Trenches of Cosmology

Hello good people, how are you?

While this blog has languished, my own attempts to share research with the world haven't (at least not entirely).

Recently I began live-streaming myself discussing cosmology research. You can find the channel where it happens here.

I will be live-streaming tomorrow (Friday) at 9pm UTC as well, on whether there might be a "mirror world" around us, making up part of dark matter. The stream is embedded below...

If you liked the Trenches of Discovery blog, hopefully you'll like the Trenches of Cosmology livestreams 😀

I'll see if I can get James and Michelle to join on some livestreams sometime in the future and the blog can re-awaken as a sort of podcast maybe? 

Let me know in the comments if you'd like that!

Cosmology Talks

On the off chance that anybody is still checking out this blog, and doesn't already know, I've made a YouTube channel with talks in it about cosmology.

Unfortunately, the channel is aimed at a technical audience, whereas this blog was aimed at the general public. So it might not be what everyone reading this is looking for. 🤷

Anyway, if you're a current (or ex) cosmologist, or want to put in a lot of background work to understand the concepts, you might want to check out the channel (and subscribe to it too!).

The video below is the latest at the channel. It's on Fast Radio Bursts and how they can be used for cosmology (the expert in the video is Amanda Weltman, a professor at the University of Cape Town). The content is really good and cosmologists should definitely check it out, although be warned the video quality before the slides are brought out isn't great due to internet bandwidth issues.

Feel free to ask any questions here or there.

The shape of physical laws

[The following is a guest post from Bjoern Malte Schaefer (see his last guest post here). Bjoern is still one of the curators of the Cosmology Question of the Week blog, which is also still worth checking out. Enjoy!]

Introduction

The aim of theoretical physics is a mathematical description of the processes taking place in Nature. Science is empirical, meaning that its predictions need to comply with experimental results, but other categories are very important (but not decisive): Theoreticians look for elegance, consistency and simplicity in their descriptions, they aim for abstraction and unification, and look for reduction of the laws of Nature to a few fundamental principles and at the same time for analogies in the description of different phenomena. The subject of this article is to show how these aspects are realized in classical physics, although many of the arguments apply to relativistic physics as well - or only show their true meaning in this context. I do apologize for some of the mathematics, and I promise to keep it as compact as possible.

Formulation of physical laws with differential equations

Physical laws are formulated with differential equations, which relate the rate of change of a quantity to others, for instance the rate of change of the position with time to the velocity. This rate of change is called a derivative. The solution to these equations usually involve an initial value of a quantity under consideration, and compute the value at each instant in solving the equation. The fact that the laws of physics are formulated with differential equations is very advantageous because they separate the problems of evolution of physical systems from the choice of initial conditions for the evolution. Using differential equation for e.g. deriving the motion of planets leads to the abstraction to what forces planets are subjected and how they move under these forces. It predicts naturally the orbits of planets without fixing a priori the orbits themselves, as for example Johannes Kepler might have thought.

Classical mechanics

Let’s discuss a straightforward example: The motion of a body under the action of a force in Newtonian dynamics. Newton formulated an equation of motion for this problem, which stipulates that the acceleration of a body is equal to the force acting on it, divided by the mass of the body. If, in addition, the acceleration is defined as the rate of change of velocity with time and the velocity as the rate of change of position with time, we get the usual form of Newton’s equation of motion: The second derivative of position is equal to the force divided by mass: This is the prototype of a differential equation. It does not fix the trajectory of the body (the position of the object as a function of time) but leaves that open as a solution to the differential equation under specified initial conditions (the position of the object at the starting time).

Already in Newton’s equation of motion there are two very interesting details. Firstly, the solution to the equation without any force is found to be one with a constant velocity, or with a linearly increasing coordinate, which is known as inertial motion. And secondly, the equation of motion is a second order differential equation, because of the double time derivative. This has the important consequence that motion is invariant if time moved backwards instead of forwards.

Classical gravity

A generalisation to this idea is the classical description of gravity. In a very similar way, the gravitational potential is linked through a second-order differential equation to the source of that field, i.e. a central mass. How would this work by analogy? In the mechanics example above, the source of motion was given by the force and both were linked by the second derivatives. Here, the second derivatives of the potential are linked to the sourcing mass again by a second order differential equation, which in this context is called the Poisson-equation, named after the mathematician Denis Poisson.

Would this idea work in any number of dimensions? It turns out that one needs at least three dimensions to have a field linked to the source by a second-order differential equation, if the field is required to vanish at large distances from the source and if the field is symmetric around its source, which are all very sensible requirements. Surely the gravitational field generated by a point mass would be the same in every direction and the attracting effect of the gravitational field should decrease with increasing distance.

Is there an analogy to the forward-backward-symmetry of Newton’s equation of motion? The field equation is invariant if one interchanges the coordinates by their mirror image, therefore, Nature does not distinguish between left and right in fields, and not between forwards and backwards in motion. These are called invariances, in particular the invariance of the laws under time-reversal and parity-inversion. And finally, there’s an analogy to inertial motion, because no gravitational field is sourced in the absence of a massive object. The mass is the origin of the field in the same way as force is the reason for motion.

Variational principles

Joseph Louis Lagrange discovered a new way of formulating physical laws, which is very attractive from a physical point of view and which is easily generalizable to all fields of physics. How it works can be seen in a very nice analogy, which is Fermat’s principle for the propagation of light in optics. Clearly, light rays follow paths that are determined by the laws of refraction, and computing a light path using Snell’s law is very similar to using Newton’s equation of motion: At each instant one computes the rate of change of direction, which is dictated by the refractive index of the medium in the same way as the rate of change of velocity is given by the force (divided by mass). But Fermat formulated this very differently: Among all possible paths leading from the initial to the final point light chooses the fastest path. This formulation sounds weird and immediately poses a number of questions: How would the light know? Does it try out these paths? How would the light ray compare different paths? It is apparent that Fermat’s formulation is conceptually not easy to understand but one can show that it leads to exactly the right equation of motion for the light ray.

