIXIE.

The prominent physicist from the former Soviet Union that sponsored this post was Rashid Sunyaev. If you stick with the blog long enough you can collect the full set (be warned, there are a lot of them).

So that gives the guaranteed signal, but spectral distortions in the CMB are also a really interesting probe of a variety of new physics possibilities. Firstly, there is the possibility of detecting the effects of the decays of exotic particles. If an exotic particle were to exist in the early universe and was to interact weakly enough with the rest of the constituents of the universe then it would not be in thermal equilibrium with them. If it were to then decay into other particles that did interact with the rest of the universe, then this would appear like an injection of additional thermal energy. If the CMB formed before the universe could reach thermal equilibrium again, then this would introduce a spectral distortion in the CMB that PIXIE could potentially measure. Also, if the primordial density perturbations had a large enough amplitude on very small scales, primordial blackholes would form. These primordial blackholes would also be out of thermal equilibrium with the rest of the universe and would also emit radiation. This again would distort the blackbody spectrum of the CMB.

This raises the interesting possibility that PIXIE could further constrain inflation on distance scales that no other probe could ever realistically constrain. The problem is that the fluctuations on these scales would need to be much larger than what we observe on the larger scales already probed. When you combine this with the fact that on the scales we have observed, the power seems to decrease at smaller scales, it does make the prospects of these spectral distortions existing less plausible. But that doesn't mean they definitely wouldn't be there.

Finally, the SZ effect (where S stands for the same Sunyaev), which is scattering of the CMB off hot gas inside clusters and galaxies, would also introduce a spectral distortion. If PIXIE were to map out this spectral distortion over the whole sky this would give a wonderful map of the large scale structure of the universe.

There is one last source of information lurking inside the CMB. On Wednesday night at the conference a public session was held. One of the attendees asked a wonderful question. He understood that the CMB we see is just an image of a surface, billions of light years away. He wanted to know how long we needed to wait until the image we see changed. I don't think the panel quite understood his question because their answer just related to the inevitable redshifting of the CMB's temperature, but as well as that the actual values of the anisotropies will change. This is because, if we wait long enough, we're literally looking at another patch of the primordial hydrogen plasma with different over/under-densities.

Thankfully Lyman Page was listening and understood the question, and, during his talk on Friday he answered it. The answer to this question is present in Stuart Lange's senior thesis and I think it's really cool. The answer is that, if we wait billions of years, the CMB will have completely changed. You can see a simulated film of this below (note the scale in years). This might then sound like it is just a cute curiosity, nice but unobservable. But it isn't quite. Using very ambitious estimates, Lange estimates in his thesis that even in a timeframe of the order of 100 years the minute differences that will have occurred might just be detectable. If they were, we could then do real-time cosmology by calculating the statistical properties of this difference map. Those will be cool days.

This is how the CMB anisotropies would change over time if we sat and watched for long enough (obviously this is only a simulation, we don't know how the real universe will change with time). What a cool senior thesis topic!

Summary

And I'm done. Hopefully I will get around to writing something about the anomalies at some point. However, given how contentious they appear to have become I want to be careful and precise whenever I do choose to write about them.

My lasting impressions of the conference were the following:

A measurement that a parameter is zero, is still a measurement. Planck has told us some genuine facts about the very early universe. Those facts might not be extravagant, but they are facts. It's really quite amazing that as a species we've managed through observation and reasoning to learn anything about what the laws of physics are like at those incredibly high energies.
Planck might not have measured a primordial bispectrum, but the fact that they have detected, with reasonable significance, the secondary bispectrum that arises from a lensing-ISW correlation is important to remember. It means is that a power spectrum is no longer enough to fully describe the statistical properties of a Planck CMB map. The era of non-Gaussianity has begun.
All of the discrepancies between Planck and other experiments potentially relate to late-universe effects. The early universe is quite well constrained now, but the late-universe is not at all. Could we be starting to see the signs of new physics in the late-universe? It is true that the most significant of these discrepancies, the under-abundance of galaxy clusters in ACT, SPT and Planck's cluster samples, could be the result of biases in the mass measurements of these clusters. However as Dick Bond said in the panel-discussion on Friday afternoon "ignore clusters at your peril". Clusters have been the unheeded heralds of new physics before, might they be trying to tell us something interesting again?

The only unquestionably statistically significant anomaly from Planck. Ignore clusters at your peril...

(Note that, in the 1990's there was a "missing mass" problem relating to the masses of galaxy clusters. People were convinced that the universe was flat, but if it was that required more energy density in the universe than what was present in clusters, hence the "missing mass". That missing energy density is what we now call dark energy, but it took the supernovae measurements before people were convinced that the cluster measurements weren't just wrong.)

Finally, just because no deviations from $\Lambda$CDM have yet been measured, does not mean that no deviations exist. Even in the early universe there is still plenty of room for surprises.

Twitter: @just_shaun

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

2013-04-08T14:55:00.000-07:00

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.

With satellites like Planck those perturbations are now being ever more precisely examined.

Mukhanov has a very different perspective to Linde regarding what inflation can or cannot explain. To him the question of whether a theory is scientific or not comes down to one thing and one thing only: has it made unique a priori predictions that can then either be verified or used to rule out the theory? From that perspective his view is that inflation has only ever predicted one set of results and those are the predictions of the first, simplest models of inflation. He makes no distinction as to whether those models are well described by a quantum field theory model or not.

I don't happen to agree with this perspective and I don't think most practising physicists would either. Inflation might be true and yet not described by one of those original models. If that is the reality, then I would want science to be able to test this reality.

However, Muhkanov deserves credit for at the very least sticking religiously to his guns. He likes to show slides during talks like this that were written on overhead transparencies in the early 90's. This dates these slides to an era before the anisotropies in the CMB were discovered, before the late-time accelerated expansion was discovered and a time when the total observed mass in the universe was indicating that the curvature in the universe might be significant (i.e. in technical terms it would be "open"). These slides make a number of specific predictions for what inflation requires (by Mukhanov's definition of inflation).

A flat universe (i.e. no curvature)
Perturbations that had a Gaussian distribution
Perturbations that were almost scale-invariant, but not quite (they would need to have a slightly larger amplitude at larger scales)
Perturbations that were adiabatic (i.e. all the constituents of the universe were perturbed in the same way)
A small, but not insignificant quantity of primordial gravitational waves

How many of these predictions have now been verified?

All but one.

The reason why Mukhanov deserves credit is that at two separate points in history at least one of these predictions has been in serious jeopardy. I mentioned above that when Mukhanov was first writing these predictions down, there seemed to be some evidence that the universe was open. At that time, some inflationary theorists (Linde amongst them) were trying to construct models of inflation that could generate an open universe. Mukhanov said in his talk that at this point of history he was considering leaving cosmology because he believed inflation could not survive as a predictive science if the universe was open. It turned out that those tentative hints of open-ness were actually the first evidence of the consequences of the accelerated expansion and that the universe is flat.

Then, last decade the WMAP satellite was showing not insignificant evidence for a large degree of "non-Gaussianity" in the CMB. If that had been verified, Linde's inflation would have survived (after all it can explain anything), but Mukhanov would have pronounced inflation dead. Planck showed that WMAP's evidence was only a statistical fluctuation and that, to Planck's accuracy, there is no evidence for primordial non-Gaussianity.

Mukhnov's view of inflation seems to be surviving quite well.

There is that one missing piece though.

These are primordial gravitational waves.

Can we ever prove inflation right or wrong?

If you will stick with me I am about to explain how it is possible that Planck's observations have simultaneously made it more likely that inflation is correct but more difficult to ever prove it right beyond doubt. I appreciate that this sounds a bit silly, but read on.

If you look at the list of predictions from Mukhanov's inflation one thing that might leap out at you is that most of the predictions are basically the absence of something (except the primordial gravitational waves, but I'll get to them). No deviations from Gaussianity (which is the default because of the central limit theorem). No curvature. The perturbations in each field are the same. The fact that each of these predictions has occurred definitely strengthens the case for inflation, but it doesn't prove it beyond doubt, because each prediction is also kind of the default.

Compare this to the Big Bang. We know the Big Bang occurred because it made a collection of very non-trivial predictions (e.g. the existence of the CMB and the fact that its temperature and polarisation would be correlated and would carry the evidence of primordial sound waves, etc). What inflation needs is to also have something non-trivial.

What many theorists were hoping for is that inflation was correct, but that it was Linde's view of inflation that was correct, not Mukhanov's. In this case, there could have been some non-Gaussianity, or some other feature. Through the analysis of these features, a distinctive signature of one of the many other models of inflation might be seen. We might rule out the simplest model of inflation, but the hope was that we would detect a more complicated (perhaps even less compelling) alternative model. The fact that any features that might exist have so far evaded our detection makes this possibility less likely.

Hence, the case for inflation has improved from Planck (i.e. the predictions of its simplest models and its most compelling models were verified), but the possibility we might one day verify it beyond doubt has decreased (i.e. the most compelling models make rather neutral predictions, without distinctive features).

A future colleague of mine, Chris Byrnes (thanks for the job dude!) showed this comic in his talk. Chris (like me) is a theorist who has worked on models of inflation that can generate non-Gaussian primordial density perturbations. The comic pre-dates Planck, but I think it explains what Planck did to these models quite well. These more exotic models could still be true, but the exotic parts of them seem to have "no influence on the Universe whatsoever". Nature can be cruel.

The are two non-trivial predictions in Mukhanov's list. I'll still get to primordial gravitational waves, but the other prediction is the almostness for the scale invariance of the primordial curvature perturbations. If inflation predicted pure scale invariance and that had been observed, it would be as bland and as neutral as flatness, adiabaticity or Gaussianity, but it didn't. It predict almostness for the scale invariance. Planck has now verified, that in the $\Lambda$ CDM model, the primordial perturbations are not scale invariant and that they deviate from scale invariance by just the right magnitude to match Mukhanov's prediction. This was non-trivial, but it is just one number. Maybe that one number coming out right was a fluke? Compared to the entire curves I showed you last week that match what we expect from primordial sound waves and thus provide irrefutable evidence for the Big Bang, getting one number right isn't quite enough to convincingly determine that inflation really did happen.

It's definitely a murder weapon, found at the scene of the crime, but it isn't a smoking gun.

So, is there a smoking gun for the simplest models of inflation?

Does inflation have a smoking gun?

And now I get to primordial gravitational waves, the only piece missing from Mukhanov's puzzle and what, if they were detected, would surely warrant, for Mukhanov, one of the most well deserved utterances of "I told you!" in the history of humanity's pursuit of knowledge. He would have spent more than twenty years, resolutely saying the same thing over and over again, while the rest of the community flitted backwards and forwards, only for them to eventually settle down exactly where he has stood, unmoved, from the beginning.

(Almost) Every single model of inflation predicts that there would exist primordial gravitational waves that are also almost scale invariant. This level of prediction is at last non-trivial. The existence of almost-scale-invariant primordial gravitational waves would indicate that, early in the history of the universe, the energy density of the universe was very large (to generate the waves) and almost constant throughout space and time (to make sure they are scale invariant). This is very nearly the actual definition of what is required to generate an inflationary epoch.

The big problem is that the amplitude of these waves depends on the model. For some models (the simplest) the characteristic effects that these waves would have on the CMB's polarisation are right on the verge of detection by Planck. For others (arguably the most compelling) they are so small that we'll never see evidence of them.

Sadly, we are starting to reach the point where Mukhanov's brand of simple inflation is going to be ruled out (I guess Mukhanov would say that he's heard this kind of statement a few times before). It still survives, but barely. If it does get ruled out, but inflation is still true, then these primordial gravitational waves will be there. But, there is no reason to expect that they will be loud enough for us to ever detect them. Maybe inflation occurred at a low enough energy scale that we'll never see the primordial gravitational waves it inevitably generated, but at a high enough energy scale that we'll never be able to probe inflationary physics with a collider. The window between those two energy scales is enormous.

This might leave us, for many generations, in the awkward position that inflation seems compelling and likely, but still hasn't quite been verified beyond doubt. But such is life for an observational, rather than experimental, science. We can only observe what nature has chosen to make observable.

If we assume inflation is true, have we learned anything about it?

I wrote above that Mukhanov's favoured simple brand of inflation and the other (arguably) most compelling models of inflation make rather neutral predictions. I also said that there were other models that made less neutral predictions. So surely, at the very least, if we assume inflation is correct, the observations of Planck have said something about inflation, even if it is just that those other models were wrong?

Correct (mostly)!

If we assume that inflation is true then Planck's observations are starting to say some kind of interesting things about what type of inflation might have generated our Big Bang. In a talk on Thursday Mattias Zaldarriaga gave a nice talk about what Planck has told us about inflation. He made some nice observations.

We know inflation must end and that the inflaton must end up in a stable vacuum state (or inflation would still be happening and we wouldn't be here now). In the language of a Taylor expansion, the first term around this vacuum would be $\phi^2$. Now, Planck is on the verge of ruling out $m^2\phi^2$ inflation. If $m^2\phi^2$ inflation is ruled out, then we can say, using a kind of Taylor expansion measure of the distance from the vacuum, that during inflation the inflaton field was far from the vacuum. Or, in other words, at least one other term must exist in the inflaton's potential!

I find that kind of neat. There isn't enough information to determine what that term is, but we know it must be there. That would be one non-zero piece of information about the particle content of the early universe that cosmological measurements have now provided us with. No collider will ever probe those energies, but, through cosmology, we have gained at least some information.

We will soon know a little bit more. If Planck does not verify the existence of primordial gravitational waves, then as you can see from the figure below, this would eventually require the potential of single field inflation models to be concave during inflation. The minimum we lie in now must be convex. Therefore, we know that at some field value the curvature of the inflaton potential must change. Again, this isn't a substantial fact, but it is a fact, a fact about the particle content of the universe at incredibly high energies.

This shows the amplitude of primordial gravitational waves (y-axis) vs how far from scale invariant the primordial curvature perturbations were (x-axis - 1.00 would be scale invariant). The blue contours show the space allowed by Planck. The black dots show $m^2\phi^2$ inflation, the simplest model of them all. I must have spent a solid six months in the first year of my doctorate staring at WMAP's version of this figure each day, mostly confused, trying to reproduce someone else's unreproducable work, and not really making much progress. Good times.

The final pieces of information we have gained relate to these non-observations of features. It was well known before Planck that any slowly rolling, single field, model of inflation could not generate observable primordial non-Gaussiniaty. This is one of the reasons many theorists were so hopeful for a detection of non-Gaussianity, because it would definitively tell us that there was something non-trivial about the early universe. The converse of this is not quite true, multiple field models of inflation can exist without generating non-Gaussianity. However there are reasonably generic things one can still say.

If one were to write down the physics describing the inflaton and parameterise the deviations from the simplest single-field slow-roll situation with a variable speed of sound and/or modified dispersion relation (a modified dispersion relation kind of describes how fluctuations of different scales act within the universe - a "modified" dispersion relation implies the physics is different for different wavelengths) then one would inevitably generate non-Gaussianity. Therefore, the fact that no non-Gaussianity has been observed tells us non-trivial things about the speed of sound and dispersion relation during inflation. There may very well be more than one field, or various other modifications, but those extra fields can't change those quantities.

That's also kind of neat. A measurement that a certain parameter is consistent with zero is still a measurement of that parameter and it does still tell us something about the nature of the very early universe. Whatever its constituents were, the speed of sound in the very early universe was very close to the speed of light.

The one caveat is that for any of those points to become facts does require the assumption that inflation definitely did occur.

Why aren't the simplest models the most compelling?

Physicists and non-physicists might have been puzzled by a distinction that crept into my language above. I separated the simplest models from the arguably most compelling. I added the word "arguably" because I don't think Muhkanov would make this distinction and neither would some others. However I am someone who would. Let me give you the argument why.

(In most models) Inflation empties the universe out of everything except the inflaton. That was actually why inflation was invented in the first place. But, when we look at the universe today it definitely isn't empty of everything except one field. We see hydrogen and lithium and helium and ever more complicated atoms and molecules. If inflation is true and inflation empties the universe of everything except the inflaton field, then, well, clearly everything we see now must have come from the inflaton.

