## Monday, May 20, 2013

### Stem cells 2.0

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

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

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

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

## Monday, April 29, 2013

### TEDx CERN

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

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

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

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

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

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

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

## Wednesday, April 10, 2013

### The human machine: setting the dials

The previous post in this series can be found here.

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

Esoteric instructions laid bare

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

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

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

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

## Tuesday, April 9, 2013

### The Trenches of Discovery

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

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

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

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

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

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

[Continued from yesterday...]

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

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

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

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

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

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

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

## Monday, April 8, 2013

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

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

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

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

Highlights

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

What has Planck told us about inflation?

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

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

## Thursday, April 4, 2013

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

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

The feature at l=1700

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

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

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

Planck's data analysed on the SPT sky

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

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

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

The result is striking.

They found a cosmology that agrees with SPT.

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

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

Power asymmetry

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

[The final summary is now available here]