Lagrange’s idea was to construct an abstract function in analogy to the travel time of the light ray, and to measure a quantity called action. Starting from his action he could find a physically correct equation of motion by constructing a path that minimizes the action, in complete analogy to Fermat’s principle. Lagrange found out that if one starts in his abstract function with squares of first derivatives of the dynamical quantities, they would automatically lead to second order equations of motions, so the basic parity and time-reversal symmetries are fulfilled. In addition he discovered, that if he based his abstract function on quantities that are identical to all observers, he could incorporate a relativity principle and make a true statement about a physical system independent from the choice of an observer.

Universality

The formulation of the laws of physics with differential equations is very attractive because it allows to describe different solutions that might exist for a physical problem. For the motion of the planets around the Sun there is a universal mathematical description, and the planetary orbits themselves only differ by choosing different initial conditions for the differential equation. There is, however, yet another feature present in the equation of motion or the field equation, which is related to Lagrange’s abstract description.

Clearly, any description of a process must be independent if the length-, time- and mass-scales involved are changed: This feature is referred to as universality or mechanical similarity, because it allows to map solutions to the equation of motion onto others. For instance, the orbit of Mercury would be a scaled version of the orbit of Neptune, the orbits can be mapped onto each other by a redefinition of the length- and time-scales involved. This was considered be an essential property of the laws of physics, because it implies that problems fall into certain universality classes and that there is no limit of validity of the solution. Coming back to the problem of the motion of objects in gravitational fields one finds Kepler’s third law, which states that whatever the orbit of a planet, the ratio between the third power of the orbital radius divided by the orbital time squared is always a constant. It is completely sufficient to solve the problem of an orbiting planet in principle, the orbits of other planets do not even require solving the differential equation again (with different initial conditions), but all possible solutions follow from a simple scaling operation. A more comical example are astronauts walking on the surface of the moon with much smaller gravity: their movements appears to be in slow motion, but speeding up the playback would show them to move perfectly normal.

Relativity

The last question is of course what the true meaning of Lagrange’s abstract function should be: It is very successful in deriving physically viable equations of motion and field equations, but before the advent of relativity it was unclear how it should be interpreted: It turns out that the Lagrange-function of moving objects is the proper time and that the Lagrange-function of the gravitational field is the spacetime curvature. Objects move along trajectories that minimize the proper time elapsing on a clock moving with that object, and the gravitational field is determined as the minimal curvature compatible with a source of the field. These interpretations require that spacetime has at least four dimensions (instead of three), and they lead to viable second-order differential equations respecting time-reversal and parity-invariance. Both quantities, proper time and curvature, are invariant under changes of the reference frame, so relativity is respected, and are invariant under choosing new coordinates - this is in fact the expression of universality. And one has learned one additional thing, which must appear beautiful to everybody: The laws of Nature are geometric, a very complicated, position dependent geometry, whose properties are defined through differential equations. The lines of least proper time are straight in spacetime in the absence of a force, and considering gravitational fields in cosmology it is even the case that the expansion of space is constant an empty universe, both as a reflection of inertial motion. But there is one new phenomenon: Gravitational fields do not vanish at large distances as Newton thought, rather, they start increasing at distances above 10^25 meters, where gravity becomes repulsive under the action of the cosmological constant, and this feature brakes scale invariance.

Summary

 The formulation of the laws of Nature led physicists to a geometric description of physical processes in the form of differential equations, and variational principles are a very elegant way of formulating the origin of equations of motion and field equations. The true meaning of the variational principles only became apparent with the advent of relativity. It is even the case that other forces, like electromagnetism, the strong and the weak nuclear force have a analogous description, involving an abstract geometry on their own. Finally, it was realised by Richard Feynman that the way in which Nature realizes variational principles was through the wave-particle duality of quantum mechanics - but that is really the topic of another article.

LIGO's search for gravitational waves.

Here is an infographic showing how LIGO searches for gravitational waves. We're happy for it to be shared, so long as it is attributed to @ashadesigns and The Trenches of Discovery.

For more details on why you should be interested in LIGO and gravitational waves, maybe start here and see where your interest takes you. The press conference where LIGO will hopefully announce a detection of gravitational waves will be webcast at the location below, apparently:

Dark energy: onus of proof reversed

[Note from Shaun: The following is a guest post by Boud Roukema. Boud is a professor at the Toruń Centre for Astronomy at Nicolaus Copernicus University. Boud is one of the coauthors of the papers on the pro-backreaction side of the debate I referred to in this post. Boud also blogs at Topological Acceleration, where the following post first appeared on 22 January this year.]

The simplest explanation for "dark energy" is that it measures recent evolution of average negative curvature. We think that it mainly represents the recent formation of cosmic voids on scales of tens of megaparsecs; these voids dominate scalar averaged quantities. In other words, the onus of proof has been reversed, in a quantified way: dark energy as something beyond classical general relativity should be disfavoured by Occam's Razor unless a relativistic inhomogeneous cosmological model is used. This seems so far to have largely gone under the radar...

Observationally, there's no disputing the existence of dark energy in the restricted sense of providing a good observational fit to several of the main cosmological observational datasets, modulo a rather unrealistic assumption of the model used in the fitting procedure. The assumption is that the class of possible spacetimes, i.e., solutions of the Einstein equation of general relativity, is the FLRW (Friedmann-Lemaître-Robertson-Walker) family. The FLRW models require that after choosing a way to split up space and time (a foliation), the spatial slice (i.e., a 3-dimensional space) is homogeneous—the density is the same everywhere, so galaxies and voids cannot exist. In fact, cosmologists usually make a hack, modelling galaxies and voids by patching Newtonian gravity into an Einstein "background"—since using the Einstein equation is more tricky. This hack bypasses the basic problem without solving it.

