Monday, 5 June 2017

ATE (What is CRISPR and how does it work?)

F asks "What is CRISPR and how does it work?"

CRISPR is not to be confused with KRISPA which, it turns out, is a highly classified, well it would be, project to take alien technologies and adapt them for civilian use. This project clearly raises many questions, the first of which is "is it nonsense or is it nonsense?"

Viruses have plenty of DNA but don't have the cellular mechanisms needed to reproduce them. Their trick is to get to get a host cell to do it for them. This host cell could be one of yours or mine, or even just a one celled organism such as a bacteria. 

It turns out that many bacteria have a trick up their sleeves for dealing with invading viral DNA. Their own DNA contains a list of the bits of viral DNA that they, or their ancestors, have encountered in the past. To keep things nice and tidy these viral DNA sequences are separated by what we might think of as DNA bookmarks. These take the form of short repeated sections of DNA letters (C, G, A or T) that read the same way backwards as forwards (i.e are palindromes like civic, kayak or racecar). So these sequences are Clustered together in a particular bacterial genome, they're Regularly Inter-spaced, they're Short, they're Palindromic and they Repeat. Hence CRISPR.

To make use of this library of viral DNA the bacteria produces a protein known as CAS9. This protein makes an RNA copy of the viral DNA sequence between the CRISPR genes and then wanders off into the cell. Should it happen to encounter a bit of viral DNA with this same sequence it attaches itself to it and disables it by snipping it in two.

When the viral DNA is snipped in two, it will attempt to repair itself but isn't likely to get it absolutely right and most of the time it's disabled and unable to carry out its dastardly deeds.

Having uncovered all this, some scientists wondered if we might be able to use this mechanism not against viral DNA but to precisely disable particular gene sequences inside other living cells. All you'd need to do is make a sample string of DNA letters matching the gene you want to target and attach CRISPR genes to each end so that the Cas9 enzyme recognises it as a gene sequence to copy. Release this combination into a cell and it will find the targeted sequence, snip it in two and disable it.

Since we now have the technology not only to rapidly sequence DNA, but also to manufacture DNA strands of any sequence we choose, this means that we can use CRISPR to selectively disable what might, for example, be a faulty gene.

Which just leaves one final trick. DNA is good at attempting to repair itself when it's been broken. Like many builders it will tend to make use of the materials at hand. Supply it with a good copy of the gene that you've snipped and there's a good chance that the good copy will be inserted in its place and the cell's DNA will have been repaired.

ATE (How does the Hydrogen bomb work?)

This is the third in a series of answers to questions put to me by students at a local secondary school. The sheet of paper they gave me was titled "Ask the Expert", but I don't really feel like "an expert" let alone "the expert" so I've changed the post title to ATE.

J asks "How does a hydrogen bomb work?"

Given the serious resources needed to put any of what follows into practice, I'm confident that J, or anyone else who reads this, will not be in any better position to actually make a bomb than they were before.

Look at an atom and you'll find that it has a very dense positively charged nucleus surrounded by a cloud of negatively charged electrons. If the nucleus was the size of a tennis ball then the atom as a whole would be about 10km across. 

The nucleus is made from positively charged protons and, as their name suggests, neutrally charged neutrons. Since like charges repel, and the closer you put them the harder they repel, there must be an even stronger force (helpfully known as the strong nuclear force) that stops the protons in the nucleus simply blasting the whole thing apart. This is the reason why there's a limit to how many protons a nucleus can contain and explains why bigger stable nuclei tend to have a larger proportion of neutrons (they provide extra glue to hold it all together).

