Synchrotron

The Canadian Light Source is a national research center located at the University of Saskatchewan. They pursue research using a synchrotron. This is a type of cyclic particle accelerator that accelerates electrons to speeds approaching the speed of light. This leads to extremely powerful beams of light that can be tuned to any desired wavelength. CLS scientist built this end station. As I understand from their description, the beam of light coming off the synchrotron enters the optics hutch, the white bit that takes up about 2/3 of the right portion of this model, via that gray nozzle on the right side. Inside the optics hutch, the beam is focused and tuned to the desired wavelength. The resulting narrow beam leaves the optics hutch and hits the experimental hutch, the white bit on the left hand side of this photo. There scientists study how the light energy affects or interacts with some sample they are interested in.

Mars Science Laboratory Curiosity Rover will be an official set

Today LEGO announced that they approved Stephen Pakbaz's Mars Science Laboratory Curiosity Rover as the next Cuusoo set. Cuusoo is a crowd-source site where LEGO builders can propose set ideas, and if they get 10,000 votes, LEGO will consider releasing them as official sets. I love the fact that they're choosing this, and not the latest proposal inspired by TV/movies/video games. This set is very much in the spirit of the Shinkai 6500 and Hayabusa sets, the first two Cuusoo sets, and also ongoing collaborations between LEGO and NASA. Stephen is a JPL engineer, and he's said that he was inspired by previous LEGO NASA sets. Here's to the future generations that will be inspired by this new set to look to the stars (er, planets)! Congratulations, Stephen! Via the Brothers-Brick.

DNA patent ruling

Here's some DNA. I'm not sure who built this, as this was at a public display and turns up in several people's photo streams. Anyway, you might ask why post this today, as I just posted a model of DNA in my last post. Well, this gives me a chance to write about the ruling from the US Supreme Court in the case of Association for Molecular Pathology v. Myriad Genetics, Inc. As I understand it, Myriad held a series of patents, and some were upheld while others were struck down. To understand this case, we have to start with a description of transcription/translation. DNA resides in the nucleus, and protein synthesis takes place at the ribosome outside the nucleus. In order to get the information from the DNA to the ribosome, a copy is made, the complementary strand of RNA. So, for instance, let's say there is a DNA strand that goes GCGCAAGC. The complementary strand of messenger RNA is CGCGTTCG (C's match with G's, G's match with C's, T's match with A's). But, let's go a little further. About 98% of the human genome is not used for making proteins. When this non-coding DNA (sometimes called 'junk DNA', but it does actually have important regulatory function) comes in the middle of a DNA sequence, it is called an intron. So the unwanted parts are removed. So, for instance, our CGCGTTCG strand could be trimmed down to just CGCGCG, and this mature mRNA would code for the protein Arg-Ala (groups of three RNA bases are called 'codons', and code for different amino acids). Okay, back to Myriad Genetics. They found that a mutation in the code for a particular protein is associated with certain kinds of breast cancer. So, in our example the healthy cell has DNA GCGCAAGC, which leads to mRNA CGCGTTCG, which is modified to mature mRNA CGCGCG, which codes for protein Arg-Ala. Let's say the potentially cancerous cell has DNA CCGCAAGC, which leads to mRNA GGCGTTCG, which is modified to mature mRNA GGCGCG, and this would code for protein Gly-Ala, and let's say this protein is associated with cancer. Myriad came up with a test for the presence of this mutation. Their test involved creating a shortened form of DNA with the introns removed, called complementary DNA. In our example this would be CCGCGC (note it is missing the AA from above). They take mRNA from the patient, and see if it binds to this complementary DNA. If it does, it indicates the presence of a mutation that could lead to cancer. They then took out patents on the process of comparing the mRNA to their complementary DNA, the sequence in the complementary DNA (CCGCGC), and also the sequence in the initial DNA (CGCGCAAGC). What the Supreme Court ruled yesterday is that the third type of patent is invalid, as the sequence of DNA in the living cell (either healthy or cancerous), is a 'product of nature'. That is, Myriad did not invent it, so they cannot patent it. OTOH, the complementary DNA is not naturally existing, and so therefor may be patented. It is also valid to patent a novel method involving this complementary DNA. So it was a mixed ruling, but IMO a correct one. The human genome is still there available for anyone to do research without fear of being sued for patent infringement, but there is still incentive for companies to produce new types of tests that they can protect with patents.

