Espresso

This is a demitasse 3D printed out of porcelain. The outside has a cubic/pixelated/voxel pattern around the cup which contrasts well with the smooth, hemispheric cup.

I designed this espresso cup just to try out 3D printing with porcelain. The piece is not actually directly 3D printed, but instead a cast is 3D printed by laser sintering. It is then filled with porcelain and fired. Even though this model was molded there is no visible seam from the mold! 

The best thing about designing with porcelain is that it is food safe and can be washed. 

It is available here.

Transistor

 

This ring is based on the weapon in the video game Transistor. It has a computer circuitry look to it. I designed this ring in 123D by Autocad. I had it printed in gold plated stainless steel to maintain the circuitry feel. It is quite top-heavy and the hole is slightly too big for my finger, so it doesn't stay perpendicular to my finger as I would like. Overall, I am very happy with the unique design and circuitry feel. It is available on Shapeways.

 

Resource Sharing

My first first-author paper, Resource Sharing Controls Gene Expression Bursting, has been published [PDF]! 

Genes express proteins in bursts of activity with periods of no activity between bursts. Burst dynamics are characterized by a burst size (duration of a burst) and burst frequency (number of bursts per time). During a burst the gene draws on a limited pool of reusable resource. Little is known about the relationship between burst dynamics and resource sharing. Here we made cell-sized reaction chambers (both PDMS plastic and POPC lipid vesicles) and observed bursting dynamics as the size of the resource pools was varied. When the size of the resource pool was increased, the number of protein made increased. This increase in protein was achieved by increasing the burst size not burst frequency. This may be due to the fact that the 100 different molecules needed to make protein became localized. Localized components suggest large transcriptional burst sizes are correlated with large translational burst sizes. This correlation is confirmed with in vivo E.coli data. Our results demonstrate the link between bursting dynamics and resource sharing.

 
 

Caveney, Patrick M., S. Elizabeth Norred, Charles W. Chin, Jonathan B. Boreyko, Brandon S. Razooky, Scott T. Retterer, C. Patrick Collier, and Michael L. Simpson. "Resource Sharing Controls Gene Expression Bursting." ACS Synthetic Biology (2016).

Whitehouse

My sister set up and ran a creative Minecraft server for a while.  She built this whitehouse at the spawn site.  I captured this model and had it printed before she shut down the server as a way to remember it.

The flag and tree are fragile (at least in sandstone) because they are only connected by a single Minecraft block.  Otherwise, the full color model is beautiful.

I used Mineways to capture the volume I wanted to print. It is easy to use. The world save is opened in a top down view, and you just select the volume to print. The Minecraft world save is converted into an stl file, ready to be sliced and printed. I found this method through erich666's L'Effie, Vokselia's Eiffel Tower and Mauricio's October 27th, 2010 blog post

This was my first 3D model, and the easiest to make. As a CAD program, Minecraft is very intuitive.

Ring

This ring was created with ShapeJS, a programming language made by Shapeways. The ring is the combination of two bands. The inner band (size 9.5 19.4 mm diameter) is 1.5 mm thick and provides a smooth surface. The outer band is made by intersecting a SchwarzD Minimal Surface with the outer band, a ring. As before, minimal surfaces are the minimal surface needed to connect given boundary conditions (like soap bubbles forming inside a ring of wire or a circus tent draped on poles. Here the minimal surface provides a quick way to make an interesting pattern. After the intersection, the corners are rounded. Currently the minimum feature size is 1mm thick, so sharp corners or very thin features need to be smoothed out for printing. To help with printing I made the SchwarzD pattern very thin with a larger period. It is not easy to get a sense of the minimal surface from the final ring design, but the pattern it produces is interesting. It reminds me of waves in sand. Here is a link to the ShapeJS minimal surface ring example.

SchwarzD ring is now available on my Shapeways store.

Terrariums

Bottles, especially bottles of alcohol, are all so beautiful and uniquely shaped. I hate just recycling them when they're empty, but keeping keeping empty bottles seems like a waste of space. I also love plants, but watering them can become a chore.  So, I've taken interesting old bottles and filled them with plants.  This way I can keep the bottles, and the plants need watering less often.

