Category Archives: Science

Why does glass, when heated, lose its color ?

I’ve been learning to blow glass and I noticed when I started to use colored glass, that when you heat it up in the furnaces, the often intense and vivid color of colored glass seems to disappear to be replaced with little but a dull orange glow. Why ? I tool me a while to find what I think is the answer. At first I thought it might be the dull glow simply drowning out the blue but it didnt make sense to be – the glow is not that intense and the color is often really intense when the glass is cold. Example: 

You can see the swirls of colored glass inside this vessel, but they just appear as slightly different intensities of reddish glowing. Once the vessel cools it will be vivdly colourful. Ok, so why ?


Color in glass is created by dissolving  various salts in the glass, often of transition metal salts, which have vivid colors. Some examples:

Compound Color
gold chloride dark red
cobalt oxide deep blue
iron oxides greens, browns
mix of mangnese, cobalt, iron black
antimony oxides white
uranium oxides yellowish green
selenium compounds reds
copper compounds light blue
tin compounds white
lead/antimony yellow

The colors arise because the electrons inside the orbitals of these compounds have quantum energy levels that have the right energetic gaps between them to absorb photons of wavelengths in the visible spectrum. Only photons with exactly the right energy will be absorbed. The absorbtion causes an electron to be promoted to a higher energy state. This electron can then return to its more stable state in a number of ways. It can either fall directly down to the original level creating a photon of the same wavelength as was absorbed previously or it can (if it has appropriate energy levels at it’s disposal) fall down in a number of smaller steps each emitting a photon of longer wavelengths (i.e. smaller) energy, say in the infrared spectrum, hence reducing the amount reflected light of the frequency previously absorbed.

So, a blue compound looks blue beacuse red and green photons are preferrentially absorbed by it. Blue does not get absorbed, only reflected and our eye will detect much more blue photons reflected by the object and hence our brains say “blue!”.

Black Body Radiation

Ok, now when you heat things (anything) it will start emitting radiation. The hotter you make it the shorter the wavelength of the emitted light. Or, in other words, the energy of the photons goes up. This radiation is called (unintuitively) “Black Body Radiation” or (more intuitively) “Thermal radiation”. Maybe sometimes when buying light bulbs or LEDs or flourescent lamps you’ve seen the label 3000K or 4500K or whatever ? That label is indicating that that light source will give off a spectrum of radiation close to what a ideal blackbody radiator will give of if it was heated to that temperature. Blackbody radiation is also what’s responsible for the glowing of the wire in your toaster or the glowing coals in your garden barbecue. The spectrum of the radiation is fairly wide but as things get hotter it moves to higher and higher frequencies. Therefore things first just feel warm (they emit invisible Infrared radiation) then glow red, over yellow to white because as things get hotter and hotter the wavelengths get shorter and shorter (frequencies become higher). In this plot the spectrum is shown for different temperatures.


The sun for example has a surface temperature of 5,778Kelvin and radiates most strongly in the yellow to green part of the spectrum (note that the reason the sun appears yellow has to do with scattering of light in the athmosphere. In space the sun looks white).

What’s interesting that this general spectral behaviour is independent from the material you’re heating. Doesn’t matter what it is, the shape will be the same (that’s not quite true and we get to that in a minute, but roughly speaking it’s true). This means you can actually tell the temperature of anything glowing red or yellow hot by noting it’s temperature. This is something glassblowers and metal smiths have exploited for thousands of years. It also means that you can relatively accurately measure the temperature of objects by looking at the amount of infrared radiation they emit. This is the basis for contact-less thermometers such as this one:


Ok, back to glass. So what I said above is actually (it turns out!) not quite the truth. What actually happens is that the amount of thermal radiation given off by a compound at a given frequency is proportional to the amount of light usually absorbed by that compound at that frequency. Or, in simpler terms, a blue thing preferentially absorbs red and blue so if I heat it it will also give off red and green preferentially to blue light. The reason is that as you heat things you’re exciting the electrons inside the compound and you promote them to higher energy states. They can then fall down back to their original states giving of photon of the exact energy corresponding to the gap. Those gaps are the same gaps responsible for absorption too! so it makes sense that those two phenomena are related.

And so here we have the answer to the original question. Imagine your’re heating a blue compound. At first blue dominates the reflected spectrum. But as you heat it, it starts giving off red and green preferentially over blue and at some temperature the two match and the compound no longer appears blue to our eyes because red and green have “caught up” with blue. This will happen no matter what the original color was. As you heat the object further though the normal spectrum of the black body radiation will dominate any electronic transitions and the thing will simply glow red–>yellow–>white like anything else.