DNA

There are a lot of LEGO renditions of DNA out there, indeed I chose one for the banner of this blog, but most don't really have an accurate structure. This one by SICP_DNA, though, is very good about keeping to the actual structure of DNA. In DNA, the strands on either side are pointing in opposite directions, and the white and gray backbones have the studs pointing in different directions here. Since the backbone sugars are asymmetric, the 'grooves' are different sizes. Another aspect of DNA is that two of the bases, the purines A and G, are larger than the other two, the pyrimidines T and C. The connections here are such that it only works out when A lines up with T or G lines up with C. They also got the sizes right here, so that one complete twist takes ten steps, and the width to height ratio is approximately correct.




Here you see a comparison between the 'real' structure of DNA, and a simplified depiction. BTW, the LEGO version below is from Nathan Sawaya's Building Bricks of Life. I certainly mean no disrespect, as it is a great model. But as Nathan has said elsewhere he's an artist, not a scientist, and he writes that he decided to go with this more artistic approach (as a commissioned piece for the Archon Genomics X Prize) rather than try to do a more accurate version. Someday I'd like to see him go back and do an accurate depiction of DNA. He's a great sculptor and I'm sure it would be quite cool.



BTW, since I've posted two Cuusoo projects in a row, I wanted to say a little about that. I was corresponding with another LEGO blogger the other day about these, and I agree with him that a great number of the things posted there are not actually viable LEGO sets, including this one (sorry, SICP_DNA). So if I blog something, it is not necessarily true that I am supporting it as a Cuusoo project. I just see Cuusoo as another place where LEGO builders post their creations, along with other photo sharing sites.

Female figs Cuusoo project

Cuusoo is a LEGO website for crowdsourcing set ideas. You propose a set, and if it gets 10,000 votes, LEGO promises to take a serious look at producing the set. Most of the sets that have made it to 10,000 have been attached to some movie/TV show/video game, and fans of that movie/show/game help push it over the top. That said, there have been two science driven sets already produced, the Shinkai submarine and the Hayabusa space probe, in the original Japan-only version of Cuusoo, and the Mars Curiosity Rover is being considered in the most recent round of creations that have reached 10,000. Now it seems that socio-political forces are pushing another to the top. Alatarial designed Female Minifigs to help correct the gender imbalance in Legoland, putting women in small scenes depicting different occupations. The cool thing, and the reason why I'm posting this here on SciBricks, is that many of those occupations are as scientists, probably because Alatarial is herself a geochemist: paleontologist, astronaut, astronomer, chemist, (falconer), geologist, and engineer (plus six others in non-science roles not shown here). I assume that this was recently posted on some social media site, or featured in some news source, because the project jumped from 2500 votes to 7500 in just three days.

NASA's Missions: Imagine and Build

I noted this a couple of weeks ago, but did not have details at that point. LEGO has teamed with NASA for a contest, NASA's Missions: Imagine and Build. Two categories (subdivided into age ranges) challenge you to either build a MOC based on a currently planned NASA mission, or to build the aircraft of tomorrow. The second category is supposed to be accompanied by a technical paper, so they're looking for someone with some knowledge, not just clicking some bricks together and swooshing the creation around your room. We're all looking at you, Apojove (jk, I know there are a ton of AFOLs out there with real science and engineering expertise).

ATV-4 "Albert Einstein"

Brainbikerider built the ATV-4 "Albert Einstein". I'll just be lazy and copy his whole description:

The ATV (Automated Transfer Vehicle) is ESA’s unmannded resupply spacecraft for the ISS. The mission of this “real world X-Wing” is not only to transport cargo and propellant, but also to reboost the Space Station into a higher orbit. Currently, it’s the most powerful resupply spacecraft with a cargo capacity of more than 6.5 tonnes. The fourth ATV, named after the famous scientist Albert Einstein, will be launched today on an Ariane 5 rocket at ESA’s spaceport in Kourou. You can read more about the ATV here.

Petri dish

As anyone who uses Google knows, today they recognized Julius Richard Petri's 161st birthday. A Petri dish, aka a cell culture dish, is a shallow round dish with a raised edge, often used by microbiologists to grow bacteria or other microorganisms (here in LEGO by MorsLEGO). Usually the dish is partially filled with a warm liquid mixture of agar and nutrients. After it cools the agar becomes a semi-solid gelatin that is an appropriate surface for growing the bacteria, which can be studies as they grow.



In a fun twist, artist Darlene Charneco made Podland Petri.