You may recall the most famous equation in physics (E = mc2). This is a consequence of Einstein's special theory of relativity and quantifies the fact that mass and energy are interchangeable. Measure the mass of all the fuel and air that goes into a coal fired power station and compare this with the mass of all the ash and flue gases that come out and you'll find that a little bit less comes out than goes in. Put this mass into the famous equation and you'll get the total energy (heat and electricity) that the power station produced.*

If you compare the mass of a nucleus with the masses of its component parts (i.e. all the protons and neutrons) you find that the nucleus weighs less than the sum of its parts. If you wanted to pull the nucleus apart you'd have to supply this missing mass (energy) and so it represents what's called the binding energy of the nucleus. If you look at a whole load of different nuclei and divide the total binding energy of each by the number of nucleons (the collective term for protons and neutrons) you get the binding energy per nucleon.

Plot a graph of this binding energy per nucleon against the size of the nucleus and you get an interesting curve.


The nuclei of light atoms such as Hydrogen and Helium are on the left and of large atoms like Uranium are on the right. You'll notice that if you were to stick two light nuclei together to make a bigger one then the binding energy per nucleon would increase. This happens all the way up to Iron (Fe). Similarly, if you could persuade a really big nucleus to split into two or more parts then the binding energy per nucleon would also increase. The first process, putting two nuclei together, is known as fusion. The second, when a big nucleus falls apart, is know as fission. 

In a conventional hydro electric power station, falling water turns a turbine and produces power. The water ends up closer, more tightly bound, to the earth than it was at the start. So, increasing the water's binding energy releases energy that's used by the turbine. Similarly if two light nuclei fuse, or a heavy nucleus splits, then energy is released. Lots of it.

The first nuclear bombs were purely fission devices. It turns out that there are particular isotopes of Uranium and Plutonium that are largely stable until hit by a neutron, at which point they fall apart. This not only releases tremendous amounts of energy but also spits out a few more spare neutrons. If one of these should hit another nucleus then that too will split and, if there's enough material (a critical mass) and its in the right shape, you can get an explosive chain reaction. 

Choose the right nuclei, and fission is relatively easy. Find ways to control the reaction so it doesn't get out of hand and you can have a nuclear power station. Fusion is much more difficult for the simple reason that to get two nuclei to fuse you've got to get them very close together and, because they're both positively charged, they really don't like this. But, it can be done provided that they're moving fast enough to overcome the repulsive electrical force. 

Now you can speed up a nucleus in two ways. One at a time in a particle accelerator, or a whole bunch of them by simply raising the temperature. Deuterium is an isotope of Hydrogen which contains a proton and a neutron rather than just a proton. To get two Deuterium nuclei to fuse takes a temperature of around 100 million degrees. The interior of the Sun is as hot as this, and its enormous gravity stops everything flying apart, but these conditions are much harder to achieve on Earth.

But, there is one place where we can get temperatures and pressures high enough to initiate a fusion reaction and that's inside a conventional fission powered nuclear bomb. So a Hydrogen bomb is simply a fission device with the right isotopes of Hydrogen carefully packed around it in such a way that, when the fission bomb goes off, they hang around long enough to start fusing into Helium.

*A 1GW station produces 1 x 109 J of electrical energy per second. It's about 40% efficient so this is about 40% of the total energy produced. Hence the total energy = 1 x 10 9 / 0.4 = 2.5 x 109 J. In a year this adds up to a total of 1.3 x 1015 J. The speed of light c = 3 x 108 m/s so putting this much energy into the equation E = mc2 gives a mass of 0.015kg (about 6 ounces). Just think of all the coal trains going in, and all the gases coming out, and I think you'll agree this might be quite difficult to measure.

Sunday, 4 June 2017

Ask the expert (The end of the world)

G writes to ask "How might the world end?" 

Here's a top of the head response.

If G means the world as G knows it, then this will probably be in the next 80 years. G can change the odds on how it will end by becoming a couch potato, eating a fast food diet and taking up smoking. For an accidental death try Everest.

If G means the Earth, then perhaps what's more important is not when it ends, but when it stops being habitable. 

Astronomers study stars by the light they give out. From measurements of a star's brightness, from the detailed spectrum of the light it emits and from how it seems to wobble around other stars nearby, you can work out it's mass, it's temperature, whether it's coming towards you or going away, how far away it is, what sorts of atoms there are in its outer atmosphere ... In particular, if you know how far away a star is you can say how long ago light must have left it and therefore how old it must have been (relative to the age of the Universe) when that light was given out. Knowing all these things means that we know a lot about different star types and their typical life cycles.