Since in reality, galaxies, clusters of galaxies, the cosmic web and voids and supervoids exist beyond any reasonable doubt, the FLRW family should be expected to go wrong at recent epochs and at small (less than a few gigaparsecs) scales. And the small-scale, recent epoch is the only epoch at which a non-zero cosmological constant (or dark energy parameter Ω_Λ) can (at present) be observationally distinguished from a zero cosmological constant. So it happens that just where and when we can expect things to go wrong with FLRW, Ω_Λ suddenly appears, provided that we assume FLRW in our interpretation of the data despite expecting FLRW to be wrong! What is it that goes wrong? The picture above shows voids on the scales of a few tens of megaparsecs from the2dFGRS. From a relativistic space point of view, expansion rates are different in different regions. This also happens in the hack of adding Newtonian galaxy and void formation to Einsteinian expansion, but in that case the expansion is forced to be rigid, by assumption, preventing the Einstein equation from being applied correctly. Even when we interpret the observations from a rigid comoving space point of view, the numbers show that the ratio of the "peculiar velocities" of galaxies coming out of voids to the sizes of the voids is big: several hundred km/s divided by something like 10 Mpc, giving a few times 10 km/s/Mpc. This void peculiar expansion rate is not much smaller than the Hubble constant, which is about 70 km/s/Mpc. At an order of magnitude level, the expansion rate is definitely inhomogeneous. This is why interpreting the observations in terms of homogeneous expansion gives a big error.

In other words, unless we use a relativistic cosmological model that takes inhomogeneous curvature and virialisation into account, we cannot claim that the "detected" Ω_Λ is anything other than a structure formation parameter of a fit through cosmological data using an oversimplified fitting function. The second picture at the right shows that going from right (early times) to left (today), the amount of inhomogeneity (the virialisation fraction) grows from almost nothing to a big fraction of the total mass density today. Alternatively, if we ignore the growth in inhomogeneity, then we get Ω_Λ, interpreted from the data assuming homogeneity, growing from almost nothing to a big fraction (70%) of the total density today. If we ignore inhomogeneity, then miraculously dark energy appears instead!

Several relativistic structure formation cosmological models are available, though still in their infancy. However, what has been a little distracting from working on these is that some observational cosmologists thought that there existed a mathematical theorem—the Green and Wald formalism—showing that dark energy could not be a "fitting function" description of curvature and kinematical backreaction, the general-relativistic effects of treating both structure formation and expansion of the Universe together. This is why my colleagues and I had to publish a clarification showing the main flaws in this reasoning. In particular, the Green and Wald formalism is not applicable to the main relativistic structure formation cosmological models that have been proposed in the research literature over the past five years or so. Green and Wald's formalism remains an interesting contribution to the field of relativistic cosmology, but it does not "save" dark energy from being anything more exotic than spatially averaged, evolving negative curvature. After a few tweets [1] [2], a blog entry, and a reblog we can get back to work. :)

The future is now! The rise of genome editing

It’s an exciting time to be a biologist! Every few years it seems like there is another significant technical breakthrough that allows biological research either to speed up exponentially, or to enter into areas that were previously inaccessible. In just the last decade or so we’ve seen the publication and digitisation of the human genome (without which most current life sciences work would be either impossible or impractical), the development of super-resolution microscopy (allowing us for the first time to see live biological processes on a truly molecular scale), the facilitation of DNA sequencing (making it economical on a large scale), and the invention or improvement of a whole range of technologies (enzyme-conjugation systems, flow cytometry, fluorescence-activated cell sorting etc.) that won’t mean much to anyone outside the field but that have revolutionised the way research is done. It’s been a long road, but it finally seems like the ambitions of researchers are starting to be matched by the available technology, whether it be computational, mechanical, chemical, or biological. The latest innovation that is taking the biology world by storm is the enormous progress that has recently been made in an area that has incalculable potential in both academic and clinical contexts: genome editing. In this post I will try to explain these recent advancements, why researchers are excited, and why you should be too!

What is genome editing?

Genome editing is pretty much what you’d expect from the name; editing the DNA sequence within the genome of a particular cell. This can involve adding DNA, removing DNA, swapping some DNA for other DNA, or moving DNA around within the genome. It is difficult to overstate how powerful a tool genome editing can be when it comes to biological research. Much of the work done in molecular life sciences is trying to work out how various molecules fit into the whole machine that is an organism – genome editing allows researchers to directly tinker with these molecules (typically proteins, which are of course encoded by a their associated DNA sequence) and observe the effects. This could involve removing the gene encoding a given protein from an organism and seeing what defects arise. Alternatively, you could introduce a specific mutation in a gene to see if that has functional relevance, or introduce DNA encoding fluorescent marker proteins into the end of your protein of interest to see where it goes and what it’s up to. Genome editing elevates researchers from the level of pure observers into direct manipulators of a system.

Hypothesis: The future of peer review?

If I could recreate the way research results are quality checked and revealed to the world, I would probably change almost all of what is currently done. I think the isolated scientific paper is a product of the 20th century, being imposed on the 21st purely because of inertia. A better solution would be to give a "living paper" to each general research project an individual researcher has. This living paper can then be updated as results change/improve. In such a system I would probably have ~5 living papers so far in my career, instead of ~20 old-style papers. Or, even better, would be a large wiki edited, annotated, moderated and discussed by the science community as knowledge is gained.

Even if you to wish to keep "the paper" as how science is presented, I think that the journal system, while invaluable in the 20th century, also exists in the 21st century only due to inertia. Pre-print servers like the arXiv are already taking care of the distribution of the papers, and the peer review, which is responsible for the quality check side of things, can (and might?) be organised collectively by the community on top of that. But why should we stick with peer review anyway? Could there be a better way?