Solar System

Last in my little mini-series on the images from my new banner is Nathan Sawaya's sculpture of the solar system. Nathan notes that he tried to put them in roughly relative scales, but he also notes that he's an artist, not a scientist. For a great side-by-side comparison tool, go to this link, that lets you compare the various planets to each other. Nathan also insists on including Pluto atop his sculpture. Seven years ago there was a debate in the International Astronomical Union about the status of Pluto. It turns out there are at least four other similarly-sized rocks out there (and Eris is bigger than Pluto). Rather than have a constantly expanding solar system as further celestial bodies are discovered, the IAU came up with classifications of 'planet' (Mercury, Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune), and 'dwarf planet' (Pluto and friends). Due to tradition, and quite possibly due to the connection with the Disney cartoon dog, many have resisted the reclassification of Pluto (for instance, it was a subplot of an episode of the sitcom Sports Night).

DNA

Continuing with my mini-focus on the models in my new banner, DNA's double helix (here by Andreas) is one of the most widely recognized structures from modern science. This wasn't always true. By the 1940's it was commonly accepted that DNA held the key to genetic information. It was known that DNA was made of four bases - G, C, A, and T - and also sugars and phosphates, but it was not known how these came together. Erwin Gargaff discoverd that each cell had an equal number of G's and C's, and also an equal number of A's and T's. Linus Pauling proposed a structure that involved a triple helix, with the phosphates on the insides. At this time, Rosalind Franklin was doing some ground breaking work on X-ray crystallography, and she determined that the structure involved a double helix, and the phosphates must be on the outside. Watson and Crick put this information together, and they came up with the now famous double helical structure shaped like a twisted ladder, where the outside strands (the blue bricks in this LEGO model) are comprised of repeating sugar-phosphate units, and the rungs of the ladder (the red and yellow here) are pairs made up of either A and T or G and C bases. Their paper describing the structure has one of the best lines ever in science writing: "This structure has novel features which are of considerable biological interest." Indeed, the base-pairing and the double helix are at the heart of explaining how DNA is copied, bringing information to the next generation of cells, and also explaining how DNA is used by the cell to make proteins.



BTW, the elucidation of DNA's structure is a great story of egos and infighting, probably sexism, and accusations of international politics. Franklin didn't get much credit for her discoveries because another scientist, Wilkins (another DNA researcher who eventually shared the Nobel with Watson and Crick) shared her data with Crick without asking her first. After she left Kings College, the research director there refused to let her continue on with her data, so she turned to other subjects, where she made ground-breaking discoveries on tobacco mosaic virus and polio virus. So one of her key papers was not even published until after her death. Another interesting side story is that Linus Pauling reportedly felt he would have come up with the structure first if he hadn't missed a flight due to passport issues, so he didn't see a talk by Franklin where she shared some of her results. The Wikipedia entry disputes the significance of this missed flight, but I first heard the story at a conference in honor of Pauling on the occasion of his 90th birthday, where several of his former students gave talks. BTW, he was there at the start of the conference, but I didn't make it until the afternoon session, so I didn't get to see him.

Platonic solids

The Platonic solids (here by OptimalControl) are defined as polyhedra (three dimensional solids) comprised of regular polygonal faces, arranged such that the same number come together at every vertex. The tetrahedron, octahedron, and icosahedron, each comprised of equilateral triangles, the cube made up of squares, and the dodecahedron made of regular pentagons, are the only polyhedra that match this description. These were described by Plato in the Timaeus dialogue, hence the name. He associated the first four with the elements fire, air, water, and earth, respectively, and the dodecahedron with the heavens. BTW, I know this is a LEGO-centric blog, and I try to stick to that, but if you are interested in geometric shapes like these, you might want to check out Magformers, a building toy made up of regular polygons with magnets along the edges, so they can easily click together to make various polyhedra.



From the Timaeus:

The first will be the simplest and smallest construction, and its element is that triangle which has its hypotenuse twice the lesser side. When two such triangles are joined at the diagonal, and this is repeated three times, and the triangles rest their diagonals and shorter sides on the same point as a centre, a single equilateral triangle is formed out of six triangles ; and four equilateral triangles, if put together, make out of every three plane angles one solid angle, being that which is nearest to the most obtuse of plane angles ; and out of the combination of these four angles arises the first solid form which distributes into equal and similar parts the whole circle in which it is inscribed. The second species of solid is formed out of the same triangles, which unite as eight equilateral triangles and form one solid angle out of four plane angles, and out of six such angles the second body is completed. And the third body is made up of 120 triangular elements, forming twelve solid angles, each of them included in five plane equilateral triangles, having altogether twenty bases, each of which is an equilateral triangle. The one element [that is, the triangle which has its hypotenuse twice the lesser side] having generated these figures, generated no more ; but the isosceles triangle produced the fourth elementary figure, which is compounded of four such triangles, joining their right angles in a centre, and forming one equilateral quadrangle. Six of these united form eight solid angles, each of which is made by the combination of three plane right angles ; the figure of the body thus composed is a cube, having six plane quadrangular equilateral bases. There was yet a fifth combination which God used in the delineation of the universe.