ORD Camp Photos and Panoramas

The Whisky fest

The Pig fest

Ord Camp 1

Ord Camp 2

Ord Camp 3

Ord Camp 4

Ord Camp Shop

Our FoldIt Paper is out in PNAS!

Algorithm discovery by protein folding game players


AlgorithmsFoldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as “recipes” and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.

Fulltext at PNAS (OpenAccess)

Beautiful Proteins in Positively Aware!

I few months back i got a request for  a bunch of renderings of HIV proteins for a non-profit magazine called Positively Aware! Now they’ve been printed :)


Sculpture No 1 & 2 done!

After several weeks of crazy long hours at the shop i finished the first two structures of Ubiquitin and KcsA.


Copper, Steel

Ubiquitin is a small regulatory protein  found in almost all tissues of eukaryotic organisms. The cell attaches short chains of Ubiquitin molecules to proteins, which labels them for destruction and subsequent recycling. The Ubiquitin tag directs proteins to the proteasome, which is a large protein complex in the cell that degrades unneeded proteins back into their amino acid constituents. These are then reused to synthesize new proteins.  The constant recycling of proteins not only ensures damaged proteins are removed quickly but also allows rapid regulation of enzyme levels in the cell.

Structurally, Ubiquitin features all of the major structural features of typical proteins including two a-helices a curved b-sheet. Its small size  (76 amino acids) makes it one of the most studied proteins for protein folding and dynamics.

KcsA Potassium Channel

Copper, Steel

Potassium channels form potassium-selective pores that span cell membranes. They are the most widely distributed type of ion channel found in virtually all living organisms. The four identical subunits are situated in a four-fold symmetrical manner around a central pore, which allows potassium ions to pass freely.  At the top of the structure, formed by four loops lining the pore, a selectivity filter is situated which prevents other ions (such as sodium ions) from passing. The correct ions are detected by their size and charge. Note that that no active pumping of ions occurs; it merely allows passive conductance of ions down the con-centration gradient between the two sides of the membrane.

The KcsA is an archetypal membrane protein with eight tightly packed membrane-spanning a-helices.  The four short helices in the center where the chain crosses half the membrane and then returns to the top are a more unusual feature.

Protein Folding in cuprum

TIG Welding Proteins

Today I swapped my MIG Welder for Kevin’s TIG welder (temporarily) and experimented with TIGing copper together. Turns out its not that hard except that the copper i’m welding is so thin that its really easy to just blow a hole in it or turn it all into a molten puddle with just a little bit too much heat. I found in the end that keeping the electrode tip fairly close but giving lots of power gives a small controllable puddle as opposed to less power and larger distance which gives a much wider puddle. We’ll see if the joints are any good once i start bending and “folding” the whole thing into shape. If they crack then i have screwed it up. I realized after welding all the parts to gether that I should have ground down the excess weld each time piece by piece rather then ding it now with all pieces attached to eachother which is much more unwieldy. And bending the loop regions into their approximate shapes is totally pointless. Might as well leave them straight (just cut to the right length at 1″/aa and bend them later in the context of the secondary structure elements. Steep learning curve but super fun. WIth the TIG too – it’s really fun and clearly a lot more practice needed but it feels really satisfying. MIGing is just metal hot glue. TIGing is so much more precise. And its lovely and quiet and looks gorgeous under the helmet – you can literally see the stream of electrons flying into the base metal like a glowing shower – not like tig where its all splatter and noise and smoke. TIG is clearly the high-class of welding :) .

Doubt on the common assertion that humans are naturally aggressive

Robert Sapol­sky’s study of a baboon tribe which was  transformation from a violent patriarchic, warnongering tribe (like humans) into a peaceful, almost egalitarian and stable society is one of the more fascinating demonstration that the ubiquitous assumtions that humnas are “naturally” violent is unlikely true.

An excellent podcast on the matter is here:

An two articles by Sapolsky:

Robert M. Sapol­sky, Ph.D., is the John A. and Cyn­thia Fry Gunn Pro­fes­sor of Bio­log­i­cal Sci­ences and a pro­fes­sor of neu­rol­ogy and neu­ro­log­i­cal sci­ences at Stan­ford Uni­ver­sity.

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

After about 2 years of work, millions of CPU hours donated by volunteers from around the globe on Rosetta@HOME and a fruitful collaboration with Daniel Keedy and Jane and David Richardson at Duke University our paper on energy landscapes is finally out! Thank you to everyone who helped and especially to Daniel Keedy @ Duke and all who have donated computing time!