So far, 750 mL bottles are a good size. They are 1/3 full of dirt and 2/3 open for the plant to grow. Each terrarium has coarse alabaster in the bottom to help drain the soil above.  Between the marble and soil is activated charcoal to help limit mold and fungi growth and release nutrients to the plants. The terrariums are left open, but with such narrow necks they stay quite damp. Plants that do well in these conditions require nearly continuous moisture. Some plants I've tried just end up dying. At first I tried sealing the bottles, but the plants quickly died. The plants in the sealed terrariums may have been too large for the container. This would cause them to use up limited nutrients before reaching equilibrium in the system. Interestingly, a similar result was seen at a much smaller scale when confining populations of cells. Chambers with few initial cells grew while chambers with many initial cells did not grow.

Slow groing plants work better. Fast growing plants tend to grow out of the neck of the bottles. Finally, they should be left to grow in bright rooms but never direct sunlight. Direct sunlight will cause the terrarium to act like a car on a hot day and cook the plant inside. 

Sharkfin

On a family vacation at Hilton Head, South Carolina about 10 years ago I bought a bottle opener just like this one. My dad wanted one too, but unfortunately it was the last one in the store and the island.  This is a perfect, almost stereotypical, scenario requiring 3D printing: the need for replicating a unique object.  It also seemed like a good beginner CAD project, so I set out to have one printed for my dad. I started with a rectangular block and took the intersection of a projected shape in all three dimensions. The fin shape was drawn by hand as a spline. The other two dimensions were an isosceles triangle (projected from the back to the front) and an oval (projected from the bottom to the top). I uploaded the STL model and had it printed in stainless steel. Now, thanks to 3D printing, a once rare object is available to anyone.

When I first got it I was worried it would break, but I've opened bottles with it no problem. The fin shape of this one is a little different from the one I was replicating because I drew it by hand. The tip of the fin is thicker than the original because of printing limitations, but no worries it still looks amazing.  Finally, the striped pattern comes from the layer resolution of the 3D printer.  I think it looks cool because it clearly sets the bottle opener apart as being 3D printed. I gave it to my dad, and he loves it! 

PhD beyond Academia

Knowing is not enough; we must apply. Willing is not enough; we must do.
— Johann Wolfgang von Goethe

Driven by the shortage of positions in academia, the purpose of the university is changing, and only a few programs are reacting.  PhDs, the highest academic degree, were traditionally for people aspiring to be professors in much the same way as medicine and law degrees are for doctors and lawyers.  However, due to an over abundance of new PhDs, programs need to adapt.

Oxford lists the purpose of a PhD as, "It is no longer just about producing an original piece of excellent research; producing a trained researcher is an equally important output. (Mary Ritter, Pro-Rector for Postgraduate Affairs at Imperial College, London and Chair of the UK GRAD Steering Group, Research Councils UK)." In some cases this is taken further to training someone suited for business, political science, or industry.

There is a crisis in academia.  As Jake Beal tweeted, only 8% of current PhD students will every land a tenure-track faculty position.  Furthermore, those 8% are likely to only come from the top schools.  PhDs are instead turning to entrepreneurship, data science, and policy.  So, how should PhD students use their degree, and how should they position themselves to succeed post graduation?

Programs like the Bredesen Center are adapting PhDs for entrepreneurship & policy, prior to graduation. The Bredesen Center is a PhD program that exists outside traditional disciplines.  Each student studies an aspect of energy.  I study what conditions affect noise in genetic circuits, but other students study everything from hydropower to plasma physics.  As part of the program we are required to take a few courses in either entrepreneurship or policy, and we are encouraged to go beyond the classroom.  This model is important for modern PhD students; learning skills outside science is important to prepare scientists for jobs outside academia.  Other programs offer post-doc short courses for turning PhDs into data scientists.  

In the spirit of the meritocratic hacker ethic, real, concrete projects are superseding credentials.  A PhD and entrepreneurship are examples of such projects.  Alex Shye discusses a few similarities between the two including experimentation, moving fast, understanding the current field of work, and unstructured work that permeates your life.  Even companies are no longer as concerned that candidates have checked all the boxes (e.g. which degrees, from where, working for whom).  They now want to see portfolios of projects candidates have completed; work can be shared directly with the world (the purpose of this website).  Professor Christine Ortiz, the dean of graduate education at MIT recently stepped down from her position to found a new type of university focused on projects, not lectures, majors, or exams.  The Thiel Fellowship goes a step further and offers driven teenagers the stability and opportunity to build their own venture (startup, non-profit) instead of attending college.  One of the driving ideas is that experience completing projects is more valuable than sitting through dictation in a classroom.  