Formaldehyde

You might have noticed that I'm making some slight changes to the look of this blog, including the graphics added to the banner at the top of this page. I tried to choose some models from a few (but by no means all) of the major disciplines covered on this blog - chemistry, math, biology and astronomy. Let's take a few blog posts to look at the models I used. Starting at the left end with one of my own, here is my model of formaldehyde (shown next to a standard organic chemistry model kit version). Formaldehyde is made up of one atom of carbon (shown in black), with a double bond to an atom of oxygen (red) and two bonds to hydrogen atoms (white). One thing that is demonstrated by this model is the shape of formaldehyde. Molecular shape is driven by VSEPR - Valence Shell Electron Pair Repulsion theory. The bonds (gray lines) are made up of negatively chaged electrons, and, since like charges repel, those bonds push each other away. VSEPR says that the best (lowest energy) arrangement of bonds will maximize the distance between the bonds. Here we have three sets of bonds around carbon, and the furthest they can get from each other is 120 degree angles (360 / 3).

Inventing Our Future of Flight

I just ran across a press release that NASA and LEGO will be sponsoring a contest along the theme of Inventing Our Future of Flight this summer. Details will be forthcoming and I'll post them here when I find them.


NASA logo by Galen Fairbanks

Colossus Mark 2

James Pegrum built the Colossus Mark 2:

1944AD 1st June, Bletchley Park, England. The improved Colossus Mark 2 starts working in time for the Normandy Landings.
The Colossus was the world's first electronic digital computer that was at all programmable. It was designed by Tommy Flowers to solve a problem posed by a mathematician, Max Newman. In December 1943 the prototype, Colossus Mark 1, was shown to work. There were ten Colossus computers in use at the end of the second world war.
The computers were used by British code breakers, giving the Allies valuable intelligence, obtained from reading many encrypted high-level telegraphic messages between the German High Command and their army commands.

Newton's cradle

I've previously described a Newton's cradle, a desktop toy that demonstrates the conservation of momentum. Derfel Cadarn has built another LEGO version.

Lunniy Korabl

The LK Moon Lander (here by Kei_Kei_Flic) was a planned Soviet landing vessel in the late 60's, roughly the equivalent of the Apollo LM. After Americans were the first to reach the moon, and following setbacks in their own space program, the Soviets decided to scrap the mission and instead to focus on orbiting space stations.

Leonardo

Leonardo da Vinci (here by Legopard) was the ultimate Renaissance man. Of course he is known for his art, but he was also a scientist. His notebooks are full of his observations of anatomy and botany, his inventions in many areas, and his writings on geometry, the formation of fossils, the flow of rivers and the reflection of light off the moon.

LEGO math fun

I spent some time doing LEGO math with my 4-year-old today. Phase 1, numbers - build stacks for each number 1-9 and put them in order. Phase 2, addition - combine stacks and see what they make. Phase 3, subtraction - take away bricks from a stack.




BTW, that's 1-year-old's hand just behind her brother in the second picture, and that's her artwork on the wall. Each kid has gone through this write-on-the-wall stage. Time to paint the kitchen again. :(

Simple machine: screw

A screw is a machine that transforms rotational motion to linear motion. When you turn a wood screw, for instance, you are adding torque, or rotational force, but the screw translates this to a forward force, pulling the screw into the wood. An Archimedes screw (known since at least the third century BC and attributed to the Greek mathematician) uses this concept to lift water. Here are two LEGO versions of Archimedes screws to move little balls up a slope, both by Akiyuky. BTW, these were built as modules in Great Ball Contraption layouts. The GBC is a collaborative LEGO project where people build different modules that move balls from point A to point B. These modules all get strung together to make huge mechanism that are fascinating to watch.

Simple machine - wedge

Another machine that is so simple that it is easy to overlook is the wedge. The idea of a wedge is that due to the angled shape, as it is pushed forward, force is exerted outward (at right angles to the path of the wedge. Think, for instance, of a log splitter - you put the log splitter in the top of the log and hit downward with a sledgehammer. You are exerting force downward on top of the log splitter, but the result pushes the two halves of the log outward. Or even just an axe is a simple example of a wedge, with really the same idea. Axe by Demonhunter.



You killed Kenny! You b... by dm_meister