This means that the inflaton field must interact with us. The interaction might be very weak (in fact it has to be) and it might even be indirect through interactions with other intermediate fields, but sooner or later the energy in the inflaton field must turn into the energy in hydrogen, helium, the CMB, etc.

This point was raised by Anupam Mazumdar late on Thursday and it is a major problem for the simplest models of inflation. For inflation to work, the energy density during inflation must be almost constant (but not quite). For this to happen the inflationary potential energy function must be almost flat (or, more precisely, must have an almost flat part of it). Any interactions with messy standard model particles will act to destroy this flatness.

Finding a potential energy function that is stable to this feature is difficult and the simplest inflationary models simply are not stable to it. This means, that even though one can calculate the predictions for the density perturbations generated by these simple models it is very difficult to work out ways of generating our universe's matter without ruining those predictions, or altering the potential so significantly that inflation would no longer even occur.

From this perspective the most compelling inflationary models are those that are complete. These models can generate both the density perturbations and the matter in the universe. Such models do exist, though they aren't without their own (arguably less severe) issues.

The problem for testing inflation is that these models occur at lower energies than the simplest models and thus the primordial gravitational waves that they generate would never be observable. It is technically possible to write down a complete model of inflation that can generate primordial gravitational waves that Planck will eventually detect, but those models aren't simple, nor are they particularly compelling.

Still, time will tell...

[the non inflation stuff has been continued here...]

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

2013-04-04T10:10:00.000-07:00

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]

The universe as seen by Planck - Day Two

2013-04-03T14:22:00.000-07:00

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.

These SZ detected clusters were what many of this morning's talks were on and the results do seem to be potentially interesting.

SZ detected clusters

One of the very nice things about detecting galaxy clusters with the SZ effect is that the probability of detection does not decrease for clusters that are further away from us. The other methods to detect clusters (e.g. by their emission of X-ray radiation) suffer from the fact that the light from the cluster gets dimmer the further away from us it is. However, because the SZ effect is not a light source being emitted by the cluster, but instead a scattering of the CMB, that is not the case. In fact, if a cluster gets too close to us it becomes more difficult to detect the cluster using the SZ effect because the scattered image in the CMB becomes too large and becomes more difficult to distinguish from an ordinary CMB fluctuation.

One of the not so nice things about detecting galaxy clusters with the SZ effect is that, because the detection efficiency is almost independent of our distance from the cluster it isn't really possible to determine how far away a detected cluster is. We can say that there probably is a cluster somewhere along a given line of sight, but not exactly where along that line of sight.

A second not so nice thing about SZ detections of galaxy clusters is that, because the CMB itself also has fluctuations, there is always a chance that one of these CMB fluctuations will mimic the SZ effect seen when the CMB passes through a cluster. This means that it is necessary to "follow up" any potential SZ cluster detection with some other probe in order to make sure it really is a cluster.

Many of Planck's candidate cluster detections had already been detected by other telescopes and for those candidates that were original detections Planck has verified their existence using the XMM X-ray telescope.

The principle behind doing cosmology with galaxy clusters is that one can use detection proxies like SZ signal significance or X-ray temperature to estimate the mass of the cluster. Then, one can use a theory to determine the number of clusters expected to exist in a given volume and given mass range. Then one can compare observation to theory.

One of the biggest problems in doing cosmology with clusters is that you don't know if you've seen every cluster that is out there. When you compare to theory you need to make sure that you are only comparing to the theoretical clusters that you definitely would have seen. Therefore, to do cosmology properly you don't just need to know the probability that a given cluster will exist, you also need to know the probability that you would have also detected it. This isn't always trivial to do. Some of the more interesting clusters are detected serendipitously (e.g. they were in the background of a photograph of another astrophysical object). Once they're detected, we definitely know they're there, but we have no idea how to quantify the probability we would have seen them. For these clusters, all we can do is wait until some other survey that detects clusters more algorithmically sees them as well. And this other survey would need to have definitely seen the cluster, without any prior knowledge. If we point a telescope at a cluster because we already know it is there, then that's cheating and we still can't quantify the probability we would have detected initially.

This is where Planck is perfect. It surveyed the whole sky and was always going to survey the whole sky. Therefore, even though it might not have detected a great number of new clusters itself, it does allow us to do cosmology with a number of clusters that we previously knew about, but had to just smile at forlornly.

Cosmology with Planck's SZ detected clusters

The results are unexpected. To create a sample of clusters to compare to theory, Planck only keeps the clusters with an SZ-detection significance above a certain value. They have seen cluster candidates with significances below this value, and they've even followed some of them up with XMM, but they haven't followed all of these up with XMM, so they don't know whether all of these lower significance candidates are real clusters. However, with their chosen threshold, they do know they have a complete sample.

The red dots are the number of observed clusters. The error bars are statistical (i.e. Planck do know the exact numbers of clusters they've observed). The green curve is what Planck's CMB measurements would suggest (note the y-axis is logarithmic - that's a lot of missing clusters).

They find that the best fit cosmological model from the Planck CMB data predicts almost twice as many clusters should have been observed compared to what was observed. This sounds very striking and it definitely is interesting, but it isn't quite as drastic as it sounds. There are two parameters in the standard cosmological model that cluster abundance is most sensitive to. These are the overall matter density (put simply, if you have more matter, you get more massive galaxy clusters) and the amplitude of the primordial density perturbations (clusters form in the peaks of the density field and if the amplitude of the perturbations is bigger, then there are more large mass peaks). The abundance of clusters is actually very sensitive to these two parameters. For example you would need to change the amplitude of primordial density perturbations by less than 10% of its value to double the expected number of clusters in Planck's sample.

However, within the standard cosmological model, these parameters have been very accurately measured and this discrepancy is still a significant one.

So what does this indicate? Why has Planck not seeing these missing clusters (100's of them)?

Here are some candidate explanations raised today during talks and in questions raised afterwards:

Neutrinos have masses. This is now known. If neutrinos have big masses, then some of the dark matter is actually neutrinos. These neutrinos will suppress the growth of structures on small scales. Essentially, those clusters are missing because the matter that was meant to fall into them didn't quite manage to collapse into a large mass cluster because some of that matter is actually neutrinos and those neutrinos were moving too fast to fall into structures.
Those clusters exist, but for some reason Planck hasn't seen them. What we predict is that a set of clusters of a given mass should exist. What we measure is a set of clusters with a given SZ-effect. What Planck does is calibrate the relationship between these two observables by looking at a sub-set of clusters for which there are multiple measurements of the clusters' masses (e.g. SZ effect, X-ray temperature, the lensing of the images of galaxies behind the cluster). An assumption is then made that certain relationships between the SZ-effect and mass found in that sub-set holds for the full sample. For Planck's observation to be explained by this assumption breaking down it would require there to be clusters that exist with large mass, but an anomalously small SZ-signal. This is actually what one might expect for the most massive clusters. These clusters are likely to be irregular, or still forming. Therefore, the hot intracluster gas might not be as hot as would be typical (for a cluster of the given mass). Therefore, they would exist, but Planck wouldn't see them. This sounds sensible, but don't forget, Planck is missing ~100 clusters (which is also about the number it has seen). That's a lot of missing, irregular, clusters.
We know the masses of clusters better than we thought! This sounds ridiculous. How could over-estimating one's errors cause half of the universe's clusters to just disappear? Well, it's not that ridiculous actually. The expected number of galaxy clusters of a given mass falls off exponentially fast as mass increases. Therefore, there are always expected to be many, many more clusters that exist with smaller mass than larger ones. Now, suppose there is some scatter between the mass of an observed cluster and its SZ-detection efficiency. This means that for a cluster of a given mass sometimes it will have a slightly higher detection efficiency and sometimes a slightly lower one. If the Planck collaboration comes along and selects only the clusters with an SZ-detection efficiency above some threshold, then, because there are so many more low mass clusters, it is actually far more likely that they are seeing lower mass clusters that have unusually large SZ-detection efficiencies than that they are just seeing large mass clusters. Pulling this all together, when Planck predicts how many clusters they should see they are including the possibility that these low mass clusters have crossed this threshold. The wider you assume this scatter can be, the lower the limiting mass you are allowing to scatter up above this threshold. As I told you above, there are exponentially more low mass clusters than large mass clusters. Therefore, widening these errors on the cluster masses significantly increases your expected number of observations.

Other SZ cluster surveys

Planck isn't the only telescope capable of detecting clusters using the SZ effect. Two ground based CMB telescopes (ACT and SPT) actually have better resolution than Planck and thus can detect clusters with slightly lower masses (though they see less of the sky). It is curious to note that both ACT and SPT also see an under-abundance of clusters.

On the left are all the cluster experiments. On the right are the CMB experiments. The measured parameter is a combination of the matter density and the amplitude of primordial density perturbations. Clearly the clusters and Planck's CMB measurements are in tension. Out of curiosity, also note SPT's CMB measurement and how strangely low it is. I've heard no explanation for a potential cause of that.

Andrei Linde "inflation can explain anything"

The last talk of the day today was by one of the founders of inflation, Andrei Linde, who boldly stated that inflation can explain anything. Inflation is most popular candidate for what generated the primordial density perturbations. One day I will try to explain what the paradigm of inflation actually is, but that day isn't today (in the meantime, google will give many other people's attempts).

A concerned reader might wonder how one can possibly do science with such a paradigm. If inflation really can explain anything, then how are we to determine whether it is true? Surely that isn't science!?

I have some thoughts on this that I've decided to share.

Yes, inflation can explain (almost) anything. But also, no, that doesn't mean we can't do science with inflation. The reason is that there are better models of inflation and there are worse models of inflation.

Before explaining why I think that matters, let me explain how I understand science works. Science works through the construction of models of nature and the observation of nature. Which model is chosen by science depends on two things: how believable the model is and how well it fits the data. Quantitatively speaking, this is just Bayes' Theorem, but I'm not going to speak quantitatively, because the "how believable a model is" aspect of science doesn't (usually) work quantitatively. Whenever a new measurement is made, all the competing models are judged on both of these criteria.

A perfect example of this is the Copernican model of the solar system vs the Ptolemaic model. When the Copernican model was first presented it actually fitted the observations of the solar system worse than the old Ptolemaic model. Nevertheless, it relatively quickly (I guess that's debatable) became established as the most believed model. Why is this? The reason is that it was just so much simpler. Instead of having epicycles upon epicycles, all of which needed to be put in by hand, there was instead just one simple assumption: the sun is at the centre of the solar system. If you're curious, the reason the model fitted the data worse is that it assumed circular orbits and the true orbits are elliptical, but the model still won.

Of course, on unsatisfying model can win too, if more and more data comes out in its favour. Cosmology has exactly this situation with the very unsatisfying dark energy (it just seems to work!).

What has this got to do with inflation? Well, when we make measurements, we test the various different models of inflation. If the measurements favour the simpler, or more believable (better) models then inflation has had a victory. If the measurements favour the less believable (worse) models, then inflation has suffered a defeat. Unfortunately, there is no alternative paradigm to inflation with an equally believable foundation, therefore no observation could (yet) cause a paradigm shift away from inflation. However, there could be observations that would make it less and less believable, fuelling desires to find alternative models. Linde is right that inflation could still explain those hypothetical observations, but if an alternative model came along that also explained those observations in a much simpler way, science would turn to that model.

So what is the true status of inflation models given Planck's results? I think many of the talks I will attend tomorrow will be on this topic. So, stay tuned... (the short answer is that inflation has done very well)

(Note however that tomorrow includes the conference dinner. Therefore, it is unlikely that I will find time to write a post tomorrow. More likely, I will write a summary of both tomorrow and Friday's talks sometime on Friday afternoon/evening)

[Some rumours from day three are now here]

Twitter: @just_shaun

The universe as seen by Planck - Day one

2013-04-02T15:37:00.002-07:00

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

Overall summary

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

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

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

The missing data feature

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

The red stuff is the galaxy. The blue/green stuff is the CMB. But what on Earth is that grey stripe? Talk about features!

Planck made quite a big deal about a number of "features" in their analysis (some of which I'll discuss below), but no mention was made of this feature that seems so obvious you can make it out by eye.

It turns out there is a well understood reason for this particular feature. Firstly, Planck had two independent telescopes on board. The low frequency instrument (LFI) and the high frequency instrument (HFI). These telescopes measured the intensity of microwave radiation at different sets of frequencies. This "feature" can only be seen in the LFI maps and is actually the result of those points on the sky being measured less often by LFI than all the others.

During one of LFI's sweeps of the sky it was hit by a cosmic ray. After this, it started taking measurements that were completely discrepant with expectations. How did LFI solve this? Just how you solve any other hardware problem. They turned it off and on again (apparently). Once back on, it was back to taking measurements that made sense. However, during all of this time, the telescope was sweeping across the sky, measuring different points on the sky. Every point that it missed during these events were therefore not measured in that sweep and remain measured one less time than the rest.

This grey band in the LFI maps is exactly that region of the sky. So, no excitement there.

Issues with polarisation

Planck hasn't just measured the temperature of the CMB, it has also measured the polarisation of the light in the CMB. If the big bang model is correct, then that polarisation should have certain statistical properties that reflect the sound waves in the primordial hydrogen, just like the temperature does.

In this release of data, none of the cosmological results from Planck have included any measurements of the polarisation. Why?

The answer to this question is that, at very large angular scales, the polarisation is not behaving well. Planck measures the temperature and polarisation at many different frequencies. The CMB should have exactly the same temperature and polarisation at every frequency. For the temperature, it does. For the polarisation, it doesn't seem to yet. So what's going on?

Well, the polarisation of the CMB is a very weak signal, much weaker than the temperature. Therefore, even though enough foreground radiation has been removed from the measured CMB to isolate the temperature signal accurately, this does not mean that the polarisation is not still contaminated.

The way that Planck can see most clearly that something is still a problem is by subtracting one map from another (i.e. two maps of the CMB temperature measured at different frequencies). If the polarisation is measured correctly then the remaining signal should be close to zero. If it isn't, there is a problem. One of the speakers showed a nice slide this morning (the slides aren't online and this isn't published so I can't show you the image) showing the amplitude of the polarisation signal in one of these subtracted maps as a function of angular scale. As the angles become small enough it definitely went to zero; however at the large angles it was still quite large.

In order to use the polarisation to obtain cosmological constraints Planck needs to understand all the angular scales correctly. Therefore, rather than work out what was going wrong, they decided to wait and solve that problem later.

Still, at the small angular scales, the polarisation data can be trusted and in this data Planck have one of their most impressive figures. The figure below shows how both the temperature multiplied by the polarisation (pixel by pixel on the sky) and how the polarisation itself varies with angular scale. The blue dots are the measured signal. Now, the red curve is not the best fit curve to this data. That is worth pausing and reflecting on. If it isn't the best fit curve, then what is it?

These curves reflect some of the best of humanity. These are the tiny fluctuations in the polarisation of a field of radiation, left over from a hydrogen plasma that permeated the entire universe, 14 billion years ago. The oscillations in the curves come from sound waves in this hydrogen plasma. The curve is our prediction for this data, with no free parameters to play with at all. Just reflect on that. I'm unable to describe how incredible this is. We don't even know whether Shakespeare wrote Shakespeare's plays, but we can predict exactly what the polarisation in the CMB should look like.

That curve is the unique prediction from analysing Planck's temperature data. There are no free parameters in defining those red lines. Once the temperature data is analysed, we can make an unchangeable prediction for what the polarisation should look like. The fact that the red line goes straight through the blue data points is absolutely remarkable. However, if one believes in the big bang and standard cosmological model, this is all that could have happened. If one doesn't believe in the big bang, then not only is there no reason to suspect that the CMB exists, or that it is polarised, but certainly not that the way the polarisation averages on particular angular scales should look like that.

I think it is worth pausing for one second longer on this. I'm about to start describing a few "features" and anomalies that might be present in the Planck data. It is tempting for a person cynical about natural science to pick up on these anomalies and say "scientists don't understand what they're doing, look at all these anomalies". The thing is, scientists are trying to understand everything. It isn't enough that the model explains almost everything, every possible failure is looked for and analysed. If someone wants to replace the big bang, or any other aspect of cosmology (or well-established science) it isn't enough just to explain how to create these anomalies. Any alternative model must also reproduce everything that works. Without the big bang the prediction for that red line would be a horizontal line through zero. That wouldn't be called an anomaly, that would be called a completely failed model.

