Holy Microscopy, Batman!!

I remember one of the best presents I ever got as a kid was a microscope. I have no recollection whatever of who it was that got it for me but I remain grateful for it to this day. Unfortunately my successes at imaging the smallest structures in biology were few, in fact they were non-existent. I don't remember managing to get a single sample to work. I didn't know that just looking at pond water or peeling an onion could yield such impressive results so easily. Mainly, then, my microscope remained in its box looking at nothing more interesting than the back of the instruction manual; but it wasn't as fruitless a situation as it sounds. Even though I couldn't use it properly I loved having it. It inspired me. I liked that someone would entrust me with this highly sophisticated piece of scientific machinery, which is what I assumed it was. The fact is, though, that microscopes aren't especially sophisticated, at least not your standard compound microscope that most of us would be familiar with from high school biology classes. It isn't entirely clear who invented it, or when, but if we said 400 years ago we wouldn't be far off the mark, though it wasn't until the 1670s that microscopy became recognised as a way of seriously studying nature as opposed to merely a gentleman's hobby.

"...green Weeds growing in Water and some Animalcula found about them" by Antonie van Leeuwenhoek.

Native of Delft Antonie van Leeuwenhoek became the stand out practitioner of the field. He was a slightly odd man who never actually published scientifically or shared the details of how he achieved his progress; he nevertheless came to dominate the field to such an extent that Robert Hooke commented he had a virtual monopoly on microscopic study and discovery. Leeuwenhoek was the very first person to see images that we now commonly take for granted. Bacteria, the cell vacuole and, ahem, sperm were all amongst his discoveries. He also coined one of my all time favourite words: animalcule. He used this to refer to the bacteria and other microorganisms he was discovering. It is only through his correspondence with the Royal Society in London, who subsequently published both his letters and accompanying diagrams, that we can see the incredibly detailed work he was able to carry out.

As we learned more about the nature of light itself it became clear that we would never be able to see anything smaller than about 200-250nm; it's just not possible. There is an equation that Ernst Abbe (a contemporary of Carl Zeiss, camera fans!) came up with in 1873 which I don't fully understand but the result happens to be approximately half the distance of the wavelength of light. For a century this remained unchanged and unchallenged but then some clever people decided to take a different tack which would improve resolution ten fold. And make some pretty pictures too.

Super high resolution image of an E. coli cell by Eric Betzig

Two methods were independently developed both of which have pretty cool acronyms (actual acronyms, not just initialisms): photo activated localisation microscopy (PALM); and the closely related stochastic optical reconstruction microscopy (STORM). It was Eric Betzig, of the Howard Hughes Medical Institute, that developed the PALM technique, so to speak. I don't fully understand how the technique works but it starts out similarly to standard fluorescent microscopy. A fluorescent molecule is tagged to the molecule of interest either using an immunohistochemical approach (antibodies) or genetically. Then the trick is to repeatedly switch the fluorescence on and off such that you obtain a high contrast between your illuminated molecule of choice and the background; subsequently you need to apply some cunning Gaussian functions to help localise the actual centre of the diffraction blur. This is made much easier if you have a small number of areas being activated at any one time and if these points are giving off a large number of photons.

Above you can see an image of a cell from a fruit fly, Drosophila melanogaster. On the right is the traditional image you could expect to get using normal microscopic techniques. On the left is the same cell using the PALM technique. You don't need to be a cellular biologist to see that there is a lot more detail to be seen using the new technique. Indeed, the image is actually 3d as the different colours represent different depths within the cell. The spaghetti like structures are the microtubules of the cell which are a sort of scaffolding that holds the whole thing together and is also very important during cell division.

In this remarkable image the same cell has been represented 3 times. In it, the mitochondria, the energy producing organelles, have been made to glow. In the left panel is the image you would expect to see using standard techniques. The right hand panel is a single cross section through the cell using the STORM technique and in the central panel is a super resolution 3d image using STORM where colour once again represents depth.  One of the differences between PALM and STORM is how they label the molecules of interest. PALM uses the genetic method and STORM uses the immunohistochemical approach. There are a couple of differences to do with the actual imaging but frankly I don't understand them well enough to be able to explain them.