Firstly, let me stress, peer review is definitely an incredibly effective way to progress knowledge accurately and rapidly. The best ideas are the ones that withstand scrutiny. The better an idea is, the more scrutiny it can withstand. Therefore, holding every idea up to as much scrutiny as possible is the best way to proceed. However, by peer review I simply mean criticism and discussion by the rest of the scientific community. I think the way peer review is currently done, at least what people normally mean by "peer review" is very nearly worthless (and when you factor in the time required to review and respond to review, as well as the money spent facilitating it I'd be tempted to claim that it has a negative impact on research overall). The real peer review is what happens in informal discussions: via emails, at conferences, over coffee, in the corridor, on facebook, in other papers, etc. The main benefit the current method of peer review has is simply that the threat of peer review forces people to work harder to write good papers. If you removed that threat, without replacing it with something else, then over time people would get lazy and paper quality would degrade, probably quite a lot.

But that would only happen if the 20th century form of peer review was removed without replacing it with something from the 21st century. I wrote above that the real form of peer review happens through conversations at conferences, in emails, etc. The rapid access to papers that we get now makes this possible. In the early-mid 20th century, because the (expensive) telephone was the only way to rapidly communicate with anyone outside your own institute, word of mouth would spread slowly. Therefore some a priori tick was needed, that confirmed the quality of a paper, before it was distributed; hence peer review. But now communication can and does happen much more rapidly. Today, if a paper in your field is good, people talk about it. This gets discussed in emails amongst collaborators, which then disperses into departmental journal clubs and the information about the quality of the paper is disseminated like that. It's worth emphasising that, at least in high energy physics and cosmology, this often happens long before the paper is technically "published" via the slow, conventional peer-review.

However, this information probably still doesn't disseminate as widely or as quickly as might be ideal, given the tools of the web today. What would be ideal is to find a way for the discussions that do happen to be immediately visible somewhere. For example, what if, instead of having an anonymous reviewer write a review that only the paper's authors and journal editor ever sees, there was instead a facility for public review (either anonymous or not), visible at the same site where the paper exists, where the authors' replies are also visible, and where other interested people can add their views? The threat of peer review would still be there. If a paper was not written with care, people could add this in a review. This review would remain unless or until the paper was revised. Moreover, negative reviews that would hold up a paper could also be publicly seen. Then, if a reviewer makes unfair criticisms, or misunderstands a paper, the authors could makes this clear and the readers can judge who is correct. Or, even better, the readers can add to the discussion and perhaps enlighten both the authors and the reviewer (with words that all other readers can see)!

Cosmological Backreaction

In the last few weeks a disagreement has surfaced at the arXiv. The disagreement concerns whether backreaction is important in cosmology.

To summarise my take on the whole thing, it seems to me that the two sides of this disagreement are, to a large extent, talking past each other. I don't doubt that there is genuine disagreement where definitions overlap, but, at least to my present understanding, much of the disagreement actually just lies in what should be considered "backreaction". There seems to be a secondary, though related, disagreement concerning whether one should start with observations and use them to methodically construct a model of the universe, or instead start with a model of the universe and then see whether it fits the data. The side that favours first constructing the model would say that a model without any backreaction is entirely self-consistent and fits the data well enough not to be concerned. To the other side this still doesn't prove that backreaction must be negligible.

But OK, what is cosmological backreaction?

Backreaction itself is quite a common term in physical sciences.

In a surprising proportion of calculations about nature we would normally analyse some sort of interesting object, existing within some external system, but in a scenario where the behaviour of the object has no measurable influence on the overall system. Then, calculating predictions essentially amounts to two independent steps: firstly, calculating what the background system is doing, and then calculating how the interesting object will react to that.

However, this type of scenario isn't always accurate. When it isn't, the background system could be described as "backreacting" to the object's behaviour.

Mysterious news stories about supervoids

Early last week a news story broke about a supervoid. The supervoid was claimed to be a number of things, from an explanation for "the cold spot", to the biggest "structure" yet found in the universe, to just "mysterious".

Whether it is a structure or not entirely depends on how you define structure, so I won't discuss whether it is or isn't a structure. However, if you do allow it to be a structure, it isn't the biggest structure yet found. It's hard to do a like for like comparison with other "superstructures". However, there are regions of the universe where the density of observable matter is smaller, for a wider range, so by any definition I can think of, this structure has been beaten.

The cold spot is a region in the cosmic microwave background (CMB) that has a temperature profile that is somewhat unexpected (due to a combination of a cold central spot and a hot ring around it). Whether this void could be the explanation of the cold spot has been explained in this paper and this blog post by Sesh. It can't, not without a significant deviation from General Relativity (and a sufficiently big deviation that it would be very strange that these deviations haven't been seen elsewhere). It's worth stressing right now that it isn't the coldness of the cold spot that is itself anomalous. This is a subtle point so just about anyone who says "the cold spot is too cold" can be forgiven for the mistake, but in reality the cold spot isn't too cold. In fact it has more or less exactly the coldness expected of the coldest spot in the CMB. What isn't expected is that there will be a hot ring around such a cold spot. Actually, it's worth stressing further that it isn't even the hot ring that is, by itself, anomalous. Such a hot ring is also quite likely in the CMB. The anomalousness of the cold spot is caused by the fact that both of these features are present, right next to each other. I explained this curiosity in this blog entry, but it is worth repeating.

I want to address now quickly the claim that this supervoid is mysterious. The quantitative source for the claim that the void is mysterious comes from the claim in the paper about the void that it is "at least a \(3.3 \sigma\) fluctuation" and that "\(p=0.007\) ... characterizing the cosmic rarity of the supervoid". However (and this is the crucial point) what these numbers quantify is the probability that something as extreme as this void could exist at a random point of the universe (or, more precisely, a random point within the part of the universe seen by a particular observational survey). What these numbers do not quantify is the probability that the whole survey could have seen something this extreme. These are two separate statistical things and the relevant one for claiming mysteriousness is the second one. I'll try to estimate this probability.