We know that big stars are brighter, hotter and have relatively short lives and that small stars are dimmer, cooler and live much longer. We also know that our star, the Sun, is a typical middle sized sort of star. It simply isn't big enough to explode in a Super Nova, or end it's life as a black hole or a neutron star. Instead, as it fuses it's nuclear fuel into heavier elements (in colloquial terms "burns up"), the pressure from the reactions inside will build up and it will swell. As it swells the surface will cool slightly and become redder. The Sun will be what's known as a Red Giant. After this phase it will spend a long time as a spinning cinder of hot rock known as a White Dwarf.

Astrophysicists think that in about 3 billion years the Sun will have expanded so much that it will completely smother Mercury and Venus and reach out almost as far as the Earth. Even though the Sun will be cooler, it will be so much closer, and cover so much of the sky, that all of the earth's water will evaporate and the conditions for life will cease to exist.

If G means the Universe, then the answer depends on whether of not it keeps expanding. 

If it does, then eventually all of the stars, and the stars formed from the remnants of other stars, will have run out of fuel and will slowly cool down as they radiate their remaining heat energy into space. Meanwhile, if space keeps on expanding we'd begin to notice not only the space between galaxies expanding, as we do now, but also that between the atoms in molecules and even the particles within the atoms. Everything will be smeared out into an ever thinner smudge.

If it doesn't, and the Universe collapses back in on itself, it won't so much end as reset. A "new" Universe will bounce back out with no memory of the one we're in now. 

This might take some time.



There'll still be rocks with Lichen when we're long gone



Ask the expert ... (string theory)

For the last few weeks I've been going in to a local secondary school on a Friday lunchtime and attempting to answer students' questions about science and the environment. When I had to be away one week I asked if they could put some down on paper and I'd return the compliment by writing down my replies. What follows is my top of the head response to the first question.

What is string theory?

Two extremely successful theories dominate modern physics. 

One of them, Quantum Mechanics (QM) covers the world of the very small and explains a huge range of phenomena from the spectrum of light emitted by different atoms, the structure of the periodic table (i.e why we have the elements we have and why they react with each other in the ways they do) all the way through to how the semi-conductor devices in our phones and computers manage to do what they do. Remembering that in science a theory isn't just a piece of idle speculation but the best available explanation of the facts, Quantum Mechanics is the most precise theory that has ever been devised (which doesn't mean, of course, that it couldn't be replaced if a more powerful theory came along)

The other, the General Theory of Relativity (GTR) not only explains the warped relationships between space, time and matter that govern the behaviour of stars and galaxies but also makes well tested predictions about the way, for example, the strength of a gravitational field affects time (to put it, simply clocks run more slowly in a strong gravitational field than a weak one). If the time signals from the clocks on the satellites that our phones use to work out our GPS coordinates weren't corrected for this then the system simply wouldn't work.   (As you move away from the Earth the gravitational field gets weaker and the clocks on a satellite run faster). Atomic clocks can now be made that are so precise that you can tell, just by looking at the time, whether they're on the floor of the lab or have been put up onto a bench.

Unfortunately these two theories, one governing the world of the very small the other that of the very large, are fundamentally incompatible. In practice, this doesn't matter very much because there are few places, apart from the inside and boundary of a black hole, where the rules of one domain need to be applied to the other. But for some physicists, those who aren't just interested in getting the sums right but also want to know that they're getting as close to the truth about the Universe as they can, they'd really like to have a single Unified Theory that covered everything. Everything from the smallest fundamental particle right the way up to the largest cluster of galaxies. 