The Bredesen Center model is working.  Justin Knowles and other students have received national recognition for their work on clean energy policy.  Tony Bova is replacing oil-based plastics with bioplastics.  Beth Papanek and I are creating a low-cost biological source of nanoparticles.  Three teams of students, including Adeola Adediran, Christine Ajinjeru, Akinola Oyedele, and Eva Mutunga, have won the local pitch competition Vol-Court.  

The future is bright.  Forget knowing and willing.  Apply and do.  Make.

Complexity

The picture on the left is an egg in a 3D printed voronoi coquetier, or eggcup.  At least on the surface, complexity seems reversed from what is typical.  That is the inorganic eggcup has a much more complex structure that the simple curved biological egg.  In contrast, the varied structures of the succulents to the right are more complex than the plain pot they're in.

While complexity between the egg and eggcup at the macroscopic scale is reversed, the minimalism of the egg hides far more complex nanostructure than the eggcup.  The egg has the potential to make a quite radical transformation into a bird with many types of tissue displaying varied structures.

Interestingly, biology and 3D printing are starting to merge and create objects that are complex across many scales.  Biobots makes printers that create biocompatible scaffolds that support cell cultures and grow organs.

The coquetier was designed by @Gregoware, downloaded from @thingiverse and printed on an @ultimaker.

Cured Ham

My friends ate a cured ham with Thanksgiving dinner a few weeks ago.  They thought something like mold or fungus was growing on the outside.  I thought it was just salt, but I collected some into an eppendorf tube to look at later.  I went home for Thanksgiving and my friends stayed and cooked the ham.  They first washed the outside (removing what we though was salt or mold) and then soaked the entire leg in water for a day.  This was to draw out the salt that was used to cure the ham.  They then cooked it in the oven and enjoyed it.

About two weeks went by until I could look at the sample under the microscope.  By the time I put the sample on a microscope slide it had collected moisture and was much wetter than when I collected the sample.  

First, I scraped some of the sample on a number 1 coverslip, and mounted it on an inverted Nikon microscope with a 20x air objective (the 100um scale bar applies to all images).  At first I saw dried salt crystals.  As I looked at the sample it was drying out.  I switched from backlit to fluorescence, and some of the crystals were fluorescent!  They lit up the crystals around them.  The center and right images are in the same location, but the center image is fluorescent while the right is backlit.  Fluorescence was excited at a peak of 532 nm (blue-green) and the emission peak was at 595 nm (yellow-green).

Then I saw this large shadow, and it was moving!  It looked like a large bug.  I recorded a video over about 7 seconds, imaging frames as fast as possible.  Just after the video was recorded it stopped moving, and I could not get a better image of the bug.  I think it was alive and either dried out or got cooked to death by the lamp illuminating the stage.  

After some searching, I learned cured meats can harbor pests, including mites.  They are about 800um long  (which this one appears to be), and they have eight legs, four in the front and four in the back, with little hairs growing off the legs.  These live on the outside of the meat only and can be easily washed off.  This was a learning experience.  I don't think the mites were harmful, but they do look gross.

Bitcoin

Bitcoin (BTC), the cryptocurrency, is supported by a network of independent miners and is always mining blocks.  Each block is a challenging computational problem, and the difficulty is adjusted based on the computational power of the entire network so that one block is mined every 10 minutes. The computer that mines the block (solves the problem) collects the transaction fees associated from any transactions processed in that block and, currently, 25 new BTC.  So, given we can estimate the reward for mining a block (in BTC) and the amount of electricity the network spend mining the block, can we quantify the value of BTC in dollars (USD)?