I don't have any reason to doubt the numbers they quote for the probability that this void could exist at a random line of sight in the survey. If I use the quoted radius, density contrast and redshift of the void I also calculate it to be a \(\sim 3\sigma\) fluctuation in the matter field. This can be done first by calculating the root-mean-square of the density (contrast) field of the universe when it is smoothed over a particular radius. This quantity, "\(\sigma_R\)", is commonly used in large scale structure. Then, the ratio of the density (contrast) of the obtained void and the \(\sigma_R\) value for the radius of the void gives you \(\sim 3.5\) so I trust that the more sophisticated analyses in the paper are correct, or at least aren't obtaining wildly wrong answers. If one assumes (probably validly) that the large scale density field of the universe has a Gaussian distribution this can be translated into a probability that the observed fluctuation could occur at any random position in the universe.

So, the crucial question that now needs to be asked before calling this supervoid mysterious is whether the survey used to find it saw enough of the universe to witness this rare an event. The size of the void in the sky is approximately \(10\) degrees (as quoted in their abstract). This means it has an area of approximately \(100\) square degrees on the sky. The void was found using data from the WISE and 2MASS all-sky surveys. However the whole sky isn't usable for robust analysis due to foregrounds, the galaxy, etc. Thankfully for our goal, the authors of the supervoid paper also wrote a paper about the catalogue of galaxies they used to find the supervoid and in the abstract of that paper they estimate that their catalogue covers 21,200 square degrees of the sky.

What does this mean when we pull it all together? Well, the catalogue used to find the 100 square degree thing, covered 21,200 square degrees of the sky. Therefore, there were \(\sim 21200/100 \simeq 200\) independent \(100\) square degree patches of the sky seen by the survey. Using their own probability for this void existing at any particular line of sight of \(p=0.007\) this gives a very approximate estimate of the expected number of under-dense regions of the universe at least as extreme as the "mysterious" supervoid. The answer is \(N \sim 200*0.007 = 1.4\).

So, not only is the supervoid not actually mysterious, it is in fact more or less exactly in line with naive expectations!

Twitter: @just_shaun

The science of three-parent children

2015 has already been a significant year in the field of human medicine as February saw the UK become the first country in the world to legalise the generation of so-called 'three-parent' children. This marks a milestone for preventative genetics and embryology and offers hope to many people around the UK and beyond who would be unable to have healthy children otherwise. The votes to bring this into law were fairly comfortably won by those in favour - 382 vs 128 in the House of Commons (the lower house) and 280 vs 48 in the House of Lords (the upper house) - however there have been a number of vocal opponents to the measure. In this post I hope to explain just what the process involves, and why it is considered necessary by the majority of British MPs.

A cellular energy crisis

Mitochondria, as you may recall from a previous post, are the powerhouses of our cells. They metabolise a range of molecules derived from food at use them to generate energy in the form of another molecule, ATP. You would not last long without them - just try holding your breath for a few minutes, since anaerobic respiration is all a cell without mitochondria would be able to manage. It is not surprising, therefore, that problems with mitochondrial function can be fairly nasty. Mitochondrial diseases are a range of genetic disorders in which the proper role of the mitochondria is disrupted due to mutations in one of the genes responsible for making mitochondrial proteins. These diseases never completely knock out mitochondrial function (since an embryo with such a disease could never survive to full development) but still cause severe symptoms in sufferers. Depending on the exact mutation, these can include blindness, deafness, diabetes, muscle weakness, cardiac problems, and problems with the central nervous system. Prognoses vary from one disorder to the next, but they invariably shorten lifespan, often severely. Sufferers of Leigh's disease, for example, rarely live past 7 years of age, and spend their short lives experiencing muscle weakness, lack of control over movement (particularly of the eyes), vomiting, diarrhea, an inability to swallow, and heart problems, among others. 

Combined constraints from BICEP2, Keck, Planck and WMAP on primordial gravitational waves

This week, the joint analysis of BICEP2 (+ BICEP2's successor Keck) and Planck has finally arrived. The result is more or less what was expected, which is that what BICEP2 saw last year in the B-mode polarisation signal of the CMB was not actually primordial gravitational waves (as had originally been hoped and claimed), but was unfortunately actually due to dust in the Milky Way. Such is life. Though we did of course have the best part of a year to come to grips with this reality.

Combined constraint on \(r\) from polarisation and temperature measurements (in blue). Freshly digitised in the spirit of modern cosmology. Gives \(r\lesssim 0.09\) at \(95\%\) confidence.

As a result of subtracting the dust component in BICEP2/Keck's signal (obtained by comparing the measurements from BICEP2/Keck and Planck), the final constraint on the "tensor to scalar ratio" (or \(r\)) from the BICEP2/Keck measurement is that \(r<0.12\) at \(95\%\) confidence. This \(r\) parameter essentially measures the amplitude of a primordial gravitational wave signal, so the net result is that the subtraction of dust takes BICEP2's high significance measurement of non-zero \(r\) and converts it into simply an upper bound.

I've seen some comments on blogs, in media, on Twitter, etc that there is still evidence of some sort of excess signal in BICEP2/Keck over and above the dust, but I can't see any evidence of that in any of their published results. The final likelihood for \(r\) (shown above in black) shows a plot consistent with \(r=0\) at less than \(1-\sigma\) (i.e. \(r=0\) is less than one standard deviation away from the maximum likelihood value). In fact, it would seem that the measurement of the dust that has been obtained by comparing BICEP2/Keck's measurements with Planck's measurements has been so good that the B-mode constraint on \(r\) from BICEP2/Keck is now competitive with (or even slightly better than) the constraint arising from temperature measurements of the CMB. This was always going to happen at some point in the future and it seems that this future has now arrived.