So asides from creating beautiful images and winning Nobel prizes, what are these new methods actually good for? Well, one exciting example was announced on the same day as the Nobels. Researchers were able to show how HIV changes its shape as it invades a T-cell thereby opening up another new avenue to explore for possible treatments or vaccine developments. This is very important work and shows science at its most creative and beautiful.

Vertical Abstraction

Whilst I was in Romania this summer I went to the beach resort of Mamaia a few times, largely considered to be the most popular beach resort in Romania, the whole resort is squeezed on to a spit of land 8km long but only 300m wide. On one of my trips there I rode the cable car back to Constanza, it takes about 7 minutes to cover the 2km distance. Although it's a bit pricey it does afford some good views of the area and saves you having to wait for the bus/walk/swim.

Like most cable cars, indeed like most other forms of transport, if you want to take any pictures you either have to get what you can through a tiny, inconveniently placed open window, or, shoot through a half inch of scratched, dirty plexiglass covered in the spit of a thousand window lickers. Neither option is ideal.

Inevitably, this was the situation that faced me. My highly creative and completely lucky resolution was to blindly fire off shots aimed straight down to the ground. Obviously I could see roughly what was coming up; a waterpark, residential blocks and so on; so it wasn't 100% chance, but it was mostly.

The one exception to this was the picture of the residential block. The setting sun gave it a wonderful orange glow that added to the already decades old feel of the building.

Lest We Forget....

Pretty much everyone in London must be aware of the various commemorative public art installations that have been happening over the past few weeks to mark the centenary of the First World War beginning. With the passing of Harry Patch in 2009 this conflict did truly become history; he was the last surviving soldier to have fought in the trenches of western Europe. It is now only through books, documentaries, films and other second hand sources that we can learn about what is sometimes called The Great War.

I'm not sure a war should ever be called great. Whilst there are certainly circumstances where it is worthwhile to take up arms to defend an ideal or way of life I don't think that we should necessarily glory in it. War should be a last resort, a terrible necessity carried out only to the extent necessary and only when no other option remains. Was the First World War one of these occasions? I honestly don't know. I've read conflicting views on this and am not qualified to make a judgement. I'm not sure that anyone is. I am sure that we must make sure nothing like that ever happens again and that is why installations like this are welcome. Each ceramic poppy in the pictures here, and I have by no means covered them all, represents a fallen soldier. I don't know how many there are, many hundreds of thousands. Too many.

The same as the first picture but original colour

The Sun: Part 2

Quite some time ago, in fact just over a year ago, I wrote this post about how completely awesome the Sun is. Its awesomeness was so overwhelming that I actually got completely sidetracked and didn't even get around to writing about the topic I had intended to: helioseismology, aka, sunquakes. I said that I would follow it up with another post but it just never happened and so it is high time that I kept my word. But first, a tangent...

Image credit: BBC

Limitless, clean, affordable power. It has been the dream and ambition of many a politician, philanthropist and crackpot perpetual-motion-machine con artist; it is, however, a reality. At least in principal, anyway. But, Jason, how can this be; I hear you say. Well, it's simple. At least in principal, anyway. All you have to do is create a star 10 times hotter than the core of our sun here on Earth. Easy! This is the idea behind nuclear fusion, the opposite process to what happens in nuclear fission, which is what currently happens in nuclear reactors across the world. In fission, a big atom of uranium-235 is hit with a neutron resulting in the splitting of that atom. This produces two smaller fission products, normally krypton-92 and barium-141, and two or three other neutrons; these other neutrons are free to go and blast into another atom of uranium-235 and so you have your chain reaction. Now, heat is simply a measure of how fast molecules are moving and, given that the neutrons produced are moving very fast indeed, one of the outcomes of this reaction is an enormous quantity of heat. In a nuclear reactor this heat is harnessed like in any other type of power station to heat water which turns a turbine and so on.