Tentative feature evidence

There are "features" in these curves. A feature is a collection of data points that are consistently above or below the red curves, over an extended range. Can you find them?

Look at the curves in the bottom panel of the figure above. These curves show the difference between the measured value of how the CMB temperature depends on angular scale and the best fit model from cosmology. Clearly some of the data points lie above the curve and some below. These data points have errors on them. We can't measure them perfectly, so this is what we expect. However, if there was a true "feature"in the data, something genuinely unlikely, then what would happen is that, over some range of $ l$ values the data points would lie either above or below the theoretical curve.

Planck claim to have found two of these features in the figure above. Before reading my next paragraph, have a look at that figure and see if you can find where these features should be. There are meant to be two, and only two (remember you're looking for a collection of data points next to each other that consistently lie above or below the theoretical line)...

Found them? Well, when Planck analyses the data, allowing for isolated features to exist in the primordial signal, they find two regions where a feature can improve the fit to the data. One is at very large angular scales (at $l\simeq 20$) and one is at very small angular scales (at $l\simeq 1700$). I think if you look carefully you can see these two features in the curve above (at least I can convince myself that the blue data points are consistently below the theoretical curve). Now, neither of these features are all that statistically significant, but introducing them does help fit the data.

There are a variety of possible models for how such features can arise but all of them require adding additional parameters to the standard cosmological model.

This would be a pretty bleak situation (i.e. the features may be real, but they may not, we'll never know) if it weren't for one thing. All of these models that would predict features in the temperature, also predict features in the polarisation. Great, you might think, let's just look at the polarisation.

Problem.

As I wrote above, one of these features is at a very large angular scale and one at a very small angular scale. I've already mentioned Planck's problems with the large angular scales. Hopefully one day they'll get this sorted (they seem confident) and we'll be able to see. Unfortunately, Planck's excellent resolution in measuring the temperature is not quite as excellent with the polarisation. And, this particular small angle feature is at angles too small for Planck to resolve in the polarisation. This doesn't make this feature untestable ever, it just means we'll need to wait for a new telescope to make these measurements.

Bispectra

All of the curves above are called power spectra. What they essentially do is tell you how the CMB's temperature or polarisation will look if you average it over two points separated by a particular angle. If the power spectrum has a larger amplitude at a particular angle, then the CMB's temperature should look more similar over those angles (i.e. if it is hotter at one point, then it should also be hotter at another point that is that particular angle away from it). If the amplitude is smaller at a particular angle, then the CMB will look less similar over those angles.

Why stick to two points though? If one can calculate an average over sets of two points on the sky one can also calculate an average over sets of three points on the sky. This is called a bispectrum. One of Planck's biggest drawcards was its ability to constrain the bispectrum of the CMB's temperature anisotropies.

And it did.

In the standard cosmological model, the primordial bispectrum should be almost zero. It should be so close to zero that no experiment yet conceived should be able to detect it. This is because the standard cosmological model predicts that the primordial density perturbations should have a Gaussian distribution and a Gaussian distribution has a zero bispectrum. You might have heard about the search for "non-Gaussianities". This is it. This is what we've been obsessing about when we talk about non-Gaussianity because the primary way in which Planck searched for non-Gaussianities was by searching for a non-zero bispectrum.

There were high hopes. WMAP, Planck's predecessor, had seen tentative evidence for a non-zero bispectrum in a number of different ways. It was known that Planck would reduce the uncertainties on the bispectrum and the hope (maybe even the expectation) was that Planck would detect it with high significance.

This just didn't happen.

Instead, Planck has constrained the bispectrum quite tightly. Each of the ways in which WMAP was seeing evidence for a bispectrum, Planck has shown it to favour zero. Of course, a two-point average depends on just one number, the angular separation of the points. However, a three-point average will also depend on how the three points are oriented with respect to each other. Therefore, there are many ways in which a bispectrum can be non-zero and Planck has only analysed some of them.

Moreover, Planck does find tentative evidence for bispectrum features. What this means is that if they search for a non-zero bispectrum that is highly localised in terms of the angular separation of the three points they see some hints of a non-zero signal. This is similar to the features in the power-spectrum I described above. This is interesting, but perhaps not compelling. The reason it isn't compelling is that they analysed a lot of possible bispectrum features. Most of these features were consistent with zero and a few weren't. If you look for a signal in enough hay-stacks eventually you will find one.

A "feature" bispectrum. See how it depends on three different angular scales? See how it is localised to one particular set of these scales (i.e. it goes white when $l$ gets big). Just as I told you. Other than that, this figure is going to have to be just eye candy. It's after midnight and I need to go to bed. Ask if you want more details.

But wait, there are features in both the power spectrum and the bispectrum, could they be related? good question. The simple answer is definitely, yes. Any model that generates a feature in one will almost definitely generate a feature in the other. However, both features should occur at the same angular scale. Here, they don't (or at least don't appear to - I'd love to be corrected if that was wrong!).

Trispectra

Well, if you can average over three-points, why not average over four? The number people use to quantify the amplitude of the bispectrum is parameterised as $f_\mathrm{NL}$. This is the number Planck has found to favour zero. A four-point average, or trispectrum, would be parameterised by $g_\mathrm{NL}$. Did Planck constrain $g_\mathrm{NL}$?

Not yet.

I've actually done some work on $g_\mathrm{NL}$, so I was eagerly searching through Planck's non-Gaussianity paper in March looking for these constraints, only to find nothing. $g_\mathrm{NL}$ is interesting because it would enhance the abundance of extreme over-densities in the universe and extreme under-densities at the same time. $f_\mathrm{NL}$ can only do one or the other, but not both. This could make $g_\mathrm{NL}$ a candidate explanation for the ISW mystery, which I've blogged extensively about.

I overheard today that the reason why no $g_\mathrm{NL}$ constraints were announced in March is the same reason for no use of polarisation data to do cosmology. That is, the $g_\mathrm{NL}$ analyses are failing "null tests". What this means, is that when the CMB maps are analysed in a way such that the result for $g_\mathrm{NL}$ should be zero, it still gives a non-zero signal. An example of this is when the maps generated from intensity measurements at two different frequencies are subtracted from each other. The CMB should cancel, and thus the four-point average should be zero. If it isn't, something is going wrong. This problem is less of an issue for the bispectrum (although not completely non-existent).

Tension between CMB and astrophysics

The tension between astrophysical measurements of some cosmological parameters and the measurements of those parameters by Planck was mentioned early today. This is one of the most fascinating things to come out of Planck.

The primary two tensions here are measurements of the expansion rate of the universe and measurements of the abundance of galaxy clusters.

It is tempting to dismiss these tensions as systematic errors being made on the astrophysics side. The justification for this relates to what I wrote in my first post about Planck; it is very easy to predict what we should see in the CMB, but much more difficult for other cosmological probes. However, these other measurements are the most honest estimates, using what we know about astrophysics, to constrain these parameters. We shouldn't be so hasty to dismiss all of astrophysics so readily. What if this is due to new physical effects instead?

This is the main topic of the talks tomorrow, but I'll leave you with an image showing, quite strikingly, that this discrepancy really does exist. It is the constraints obtained on the amplitude of primordial density perturbations on a given distance scale plotted against the constraints on the density of matter in the universe. The blue curves come from the abundance of galaxy clusters (detected by Planck) and the red curves come from Planck's CMB measurements.

Now that is what I call a feature in the Planck data. The blue curves are what Planck's clusters tell us about cosmology. The red curves, what Planck's CMB measurements tell us. The way to interpret curves like this is that the preferred value of the parameter is the one inside the curves. I think I can see this feature by eye.

Something is clearly going on...

(Feedback and questions are welcome. was this too technical, not technical enough? Do you want more figures or less figures? Would you like me to quote actual numbers for the parameters I mention, or are you happy with descriptions?)

[The second day's summary can be found here]

Twitter: @just_shaun

The universe as seen by Planck (conference)

2013-04-01T14:55:00.000-07:00

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.

This week the talks will be aimed at cosmologists, astronomers and astrophysicists and the public will have to put up with bloggers like me who try their best to make the talks intelligible to the interested member of the public.

But that's not my only motivation. I also want to learn things myself. Conferences like this are tiring. Trying to take in information over the full week is difficult. By forcing myself to try to write something every day about the conference I will also force myself to pay more attention during the week.

Most importantly, I hope that if I write something here that is wrong, or is some sort of misconception on my behalf, that somebody reading will call me out on it (so please do, for my sake and for the sake of the other readers). Similarly, if I don't understand something during a talk I will write down questions here. If you know the answer, please let us know. Also, whether you're a cosmologist, or member of the public, if you've got a question about the conference, please ask. Either I can answer you, another reader can answer you, or I can ask someone at the conference and get an answer for you that way.

What will I post about?

There will be many talks each day on a variety of topics. I would not be able to summarise every talk, even if I wanted to. So, I won't. What I will do is write about a selection of events and talks from the day that satisfy any the following criteria:

I found it interesting (this is my blog, so fair is fair)
It generated a lot of conversation and/or controversy at the conference
Things that I think might have human interest value
And... finally, the things that I think will be interesting to readers and other physicists, even if I'm not so interested myself.

I can't cover everything, so if you were at the conference and you stumble across this blog and I didn't write about your talk, I'm sorry. I promise that if people interact with me through the comments and/or Twitter, the chances that I will cover what they talk about will astronomically increase.

Highlights to expect

The conference hasn't started, but we've all seen the papers, and the conference programme can be found here. There may be surprises and unexpected controversies, but here's a few things to look out for during the week (from my perspective):

Andrei Linde. Proof that cosmology can make you rich (if Mr Milner chooses to give you $3,000,000). But is inflation correct? And has Planck made it more believable, or less testable, or both?

What is the community's perspective on inflation models post-Planck? Andrei Linde and Slava Mukhanov will both be at the conference and are members of the founding gang of the theory of inflation, which is the leading candidate for how the primordial density perturbations in the universe were generated. There are better models of inflation and there are worse models of inflation. Arguably, what Planck saw is more in line with what the more believable models of inflation predict. It will be interesting to see what the conference's consensus is on inflation and what these two very vocal Russian physicist's perspective will be. Is it now 100% verified (I wouldn't support this)? Has it been given a boost in believability (probably)? Does the lack of observation of new effects in the primordial universe starve us of insight into the nature of inflation (I expect some will argue this)? We will see...
Planck detected fewer galaxy clusters than it was expected to. It detects these cluster from the way they affect the CMB as it passes through them. One possibility is that their are fewer galaxy clusters, which would be a consequences of neutrinos having relatively large masses. Another possibility is just that Planck is under-estimating the masses of these clusters. I'm curious to see conversations develop around this issue.
There is tension between the results from Planck and local measurements of the expansion rate of the universe. Have these local measurements just made a mistake, or is this a sign of interesting local, or late-universe physics? Similarly, the South Pole Telescope seems to have results that are slightly discrepant with Planck. Have SPT made a mistake, or is the sky anisotropic and SPT have seen a genuine effect?

How have the more ambitious theorists reacted to Planck's abundance of null results? Verifying that cosmology requires no new epicycles was a triumph for cosmology and humanity's pursuit of knowledge, but where will theorists turn to now? There are still unanswered questions in cosmology, even if no new clues as to how to resolve them. Moreover, just because we haven't yet observed deviations in the early universe, doesn't mean there aren't more subtle deviations still waiting to be found.

The keynote talks. On Tuesday and Wednesday there will be keynote talks at 17:00 CET and on Friday at 14:00 CET. Whether you are a scientist or not, these talks would be well worth tuning into the webcast to listen to. They will be more general and more speculative than the rest of the talks. On Wednesday there will also be a public session immediately following the keynote talk and on Friday, the conference summaries will follow the keynote talk. So you should also tune into the webcast to watch them.

I ask for your forgiveness in advance

Each of the posts I manage to write this week will be written under immense time pressure. The conference ends each day at about 6-7pm and starts the following morning at 9am. I also have to eat. I won't have time to carefully read over anything I post, nor to thoroughly check the physics. I'll do my best.

This is also the first time I've attempted anything like this. Hopefully I'll learn and do it better next time. Any feedback, advice or suggestions would be more than welcome.

Because of the above, I should add the usual disclaimer that any views expressed by me over the next four days certainly don't reflect the views of the conference organisers, nor my employers. But I'll add an additional disclaimer too. The views expressed over the next four days will possibly not even reflect what my own views would be upon reflection.

I might have a go at live-blogging, if I get adventurous later in the week. Or, I might tire myself out and skip a day. We will have to wait and see.

I will do my best to Tweet a bit and follow Twitter during each day. You can follow me at @just_shaun and the obvious hasthag to follow is #Planck. that is the one I will try to follow.

Summary

Noordwijk. Does anyone else think that ESA should have released Planck's results in June? I'm still tempted to go for a swim on Friday.

This week ESA is hosting a conference in Noordwijk, in The Netherlands to analyse and discuss the cosmological results from the Planck satellite. I will be here and will try to write daily summary posts about the most interesting talks and discussions from the day. You can follow the conference through its webcast, which is presented live here. You should pay particular attention to the keynote talks each day, which are at 17:00 (CET) on Tuesday and Wednesday and 12:00 on Friday, as well as the public session following the keynote talk on Wednesday and the conference summary following the keynote talk on Friday.

Please ask questions in the comments during the week if you want me to clarify anything (whether you're an expert or not). If you think I've written something that is wrong, please point this out in the comments. Half of the reason I am doing this is to learn myself and if I have any misconceptions I really want them to be pointed out. Also, if you know the answer to any questions I happen to ask, please provide them in the comments. If you want me to cover anything specific, please point this out in the comments.

This won't be easy so any encouragement and/or sharing of these posts that you wish to do/give will be most welcome!

[The first day's summary is now here]

Twitter: @just_shaun

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

2013-03-24T18:09:00.001-07:00

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

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

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

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

Why I found what Planck saw to be incredible

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

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

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

The red bits are the measured data, the green curve is the best fit model. The line only needs six parameters to describe it and it just goes straight through the data. Somehow, a crazy species of ape that spends half its time trying to kill itself has managed to both predict this curve so accurately and then put a satellite in space, cool this satellite so that it is colder than space and measure the curve. Awesome.

Anyone who isn't a fan of dark matter and dark energy should take a moment and think about the following: Only one of those six parameters was included in the cosmological model in order to explain an aspect of the temperature fluctuations in the CMB. However, each and every one of them will affect the CMB in non-trivial ways that Planck can see. And finally, everything that Planck saw can be described by this model.

Here are the six parameters (in one particular parameterisation) and why we first needed them in cosmology.

The Hubble parameter: The Hubble parameter describes the expansion rate of the current universe. We've needed a Hubble parameter since Hubble first noticed the expansion of the universe. This was at the beginning of the 20th century, long before the Big Bang model even existed, let alone measurements of the CMB or its anisotropies.
The density of dark matter today: Dark matter also pre-dates the Big Bang and the CMB. It was first postulated to explain why galaxies were rotating too fast
The density of dark energy: "Dark energy" has been required by modern models of cosmology because the expansion of the universe appears to be accelerating today.
The amplitude of the primordial density fluctuations: There are galaxies in the universe. Therefore, there needed to be very small fluctuations in the density of the very early universe, around which these galaxies could form. Precisely how big these fluctuations were, is a free parameter.
The spectral index of the primordial density fluctuations: The amplitude of these density fluctuations could depend on their physical size. Fluctuations in the density could be more pronounced on small distance scales, or on long distance scales. Note that this is the one parameter that could be argued to be required as a consequence of the CMB

The optical depth due to reionisation: After stars form, they emit enough energy to partially ionise the neutral hydrogen remaining in the universe. By the time this happens, the hydrogen is very diffuse and therefore the universe does not become opaque again. However, the CMB will sometimes scatter of the released ions. The "optical depth" measures how far back in time this reionisation process occurred. While the optical depth is not a fundamental cosmological parameter, we don't understand the reionisation process well enough yet to remove it from the model. Once this one parameter is fixed though, we have no more freedom to play with.