Why is Ebola so scary?

Unless you've been living under a reasonably sizable rock for the last few months, it can't have escaped your attention that the world has yet another terror to throw on the mountain of things we should be scared of: Ebola. The ongoing situation in Africa is the largest Ebola outbreak in history and has seen the disease spread beyond Africa for the first time. At the time of writing this, nearly 10,000 people have become infected, almost half of whom have died. This number is growing...rapidly.

Ebola cases and deaths in the 2014 outbreak.

In this post, I will describe what Ebola is, why it is so scary, and what chances we have of defeating it.

What is Ebola?

'Ebola' as a biological term actually refers to a group of five viruses within the Filoviridae family, of which four can cause the disease generally called Ebola, but more specifically known as Ebola virus disease. The recent outbreak has been caused by just one of these viruses, which used to be known as Zaire Ebolavirus, but is now simply 'Ebola virus' given that it is the most common among humans, and Zaire no longer exists! It doesn't look a whole lot like most viruses, it has to be said - with long, tubular filaments waving around rather than the tight, spherical viruses we're used to seeing for 'flu, HIV, and most others.

The Ebola virus.

Comparing Planck's noise and dust to BICEP2

In case anyone reading this doesn't recall, back in March an experiment known as BICEP2 made a detection of something known as B-mode polarisation in the cosmic microwave background (CMB). This was big news, mostly because this B-mode polarisation signal would be a characteristic signal of primordial gravitational waves. The detection of the effects of primordial gravitational waves would itself be a wonderful discovery, but this potential discovery went even further in the wonderfulness because the likely origin of primordial gravitational waves would be a process known as inflation which is postulated to have occurred in the very, very early universe.

The B-mode polarisation in the CMB as seen by BICEP2. Seen here for the first time in blog format without the arrows. Is it dust, or is it ripples in space-time? Don't let Occam's razor decide!

I said at the time, and would stand by this now, that if BICEP2 has detected the effects of primordial gravitational waves, then this would be the greatest discovery of the 21st century.

However, about a month after BICEP2's big announcement a large crack developed in the hope that they had detected the effects of primordial gravitational waves and obtained strong evidence for inflation. The problem is that light scattering of dust in the Milky Way Galaxy can also produce this B-mode polarisation signal. Of course BICEP2 knew this and had estimated the amplitude of such a signal and found it to be much too small to explain their signal. The crack was that it seemed they had potentially under-estimated this signal. Or, more precisely, it was unclear how big the signal actually is. It might be as big as the BICEP2 signal, or it might be smaller.

Either way, the situation a few months ago was that the argument BICEP2 made for why this dust signal should be small was no longer convincing and more evidence was needed to determine whether the signal was due to dust, or primordial stuff.

The Cold Spot is not particularly cold

(and it probably isn't explained by a supervoid; although it is still anomalous)

In the cosmic microwave background (CMB) there is a thing that cosmologists call "The Cold Spot". However, I'm going to try to argue that its name is perhaps a little, well, wrong. This is because it isn't actually very cold. Although, it is definitely notably spotty.

That's the cold spot. It even has its own Wikipedia page (which really does need updated).

Why care about a cold spot?

This spot has become a thing to cosmologists because it appears to be somewhat anomalous. What this means is that a spot just like this has a very low probability of occurring in a universe where the standard cosmological model is correct. Just how anomalous it is and how interesting we should find it is a subject for debate and not something I'll go into much today. There are a number of anomalies in the CMB, but there is also a lot of statistical information in the CMB, so freak events are expected to occur if you look at the data in enough different ways. This means that the anomalies could be honest-to-God signs of wonderful new physical effects, or they could just be statistical flukes. Determining which is true is very difficult because of how hard it is to quantify how many ways in which the entire cosmology community have examined their data.

However, if the anomalies are signs of new physics, then we should expect two things to happen. Firstly, some candidate for the new physics should come up, which can create the observed effect and produce all of the much greater number of other measurements that fit the standard cosmological model well. If this happens, then we would look for additional ways in which the universe described by this new model differs from the standard one, and look for those effects. Secondly, as we take more data, we would expect the unlikeliness of the anomaly to increase. that is, it should become more and more anomalous.

In this entry, I'm not going to be making any judgement on whether the cold spot is a statistical fluke or evidence of new physics. What I want to do is explain why, although it still is anomalous, and is definitely a spot, the cold spot isn't very cold. Then, briefly, I'll explain why, if it is evidence of new physics, that new physics isn't a supervoid.

So, what is the cold spot, and why is it anomalous?

The human machine: obsolete components

The previous post in this series can be found here.

In my last post in this series I described some of the ways in which gene therapy is beginning to help in the treatment of genetic disorders. A caveat of this (which was discussed further in the comments section of that post) is that currently available gene therapies do not remove the genetic disorder from the germline cells (i.e. sperm or eggs) of the patient and so do not protect that person's children against inheriting the disease. This could be a problem in the long run as it may allow genetic disorders to become more common within the population. The reason for this is that natural selection would normally remove these faulty genes from the gene pool as their carriers would be less likely to survive and reproduce. If we remove this selection pressure by treating carriers so that they no longer die young, then the faulty gene can spread more widely through the population. If something then happened to disrupt the supply to gene therapeutics - conflict, disaster, etc. - then a larger number of people would be adversely affected and could even die.

Although this is a significant problem to be considered, it is one that is fairly simply avoidable by screening or treating the germline cells of people undergoing gene therapy in order to remove the faulty genes from the gene pool. This is currently beyond our resources on a large scale, but will almost certainly become standard practice in the future.