Fusion is the opposite of this where instead of breaking large atoms into smaller ones we try to stick small atoms together to make bigger ones. To go into a little more detail, fusion is when we take two hydrogen nuclei and force them together to form a helium nucleus, but we don't use your common-to-garden variety of hydrogen. Most elements in the Periodic Table can come in a variety of forms called isotopes. For example, there are three stable isotopes of oxygen; oxygen-16, oxygen-17 and oxygen-18. Oxygen-16 is the isotope that occurs most naturally and makes up over 99% of what we find in the atmosphere. Its nucleus contains 8 protons and 8 neutrons; oxygen-17 has one extra neutron and oxygen-18 contains yet another extra neutron. These are all still oxygen atoms as it is the number of protons in a nucleus that determines what the element is not the total atomic mass. Hydrogen also has a number of isotopes; hydrogen-1, hydrogen-2 and hydrogen-3, also called protium, deuterium and tritium respectively. Protium is just one proton all on its lonesome, in deuterium the proton has a neutron buddy along with it and tritium... you get the picture.

So in fusion we are actually pushing together one atom of deuterium and one of tritium, this produces an atom of helium-4 and one spare neutron that goes whizzing off to make a life of its own. One of the great potential boons of fusion power is that the fuels required, these heavier isotopes of hydrogen, aren't too hard to come by. Deuterium is found abundantly in the oceans of the world, no problem there. Tritium is quite rare but it is believed that by installing plates of Lithium in the walls of a fusion reactor it can produce its own tritium as lithium bombarded with high energy neutrons will do just that. Another massive plus is that there are no radioactive byproducts produced like there is in fission reactors. The by-products are heat, which is what we want; neutrons, which we can use to produce the next round of tritium; and helium, which is great because we're actually running short of it on Earth. The radioactive krypton and barium produced in nuclear fission has a very long half life and can be expected to stay radioactive for approximately 100,000 years. To put that into perspective; 100,000 years ago modern humans were still trying to find their way out of Africa using nothing more than spears and hand axes, or to put it another way, we are going to have to keep today's radioactive waste safe until the Earth has undergone another three Ice Ages (and I don't mean the next three instalments of the popular kid's film). I wonder if the cost of that is taken into account when nuclear energy is claimed to be cheap?

Image credit: ITER

So far so simple; there is a problem, though. As hydrogen atoms comprise of a positively charged proton and electrically neutral neutrons the overall charge of the nucleus is positive and as any 12 year old knows: opposite forces attract and similar ones repel each other so forcing together two positively charged nuclei is what's known in the trade as a non-trivial problem. Anyone who has tried to push together the two north poles of a pair of bar magnets will know that this is not something they want to do; they repel each other. It was James Clerk Maxwell in the 1860s that produced the equations that show electricity and magnetism are merely two sides of the same coin, hence electromagnetism: the force that stops two similarly charged objects getting too near each other, one of the four fundamental forces of nature. The force that holds the protons and neutrons in an atom together is the strong nuclear force, another one of the four forces; the other two being the weak nuclear force and gravitation. The goal of fusion is to push the repellent atoms close enough such that the strong nuclear force overcomes electromagnetism. Put another way, in a fission reaction we use the kinetic energy of a fast moving neutron to overcome the strong nuclear force of a uranium atom, thereby releasing energy. In fusion we are trying to use kinetic energy to overcome the electromagnetism between protons such that the strong nuclear force can take over and bind hydrogen nuclei together to form a helium nucleus, thereby releasing energy.

The reason that I'm talking about this whole nuclear fusion thing in the first place is that this is how the sun works, it is a giant fusion reactor. It has been doing this for approximately 4.5 billion years and it will carry on doing this for about another 4.5 billion years at which point it will become a red giant and swallow up the Earth. If we could harness this process here on the 3rd rock then we would have that clean, limitless energy source that I mentioned earlier. Now, obviously we don't want to turn the whole planet into a pit of hell fire so we need to do this carefully and in a controlled manner. So what are the conditions we need to achieve to get fusion to work on an industrial scale? In the core of the sun, where fusion is an every day occurrence, the temperature is approximately 15 million degrees Celsius and the pressure is 250 billion bar, 250 billion times the air pressure on Earth at sea level. They're some pretty extraordinary numbers. We can actually heat things to that temperature but achieving that pressure is beyond us; to compensate we need to up the temperature. This is why, in the experimental reactors currently being built and tested, the temperature we're aiming for is more like 150 million degrees Celsius. That's a spicy meatball.