And that's all the freedom there is in the simplest cosmological model. Fix those 5+1 numbers and everything the CMB could show us is fully predicted by the model. If we know the constituents of the universe today and how fast it is expanding, we can run the clock back and work out what the universe looked like when the CMB formed.

There was no guarantee that the real world would follow suit and produce a CMB that matched this prediction, but it did. The fact that we only need those 5+1 numbers to describe such a rich range of cosmological phenomena is itself surprising and I happen to find that remarkable.

One curious observation

The greatest mystery in modern cosmology is what "dark energy" actually is. Planck was never going to shed much light on this because the CMB is a probe of the early universe, whereas dark energy primarily affects the late universe. In fact, Planck on its own does not constrain the nature of dark energy strongly at all. It is curious to note that both of the anomalies I mentioned at the beginning of this post (the ISW mystery and the under-abundance of galaxy clusters) relate not to the primordial CMB, but to how local structures have affected it. If dark energy were not the simple constant our model assumes it to be then it is much more likely to show up in these probes than any other aspect of CMB physics.

Where to now?

Next week I will be attending the scientific conference related to Planck's release. There will be many talks given by Planck scientists and many by scientists outside of Planck. I am going to try my absolute best to write a post each day, summarising what I found interesting and what I learned from that day's talks. This won't be an easy task I'm sure, but it is also partially for my own benefit. Forcing myself to write coherent blog posts on the day's talks will force me to concentrate and think about them during the day. Also, if I am confused by something I can write it here and hopefully someone will answer. Finally, if I have any misconceptions, hopefully I will write them down here and have somebody call me out on them, allowing me (and every reader) to learn the truth.

If any readers are interested in any particular talk or Planck-related subject, let me know in the comments or on twitter and I will try to pay particular attention to that talk.

At the end of the conference, I will write a summary of what we've learned from Planck and speculating on where cosmology will head to next. Reader's thoughts (both now and during the conference next week) will be very welcome.

Twitter: @just_shaun

Following Planck's results today

2013-03-21T00:42:00.002-07:00

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

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

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

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

Enjoy the day!

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

Twitter: @just_shaun

Planck rumours will soon become Planck results

2013-03-19T19:05:00.000-07:00

On Thursday, the Planck satellite will be revealing its first cosmological results. In terms of fundamental physics, this will be the biggest event since the Higgs discovery last year. In the cosmology community it is the biggest event for the best part of a decade (possibly in both directions of time). If you don't follow cosmology too closely, you might wonder why this particular experiment might generate so much excitement. After all, aren't there all sorts of experiments, all of the time?

If so, I hope you've come to the right place.

The sky as seen by Planck in 2010. Only, they hadn't removed the foregrounds yet. There's a whole Milky Way galaxy in the way. Why must they make us wait so long?

If you're unaware, Planck is a satellite put in space by the European Space Agency to measure the cosmic microwave background (CMB). The CMB is an incredibly useful source of cosmological information. The impending release of Planck's results on Thursday is big news because Planck has measured the CMB with better resolution than any other experiment that can see the whole sky. Planck might have discovered evidence of interesting new physics, such as extra neutrinos or additional types of dark matter. It might even reveal some effects relating to how physics works at energies we could never probe on Earth. But even if it hasn't discovered anything dramatically new, the precision with which Planck has measured the parameters of the standard cosmological model will immediately make it the new benchmark.

There have been surprisingly few rumours leaked to the rest of the cosmology community about what to expect on Thursday. This has resulted in the most pervasive rumour being that they have simply not found anything worth leaking. Whatever the reality, on Thursday rumours will become results.

What has Planck actually done that is so interesting?

Put most simply, Planck has measured the temperature of the CMB along various directions in the sky. The temperature of the CMB is almost uniform, but not quite. There are tiny fluctuations in the temperature of the CMB. These fluctuations are approximately one-millionth the size of the average temperature. To put this in perspective, measuring these fluctuations is like measuring the height of a building that is 100 metres tall, in tenths of a millimetre.

Many other experiments (COBE, BOOMERANG, WMAP, ACT, SPT) have measured these fluctuations. So what makes Planck so special?

A map of the fluctuations in the CMB as seen by COBE. Pretty poor resolution, but the first ever to see them. The big red band along the middle is residual foreground from our own galaxy

In order to determine the temperature of the Cosmic Microwave Background it is necessary to measure its intensity as a function of its frequency. Unfortunately, the CMB is not the only microwave radiation in the universe. In order to properly determine the CMB's temperature along any given line of sight it is first necessary to determine what parts of this microwave radiation are the CMB and what are from some other source. The wider the range of frequencies at which you measure the microwave radiation, the easier this gets. Compared to comparable experiments, Planck does just this. The effects Planck has been looking for are subtle; therefore, removing this foreground is very important.

Most importantly though, Planck has measured the CMB with better resolution than any other space-based telescope. The Atacama Cosmology Telescope and South Pole Telescope have measured the CMB with a similar resolution; however, as their names suggest, they are Earth based and can only see a small fraction of the sky. Planck, being space based, can obviously see in every direction.

This means that Planck is the first telescope that will be able to tell us about both the smallest scales (i.e. the good resolution) and the largest scales (i.e. the full sky coverage) at the same time. This is Planck's most powerful feature.

But why is the CMB so interesting?

There is lots of stuff in the universe that can give us interesting cosmological information. Moreover, there are many other telescopes making measurements of this other stuff right now and reporting back to us. What is it about the CMB that always gets everyone so much more excited?

The customary reason to give for this is the fact that the CMB is the closest we can get to an image of the Big Bang. The CMB formed only 400,000 years after the Big Bang began and before that time, the universe was opaque. Therefore no light from any event before the formation of the CMB can reach us. This is true, but I think it doesn't quite capture the real reason why the CMB is so interesting.

The temperature fluctuations in the CMB as seen by WMAP. The resolution is much better than COBE (and someone nicely removed the galaxy). In fact the resolution is so good that you can even make out the initials of a prominent cosmologist. One of the disputes I expect that Planck will help settle is the true identity of this cosmologist.

This "real reason" is that, for most cosmological models, we can predict very accurately what the CMB should look like. We can then compare the measured CMB to the accurate predictions and see which predictions were closest to the reality. The reason we can be so precise is that, at the early time when the CMB formed, the universe was very nearly homogeneous. That is, the temperature and density at every point of the universe was almost the same. You should compare that homogeneous, early, universe to the current universe where we have galaxies, stars, quasars, enormous regions empty of almost all matter and a whole host of other things occupying the universe. When the CMB formed the universe was more like a uniform soup of dark matter, hydrogen and radiation. This smoothness makes the calculations a lot simpler.

The second point that is often made is that, after it was formed, the CMB has only interacted very weakly with anything else in the universe. This is mostly true, although CMB science is now so precise that even these incredibly weak interactions are now useful cosmological probes. For example, Planck will have discovered a number of massive galaxy clusters because of how the CMB scatters of hot electrons within those clusters.

Despite all of this, eventually the CMB will no longer be the optimal cosmological probe. The information contained within the CMB is limited. Studying the CMB can only tell us what the density of the universe was, billions of years ago, on a thin shell, billions of light-years away. It is much more difficult to extract information about the primordial (or even current) density everywhere within that shell, but once we can, the wealth of information provided will be much more significant. These observations will be what comes next in cosmology. That is, very detailed observations of the structures in the universe. The major, expensive, satellite that will be the next generation's Planck (~20 years from now) is called Euclid, which will measure the location of hundreds of billions of galaxies. In the mean time there will be many interesting surveys (e.g. e-Rosita, DES). CMB science may soon be at the point of exhaustion, but observational cosmology will continue for at least the rest of this century.

The CMB's temperature fluctuations as seen by the South Pole Telescope. Even better resolution than WMAP, but only a small fraction of the sky. Planck will see this level of resolution, but over the whole sky.

Then, after that century has passed, we (or whoever is still around by then) can start real-time cosmology. That is, observing the changes in time of the temperature of the CMB and the locations of structures. These changes will be small, but the longer we wait, the bigger they become. It is conceivable that just at the end of the life-time of the youngest people alive today the first of these measurements will be beginning to occur.

What if nothing new is revealed?

The rumours surrounding Planck and what new things it might discover have had one notable feature to them: they haven't really existed. This has caused one persistent rumour to develop and that is that there is actually nothing interesting to leak.

What would this mean?

Firstly, I won't lie, it would be kind of sad. I'm a young researcher, I'd love to have something new and exciting to contemplate and work on.

But, the situation wouldn't be quite as grim as the corresponding scenario for particle physics will be if all the LHC finds is the Higgs. The reason for this is that the standard model of particle physics is much more strongly established than the corresponding cosmological model. There are also a number of future experiments already taking measurements, or with allocated funding, that will further explore cosmology. If none of them find anything new and I'm writing blog posts like this in twenty years, I will start to use the word grim for cosmology too. The standard cosmological model (SCM) has its problems (such as what dark energy actually is) and, if nothing unexpected shows up, then we can't gain any insight into these problems and future generations might just have to learn to live with them.

But for now, Planck will still be doing a great service. Firstly, and this shouldn't be ignored, it will verify WMAP's measurements. The LHC is great because it has two detectors. If one made a mistake, it is unlikely that the other made exactly the same mistake. So, if both see something, we can be confident it is there. So far, for large enough scales, WMAP is all we've had. Maybe WMAP made a mistake? We wouldn't know. But, on Thursday, we will because a completely different telescope, analysed by different people, will have made the same measurements. Any physics and results based on WMAP will gain that important confirmation step.

Secondly, Planck will narrow the uncertainty on all of the parameters of the SCM (e.g. the density of dark matter, the density of dark energy, and the nature of the primordial density fluctuations). Planck will therefore allow us to make much more precise predictions about what other cosmological events should occur, if the SCM is correct. This will help us decide what types of telescopes and detectors to build and how to analyse the data produced. For very rare events, small changes in these parameters can even make the difference between expecting to see something or nothing. This sounds less interesting than exciting new physics, but it will still advance science significantly.

The closest I can give you to rumours

I have heard a few genuine rumours (I'm not going to identify any sources or make any claims regarding the veracity of these rumours). Here they are:

The initial "ISW mystery" is still present in Planck's observations.
When combined with extra data sets (including, I expect, galaxy clusters detected by Planck), there will be some evidence for non-zero neutrino masses, enough to make this become quite a popular field of (cosmological) research.
With respect to non-Gaussianity, Planck will see evidence for non-Gaussianity at a level comparable to what WMAP has seen (i.e. 2-3 $\sigma$).

That's it though, that's all I've heard...

The release

The teaser video for the Planck release. Someone in Planck is a fan of 1970's spy movies. Maybe this explains the lack of any leaks regarding their results. If you leak, you pay the consequences, 1970's spy movie style.

The release of Planck's results happens on Thursday. You can watch the press conference live here. It will be aimed at journalists, so if you're a lay person, don't be afraid.

If you have questions, please ask.

Twitter: @just_shaun

The human machine: probing the mechanics

2013-02-25T08:46:00.000-08:00

The previous post in this series can be found here.

This week, inspired by Shaun's most recent post covering exciting new results in cosmology, I have decided to also take a quick look at one of the fascinating recent findings of molecular biology. I hope to give some insight into how this work is done, and why it is not only intellectually interesting, but also potentially practically useful.

What do we know?

Those of you who have been following this series for a while might remember a post that I wrote last year (biological batteries and motors) where I discuss how energy is converted from myriad chemical forms in your food into the single energy currency of the cell, ATP. The system by which this is achieved is quite beautiful, chemical energy is converted into an electrical current within the mitochondria of your cells, which is in turn converted into a current of protons. This proton current drives a motor (ATP synthase) that churns out ATP, thereby converting it back into chemical energy. I'm not going to go into the whole process again here, but if you'd like a quick refresher then just hop back to my older post here, go on - you know you want to! I don't mind waiting.

So, a key player in this whole process is the so-called respiratory complex I (or NADH dehydrogenase), which is the first link in the chain that converts electrical current into proton current. Complex I takes electrons from a molecule known as NADH, which is produced from energy in your food by a range of complex metabolic chemical reactions. It moves the electrons that it takes from NADH and sticks them onto a molecule called ubiquinone, which then moves on to the next stage in the process: the perhaps confusingly named complex III.

Complex I is not just a relay for electrons, though. In fact it also directly moves protons from one side of the mitochondrial membrane to the other, thereby contributing to the aforementioned proton current that drives ATP synthase. For every electron that it transfers from NADH to ubiquinone, four protons get moved across the membrane. Until recently we knew little more than this because we didn't really know what complex I looked like. Molecular biologists had been able to purify it out from our cells and determine that it is pretty massive (containing 44 individual proteins arranged together) and identify a couple of candidate proteins in that mess that might be responsible for some of the complex's functions, but we didn't know how they all fitted together and so how they might work on a large scale. This is important because mutations in complex I are the most common cause of human neurodegenerative diseases. This is because a mutated complex I can go a bit wrong and start sticking electrons where it isn't meant to - most significantly onto oxygen-containing molecules to generate reactive oxygen species that cause damage to mitochondrial DNA and so impair neuronal function in particular. Parkinson's disease and Leigh's disease are two of the more common disorders associated with complex I, but there is also evidence that the speed of ageing is also linked to the activity of your complex I assemblies. It is, needless to say, quite an important protein.

Recent developments

As you may have already guessed from the overall tone - there has recently been some light shed on the mystery that is complex I. Last week, Nature published a study by Leonid Sazanov's research group in Cambridge in which they uncover the full structure of complex I for the first time. Bits of the structure had been known before, but this is the first time that we've had the whole thing revealed before us!

Sazanov's group have achieved this by using a technique commonly used in structural biology - X ray crystallography. I touched briefly on crystallography in my post looking at G protein-coupled receptors in case the term seems vaguely familiar. The problem that arises when looking at very small things is that light is actually too big to use as a tool to see things. By "too big", what I mean is that the wavelengths of what we would generally call 'light' (i.e. the visible and near-visible spectrum) are actually larger than the fine details of the thing you want to look at, so there is an inherent maximum resolution that can be achieved. In order to go into finer detail we need to use electromagnetic radiation with a much higher energy and so shorter wavelength - X-rays.

When you fire a beam of X-rays at a protein, some of the X-rays interact with the electrons in the protein's constituent atoms. These interacting X-rays are then scattered out in various directions and so if you detect them then you can use some clever tricks to work out how the atoms in the protein are arranged. However, the vast, vast majority of X-rays will not interact with the electrons in your protein and the scattering will be pretty damn weak. In order to bulk up the signal you need to get many copies of your protein (millions of millions of copies) and arrange them into an ordered fashion so that they all scatter in the same way. To do this you have a grow your purified protein into a crystal where each one is identical to the next and in exactly the same orientation. This is the tricky bit. Biochemists have been making protein crystals for over half a century with great success, but the bigger and more complicated your protein is then the harder it is to crystallise. Moreover, if you protein usually sits in a membrane then it makes it even more difficult to force into a crystal. Complex I ticks both these boxes and so making a successful crystal is nothing short of a scientific miracle! They don't say in their paper, but I imagine that Sazanov and colleagues have been trying to get this crystal for a LONG time! It was, however, undoubtedly worth it. The structure is quite beautiful.

The structure of respiratory complex I - taken from Baradaran et al, Nature, 2013.

Revelations

The multi-coloured structures in the figure above represent the individual proteins involved the complex, with different peptide structures represented as different shapes (ribbons, loops etc). What is immediately apparent is that there is a large region that is embedded in the membrane (the flat bit at the bottom) and a separate segment that extends upwards and away from this membranous section (the bit at the top right). Analysis of the amino acids present at different regions reveal that the top-right protrusion is the binding site for NADH and ubiquinone, and so is where electron transfer must occur. Conversely, the membrane-embedded regions are where the protons get pumped across the membrane, so the two processes must be coupled in some way.

This structure allows us to suggest mechanisms in which the two might be coupled as it identifies 4 distinct channels through which protons can cross the membrane. As I mentioned earlier - the transfer of one electron from NADH to ubiquinone results in the movement of 4 protons across the membrane, so the fact that there are 4 proton channels seems to fit neatly with the idea of one proton moving through each channel.

Three of the four proton channels identified by Baradaran et al. The paths that protons take through the protein are shown as blue arrows.