All of this got me thinking: are there any other genes that might be becoming more or less prevalent in the population as a result of medical science and/or civilisation in general? If so, can we prevent/encourage/direct this process and at what point do we draw the line between this and full-blown genetic engineering of human populations? This is the subject of this post, but before we get into this, I want to first give a little extra detail about how evolution works on a genetic scale.

Imperfect copies

Evolution by natural selection, as I'm sure you're aware, is simply the selection of traits within organisms based on the way in which those traits affect that organism's fitness. An organism with an advantageous trait is more likely to survive and reproduce and so that trait becomes more and more common within the population. Conversely, traits that disadvantage the organism are quickly lost through negative selection as the organism is less likely to reproduce. The strength  of selection in each case is linked to how strongly positive or negative that trait is - i.e. a mutation that reduces an animal's strength by 5% might be lost only slowly from a population, whereas one that reduces it by 90% will probably not make it past one generation. In turn, the strength of that trait is determined by the precise genetic change that has occurred to generate it.

The human machine: replacing damaged components

The previous post in this series can be found here.

The major theme of my 'human machine' series of posts has been that we are, as the name suggests, machines; explicable in basic mechanical terms. Sure, we are incredibly sophisticated biological machines, but machines nonetheless. So, like any machine, there is theoretically nothing stopping us from being able to play about with our fundamental components to suit our own ends. This is the oft feared spectre of 'genetic modification' that has been trotted out in countless works of science fiction, inexorably linked to concepts of eugenics and Frankenstein-style abominations. Clearly genetic modification of both humans and other organisms is closely tied to issues of ethics, and biosafety, and must obviously continue to be thoroughly debated and assessed at all stages, but in principle there is no mechanistic difference between human-driven genetic modification and the mutations that arise spontaneously in nature. The benefit of human-driven modification, however, is that it has foresight and purpose, unlike the randomness of nature. As long as that purpose is for a common good and is morally defensible, then in my eyes such intervention is a good thing.

One fairly obvious beneficial outcome of genetic modification is in the curing of various genetic disorders. Many human diseases are the result of defective genes that can manifest symptoms at varying times of life. Some genetic disorders are the result of mutations that cause a defect in a product protein, others are the complete loss of a gene, and some are caused by abnormal levels of gene activity - either too much or too little.  A potential means to cure such disorders is to correct the problematic gene within all of the affected tissue. The most efficient means to do that would be to correct it very early in development, since if you corrected it in the initial embryo then it would be retained in all of the cells that subsequently develop from that embryo. This is currently way beyond our technical limitations for several reasons. Firstly, we don't routinely screen embryos for genetic abnormalities and so don't know which ones might need treatment. Secondly, the margin for error in this kind of gene therapy is incredibly narrow as you have to ensure that every single cell that the person has for the rest of their life will not be adversely affected by what you do to the embryonic cells in this early stage - we're not there yet. Thirdly, our genetic technology is not yet sophisticated enough to allow us to remove a damaged gene and replace it with a healthy one in an already growing embryo - the best we can do it stick in the healthy gene alongside the defective one and hope it does the job. There is certainly no fundamental reason why our technology could not one day reach the stage where this kind of procedure is feasible, but we are a long way off yet.

So, for the time being what can we do? Well instead of treating the body at the embryonic stage, the next best approach is to treat specifically the affected cells later on in life.  This involves identifying the problematic gene and then using a delivery method to insert the correct gene into whatever tissues manifest the disease, preferably permanently. This is broadly known as gene therapy, and is one of the most promising current fields of 'personalised' medicine.  

A new cosmological coincidence problem?

One of the consequences of the BICEP2 data from last week, should it hold up to scrutiny, and be seen by other experiments (I hope it holds up to scrutiny and is seen by other experiments), is that there is a significant lack of "power" in the temperature anisotropies on large angular scales.

What that sentence means is that when you look at the CMB in very large patches on the sky (about the size of the moon and bigger) its temperature fluctuates from patch to patch less than we would expect.

This was already somewhat the case before the BICEP2 discovery, but BICEP2 made it much more significant. The reason for this will hopefully turn into a post of its own one day, but, essentially, the primordial gravitational waves that BICEP2 has hopefully discovered would themselves have seeded temperature anisotropies on these large angular scales. Previously, we could just assume that the primordial gravitational waves had a really small amplitude and thus didn't affect the temperature much at all. Now, however, it seems like they might be quite large and therefore, this apparent lack of power becomes much more pertinent.

That's all fine and is something that any model of inflation that hopes to explain the origin of these gravitational waves will need to explain, despite what many cosmologists already writing papers on the ArXiv seem to want to believe (links withheld). As a side, ever-so-slightly-frustrated, note, the only papers I've seen that have actually analysed the data, rather than repeating old claims, have confirmed this problem that was clear from, at the latest, the day after the announcement.

But why does it imply a "cosmological coincidence problem"? And why is it a new coincidence problem? What's the old one?

The human machine: finely-tuned sensors

The previous post in this series can be found here.

All good machines need sensors, and we are no different. Everyone is familiar with the five classic senses of sight, smell, touch, taste, and hearing, but we often forget just how amazingly finely tuned these senses are, and many people have little appreciation of just how complex the biology behind each sense is. In this week's post, I hope to give you an understanding of how one of our senses, smell, functions and how, in light of recent evidence, is far more sensitive than we previously thought.

Microscopic sensors

The olfactory system is an extremely complex one, but it is built up from fairly simple base units. The sense of smell is of course located in the nose, but more specifically it is a patch of tissue approximately 3 square centimetres in size at the roof of the nasal cavity that is responsible for all of the olfactory ability in humans. This is known as the olfactory epithelium and contains a range of cell types, the most important of which is the olfactory receptor neuron. There are roughly 40 million of these cells packed into this tiny space and their job is to bind odorant molecules and trigger neuronal signals up to the brain to let it know which odorants they've detected. They achieve this using a subset of a huge family of receptors that I've written about before, the G protein-coupled receptors (GPCRs). These receptors are proteins that sit in the membranes of cells and recognise various ligands (i.e. molecules for which they have a specific affinity) and relay that information into the cell. There are over 800 GPCRs in the human genome and they participate in a broad range of processes, from neurotransmission to inflammation, but the king of the GPCRs has to be the olfactory family, which make up over 50% of all the GPCRs in our genome.