This picture of the sun is here simply because it looks amazing. Image credit: NASA

You won't be too surprised to hear that there is no substance on Earth, nor anywhere else in the universe, that could hold a cup of plasma that's 150 million degrees Celsius; it would melt, and so the trick is to create these ridiculously extreme conditions without letting them touch anything. This is done by creating a plasma and then controlling it using superconducting magnets in a torus (doughnut) shape - known as the tokamak model. There are fusion reactors in almost every modernised country in the world, they've been there for over 50 years; but they haven't been able to undergo fusion on the scale that would be required to make it sustainable as an industrial power source.

Our best hope for that lies in the ITER project in southern France (they have a great website if you want more detail and pictures of the enormous construction). This is an international collaboration between China, India, the US, Korea, Japan, Russia and the European Union; more than half of the world's population is being represented. Its inception was at the 1985 Geneva Convention, its design was approved in 2001 and in 2006 the ITER organisation was officially brought into existence. Construction and initial testing is expected to take well over a decade with the deadline for it to be fully operational being November 2020. Only then will we know for certain if the dream of limitless clean energy is a realistic one on an industrial scale. Unfortunately even ITER is only ever intended to be an experimental proof of concept. If it is successful then the world can get on with making the very first demonstration units through the 2020s into the 2030s. Personally, I don't see us having the first proper fusion reactor online til the second half of this century. The wait, though, will be worth it.

Sadly, the wait for a blog post on helioseismology is going to have to wait even more; again. I have written another thousand-odd words without getting to the point. I'll try to revisit the topic in less than a year this time.

The Lomo Effect

Well it's been a few weeks so I thought I'd better come up with something for the blog and, so, I've investigated the Lomo style of photography and come up with a little guide on how to take a bog standard snap and give it a bit of the old Lomo magic. 

For those of you that haven't heard of it I should probably describe what the Lomo style, or Lomography, actually is. I guess it's actually two things; one of which is easy to define, the other of which isn't. The easy one is the physical look of the photos; there tends to be a vignette (darkening at the corners), the colours are very rich (due to the use of slide film and the common practice of cross processing the negatives) and the quality is generally low with blurriness, poor exposure and even light leaks frequently featuring. Most of these properties, normally avoided at all costs by most photographers but sought out by the lomographer, are down to the very low build quality of the lomo camera. Think 1980s, Russia, plastic.

The element that is more difficult to pin down is the style and composition. Perhaps a good place to start would be with the motto of the movement: Don't Think, Just Shoot. Although it could easily be confused with the motto of the American military it is actually a style encompassed by The Ten Golden Rules of Lomography as laid out on their website. These include such adages as Take Your Camera With You Everywhere You Go, and, Lomography Is Not An Interference In Your Life But A Part Of It. Basically, they try to encourage you to break every traditional rule of photography that ever existed. The Rule of Thirds would be anathema to a lomographer. I highly recommend a look at their site to get more of a feel for this unusual brand of photography; you'll probably either like it or you wont.

The question is: how did such an odd, counter-intuitive and niche movement even get started, nevermind become an international phenomenon? It all started as recently as 1992 when a group of Viennese art students came across an old Lomo camera whilst on a tour in Prague. They found it in an old camera shop and used it in a very casual kind of way, often not aiming, shooting from the hip and generally just mucking about. Upon returning home and developing the film they were charmed by the "unique, colourful and sometimes blurry images" that were produced. Interest amongst friends and family rapidly grew and the following year they founded a society in honour of the strange new camera. The camera in question was a Lomo LC-A Compact Automat, produced some ten years previous in the USSR. The build quality of the device was.... well, there was no build quality; but this leant itself perfectly to the students shooting style.

There was a problem, however; with the fall if the USSR also came the end of the production of the camera and the prospect of a ready supply of the student's new favourite toy. Undaunted, the students flew to St. Petersburg, where the Lomo factory was located, to make a deal for tax breaks so as to make it economically viable to continue production. They successfully got the special permission required from the mayor of the city, a very amiable and friendly chap, one V. Putin. The rest, as they say, is Lomography. Production has since shifted to China and production continues to this day; the future of Lomography seems secure and Lomo cameras remain cheap and affordable for all to try. The film is now the increasingly expensive part.