Looking at both the electron-transporting and proton-transporting sections has allowed the creation of a model of just how the two transfer processes are linked. To start with, the proton channels are open at the end facing into the cytoplasm (the side of the membrane from which protons will be removed) and closed to the periplasm (the side to which they will be released). The transfer of an electron from NADH to ubiquinone causes a wave of shape changes that start in the non-membrane embedded region and then cascade throughout the whole protein complex. This causes the proton channels to switch so that they are now closed to the cytoplasm and open to the periplasm; free to release their protons. Thereby, 4 protons are moved over the membrane for every electron transferred.

Electron transfer coupled to proton transfer. (NB. H+ is a proton in this representation)

The complexity of this whole system is quite astounding, doubly so when you consider that every complex I in your body is doing this thousands of times every second, and that there are billions of billions of these complexes in your whole body. What's more, now that we know how it works, we can start to make sense of how it can go wrong in neurodegenerative disorders and so potentially one day come up with effective treatments that benefit millions of people.

The story of complex I is an excellent example of just how unbelievably well engineered we are as biological machines, yet also how ingenious we can be and have been in our efforts to understand our own engineering. Moreover, it's a demonstration of how research is always progressing in the background, largely ignored by wider society but still delving deeper and uncovering more about what and who we are.

The next post in this series can be found here.

Citation:

Baradaran, R., Berrisford, J., Minhas, G., & Sazanov, L. (2013). Crystal structure of the entire respiratory complex I Nature, 494 (7438), 443-448 DOI: 10.1038/nature11871

David J. Wineland: trapping ions for clocks and computers

2013-02-12T00:47:00.000-08:00

Simon Thwaite recently completed a D.Phil. in Atomic & Laser Physics at the University of Oxford, and is currently a postdoctoral researcher at the Ludwig Maximilian University in Munich. The first part of his post series commenting on the 2012 Nobel Prize in Physics can be found here.

In this post he gives an overview of the field of trapped ions, describes two of its most important applications, and describes what goes on behind the scenes when a trapped ion interacts with a laser beam.

David J. Wineland – probing trapped atoms with light

David Wineland, an experimental physicist at the National Institute for Standards and Technology (NIST) in Boulder, Colorado, is one of the leading researchers in the field of trapped ions: that is, the study of how positively-charged ions (i.e. atoms stripped of one or more electrons) may be trapped, cooled, and manipulated. This field shares many similarities with experiments on neutral atoms (laser cooling, for example, is just as useful for ions as it is for neutral atoms), but also has a number of significant differences. The most important difference that distinguishes ions from atoms is, obviously enough, the fact that ions have a non-zero net electrical charge. This has two very important consequences.

Trapped ions: trapping and interactions

A string of trapped ions (red dots) lined up in a Paul trap
can be imaged with a tightly-focused laser beam and CCD camera.

Image credit: Rainer Blatt experimental group, University of Innsbruck.

Applying an electric field to an ion produces a force on the ion: positive ions are drawn in the direction of the field. [In contrast, applying an electric field to a neutral atom changes the ‘shape’ of the atom slightly, since the positively-charged nucleus and negatively-charged electron cloud are drawn in opposite directions, but produces no net force.] Consequently, whereas traps for neutral atoms must rely on combinations of laser light and magnetic fields, ions can be trapped just by electric fields. Most of the recent trapped-ion experiments use some variation on the Paul trap (a.k.a. the quadrupole ion trap) which uses a combination of static (DC) and oscillating (AC) electric fields to trap ions along a 1-dimensional line.

Images of ion strings containing (L to R)
1, 2, 3, 6, and 'some' ions. These images
were created by using laser light to
illuminate the ions in the string.

Image credit: phys.org

The second important point is that ions interact with one another far more strongly than neutral atoms do: two positive ions repel one another strongly through their mutual Coulomb interaction. [In contrast, neutral atoms typically interact very weakly, and behave essentially like hard spheres: they are ignorant of the presence of one another unless in direct contact.] Consequently, ions held in a Paul trap are subject to two competing tendencies. Firstly, the ions are drawn towards the center of the trap in order to minimize the trapping potential energy; secondly, they strongly repel one another in an attempt to minimize the ion-ion interaction energy. By way of compromise, the ions line up like a string of beads, with inter-ionic distances of the order of a few tens of microns. This is, experimentally speaking, a very convenient state of affairs, since it means that each ion can be individually addressed by a tightly-focused laser beam.

Applications of trapped ions

Strings of laser-cooled ions held in a Paul trap can be put to a variety of uses. One important application lies in the realm of high-precision spectroscopy and frequency standards. Securely trapped, well isolated from the environment, and cooled to a standstill, a single laser-cooled ion in a Paul trap is an ideal subject on which to make precision energy-level measurements (or, equivalently, measurements of the frequency of the electromagnetic radiation that the ion absorbs and emits).

Since frequency is just the inverse of time, a well-defined frequency can be used as a reference point for defining exactly what a ‘second’ is. Single trapped ions thus form an excellent basis for atomic clocks. Such clocks show significantly improved accuracy over those based on the radiation emitted by neutral cesium atoms (the kind which, since 1967, has formed the basis for the SI definition of a second).

Storing information in the electronic state
of a single ion or atom opens the door to
the development of information-processing
schemes that take advantage of quantum mechanics.

A second important application of trapped ions is their use in the field of quantum information processing (a.k.a. quantum computing). This field is founded on the realisation that the laws of quantum mechanics appear to allow for a more powerful model of computation than the (classical) Turing paradigm that underpins computing as we know it. Although this result hasn’t yet been mathematically proven, at this point in time it seems extremely probable that computers that are designed to take advantage of the intricacies of quantum mechanics can efficiently solve problems that are completely intractable for a classical computer.

The best-known example of such a problem is the division of a large integer into its prime factors (e.g. 15 = 3*5; or 70 = 2*5*7) This task is generally believed to be impossible to efficiently solve on a classical computer; indeed, we currently believe so strongly in the hardness of this problem that an entire cryptographic system (i.e. a method for encoding and decoding information or messages) is based on it! However, it was shown way back in 1994 that a ‘quantum computer’ (i.e. a computer exploiting the laws of quantum mechanics) could efficiently solve the problem of splitting an integer into its prime factors. This is a hugely important result, since it essentially means that if and when it becomes feasible to build quantum computers, the enormously popular RSA cryptosystem will be breakable.

This image came up when I Googled
'quantum computer'. It's kind of cool.
Unfortunately, any quantum computer
that we do end up building is unlikely
to look like this.

Image credit: extremetech.com

It is probably fair to say, therefore, that building a quantum computer is Kind Of A Big Deal. A wide range of different physical architectures, with various strengths and weaknesses, have been proposed and investigated for building a quantum computer. A string of ions trapped in a Paul trap currently forms one of the most promising architectures, at least in terms of proven experimental results.

Probing an ion with laser light

Of fundamental importance to any use of trapped ions is the controlled interaction of an ion with a focused beam of laser light. Despite its importance, the basic process that occurs when a laser beam strikes an ion (or a neutral atom) is straightforward, and can be understood with the help of the following model.

Firstly, let us assume that the outermost electron in the ion can occupy one of only two possible energy levels. We label these energy levels (or states) A and B. Further, let us assume that the laser light is of exactly the right frequency that (energy of state A + 1 photon of light) = (energy of state B) is a true statement. In this case, the photons in the laser beam have precisely the right energy to promote the electron from state A to state B; we say that the laser is resonant with the A-B transition.

When the resonant laser beam strikes the two-level ion, the electron absorbs energy from the light and is promoted from state A to state B. However, this happens in a very curious way: the electron does not simply jump from A to B and then stay there, but instead begins to oscillate between the states: when the laser is first switched on, the electron is in state A; after (say) 10 microseconds interacting with the laser, it is in B; after 20 microseconds, in A; after 30, back in B, and so on. The frequency of these oscillations is determined by the laser intensity: a stronger laser would cause the electron to oscillate between A and B more rapidly.

Superposition states, and the problem of decoherence

Now a simple but penetrating question presents itself: if the electron is in state A when the laser is first switched on, and state B 10 microseconds later, what kind of state is it in at an intermediate time – say, 5 microseconds? Is it in state A, or state B, or some mixture of the two?

If you picked the third option: well done! It turns out that after 5 microseconds the ion is actually in a state that is best written as “A + B”. If the ion is measured at this instant, it is found in state A with 50% probability, and state B with 50% probability. This “A + B” state is an example of what’s known as a ‘superposition state’: the ion is, in a very real sense, in “both A and B at the same time”.

This superposition state is uniquely quantum-mechanical (classical physics doesn’t allow anything to be in two states “at the same time”!), extremely useful, and also very fragile: as soon as the ion is measured, it is forced to “choose” whether it is “actually” in state A or state B, and its state changes in accordance with the result that we find. For example, if a measurement of the ion finds it in state A, then at the same time the measurement actually forces the ion back into state A. In the language of the field, the very act of measurement ‘collapses’ the superposition “A + B” back to A (or B, if the result of the measurement was state B).

I couldn't find a good picture of a quantum-mechanical
superposition collapsing due to the act of measurement,
so to congratulate you on getting this far, here's a picture of a sloth.

He also seems to have collapsed to his lowest-energy state upon
being measured. Perhaps sloths are quantum systems?

Image credit: here.

The fact that measuring a trapped ion actually affects the state of the ion has an unwelcome, if interesting, side effect. While trapped ions are generally very well isolated from the surrounding environment, experimental imperfections and noise, such as stray electric and magnetic fields, are always present. It turns out that such experimental imperfections have an effect on superposition states similar to an act of measurement: that is, they act to destroy fragile superposition “A + B”-type states. How to best prepare and protect superpositions, even in the presence of experimental noise, is thus an important and ongoing topic of research.

Conclusion

So this, in a nutshell, is what David Wineland’s research is all about: finding clever ways to trap and manipulate ions with combinations of electric fields and laser light; to prepare fragile superposition states and to protect them from interactions with the environment; and to use these uniquely quantum-mechanical states as a resource to build atomic clocks and perhaps, one day, a trapped ion quantum computer. What a great job to have!

The “ISW mystery” deepens considerably (II)

2013-02-05T08:00:00.000-08:00

[... continued from yesterday]

[Note added April 29: Through correspondence with some of the authors from what I label as the "French group" below I have learned that the density threshold was actually applied in their work as well. This makes things rather confusing as it means that their methods and the methods of "the DHB" are much more similar. However, they have also updated their paper to reflect new knowledge about the void catalogues and see a slightly more significant signal, similar to what Planck find (see note below). Everything is rather confusing right now. Again, once the dust has settled, I will write a post clearing everything up.]

[Note added March 21: Wow, sometimes science moves quickly. Today Planck released its data. They appear to confirm the anomalous spots in the original "Granett" (Hawaiian) result. They also appear to confirm the new anomalous result that was present in the paper that is now retracted (see the note below from March 19), albeit with a slightly reduced significance. It is unclear exactly what is going on, but it is clear that it is something interesting. I will keep you informed as things progress.]

[Noted added March 19: The paper described in the second half of this post (I called its authors the DHB) has been withdrawn from the journal it was submitted to (see the new abstract at this link: http://arxiv.org/abs/1301.6136). It is unclear whether the problems that the authors found in their analysis will affect their conclusions. However, I suggest you are cautious regarding how you interpret the conclusions I have drawn below based on this paper. I will keep you informed as/when things progress.]

A really neat figure from arXiv:1301.5849 showing the locations and sizes of the various catalogues of voids being examined. A larger redshift means the void is further away from us and one Megaparsec (Mpc) corresponds to three million light years. The purple "Granett et al." box is the original catalogue used by the Hawaiian group back in 2008.

Isn't this just "a posteriori" statistics?

There is another possible explanation for the mystery. The probability of ZOBOV picking out these lines of sight at random is exceedingly small (less than 0.003), but it isn't zero. Might this have just been a crazy fluke?

Suppose 100 different groups of physicists look for unexpected, but interesting, signals in cosmological data. Then, even if each group is very careful you still expect one of them to find something that would seem to them to be unlikely. Unfortunately, they would be the only ones to publish their results. So we wouldn't see one “detection” paper and ninety-nine papers consistent with no detection. We would just see the one “detection” paper.

The best way to determine whether this is what happened is to look for the signal in other surveys. If the original measurement was a fluke, it won't show up anywhere else. But, if it does show up again, then the chances that it was a fluke will significantly diminish.

The Friday before last a paper appeared that did exactly this. A French group took two catalogues of voids (so no over-densities), which have been produced by applying ZOBOV to a new catalogue of galaxies (these ones are closer to us). The French group then did more or less the same thing as the Hawaiians did. They examined images of the CMB along the lines of sight of these voids, averaged the temperature in all the images and checked whether the resulting signal could have happened at random.

They found no significant result.

This was quite sobering to read on the day. The paper did verify the significance of the original measurement, but not finding it in the new catalogues was highly suggestive that the story I painted above of a sort of community wide “look elsewhere effect” was true.

Hold on though!

Things at this date in time did look bad for the anomaly, but there was one important piece missing from the French group's analysis. The Hawaiians only used the most extreme over and under-dense regions in their analysis. ZOBOV found many more than 50 regions for them and if they had used all of them, they also wouldn't have obtained a statistically significant signal. This was always a crucial part of their analysis because we already knew from other observations that the observed ISW effect from most of the universe is as small as the predicted signal.

What would the French group have seen if they had only examined the most extreme voids?

A new observation

Apparently it is a rule of thumb for observers, that the more interesting your observation is, the more boring you are meant to make your title. These guys probably deserve a promotion. The paper is here.

Three days later (last Monday) a mixture of physicists from Durham, Hawaii and Baltimore (the DHB) released a paper. It answered the question posed above. For anybody interested in finding new physics, the answer is very exciting.

In their paper, the DHB repeated almost exactly the same analysis as the French group. Except, they made the crucial additional step of removing all the voids that weren't below a certain density threshold.

Figure C. This is what ZOBOV should be seeing. On the left is the average ISW temperature shift around simulated voids selected by ZOBOV. Note the clear cold spot, surrounded by a hot ring. On the right is the average radial profile for both the density contrast of the selected voids and the ISW temperature shift. Taken from arXiv:1301.6136.

The DHB also did something else important. They applied ZOBOV to simulations of the universe with accompanying simulated ISW maps. Therefore, they were also able to finally obtain accurate predictions for the expected signal, rather than just conservative over-estimates. This verified that the conservative over-estimates are indeed very conservative as the accurate expected signal is much smaller. But also, the DHB were able to use these simulations to determine the angular size of CMB patch that should give an optimal ISW signal for a given void. This corresponded to about three fifths of the radius of each void.

On to the exciting bit.

How did they analyse the data? Firstly, they took one of the same catalogues of voids used by the French group. Then they kept only the voids that have a number density less than 0.2 of the average number density of galaxies in the survey. Then, they isolated patches of the CMB along the lines of sight of the remaining voids. Finally, they rescaled each patch of the CMB proportionally to the radius of the void that selected it. A stacked image of all of these patches can be seen in figure D. When compared to the same image obtained from simulations (figure C) it actually looks quite similar (don't forget this one also has statistical noise in it), except look at the scales. It might look the same, but its magnitude is significantly larger.

Figure D. One of the more exciting images on this blog. The average temperature in CMB patches centred around voids found through observation. Even by eye, a cold spot can be made out with a surrounding hot ring. Just like from simulations, but note the different scale! The right panel is (close to) the data equivalent to the red curve in figure C. The profile is quite similar, but the magnitude definitely is not. Taken from arXiv:1301.6136.

The real test is the probability that this spot could have arisen randomly. To determine this, the group first rescaled each CMB patch to three fifths of the radius of the void that selected it (i.e. the theoretical optimal radius). They then sampled patches of the CMB along the same number of randomly chosen lines of sight and rescaled these by the same factors. They repeated this random sampling many times. Finally, they calculated the average temperature in each set of rescaled patches. This allowed them to compare the patches with voids behind them to the randomly selected patches. The result is in figure E. The top, coloured, curves are the observation (as a function of number of voids). The dashed curve shows the observational uncertainty, determined from the randomly selected patches. And the curve right at the bottom is the theoretical expectation for an ISW effect, obtained from their simulation. The lower panel of the figure shows the total “signal to noise” of the observation. You can see that the observed signal is consistently three standard deviations larger than the random fluctuations.