Preliminary: Cosmological impacts of BICEP2 + Planck

If anybody is interested, I'm currently drip-tweeting some of the constraints one can obtain from considering Planck and BICEP2 data together. BICEP2 did do a bit of this in their paper, but they only considered specific scenarios. They were also often a bit coy about the implications of the combined analysis. I'll try not to be ;-).

The results should only be seen as indicative, these aren't published, and never will be in this form (maybe they could be cited if used in a paper though!). They were provided to me by Sussex Uni's resident obtaining-cosmology-from-the-CMB expert Antony Lewis, after a hurried Tuesday adding the BICEP2 data to the Planck cosmology pipeline (i.e. CosmoMC) and may contain mistakes.

Antony has himself also made some of these results public at the Cosmo Coffee website.

Questions here, or on Twitter are most welcome. If you want to see specific cosmologies, I'll do my best to show them (if I have them), or ask Antony very nicely to provide them (no guarantees, of course).

You can find my Twitter account here: @just_shaun. Feel free to share!

"A major discovery", BICEP2 and B-modes

[Added note (on Monday): Well, wow, the rumours were, if anything, understated. I'm happy to go on record that, unless a mistake has been made, this is the greatest scientific discovery of the 21st century, and may remain so even once the century is over. I (and others) will write many more detailed summaries of what was observed over time, but BICEP2 have announced a discovery of primordial B-modes, which is extremely strong evidence of cosmological inflation (if it turns out to be scale invariant, inflation is as true as most accepted science). Matt Strassler has a good hastily written summary here. As does Liam McAllister at Lubos Motl's blog, here. Of course, this is just one experiment and maybe they've made a mistake, but the results look very robust at the moment.

Congratulations on being alive today readers! We just learned about how particles work at energies \(10^{13}\) times greater than even the LHC can probe, and about what was happening at a time much, much less than a nanosecond after the beginning of the Big Bang.]

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[Added note (on Sunday): It seems highly probable that these rumours are essentially true. Although the precise details of the results aren't yet public, the BICEP2 PI, John Kovac, has sent a widely distributed email with the following information: Data and scientific papers with results from the BICEP2 experiment will go public and be viewable here at 2:45pm GMT on Monday. At the same time a technical webcast will begin at this address.

It's going to be an exciting day!]

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The cosmology rumour mill exploded today. Harvard Astrophysics have issued a press release stating that, on Monday, they will announce a "major discovery".

This is the only hard-evidence of anything interesting on the way and it could be an announcement of anything that fits under the label of "astrophysics". This is important to keep in mind. However, for one reason or another (that is hard to nail down), cosmologists are suggesting that it is going to be about cosmology. The speculation is that it will be about the BICEP2 experiment, which has been measuring the polarisation in the CMB. The speculation is that BICEP2 have seen primordial "B-mode" polarisation.

If this speculation is true, this would be a result immense in its significance.

Primordial B-modes would be a smoking gun signal of primordial gravitational waves. This, alone, makes such a discovery important. Gravitational waves have not yet been observed, but are a prediction from general relativity. Therefore, such a discovery would be on the same level of significance as the discovery of the Higgs particle. We were almost certain it would be there, but it is good to finally see it.

However, the potential significance of such a result goes further because these primordial gravitational waves would need a source. The theory of cosmological inflation would/could be such a source. Inflation is a compelling theory, not without some problems, for how the universe evolved in its very earliest stages. If it occurred when the universe had a large enough temperature, it would generate primordial gravitational waves large enough to tickle the CMB enough to make these B-modes visible in the polarisation. As of yet, inflation has passed quite a few observational tests, but nothing has been seen that could be described as smoking gun evidence. A spectrum of primordial gravitational waves would very nearly be such a smoking gun. If the spectrum was scale invariant (i.e. if the gravitational waves have the same amplitude on all distance scales) that would be a smoking gun for inflation and accolades, Nobel Prizes, etc, etc, would flow accordingly.

All of this is just speculation, but some of it does seem to be coming from reputable sources. And some of my colleagues have been talking about tip-offs from people who wish to remain anonymous, so I figured I'd collect all the speculation I know of here in a post (let me know if I've missed anything):

• Richard Easther, on the rumour and its implications
• Bruce Bassett, on the probability that the rumours are true
• The Guardian (the first major news source to pick up on this) with comments from various prominent cosmologists
• Jester/Resonaances on the context (i.e. earlier constraints on primordial B modes)
• Lubos Motl, amongst other things, explains what B mode polarisation actually is
• Philip Gibbs, at viXra log
• Peter Coles, amongst other things, on why gravitational waves mean there should be B-modes in the CMB polarisation
• Sesh Nadathur on why, amongst other things, the rumoured measurement would appear to be in tension with results from Planck and WMAP

• Sean Carroll has written a very thorough overview of the implications for cosmology (if the rumours are true).

The PI of BICEP2, John Kovac, gave a talk at the annual COSMO conference last year that had some pretty ambitious claims for how sensitive BICEP2 and similar experiments were going to be, so... well... we'll know on Monday. It should also be noted that, although the existence of these gravitational waves is a prediction of inflation, their amplitude is a free parameter and an amplitude this big is potentially a little surprising (for me, lower temperature inflation models just seem more compelling, others might disagree).

Twitter: @just_shaun

[Edit: The video of John Kovac's talk can be found here]