Fundamentally, the value of BTC should be greater than or equal to the energy cost needed to keep the network running.  If miners receive less value from the BTC they earn than from the electricity they put into mining they will leave the network, and the average amount of BTC each remaining miner receives will increase.  If the value of BTC is excessively high compared to the electricity input miners will enter the network and the average amount of BTC each miner receives will decrease.  The decision to enter or leave the market is unique for each miner, but we assume the long run average value of BTC in dollars is greater than or equal to the cost of mining.  So mathematically,

(transaction fees + new BTC) = cost of electricity * energy input

The left hand side of the equation is the number of BTC per block.  We have already covered new BTC.  This amount of new BTC decreases by half every 4 years, and the last new BTC is expected to be awarded in 2140.  So why mine blocks when no more coins are being awarded?  When the block is mined, transactions are processed.  These are other people, not necessarily the miner, exchanging BTC.  If someone wants a transaction processed they attach a fee.  These fees are awarded to computer that mines the block.  In the long run individuals will only continue to mine if the reward, transaction fees, offsets the cost of mining, electricity costs.  We will ignore capital and overhead costs (e.g. taxes, cost of buildings, miners, and labor) to simplify the analysis, but including these will increase the lower bound of dollars per BTC.

The right hand side of the equation is the dollars spent mining each block and relies on electricity being priced in traditional fiat currencies.  A reasonable estimate for the average price of electricity across the network is $0.05/kWh.  This is slightly less than the world average because large scale BTC mining is done in cooler climates to ease cooling costs or areas with cheap electricity.  Energy input, like cost of electricity, is an average across the network.  The energy consumption per Gigahash is continuing to improve, but current ASIC miners are estimated to consume 5 Watts/(Gigahash/second), also here.  The size of the network, measured as hashrate, is readily available.  Below are the variables used with estimated values:

We rearrange the first equation to get dollars per BTC.  The 1/6 hour is assuming one block is mined every 10 minutes.  This is not always the case.

$/BTC = (<EC> * <Eff> * HRN * kW/W * 1/6) / (BTCtc * <TB> + BTCnew)

With the assumptions above, the equation predicts $830 for 1 BTC.  This is slightly above the current exchange rate of about $420.  Indicating that BTC is currently undervalued relative to the resources used to make those BTC (the amount of electricity used to make BTC is greater than the worth of those BTC when converted into USD).  The calculated exchange rate is quite sensitive to the average cost of electricity across the network and the average efficiency of the miners used.  If the cost of electricity is instead $0.01/kWh the exchange rate drops to about 1BTC=$166.  Similarly, if the miners are more efficient, say only 0.5 Watt/Gigahash, the exchange rate drops to only 1BTC=$83.  Other explanations for people paying more in electricity than the value they get include people mining for fun, as insurance against holding centralized currencies, or expecting the value of BTC to increase dramatically.  For example, after the next halving, expected in 2016, the reward of new BTC will drop to 12.5 per block, and the exchange rate predicted by the equation jumps to about $1,653.  In the extreme case, when new BTC are no longer released and the only reward for mining is transaction fees, the exchange rate predicted is 1BTC=$208,000 (assuming the cost of electricity, mining efficiency, number of transactions per block, and transaction fees are the same in 2140 as they are today, lol). With the new BTC rewarded at zero, the hashrate of the network would have to drop to only about 500,000 Gh/s, from the current 500,000,000 Gh/s, for the exchange rate to be about today’s rate.  

In the end, this was a fun exercise to put some numbers on the resources being put into BTC and compare those to the current value of BTC.  This analysis suggested BTC is currently undervalued, but in reality, BTC's value derives from many different sources including an alternative to restrictive currencies, purchasing drugs, or protection against inflationary policy.

Baymax

Big Hero 6 is an awesome Pixar movie from last year.  While the main plot follows superheroes fighting a villain, the beginning of the film really idolizes science and maker culture.  The main character, Hero Himada, uses homemade bots to win illegal robot fights in the streets of San Fransokyo (San Francisco / Tokyo mashup).  His older brother, Tadashi, is a student at university engineering a healthcare robot, Baymax.  The scene where Tadashi's lab is introduced is really cool, and in some ways captures the excitement of scientific (and engineering) research.

My sister helped me print RyanMark's Baymax model.  I chose this model because it is designed to not need supports.  Baymax is a difficult shape to print because both the top and bottom are rounded.  Additionally, his hands and fingers create an overhang.  This model is printed in two halves to avoid these problems.  This way each half is printed from a stable base and any small parts (fingers) are printed out from the main structure.  We printed Baymax at 20% fill to save materials.  Because the plastic we printed with is clear you can see the fill as crossed lines across Baymax's body.  After the print finished I used a toothpick to paint the eyes with Testors black enamel model paint (though liquid rubber would have worked well too).