But what if you don't want to faff about with film and developing and such like and just want to create the same effect using your existing DSLR and a bit of canny processing? Well, I'll show you how - so long as you intend to use Adobe Elements, although many applications are broadly similar these days. Those of you not interested in the technical parts can just skip to the pretty picture at the bottom.

The picture we're going to start with is no great shakes. The exposure isn't great, I should have got my neutral density filters out, the sky is overexposed and there's some lens flare; but as we're aiming for the Lomo style none of this should matter, if anything it'll help. So there are two main things we need to do here; create a vignette and achieve a cross-processing effect by increasing saturation and contrast. There is more than one way to do each of these steps including just clicking through the guided Lomo Camera Effect wizard, but where would the fun be in that?

There are two easy ways to create a vignette. The first is to simply go to Filter>Correct Camera Distortion and use the sliders in the vignette tool, which are normally used to remove a vignette, not to create one. I'd normally go for somewhere around -40 to -50 but it's totally up to you.

The second way is a little more involved but gives you more control. Take the Lasso tool and, having selected a feathering level of, shall we say, between 100-200 pixels, draw a vaguely circular shape in the middle of the photo. Again, we're not aiming for perfection here. We want to alter the outside of this circle not the inside and so you need to click Select>Inverse. Now create a Levels layer and slide both the shadows and the midpoint markers to the right a little, this will add to the vignette effect. I actually prefer to use a combination of these two methods to make my vignettes.

That's the vignette sorted but now we need to work on the distinctive colour palette of lomography; again, there are a couple of ways to go about this and I like to use a combination of each. First up: colour curves. Click on Enhance>Adjust Colour>Adjust Colour Curves... (yes, it really does have the three little dots after it). Here you are presented with a straight diagonal line on a grid. The left hand side of the grid represents dark colours, the left hand side highlights, and the middle is the midtones. There are several preset options available but you can also drag the points on the line to warp it. Moving any given point on the line either up or down will make the corresponding band of colour more or less intense. We want to make the curve look like an S; this will have the effect of making the highlights brighter and the dark parts darker, i.e. increasing contrast. If your line looks something like the one in my example below then you're on the right track. Press okay when you're happy with the effect achieved.

I would also recommend increasing the saturation, this will help to achieve the cross processing effect that is so synonymous with the Lomo style. To do this you can either click on Layer>New Adjustment Layer>Hue/Saturation... or simply click on the button with the diagonally divided circle on it on the right hand side and select Hue/Saturation... Use the slider for Saturation to give your colours a bit of a boost. For a 'normal' photo I wouldn't want to push this much past the mid teens, but for the Lomo style you can probably get away with numbers in the 30s, 40s or even higher depending on the photo.

In the same way that you got your Hue/Saturation... layer you can now select a new Brightness/Contrast... layer. Here, I wouldn't say that the Brightness has to go one way or the other, this really depends on what look you want to achieve with any given individual photo, but I would recommend increasing the contrast a little.

Lastly, I would say it's worth while putting a Fill layer in. To do this, select Layer>New Fill Layer>Solid Colour... Call the new layer whatever you like or leave it as the default and click Ok. This should default to a layer of pure black and you will completely lose the picture you have so carefully created. Fortunately it is only hiding behind the black layer and we now have to blend the two together to reveal the finished product. Click Ok again. At the top right in the Layers panel you will have a drop down box with various different blending options; I would recommend Soft Light or Hue or Saturation and an Opacity of something like 30-50%. This should really help bring about that cross processing look. Cross processing, by the way, is where you develop film using non-standard chemicals. There are two main film types; standard 35mm and Colour Slide film. Each of these sets has their own chemicals used in their development, C41 for 35mm and E6 for Colour Slide film; however, lomographers noticed that you can get some really cool results if you swap these up. As I understand it the more common option is to use Colour Slide film and process it with 35mm chemicals.

That's about it. With any luck you should now have a photo worthy of the annals of Lomography, or at least something that looks a little old timey; you can see my effort below. None of the techniques I have mentioned here are set in stone; indeed, that would go against the whole freestyle notion that made Lomo popular in the first place. The idea is not to be constricted by the traditional norms, to break the rules and not to worry about the consequences. As Rule #10 of Lomography says: Don't worry about any rules.