Physicists have had over 100 years to get used to the idea that the three dimensions of space and the one dimension of time can't be considered separately from one another and instead have to be thought of as a unified 4 dimensional entity space-time. Now whilst it can make your head hurt to try to think of 4 dimensions, all a physicist has to do is describe an event using 4 numbers ( x, y, z and t) and then, for example, use the appropriate equations see what would happen to these 4 numbers if the event happened to be observed by someone travelling past Earth in a high speed rocket. 

The most promising attempts to unify these two theories have been built around the concept of a field. Just as the strength and direction of a gravitational field describes the force a mass would experience if it happened to be there, so the strength of an electric field describes the force that a charged particle would experience if it happened to be there (it turns out that magnetic fields arise when charges are in motion and the two fields, electric and magnetic, are actually the same thing but seen by someone who is either stationary with respect to the charge (electric) or moving relative to the charge (magnetic)). 

It turns out that gravity and electromagnetism are not the only forces that apply in nature. There's also the strong nuclear force, that holds an atomic nucleus together and the weak nuclear force that prevents some nuclear decays (e.g stops the neutrons in a nucleus from spontaneously decaying into a proton and an electron (which is what they do if they're left on their own)) Each of these forces is associated with it's own field and the particles, for want of a better word, that transmit the forces can all be regarded as vibrations in their respective field. Unfortunately, whilst this can be done for Electromagnetism, the Strong Force and the Weak force, it can't be done for Gravity where the big problem is explaining why gravity is so weak.*

String theory uses this idea of fields and vibrations, along with all the complicated mathematics, to describe all of the fundamental particles, and not just the force carriers, as vibrations in their own fields. By doing this they have a theory that unites QM and GTR. So, rather than just using 4 numbers to describe an event you need even more to describe the state of all these other fields and hence specify which particles are there and how they're interacting. If you think of each of these fields as being another dimension then the various fundamental particles are simply one dimensional vibrations in these different dimensions. It is proposed that gravity leaks into all these additional dimensions, which explains why it is so weak in the 3 that we're familiar with. And what one dimensional objects are we familiar with, pieces of string.

* I used to do a calculation with A level physics students about what would happen if the charge on an electron was a tiny bit different in size to that of a proton. This would mean that instead of being electrically neutral we'd each carry a net negative or positive charge (depending which was bigger). Since like charges repel I asked them to estimate the force between themselves and their nearest neighbour. For want of doing the sums again I seem top remember that if they differed by one part in a million million million (i.e not a lot) the repulsive force between two typical students 1m apart was of the order of 90 tonnes.

Assume a mass of each person of about 70kg, assume they're made entirely of water, use atomic masses and Avogadro's constant to estimate the number of water molecules and hence the total number of electrons or protons (18 of each per water molecule). look up the charge on a single electron to work out the total negative charge on the person, assume that this differs slightly from the total positive charge and then use Coulombs law calculate the force between two adjacent students.


Three dimensions into two doesn't really go

Thursday, 9 February 2017

A simple plan to get more people walking

There's little doubt that if we could get more people to walk or cycle for short journeys there'd be less pollution, less congestion and their health would improve. Wouldn't it be nice if you could just point out the benefits, assume that people would see what's in their best interests, abandon their ingrained social habits, put on their sensible shoes, leave the car keys at home, and walk. Not likely to work. Sad.

What's needed is a plan. First, to give the very clear health message that if you want to live a long and healthy life then one of the best things you can do is to keep walking. Second, to give regular reminders that walking short journeys doesn't actually take that long. Third, to develop public infrastructure so that walking and cycling are not only easier and safer but also have higher status.

Now whilst I might be won over by health messages, evidence suggests that, in general, just telling people something is good for them doesn't work. Indeed it can often provoke a defensive backlash. With any communications strategy there's a time and place and the right time and place for messages about health is when people are visiting the doctor. Suppose that next to the reception at your GP's surgery there was a simple poster showing a map of the local area with the surgery at the centre. Concentric circles around the surgery could be labelled with the typical time it would take to walk there. At the top of the poster would be the surgery's name and address and at the bottom the simple message "Walking is good for you". Put up a few more posters in the waiting area with the simple message "For a healthy old age keep walking". It's a simple message, delivered in the right place to the right people and, because it's in a doctor's surgery, clearly carries medical authority.