Figure E. Possibly the most exciting figure on this blog. In the top panel, the three coloured curves are the observation, the dotted line is the observational uncertainty and the dashed line is the theoretical prediction. The different colours correspond to different frequency bands. The fact that all three are almost identical suggests this is unlikely to be the result of foregrounds. The bottom panel shows the ratio of the signal to noise, which is consistently $\sim 3 \sigma$. Taken from arXiv:1301.6136.

The probability of one “$3\sigma$” fluctuation is less than 0.003. However, this measurement is not the only measurement of this type. It is, in fact, a verification, from a different part of the universe, of the previous observation made by the Hawaiian group. That previous measurement was even less likely than this one (i.e. a “$4\sigma$” fluctuation). The chances of this being a fluke have greatly diminished. In fact, if you want to combine the significances, this is perilously close to, if not beyond, the magical (and completely arbitrary) “$5\sigma$” mark required by some to declare a discovery of new physics.

I don't know about you, but I find this incredibly exciting. Many anomalous measurements show up in science (especially cosmology). Most often it turns out that one of the following is true: we didn't understand our own models well enough; someone made a simple mistake; or it was a fluke and it goes away. As I've argued in this post, for this anomaly, all of these possibilities have now been rigorously checked. Firstly, the ISW effect cannot be this big. Secondly, the original measurement has been verified by a number of groups, so the Hawaiian group did not make a mistake. Finally, the signal has been found somewhere else, with strong significance, so the first measurement was not a fluke.

The one lingering concern is that this is a “fake CMB” being emitted by galaxies, or perhaps that something very, very subtle is being missed in the analysis (if you think you know what that might be, please leave a note in the comments). However, as I've argued above, there are certain properties a “fake CMB” would be likely to have and this signal does not seem to have them. In fact, it actually looks very, very similar to what we would expect from an ISW effect, except for the fact that it is just far too big.

So, if this is new physics, what does it mean?

That's a very good question and I don't know the answer. The signal is so much bigger than expectations that it is difficult to reconcile these observations with many well motivated “new physics” models. But we are trying to find out. The most important thing now is to explore this signal in as many ways as possible in as many regions of the universe as possible. If we can understand what makes it bigger; what makes it smaller; how it changes with void size and with void depth; etc, then we can get clues as to what is causing it (whether that is new physics or fake CMB).

Maybe we are on the verge of a new discovery. I'll keep you posted, it should be exciting times...

…...........................
Questions on any of the above are very much welcomed. If you don't understand anything, or think I/we've missed something obvious, please leave a comment. Maybe your question/observation will show the way to resolving the mystery.

Twitter: @just_shaun
................................

References:

Yan-Chuan Cai, Mark C. Neyrinck, Istvan Szapudi, Shaun Cole, & Carlos S. Frenk (2013). A Detection of the Cold Imprint of Voids on the Microwave Background Radiation arXiv arXiv: 1301.6136v1
S. Ilic, M. Langer, & M. Douspis (2013). On the detection of the integrated Sachs-Wolfe effect with stacked voids arXiv arXiv: 1301.5849v1

The “ISW mystery” deepens considerably

2013-02-04T17:13:00.000-08:00

Other than my initials, what secrets does the CMB hide that are waiting to be seen only when the CMB is examined in just the right way?

This time last year I wrote a few posts describing what I called the “ISW mystery” (Part I, II, III and IV). A year has passed, it is time for an update on the mystery.

The very short summary is that things are starting to get more than a little bit exciting. All of the plausible ways in which the calculation of the expected ISW signal could have been wrong have been checked and eliminated as possibilities; if the measured signal is real, it is too large for the standard cosmological model. Much, much more excitingly, the observation that generated the mystery has now been repeated in another region of the universe and a very similar and equally anomalous signal was found; the apparent anomaly was not a statistical fluke.

The preprint of the paper describing this new observation was released just a week ago.

What is the “ISW mystery”?

The image that began the mystery. Why is that spot so hot, and how did it get that cold ring around it?

A quick recap will probably be useful. The integrated Sachs-Wolfe (ISW) effect describes the heating and cooling of light as it passes through gravitational peaks and valleys late in the evolution of the universe. In the standard cosmological model, these peaks and valleys decay with time, so a light ray gains (or loses) more energy entering an over-dense (or under-dense) region of the universe than it loses (or gains) leaving it. The effect is very, very small. Almost every source of light in the universe is not known well enough to be used to detect it. Only the cosmic microwave background (CMB) is uniform enough that these tiny fluctuations could ever be detected.

However, even then, the primary fluctuations in the the temperature of the CMB are bigger than the secondary ones created by the ISW effect. We can measure these fluctuations but we could never know how much is due to the ISW effect and how much is primordial. The only thing we can do is look at the structures in the universe nearby and see if on average the CMB is slightly hotter (colder) along lines of sight where the nearby universe is over-dense (under-dense). The bigger, primordial fluctuations in the CMB should have nothing to do with local structures (the CMB has come from much further away). Therefore, if this signal were to be found in the CMB, the most plausible explanation would be an ISW effect.

A group in Hawaii decided to look for this signal in a slightly unusual way. Firstly, they made a catalogue of significant over and under-dense regions in a particular survey of galaxies. Then, they only examined patches of the CMB that existed along the line of sight of each of these regions. They then found that the patches aligned with over-densities were hotter on average than a randomly selected patch and those aligned with under-densities were colder (with more than “$4\sigma$” significance). This is what one would expect from an ISW effect. The “ISW mystery” is that these patches were too hot and too cold. The ISW effect simply shouldn't be that big.

The importance of checking the anomaly from every angle

If this signal really is there and really is bigger than expected, then some new physical effect must be heating and cooling the CMB as it passes through these over/under dense regions. Clearly that would be big news. It would not be quite as dramatic as genuinely faster than light neutrinos would have been, but it would certainly require consideration of exotic things like modifying gravity, changing the primordial density perturbations of the universe, or having something other than a cosmological constant causing the accelerated expansion of the universe. Therefore, it is very important to be careful before jumping to conclusions.

How do we know the ISW effect can't be this big?

From arXiv:1212.0776. Two different methods to arrive at very conservative over-estimates of the expected ISW signal. The solid line uses the hottest and coldest lines of sight, the dashed line uses spherically symmetric peaks in the density of the universe. The observed signal was $ 9.6\pm2.2 \mu K$.

The structures that determined which lines of sight to use were found with a particular algorithm (called ZOBOV for under-densities and VOBOZ for over-densities). We can't see most of the matter in the universe (i.e. dark matter). Therefore it is necessary to instead apply ZOBOV/VOBOZ to the number density of objects that we can see (e.g. galaxies). Without doing a full simulation of the growth of structure in the universe, as well as estimating where astrophysical objects would form in this simulation, it is difficult to precisely determine what lines of sight ZOBOV (I'll just use ZOBOV, hereafter, to refer to both algorithms) would pick out.

In late 2011 my collaborators and I tried to get around this with a very conservative calculation. Although ZOBOV can only see galaxies, it is the total matter distribution that generates the gravitational wells that affect the CMB. Therefore, instead of trying to model ZOBOV accurately, we calculated the ISW signal from the widest and most under/over-dense, spherically symmetric, peaks expected in the total matter distribution. ZOBOV should miss some of these peaks and therefore this calculation should significantly over-estimate the ISW signal. However, perhaps ZOBOV is managing to see some other, non-spherical, structures that happen to give a bigger signal. This seemed unlikely, but we decided to check.

To do this we took our conservatism one step further. This time we asked “what is the maximum ISW effect expected along any line of sight?” If the answer to that question was a signal smaller than the observed signal then, irrespective of how ZOBOV picks its lines of sight, the observed signal has to be anomalous. This is exactly what we found. There is no wiggle room left on the theoretical side of this anomaly. If the signal is real, it is too big.

Are we really sure it isn't foregrounds?

Figure A: The expected angular profile of a "fake CMB" with an amplitude proportional to the matter density. From arXiv:1212.1174.

Can we trust the measurement?

The short answer is yes, because there is surprisingly little room for things that could have gone wrong.

Let's briefly review the measurement. Without looking at the CMB, a group in Hawaii came up with a bunch of lines of sight on the sky where they expected the ISW effect to produce the hottest hot spots and coldest cold spots. When they then looked at the CMB along those lines of sight, they found that the “hot” lines of sight were statistically hotter than average and the “cold” lines of sight were statistically colder. Either this was a very unlikely fluke, or some aspect of the method the Hawaiians used to pick these lines of sight must be related to the temperature of the CMB.

The algorithm that picked these lines of sight looked only at a collection of luminous red galaxies (LRGs). Therefore, those LRGs must be related, in some way, to something that is affecting what we measure to be the CMB temperature.

One very plausible candidate was the ISW effect. But we know now that the observed signal is far too big for an ISW effect, so what else could it be?

The next plausible explanation is that the LRGs are themselves emitting light that looks like the CMB. If they were, then this measurement might make sense. Where there are more LRGs, more fake CMB is being emitted, so we measure the CMB as hotter. Where there are fewer, less fake CMB is being emitted, so we measure the CMB as colder.

However, a number of checks have now been made to examine whether the measured signal has the properties one would expect of “foreground” radiation from the LRGs. Every one of them has come up false. If it is foreground radiation, it is quite a strange foreground.

Figure B: The observed angular profile of the mystery "ISW" signal. Notice how different it is to what would be expected from a fake CMB (see figure A). From arXiv:1212.1174.

Here are some of the tests:

The CMB has a very well known, blackbody, spectrum (i.e. intensity of light as a function of its frequency/wavelength). The anomalous “ISW” signal is present, with equal magnitude, in all of the frequency bands measured by WMAP. If the signal is due to foreground, that foreground must look very similar to a blackbody.

If the signal is coming from LRGs, it would be natural to expect the magnitude of the signal to be proportional to the number density of LRGs. A group based in Munich and Teruel tested exactly this possibility. As part of a recent paper, they took a simulation and added a fake CMB signal that was proportional to the matter density in the simulation. When patches of the fake CMB are examined along the lines of sight of these LRG-type objects, the size of the signal as a function of the size of the patch (the angular profile) is completely different to what was observed (see figs A and B). It is worth noting that the expected angular profile of the ISW effect does match the observed signal closely.

[Continued in part two...]

.......................

References:

Samuel Flender, Shaun Hotchkiss, & Seshadri Nadathur (2012). The stacked ISW signal of rare superstructures in ΛCDM JCAP arXiv: 1212.0776v2
Carlos Hernandez-Monteagudo, & Robert E. Smith (2012). On the signature of nearby superclusters and voids in the Integrated Sachs-Wolfe effect arXiv arXiv: 1212.1174v1

[I have corrected a mistake in the caption to the third figure in this post. The descriptions for the dotted and solid lines were swapped.]

The human machine: decommissioned components

2013-01-14T10:34:00.000-08:00

The previous post in this series can be found here.

Happy 2013 from all of us here in the Trenches! We successfully made it one more time around the sun, and if that's not a good excuse for a party I don't know what is! Sadly, however, not all of your cells have been having such a swimmingly good time since the calendar ticked over to January the first - in fact nearly one trillion of them have died in the past fortnight alone, at a rate of roughly 70 billion a day, or 800,000 per second. Don't be alarmed, however, as this has been going on for your whole life and is a vitally important part of being a multicellular organism such as yourself. A human without cell death would be like society without human death - overcrowded, unpleasant, and rife with infirmity. Your body needs a system by which damaged, old, or infected cells can be removed in a controlled manner; this process is known as apoptosis.

In this post I will be discussing what we know about how apoptosis works and how it is a key player in the development of cancer and the fighting of infectious disease. I'll also show how our understanding of how this process works has allowed us to devise targeted therapeutics against a number of debilitating conditions.

Cellular suicide - picking the moment

Your cells are team players - they're willing to do anything to serve you, including laying down their lives. Apoptosis depends on this loyalty because it is actually a form of suicide that your cells perform on themselves. Arguably the most important aspect of this is timing - if your cells are in the habit of committing suicide before it is necessary then you'll waste a lot of energy and resources building replacements that shouldn't be needed. On the other hand, if the cell leaves it too late to kill itself then it may find itself incapable of doing so.

So, how does a cell know when to die? Well the most obvious markers for cell death are simply the various forms of damage that can occur to the components of the cell itself. If a cell's membrane becomes damaged, for example, this can cause excess calcium to leak into the cell and so be sensed by a number of calcium-binding proteins, such as calpain, which in turn signal that apoptosis should begin. Similarly, damage to DNA is sensed by the complex machinery of the DNA repair pathway. For example, PARP is a protein that binds to single-strand breaks in DNA caused by DNA damaging agents such as radiation (think sunburn!) or chemical mutagens like free radicals. PARP and other DNA damage sensors relay their information to a number of signalling proteins, most importantly p53. If p53 is activated in response to DNA damage it signals to stop the usual processes of cell division and begin DNA repair, but if the damage is just too bad it makes the call to start apoptosis and destroy the cell.

These causes of apoptosis are known as 'intrinsic' factors because they emerge from effects sensed within the cell. Other intrinsic factors include heat damage to the cell; sensing viral or bacterial proteins inside the cell (a clear sign that it's been infected and must die asap!); the lack of nutrients in the cell's metabolic processes; and a lack of oxygen (hypoxia). Hypoxia is possibly the most clinically relevant cause of apoptosis because it is responsible for the lasting damage caused by blood flow disorders such as occur during a heart attack or stroke. In these events, blood flow (and so oxygen supply) to either the heart or brain tissue is temporarily cut off, inducing widespread apoptosis in that area and so causing significant damage to the affected organ. Studying the genetic predisposition of individuals to hypoxia-induced apoptosis is an expanding area of research as it will allow better predictions of the severity of stoke or heart attack damage and so allow treatment to be tailored accordingly.

'Extrinsic' activators of apoptosis are ones that are presented by other cells in order to instruct a cell to die. This is most often the case when a cell is infected with a virus but the viral components have evaded detection within the cell. In this situation, killer T cells (which I've discussed in a previous post - here) detect viral components on the surface of the infected cell and so give it its final orders in the form of a protein called the Fas ligand. The Fas ligand is presented on the surface of the T cell and binds to the Fas receptor on the surface of the infected cell, which kick starts the whole process of apoptosis.

Going from initiation to action

So, our unhappy cell is ready to go, it's had its orders and needs to start the process of packing itself up. What happens now is dependent on whether the initial signal was intrinsic or extrinsic, but both have the same outcome. Ultimately, both pathways cause the activation of a host of enzymes that deconstruct the cellular skeleton, dismantle its organelles, and demolish its DNA. Taking the last of these as an example, DNA in an apoptotic cell is slowly condensed into a single mass (pyknosis) before being released from its usual home of the nucleus and into the rest of the cell (karyorrhexis), and then finally enzymatically chopped up and disposed of by a family of proteins called the DNAses (karyolysis). Similar events happen for every component of the dying cell until the cell begins to break apart into small blobs called apoptotic bodies that are then devoured by roaming macrophages and the cell is finally no more.

The death throes of an apoptotic cell breaking up into apoptotic bodies and being consumed.

As I say, however, how we get to this point depends on where the cell's instructions came from, but both rely heavily on a group of proteins called caspases (short for 'cysteine-dependent aspartate-directed proteases', but which I like to think were named after Casper the friendly ghost). Caspases are enzymes that cleave other proteins, particularly other caspases. Normally, caspases are not active in a cell because their full structure is self-inhibiting, but they can become activated by cleaving off a small part of their structure. This means that an active caspase can activate other caspases, which then activate more caspases and so on in a cascade of caspase activity. This is irreversible - once the caspases are firing a cell's time is up!

Extrinsic death signals usually cause the formation of the death-inducing signalling complex (DISC), which forms around the aforementioned Fas receptor at the cell membrane. DISC contains two caspases, caspase 2 and caspase 8, which become active within the complex. Their activity has two main effects: the activation of caspase 3, which is the caspase responsible for activating most of the demolition machinery mentioned earlier; and the activation of a protein called tBid. The role of tBid is linked closely to the mechanism of intrinsic apoptosis.