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

Michael D. Tyka, Daniel A. Keedy, Ingemar André, Frank DiMaio, Yifan Song, David C. Richardson, Jane S. Richardson and David Baker

contributed equally

What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR describes structure in solution but using less data. NMR structures display more variability, but is this because crystal contacts are absent or because of fewer data constraints? Here we report unexpected insight into this issue obtained through analysis of detailed protein energy landscapes generated by large-scale, native-enhanced sampling of conformational space with Rosetta@home for 111 protein domains. In the absence of tightly associating binding partners or ligands, the lowest-energy Rosetta models were nearly all < 2.5 Å CαRMSD from the experimental structure; this result demonstrates that structure prediction accuracy for globular proteins is limited mainly by the ability to sample close to the native structure. While the lowest-energy models are similar to deposited structures, they are not identical; the largest deviations are most often in regions involved in ligand, quaternary, or crystal contacts. For ligand binding proteins, the low energy models may resemble the apo structures, and for oligomeric proteins, the monomeric assembly intermediates. The deviations between the low energy models and crystal structures largely disappear when landscapes are computed in the context of the crystal lattice or multimer. The computed low-energy ensembles, with tight crystal-structure-like packing in the core, but more NMR-structure-like variability in loops, may in some cases resemble the native state ensembles of proteins better than individual crystal or NMR structures, and can suggest experimentally testable hypotheses relating alternative states and structural heterogeneity to function.



Alan Turing

Friday I saw an intensely moving and fascinating play on the life and work of Alan Turing (Breaking the Code, written 1986 play by Hugh Whitemore; produced by Strawberry Theatre Workshop; Thu/Fri/Sat 7.30pm @ Erickson Theatre, Seattle). Many years after Turnings work on the Enigma which may well have determined the outcome of the war against Nazi Germany, he was prosecuted by the Governement for his homosexuality and sentenced to chemical sterilization – two year later he commited suicide.

How ironic how often those who fight for freedom against the inhumane oppressors end up being the oppressors and persecutors themselves.

It is sickening how persecution of minority groups continues into so very recent history and to this day. Apparently we have learned nothing. Hey human race, can we please get over this ?

I looked up the official apology issued in 2009 by Prime Minister Gordon Brown on behalf of the UK government:

2009 has been a year of deep reflection – a chance for Britain, as a nation, to commemorate the profound debts we owe to those who came before. A unique combination of anniversaries and events have stirred in us that sense of pride and gratitude which characterise the British experience. Earlier this year I stood with Presidents Sarkozy and Obama to honour the service and the sacrifice of the heroes who stormed the beaches of Normandy 65 years ago. And just last week, we marked the 70 years which have passed since the British government declared its willingness to take up arms against Fascism and declared the outbreak of World War Two. So I am both pleased and proud that, thanks to a coalition of computer scientists, historians and LGBT activists, we have this year a chance to mark and celebrate another contribution to Britain’s fight against the darkness of dictatorship; that of code-breaker Alan Turing.

Turing was a quite brilliant mathematician, most famous for his work on breaking the German Enigma codes. It is no exaggeration to say that, without his outstanding contribution, the history of World War Two could well have been very different. He truly was one of those individuals we can point to whose unique contribution helped to turn the tide of war. The debt of gratitude he is owed makes it all the more horrifying, therefore, that he was treated so inhumanely. In 1952, he was convicted of ‘gross indecency’ – in effect, tried for being gay. His sentence – and he was faced with the miserable choice of this or prison – was chemical castration by a series of injections of female hormones. He took his own life just two years later.

Thousands of people have come together to demand justice for Alan Turing and recognition of the appalling way he was treated. While Turing was dealt with under the law of the time and we can’t put the clock back, his treatment was of course utterly unfair and I am pleased to have the chance to say how deeply sorry I and we all are for what happened to him. Alan and the many thousands of other gay men who were convicted as he was convicted under homophobic laws were treated terribly. Over the years millions more lived in fear of conviction.

I am proud that those days are gone and that in the last 12 years this government has done so much to make life fairer and more equal for our LGBT community. This recognition of Alan’s status as one of Britain’s most famous victims of homophobia is another step towards equality and long overdue.

But even more than that, Alan deserves recognition for his contribution to humankind. For those of us born after 1945, into a Europe which is united, democratic and at peace, it is hard to imagine that our continent was once the theatre of mankind’s darkest hour. It is difficult to believe that in living memory, people could become so consumed by hate – by anti-Semitism, by homophobia, by xenophobia and other murderous prejudices – that the gas chambers and crematoria became a piece of the European landscape as surely as the galleries and universities and concert halls which had marked out the European civilisation for hundreds of years. It is thanks to men and women who were totally committed to fighting fascism, people like Alan Turing, that the horrors of the Holocaust and of total war are part of Europe’s history and not Europe’s present.

So on behalf of the British government, and all those who live freely thanks to Alan’s work I am very proud to say: we’re sorry, you deserved so much better.

Gordon Brown