A few years ago responsibility for public health in England and Wales was handed over to Local Authorities. These are also the bodies responsible for things like waste disposal, schools, social care and highways. At an institutional level I've no doubt that they recognise the importance of encouraging everyday physical activity, but for a number of reasons it hasn't been far up their priorities. There are clearly opportunities to promote the message in schools (encouraging parents to walk their children to school rather than drive) and in social care (making sure looked after people are given the opportunity to get out and walk) but also in the ways in which we draw attention to existing infrastructure.

Over the years we've made a number of improvements to the old Scarborough Whitby railway line. One of the ones I'm most proud of is the Candler Street ramp in Scarborough. This connects a densely populated set of streets directly to the track in a place where there was once just a retaining wall. When the ramp was first installed it wasn't used by very many people. It took about a year to be discovered and then incorporated into everyday journeys. Now it's simply taken for granted and in near constant use. 

A good way to remind people that they could choose to walk is to put up signs that give directions to key destinations along with typical walking times. Each time you're sat in a traffic jam alongside a sign you'd not only be reminded that you could have chosen to walk but also that at least someone thinks this might be a good idea.

So, part 1 = simple messages in GP surgeries and hospitals, part 2 = well signed walking routes with times and distances, part 3 = raise the quality of the infrastructure for walking and cycling so that it has a higher status and feels safe.



Candler Street Ramp 

Tuesday, 31 January 2017

Bike Walk (a proposal)

In common with many people I do my best thinking when out walking or cycling. Of course, what you end up thinking about isn't necessarily what you might have intended and is often inspired by the places you find yourself.

Anyone who's read more than a few of my blog posts will know that I write a lot about everyday physical activity, it's importance in public health and the psycho, social and political barriers that stop it rising up the political agenda, and, while there's an increasing number of people setting their own fitness goals, joining boot camps and posting their achievements on Facebook, the real challenge is getting the habitually sedentary to take the first step.

There's no doubting that the bicycle is one of the world's greatest inventions. It's the most efficient means of land transportation that has ever been devised and is better than any animal that has ever evolved. Those of us who ride a lot, though nowhere near as much as some, even enjoy riding up hills and will deliberately seek them out. Part of this is the personal pleasure of the challenge, the rhythms of legs, breathing and heart rate, the flush of endorphins and the sheer satisfaction of achievement, but part is also the changing views as you climb and the revealed vista when you go over the top. It's about having a direct personal relationship with the landscape.

But if you're not particularly fit (yet), the hills are a barrier and not a source of pleasure. We might advise you to get in a low gear and then go steadily at a pace you can maintain, but this isn't much help if the gears on your bike just don't quite go low enough. When that happens the only choice is to get off and walk and in some cycling circles this is seen as a defeat.

Yesterday's ride took me out of Scarborough and up Harwood Dale. The roads are hilly but quiet, with good lines of sight and some delightful views. 



Looking up Harwood Dale

Just before taking this picture a thought bubbled to the surface. Why not organise some Bike Walks? You could either think of this as a ride where it's OK to get off the bike and walk, or a walk where you sometimes get on the bike and ride. 

In this case, the two end points could be the Yew Tree Cafe in Scalby and the Grainary about 6 miles away up Harwood Dale. Participants could either bring their bikes by car up to Scalby or, if coming from central Scarborough, simply up the Cinder Track and turn left along Station Road. 

As well as being able to enjoy the scenery and the company, they'd get well needed exercise and the chance to learn a bit of road-craft on the bike. What goes up must come down, so the only requirement is brakes that work.