Apoptosis caused by intrinsic or extrinsic signals - different routes, same outcome.

The intrinsic pathway for apoptosis is closely linked to the energy-releasing organelles of the cell, mitochondria (whose role I've discussed before - here). Within mitochondria are a range of proteins of the Bcl-2 family. Some of these a pro-apoptotic (e.g. Bax, Bad, Box etc.) whereas others are anti-apoptotic (Bcl-2, Bcl-xl, Bcl-w etc.). Whether apoptosis occurs due to intrinsic signals depends on the balance of the pro- and anti-apoptotic proteins in the mitochondria. The intrinsic causes of apoptosis that I mentioned above cause the activation of a number of pro-apoptotic proteins and the inactivation of the anti-apoptotic ones, primarily though signals relayed through the aforementioned p53 protein. tBid, activated by extrinsic signals, also promotes the pro-apoptotic cause in mitochondria by inhibiting the anti-apoptotic proteins. Going through exactly what all these various proteins do would take me a lot longer than I have here, but it is the outcome that we're interested in anyway! A mitochondrion in which the pro-apoptotic proteins are winning becomes extremely porous, spewing much of its internal components into the rest of the cell. These include a number of proteins that bind to IAP (inhibitor of apoptosis) proteins and block their activity. IAPs usually bind to and inactivate caspases, so their inhibition by mitochondrial proteins causes caspase activation - thereby starting the whole business of packing up the cell.

One very interesting example of a mitochondrial protein promoting apoptosis is cytochrome c. As discussed previously, cytochrome c is usually involved in the mitochondrial electron transport chain, where is acts as an electron-carrier in cellular energy processing. However, once it is free of the mitochondria, cytochrome c is able to bind to a protein called Apaf1. This binding event alters the structure of Apaf1 such that it starts to cluster together into a wheel-like structure containing 7 copies of Apaf1 and 7 or cytochrome c. This structure is colourfully referred to as the 'wheel of death' (or more boringly, the apoptosome) because, once formed, it is able to activate caspase 9, which in turn activates caspase 3 and voila we have apoptotic lift off!

The wheel of death! The apoptosome is a key player in cell suicide (structure from Yuan et al. 2010, Structure of an apoptosome-procaspase-9 CARD complex).

Fine tuning the machine

Apoptosis is, as I say, a process vital to the health of the body as a whole. When it goes wrong, things can get nasty. Cancerous cells have almost always developed partial or complete resistance to apoptosis such that they never die and so are free to divide perpetually and beyond their physiological role. Cells can develop such resistance by accumulating mutations in the proteins that regulate apoptosis such that the death signals are no longer effective. These are grouped into two categories: tumour-suppressor (TS) genes, and oncogenes. A TS gene is one for which a mutation that knocks out its activity can promote cancer. For example, the gene that encodes p53 (TP53) is a TS gene, as without p53 intrinsic death signals cannot be relayed from their initial signals to the mitochondria and so are ineffective. Oncogenes, on the other hand, are genes whose over-stimulation can promote cancer. One such gene is XIAP (X-linked inhibitor of apoptosis protein), which normally regulates apoptosis by binding to and inactivating caspases 3, 7 and 9. Deregulation (i.e. overactivity) of XIAP activity is a factor in a number of lung, prostate, and bowel cancers.

A cruel fact of apoptotic failure is that cancerous cells that are resistant to apoptosis are therefore resistant to the signals that halt cell division upon DNA damage. This means that the cell can continue to accumulate more and more mutations without undergoing the repair pathways that would become active in a non-cancerous cells. Thanks to this, the rate of mutation in cancerous cells can be up to 100 times higher than in non-cancerous cells and so tumours can deteriorate rapidly.

Thanks to our understanding of apoptosis, however, we are now at the stage where we are starting to fight back against death-resistant cells. A number of widely-used anti-cancer drugs, such as Herceptin, Iressa, or Gleevac, work in part through the induction of apoptosis by blocking cellular survival signals, thereby circumventing some of the blocks to the apoptotic machinery that have accumulated due to mutation. Some other treatments target tumour suppressor genes, such as p53, and attempt to reactivate them in the cancerous cells. Future targetted gene therapies may be capable of replacing damaged TS genes in those cells, thereby reconnecting the wiring within cellular signalling that was blocking apoptosis.

Knowledge of apoptosis has also allowed us to connect the dots between some cancers and specific viral infections. A virally infected cell must die as quickly as possible to prevent the virus from spreading. This, needless to say, is bad news for the virus, which will try to stop it at all costs. Some viruses are so effective at this that a by-product of their efforts is a fully cancerous cell. Epstein-Barr virus, for example, has its own version of the Bcl-2 proteins that inhibit apoptotic activation of mitochondria, and so can cause various lymphomas and leukaemias. Similarly, Human Papillomavirus (HPV) is now vaccinated against in young women in many countries because it was discovered its inactivation of p53 and pRb (another TS gene) lead to nearly half a million cases of cervical cancer annually worldwide and 270,000 deaths. Without an understanding of how apoptosis works, such translational treatments would not be possible.

The future

Apoptosis research is still a fairly young field and there is much left to be learned about how apoptosis is regulated in different tissues. One hurdle to such research is that the cell lines molecular biologists usually work with are derived from cancers so that they grow nicely, but these do not display usual apoptotic behaviour and so aren't suitable for work on cell death. As our understanding of apoptosis improves, however, we are better able to say what is and isn't usual in these cell lines and so accommodate the abnormalities accordingly, thereby making research more efficient. Future work promises to undercover in great depth the complex regulatory processes that govern apoptosis, and present more and more targets for treating cancer and other disorders of cell division.

The next post in this series can be found here.

A three dimensional fractal in 3D

2012-12-17T18:18:00.002-08:00

The video below is a fractal. It is also three dimensional. It has also been rendered from two different locations very close to each other. Therefore, you can also see it in three dimensions.

If you're not used to using YouTube's 3d capabilities then don't worry, this guy has a tutorial video explaining how to see the full three-dimensionality of the video without the need for glasses. It's just like magic eye in reverse, basically (though I'm not sure how good it is for your eye muscles).

If you liked that you should read the description of how the Mandelbulb was discovered. The Mandelbulb was made by people looking for a three dimensional analogue of the well known Mandelbrot set. If you don't know what the Mandelbrot set is, first watch this video, then read about what you just saw at Wikipedia.

None of the Mandelbulb, or the Mandelbrot set or the 3d fractal (a Mandelbox) shown above were designed by a human mind. All of the complexity found in the images comes about from defining structures in two or three dimensional space as the set of points that are or are not solutions to relatively simple mathematical algorithms. For example, the algorithm describing the Mandelbrot set can be described in just one line:

"... the Mandelbrot set is the set of values of c in the complex plane for which the orbit of 0 under iteration of the complex quadratic polynomial $z_{n+1} = z_n^2 + c$ remains bounded".

All of the complexity you can see in the entire ten minutes of the Mandelbrot set video I linked to above is defined in that one simple sentence.

Twitter: @just_shaun

Cinema verité - biology style

2012-12-10T14:41:00.000-08:00

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

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

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

The human machine: circuits and wires

2012-12-04T04:11:00.001-08:00

The previous post in this series can be found: here.

In the first post of this 'human machine' series, I explained how 'energy' (that abstract entity) is processed and used by our bodies in order to converted the chemical energy in our food into the work energy required to keep us ticking over nicely. I discussed in this how we are all actually powered by electrical circuits that buzz along in the internal membranes of our cell's power stations, the mitochondria. Better yet, not only are we powered by currents of electrons, familiar to us as standard electricity, but also by currents of protons, and so are actually working off energy being extracted from two forms of electrochemical potential. We're pretty sophisticated machines!

The work energy generated by these processes is used in myriad ways, but one very important one is the creation of another electrical current that is the foundation of everything you've ever done and every thought you've ever had: the neuronal action potential. This is the electrical signals that run along the neurons in your brain and body in general, constantly relaying information back and forth throughout the whole complex machine. Without it we would be like plants, with one part of our bodies completely unaware of what's happening to the rest of it, and animal life as it is familiar to us would be entirely impossible. Most people have, I expect, heard of the notion of electrical signals running throughout our bodies (it's why the machines built the Matrix, right?), but few will actually know what that means. In today's post I'm going to be talking about what neuronal signals actually are, and so explain why being hit by lightning is a bad thing but being defibrillated (like in ER) can be a good thing.

Neurons - shooting the messenger

Your body is an intricately wired piece of equipment - neurons connect every part to every other via the nervous system. In my last post in this series, I discussed how cells talk to one another; well the role of the nervous system is to allow tissues to talk to one another. This is often dictated by the central nervous system, made up of the brain and spinal chord, which is obviously vital for any concious decisions you might want to relay to the rest of your body, yet the majority of the signals coming from the brain are completely subconscious - regulating the conditions of your body, for example. The peripheral nervous system, made up of all of the non-CNS neurons, tends to be less involved in the decision making, and more acting as a simple relay of information; either sensory signals working their way back to the brain, or important instructions being handed down from the CNS to the peripheral tissues like muscles.

This entire network is dependent on a single family of cells: neurons. These are a highly-specialised type of cell that have evolved solely to pass information along from one cell to the next. This specialisation is immediately evident in their structure. Neurons are a hell of a lot longer than most cells, most of their length coming from an extended segment called the axon, or nerve fibre. Most neurons have just one axon but some, particularly in the brain, can have several. At one end of the axon is the cell body that contains the vast majority of the organelles of the cell - i.e. the bits that do the work - mitochondria, nucleus, endoplasmic reticulum etc. Dendrites, from the Greek for 'fingers', extend from the cell body and contact other neurons or cells. At the end of the axon furthest from the cell body is the axon terminal; simply the end of the cell. Both the dendrites and the axon terminus form structures known as synapses, which is really just the point at which a neuron comes into contact with another cell.

The humble neuron - simple but effective.

The axon itself is usually surrounded by a sleeve of other cells called the myelin sheath (made up of either Schwann cells or oligodendrocytes, but let's not go into that here!) that act as insulation for the electrical signal. And that's basically it - nothing all that fancy in the structure, it's very to-the-point. If I had to design an information-relaying cell I can't think of a better shape for it than a long, thin and simple design with synapses at both ends to allow information in and out. So, while elegant, the structure of the cell itself is not that astounding. It is instead once you start to look at the mechanism by which information travels along these cells that you really start to see the brilliance in its engineering.

Travelling down the wire

A firing neuron is a busy thing. The popular perception is that electricity travels down neurons much like it does in a copper wire, with electrons moving down an electrical potential from one end to the next. This is not the case in neurons. For a start, one end of the cell has no more electrons than the others, so there is no electrical potential (which just means a gradient of electron concentration) for them to move down. Then you'd have the problem of how to move the electrons - they can't move freely along the cell membrane because it's made of fats that don't conduct electricity well, and to pass it through the water-filled centre of the cell would likely do a lot of damage (errant electrons are dangerous things)! Instead evolution has come up with an ingenious way around this by developing a mechanism to skim an electrical signal along the outside of the neuron. This is done not by moving free electrons, but instead by moving charged particles called ions. Atoms have no charge when they contain the same number of negatively charged electrons as positively charged protons, but this can change if they either gain or lose electrons, thereby becoming either negatively or positively charged ions, respectively. The main ions that take part in neuronal signal transduction are sodium (Na+) and potassium (K+), both of which have a single positive charge per ion. It's the redistribution of these ions relative to a resting neuron that constitutes the electrical signal in a firing neuron.

The process by which this occurs is called the 'action potential'. In a resting neuron, the number of negatively and positively charged ions on either side of the cell membrane is not equal, and so the two sides of the membrane have different overall charges. In quantifiable terms, the inside of the cell is 70mV more negatively charged than the outside because there are more negative ions (like chloride) on the inside and more positive ions (like Na+) on the outside. This difference is maintained by the fact that the cell membrane is semi-impermeable to ions and so they cannot redistribute spontaneously, and by active ionic pumps that sit in the membrane and make sure everything is where it should be. The action potential is essentially a pulsed disruption of this equilibrium such that for a very brief moment the outside of the cell becomes more negatively charged than the inside. This effect zips along the surface of the cell very quickly, almost like a Mexican wave (or just 'The Wave' as I'm given to understand it's called in the US!) of charge displacement.

So what causes this change? Well our key players, as I mentioned earlier, are Na+ and K+. In the resting neuron, there is more Na+ outside the cell than inside, whereas there is more K+ inside the cell than outside. At the start of an action potential, channels open in the cell membrane that allow Na+ (and only Na+) to enter the cell because of simple diffusion down their chemical gradient. The absolute numbers of Na+ ions that enter the cell aren't very large, but they have the significant effect of reversing the polarity of the membrane such that the outside is now more negatively charged to the tune of around 40mV. This change in polarity causes separate K+ channels to open and so allow K+ to exit the cell, which thereby cancels out the exterior negative charge and brings the cell back to a resting membrane potential. After the action potential the distribution of K+ and Na+ is restored to normal by an Na+/K+ pump, which uses our old friend ATP to power the exchange of one exterior K+ for one interior Na+ until the balance is restored. The fact that this pump has to work pretty much constantly in active neurons makes them incredibly energy-hungry cells, which is why your brain uses 20-25% of your total calorific consumption - I hope you're putting it to good use!

The neuronal action potential.

And that's it, basically. This depolarisation and subsequent repolarisation of the membrane starts at one end of the cell and then shoots along the membrane to the other where it reaches a synapse with another cell and so either passes the signal along to the next neuron via the release of neurotransmitters, or induces whatever the desired response is from another type of cell (e.g. causing muscle contraction). The firing of the action potential on one part of the membrane partially depolarises the next bit, in turn causing it to fire and set of the next bit etc. This can be disrupted by outside sources of charge, principally the negative charge that comes with electrical current. This is the principle behind a defibrillator; if your heart is beating erratically the electrical pulse from the defibrillator overwhelms the effect of the action potential to very briefly inhibit neuronal firing in the heart so that it can restart with a normal rhythm (it doesn't, contrary to popular belief, restart a heart that has stopped beating). A similar thing happens if you are struck by lightning - aside from the burns caused by the heat of the strike, the action potentials in your neurons are disrupted and so this can cause brain damage or stop the heart from beating.

The moving parts of the machine

Whilst it's very interesting to know how the events of this cycle result in neuronal transmission, as a molecular biologist I am most interested in the engineering behind the whole thing. It's a fairly simple process but it requires some absolutely astounding biological machines to make it work. Principally what I am talking about are the two channels mentioned above: the Na+ channel and the K+ channel. These are remarkable bits of equipment - they have to be specific only to their designated ion and also be sensitive to the membrane potential such that they are open or closed at the correct stages of the action potential. For this reason, they are known broadly as 'voltage-gated ion channels'. These channels have been the subject of intense research for half a century and their architecture and inner workings are now quite well understood. I'm going to give a brief overview of how the K+ channel works to give you a sense of just how unbelievably well evolution has engineered these things to work, and really just how sophisticated a machine you are!

The human voltage-gated K+ channel - a thing of beauty! So much so that it has inspired art.

Let's start with the first point I raised: how does the K+ channel stay specific to K+ ions? The channel is, like all channels, a protein - a string of amino acids linked together in sequence and then folded up to produce the final product. Different amino acids have different chemistries, some even have negative and positive charges. That is stage one of the solution - since K+ is positively charged, lining the inside of the channel with negatively charged residues will not only attract K+ in, but also repel negatively charged ions, thereby giving some specificity. However, Na+ is also positively charged, so how to stop it from going through? This where the engineering gets really clever! The K+ channel has a segment in the centre of its pore called the 'P loop', which is made up of 5 amino acids. 4 of these P loops some together in the full channel to made a section known as the 'selectivity filter', which, as the name suggests, gives selectivity to the channel for K+ over Na+. It does this by forming bonds with K+ ions passing through the channel to stabilise their overall charge and so make the whole process energetically favourable. Na+ is smaller than K+ and so is not able to efficiently form these bonds with the selectivity filter, thereby leaving Na+ passage as an energetically unfavourable process.

The selectivity filter of the K+ channel. K+ ions passing through it are shown in red and purple; they fit perfectly in the spaces created between the P loops, whereas Na+ would be too small to fit optimally.

So, on to the next problem: how are they able to open and close in response to changes in membrane voltage? We are still working towards a full understanding of voltage-gating in these channels but nonetheless understand the general principles. Both this and the Na+ channel can exist in 3 distinct states: deactivated (closed), active (open), and inactivated (closed). The channel is capable of switching between the deactivated and active states by subtle changes in the positions of amino acids on its intracellular and extracellular sides. These amino acids alter their charge as the membrane voltage changes, which in turn causes them to shift position and pull the rest of the protein with them. In the deactivated state they are positioned such that the 5 amino acids of the selectivity filter collapse to block the central pore of the channel, whereas in the active state they help to stabilise the conformation shown above. The third state ('inactivated') is also impermeable to K+ ions but instead occurs after the channel has been active for some time. This state cannot easily revert back to the active form and so stops K+ passage entirely. This state is reached when a ball-like segment of the channel becomes correctly charged so that is will insert itself into the central pore and block it like a plug. In order for the channel to become open again the ball must be removed, which only happens after the action potential is fully finished. Unsurprisingly, this is known as 'ball and chain' inactivation.

The three states of K+ channels.

The intricacy of these proteins is quite beautiful, and it is worth remembering that they do their jobs over time-scales that are imperceptibly small to us; a neuron can fire 100 times per second quite easily, which means these channels are opening and closing on the order of nanoseconds. I think it's always important to remember that things are often more complicated than they are typically portrayed, and the complex processes governing such a ubiquitous event as neuronal transmission is a good example of this. I hope I've given you a better sense of what those vague 'electrical impulses' actually are, and that you can see just how unbelievable our construction really is!

The next post in this series can be found here.

Open Sesame! - Diplomacy through science

2012-11-26T08:39:00.000-08:00

For as long as I can remember being even remotely aware of international politics I have known one thing to be certain: Arabs and Israelis don't get on! It's a fact that I've grown up knowing and has been reinforced time and time again in recent years with seemingly unbreakable cycles of violence and ever more dangerous and confrontational political rhetoric from both sides. The most recent exchanges of ammunition between Gaza and Israeli cities is simply the latest chapter in this sad tale of a fractured region.

But how will the story end? Little diplomatic progress has been made in the resolution of the conflict in the 60 years that it has been raging, and indeed the conflict has spread to bring countries such as Iran and Pakistan into the front line of political warfare. The historic, cultural, and religious differences between the two sides seem simply too insurmountable to overcome, and so a bloody (and potentially radioactive) conclusion seems a terrifyingly possible outcome.

Yet, in the midst of all the hatred and mistrust, there is a glimmer of hope on the diplomatic front that has come in the form of a collaborative scientific project. Sesame, which stands for 'Synchrotron-light for Experimental Science and Applications in the Middle East', is a multi-million dollar particle accelerator currently under construction near Amman, Jordan. Synchrotrons are fantastically useful facilities capable of producing a form of light known as synchrotron radiation that can be harnessed to investigate materials on unbelievably tiny scales. One such application is the study of proteins and other biological molecules down to atomic scales such that their structure and function can be better understood, and potentially so that we can develop more sophisticated drugs to target them. I recently wrote about the 2012 Nobel Prize for Chemistry awarded to Robert Lefkowitz and Brian Kobilka, which would have been entirely impossible without facilities such as Sesame.

Synchrotron light, which gives the Crab Nebula (above) its blue haze, can be made on Earth to investigate protein structures down to minute scales, like the one shown below.

Sesame will be the first synchrotron in the Middle East and will provide a huge boost to the scientific community in the area - not just in molecular biology but also particle physics, materials science, chemistry, and engineering. That said, however, there are about 60 synchrotrons worldwide so even though Sesame will provide a vital local service, it isn't going to be a game-changer in the world of international science. Instead, what is truly remarkable about Sesame is the way in which it has fostered a sense of cooperation and communication within some areas of otherwise polarised societies. The project is joint funded by the governments of Israel, Iran, Jordan, Turkey and Pakistan, as well as the EU. Many of these governments are overtly hostile towards one another: neither Iran nor Pakistan has any formal relations with Israel; Iran is openly committed to the destruction of Israel; and the Israeli government has threatened on numerous occasions to launch pre-emptive strikes against Iranian nuclear facilities. The idea of these old adversaries working together is staggering!

And yet it seems to be happening. Sesame's facilities are well under construction, and even though there is still a $10 million shortfall in the funding needed to complete the project, those in charge are confident that it will be up and running by 2015. Scientists often talk about the universal nature of science and its ability to bring people together in a sense of united curiosity and progress, but in Sesame this ideal is becoming reality. This is further exemplified by the fact that, along with the countries listed above, Cypriot researchers are also amongst those who will be the principle users of the facility despite the fact that their government does not share any diplomatic relations with the government of the Turkish scientists alongside whom they will be working. The gathering of Sesame's principle future users saw Palestinians mingling with Israelis, Iranians, Egyptians, Jordanians, Cypriots, Turks, and Pakistanis, all openly and calmly engaging in unbiased discussion about the future of the project and the state of science in the region. The significance of this is difficult to comprehend given the sheer level of mistrust that usually exists between these countries. Prof. Eliezer Rabinovici of the Hebrew University of Jerusalem described Sesame as "a beacon of hope for many in the area who dare to believe.", whilst Dr Jamal Ghabboun, a Palestinian physicist from Bethlehem University, hopes that "science will open the door to further understandings concerning other issues - we will begin with science and somehow we will open the doors that are closed for years or centuries."

I am a great believer in the potential of science to bring unity to civilisation and to fractured societies. So many of the arguments and conflicts that we hear about on the news are born out of fundamental differences of opinion over one thing or another, whether it be religious or historical fact. Science is impartial and universal; it is an absolute, all we can do is hope to understand it in ever greater detail. In that sense science is immune to the petty bickering that we humans so often have over the minute differences that we focus on rather than on the enormous similarities that we share. Prof. Sir Chris Llewellyn Smith, who heads the governing council of Sesame, describes science as a "common language" that can transcend cultural and national differences and promote peace and understanding. Sesame is not the first example of this: CERN, of Large Hadron Collider fame, was established after the chaos of the second world war as part of the larger concerted effort to promote common goals across Europe and so prevent future conflict.

So, I am hopeful that Sesame will achieve its dual aims of fostering discourse between the fractured peoples of the Middle East by it foundation, and of directly furthering scientific understanding by its operation. Who knows, it may also promote the expansion of science in the region and slow the current 'brain-drain' from the countries involved, as has happened in countries like Brazil and Taiwan when synchrotrons have been built in the past. Increasing the proportion of the population who are scientifically engaged in these countries can, in my eyes, only be a good thing. It's a long way off, but I desperately hope that my grand-children do not grow up with the 'fact' of Arab-Israeli hatred, but rather with the understanding that our knowledge of existence is in its infancy and our journey towards fully understanding it is one that we will only complete if we take it together.

Solar Eclipse

2012-11-20T14:31:00.001-08:00

Southern Hemisphere view. This eclipse was only visible from New Zealand, Australia, and Chile.

Shaken not stirred - how to extract your own DNA

2012-11-12T12:40:00.002-08:00

Last week I eagerly sat down to watch the first episode of a new series: Dara O Briain's Science Club. For those of you from outside the British Isles, Dara O Briain is an Irish comedian who, in recent years, has become one of the most popular comedians and broadcasters in the UK. Not only is he a very funny guy, he's also got a pretty sharp mind inside his (frankly massive) shiny head: he studied mathematics and theoretical physics at University College Dublin and has managed to hang on to his love of science despite moving into the world of entertainment. He, along with other big names like Brian Cox and James May, has been instrumental in advancing British popular science broadcasting in the last decade and has presented a number of science programmes, such as School of Hard Sums and Stargazing Live, giving science that much-needed welcoming and friendly face.

His new series is most definitely worth watching and I await the next episodes with bated breath. The first was on the subject of genetics and epigenetics and my curiosity was more about how these complex topics would be presented rather than actually learning something (I'm already fairly familiar with the fields)! I was delighted by the casual and approachable way in which it was structured, and how debates about scientific funding and application were mixed in with the hard facts.

Possibly my favourite moment, however, was when we were shown how to perform a simple task that I am very used to doing in the lab, but in your own home: extracting DNA. Perhaps appropriately given the latest addition to the James Bond franchise, this entailed the use of cocktail-making equipment and the kind of very strong vodka needed to make that perfect Martini. Some might think of this as a big gimmicky and irrelevant, but I quite like the idea of making somewhat abstract scientific principles more tangible in the mind of the general public. Bringing such a standard research procedure into people's homes helps to demystify the scientific method and hopefully give people a greater sense of ownership over this work than they might otherwise have.

So, today's post is a shameless plug for Dara O Briain's Science Club with the aforementioned DNA recipe thrown in for those of you unfortunate enough not to be able to watch it online! Enjoy.

1. Collect some of your cheek cells by swishing some (around 100ml) salt water around your mouth for 30 seconds or so. The solution will be a bit cloudy afterwards.

2. Add a few drops of washing-up liquid (to dissolve the cells' membranes) and a shot of pineapple juice (the proteases in this will degrade the myriad proteins found in your cells). Pop it all into a cocktail shaker and give it your best shake!

3. Pour through a cocktail strainer to remove bubbles, ideally into a martini glass or something in which it's easy to layer different liquids.

4. Chill some very strong (>80% abv) vodka on ice and they carefully layer over the top of your mushed up cell solution. At such a high concentration of alcohol DNA comes out of solution and so precipitates at the boundary between the two solutions. This looks like a white cloud forming at the bottom of the vodka layer, which can be scooped out by wrapping it around a toothpick or something similar. Et voilà! It may not look like much, but you have successfully extracted the chemical instructions that make you you. Not bad for 5 minutes work.

Science and Video Games

2012-11-06T07:25:00.000-08:00

A long time ago I posted about an online game called FoldIt. After I made that post various other examples of crossovers between video games and science have been brought to my attention. Many of these, I have linked to from The Trenches of Discovery's Facebook and Google+ pages and some I've been saving for a rainy day. (Note, we often post links/comments to those pages when we don't consider them worth a whole blog post. If you read this blog, but aren't following either of those pages, you're missing out on some interesting stuff. You should remedy this.)

Well, it isn't rainy, but it is foggy, so the day has as good as come. What follows is a run through of some of the various science/video game crossovers I'm aware of. Some of these are neat video games, designed to either teach an aspect of science, or try to give a phenomenological experience of what that aspect of science means for the world. Others are more like FoldIt, they are puzzle games that you try to solve, and in the process you're actually helping the scientists solve their research problems.

Phylo

Phylo is a puzzle game where your actions could help the researcher learn something. You arrange blocks in a set of lines and try to get as close a match between the various lines as possible. This sounds like a pretty generic puzzle game, but behind the scenes your set of blocks is actually a genome and the different lines correspond to different species. By moving the blocks, looking for matches, and finding the optimal line up you are find connections between the two species. Given that there are billions of base pairs in a genome, a computer algorithm cannot iterate every single possible arrangement to find the optimal one. The human eye is great at seeing patterns and we can immediately dismiss many possible arrangements, all of which a computer would still iterate.

The results from Phylo are quite similar to FoldIt. They find that, ultimately, the computer alone still does a better job than humanity alone; however the computer guided by the collective human choices arguably does the best job. Unlike FoldIt, however, there isn't a nice newsworthy story of something entirely new discovered just on the human side. You can read the paper they published if you want.

If you're bored one evening and want to help out with the scientific cause, you might want to have a go at Phylo.

Velocity Raptor

Velocity Raptor is one of my favourite things on the internet. It is a simply two-dimensional browser game where you navigate a dinosaur (the velocity raptor) through various puzzles. Some involve evading water traps, some involve dodging slow bullets, some involve getting lights to match up, some involve timed trapdoors and other possible complications. If that was it, the game would be a somewhat bland and ultimately useless puzzle game (the puzzles are all very simple).

However, that is not it. After you easily navigate the first few levels, the speed of light is dramatically lowered. Therefore, all the effects of special relativity suddenly become relevant. As you move Velocity Raptor you witness time dilation, length contraction, relativity of simultaneity and relativistic Doppler shifts in the colours of lights. Suddenly the trivial puzzles are much more difficult.

That isn't the end of it either (and this feature will probably mess with most physicists' intuition too). At first, when the speed of light is lowered, you see the world the way it actually is, that is, the way you would measure it. A clock tells the actual time you would measure it to have at each instant, distances are the actual length you would measure them to be. But then, the game gets even tricker.

Here's how. One other issue with relativity is that light travels at a finite speed. It takes time to get from its source to an observer. This is actually something we deal with in cosmology all the time, we see objects in the sky as they were in the past, not as they are now. What this means for someone living in a world with a small speed of light is that what they would perceive when just looking at things is actually quite different to what is really there. For example, extended objects moving towards you will appear to bend because the light from their edges will take longer to reach you and thus the edges will appear to be further away (even though they actually aren't). The next level of difficulty in Velocity Raptor shows you the world as you would actually see it if you were travelling at speeds close to the speed of light.

I love this game because it gives the viewer a real feeling for what relativity means for the universe without the viewer needing to learn and understand the background maths. It doesn't help acquire new knowledge in a scientific sense, but it does give us a way to grasp phenomenologically what relativity means. And, the world is relativistic. Keep in mind when playing the game that everything that happens in Velocity Raptor also happens on Earth while you're travelling to work, only much more subtly.

A Slower Speed of Light

As soon as I discovered Velocity Raptor I was convinced that a really cool idea would be to take a first person style game (i.e. Doom, Half-Life, Portal, etc, etc, etc, etc, etc) and make the speed of light small. Last week, Santa brought me an early Christmas present.

A collaborative team of physicists, programmers, game designers and artists have made a prototype of exactly this game. They were based at the MIT games lab and they've called the game “A Slower Speed of Light”. Embedded below is a trailer for the game. You can see in the video various relativistic effects (Doppler shift) and some of the effects of perception I mentioned above (i.e. the bending of straight objects).

The makers are incredible people and so they intend to make this game open source. I hope one day there will be all sorts of versions of this idea populating the internet. Someone on facebook suggested a Portal mod would be great. I agree.

I think games like this aren't just fun. The divide between what small groups of people have worked out about how the world actually works and how most of society think the world works is a dangerous divide for society to have. If games like this can show people what relativity actually physically means without them needing to learn the mathematics then that has immense importance.

I would go as far as saying that playing this game should be a compulsory part of high-school science curricula.

Gamify your PhD

The people at the Wellcome Trust had a particularly interesting idea. They hosted a competition for people to make games out of their doctoral research.

The results are now in and can be downloaded and played.

I haven't played any yet, but I will try to find time soon. Watching some of the videos of the games I am impressed that people doing doctoral research also have the skills to make these games (though I think they did all have considerable help).

Wellcome have a write up of the awards on their own blog.

International Science and Engineering Visualisation Challenge

Finally, there is the set of games submitted to the International Science and Engineering Visualisation Challenge. So far, I have only played one these games, and that is Velocity Raptor.

By the way, the voting is still open and Velocity Raptor is not winning, so either go vote for it or find out why the two beating it are better.

For the same reasons that I think Velocity Raptor and A Slower Speed of Light are important, I think competitions like this are a great idea.

Policy debate - Do we need more Scientists in Parliament?

Finally, and this has nothing to do with games, I have mentioned before that there are few scientists involved in politics. This generated a bit of discussion, as well as a post by Sesh. Part of the consensus reached was that politics would benefit from having more experts of any form (i.e. not just scientists), but, the benefits gained in politics from being deliberately misleading will naturally turn away experts.

In any case, the following event was brought to my attention. The Society of Biology in the UK apparently also believes that scientists should be more engaged in politics and in particular in parliament. Or at the very least they think there should be more discussion on the matter. On November 28 they are holding a public debate on the matter in London.

I would attend if I was a UK resident. The registration for the event is full, but you can add your name to a wait-list if you want.

It would be interesting to know what comes out of it. A podcast of the event will be made available afterwards.

Twitter: @just_shaun