Friday, 20 January 2017

Litter in storm drains

What's the problem


You'll have seen pictures of sea birds who've died with their guts full of discarded plastic objects. You'll know that turtles can easily mistake a plastic bag for a jelly fish. You'll know that microplastic particles pose an increasing threat to marine ecosystems. You'll know that litter isn't just unsightly but has a direct impact on the environment. But one thing that I hadn't appreciated until recently was that in many parts of the world litter is making urban flooding much worse. A contact in Zambia is particularly concerned with this problem so I'm writing this simple blog post in the hope that it might help.


Blocked storm drain in Harare


Litter isn't what it used to be


Archaeologists make a good part of their living from studying ancient litter; the broken pots, discarded stone tools, bones and shells, lost copper bracelets and rusted old knives of the ancient world. It's only on rare occasions that organic material, such as wooden foundations and bits of old boats, will survive (e.g. at Star Carr, the earliest known site of habitation in the UK, and just a couple of miles south from where I sit, wooden objects have survived 9000 years by being buried in peat). The invention of plastics will make it much easier for the archaeologists of the future to find out about us.


Reducing the amount of litter generated.


One way to reduce litter is to cut off the supply. A few years ago it was possible to identify the nearest supermarket by the colour of the discarded plastic bags. Orange for Sainsbury's, blue and white for Tesco's, yellow and black for Morrison's. Since we've  had to pay for them demand has dropped by 85%. Many countries have deposit schemes on plastic bottles and aluminium cans so that even if the original user doesn't take them back there's a good chance that someone else will. 


First step = municipal waste collection


Unless a town or city has an effective system for collecting domestic waste then any other efforts to reduce litter are likely to be in vain. Of course there are expenses involved in doing this, but flooding disrupts communities, can spread disease and costs money to clear up.


Changing behaviour


Persuading people not to drop litter in the first place is more difficult. We're more responsive to what the people around us actually do than any official message. In the obscurely titled blog post "The exception proves the rule" I looked at one of the few studies of littering behaviour I could find. The simple conclusion of this study was that litter breeds litter. Unless you actually get rid of most of the existing litter it's very hard to stop people simply dropping more. 


First big clean up


Once you've got an area cleaned up, which might involve paying local people to help do it, the challenge then is to keep it clean. Eating food on the street is now an established habit across the world and is unlikely to end. So unless there are convenient bins for people to put their litter in, which are emptied before they start overflowing, the problem will simply recur.


Litter bins


When we were addressing the problem on the old railway line in Scarborough (which is now a quiet route for walkers and cyclists) we made sure that there was a bin at every point of access. Not only did this reduce the amount of litter left on the track but it also meant that casual litter pickers, such as myself, had somewhere convenient to put the litter that we'd picked. We've been  surprised how many fellow citizens now respond to the sight of someone else's litter by picking it up and putting it in the bin. An additional advantage of keeping the track relatively clean is that it feels like a safer, looked after, space and more vulnerable people are happier to use it.


Community participation


But every now and then, particularly in winter when the vegetation dies back and hidden litter is revealed, we do have to have an organised litter pick and to do this you need to have active citizens who are prepared to join in. And this, in turn, needs people to have a sense of ownership of the public space.


Other cultural norms are possible


Changing cultural attitudes to litter is difficult but not impossible. Most of us live within the social norms that are set by the people around us and these are different all over the world. We like going on holiday to the Dalmation coast of Croatia. One of the things we like about it is that there is a walking culture. In the evenings it's the habit for everyone to go out and promenade, the paths and footways are all maintained and there's very little litter. Having spoken to Croats about this the response was simple "it's just not something we do". They either put it in a bin or take it home. Indeed, when we spent a week last year wandering around the island of Mljet I saw only one piece of litter and couldn't help taking a picture.




The only piece of litter we saw on Mljet (august 2016)

Just so you don't think I spent all my time staring at the ground......



Looking down on the the salt water lakes of Mljet

A couple of links

Here's a proposal for a study in Cape Town. which suggests using litter traps on storm drains and then correlating the amount trapped this with different strategies used to reduce litter in different catchments. I was not able to find out if this work actually took place

A summary of Behavioural interventions that might be taken to reduce littering in the UK