Shade

"Complexity is free" is one of the popular saying about 3D printing.  It means that unlike traditional manufacturing, more complex shapes are just as easy to make as simple ones.  Biologically inspired shapes are a great way to show off "complexity is free."  I wanted to print a really cool, flowing, organic shape that was also functional, so I chose the Julia Vase #011 by virtox as the lamp shade.  My sister helped me print it out of a tough, clear plastic.  The model is hollow so the printer generally just traced the edges.  

Ideally the lamp would be self contained within the shade to avoid disrupting the unique, complex surface.  I decided on powering the lamp with induction coils for a sleek design.  In theory the lamp shade could be printed to completely enclose the lamp.  The lights need to be LEDs to avoid generating enough heat to melt the plastic and to fit inside the shade.  I followed this guide by Tyler Cooper on Adafruit to get the parts list and get the wiring right.  All parts were ordered from Adafruit.  The circuit is really simple.  The wall plug is soldered to the coil supplying power.  The coil receiving power is soldered to a resistor (to avoid overloading the LEDs) and a few LEDs in parallel.  

There are a few things could be changed.  The LEDs are a little dimmer than I expected.  I think this is because of the resistor I used (1kOhm).  If it has less resistance there would be more current and brightness.  The LEDs light up around 3cm above the coil.  Again, if the resistor were smaller it would probably light up further from the coil.  Finally, the transmitting coil is bare, so I'll need to make a small case for it (and a stand for the shade).  Overall I am really happy with the result.  The lamp shade is especially beautiful when lit from the inside.

 

Cell-free Scalability

Biotechnology has so far relied on microbes.  They produce beer, bread, cheese, yogurt, insulin, chemicals, flavors (like vanillin), and many other products.  Some of these microbes were found naturally and others were altered with metabolic engineering.  The output of a product from engineered microbes generally depends on the scale of the reaction.  On the lab scale, microbes may show high concentrations but when the bioreactor is scaled to industrial levels the concentrations drop.  This presents a major challenge for researchers engineering microbes.  Their lab scale microbes perform wonderfully but commercialization fails.  Cell-free synthetic biology is becoming an alternative to metabolic engineering.  Cell-free reactions only use parts of cells to carry out reactions, so nothing needs to be kept alive.  Additionally, the only reactions happening in the system are those that contribute to the desired product (when using cells many reactions are necessary to just keep the cells alive).  Cell-free reactions are easier to manipulate and quicker to run.  Fortunately they are also scale independent.

 Zawada et al. tested the scalability of cell-free reactions for cytokine production.  The plot to the right shows their main finding.  Concentrations of products are plotted versus time.  The different curves represent different scale reactions from 250 microliters to 100 liters.  Note that all the curves line up, so at any scale these reactions happen at the same rate (produce the same amount of product per time).  This is another benefit of using cell-free reactions.

Ubiquitin

The function of proteins is determined by their shape.  Proteins are made of chains of building blocks, amino acids.  The amino acid sequence is the primary structure of the protein.  Amino acids all have unique properties (size, charge).  Protein shape determines if the protein prefers interactions with water (hydrophilic) or oil (hydrophobic), binds oxygen, or harvest light.  The study of protein structure (crystallography) is a very important.  There are two main approaches to determining protein structure: X-ray crystallography, and nuclear magnetic resonance (NMR).  Structures are then stored in the Protein Data Bank, which currently has 100,000 structures.  

3D printing proteins could be an easy way to interact with their structure.  I'll be following this guide written by Forrest Yeh.  I chose to print ubiquitin because as its name suggests, it is ubiquitous in eukaryotic organisms.  It attaches to proteins after they've been made (post-translation) and regulates their activity, location, live span, and other cell processes.

After downloading the .pdb 3D crystal structure from Protein Data Bank, the best way to view the structure is with UCSF Chimera.  You can change the way the structure is visualized from spheres for each atom to a cleaner and more informative ribbon with alpha helices and beta sheets (secondary structures).  The visualized protein can then be exported as a .stl file which can be input into a slicer program to convert the model to G-code (3D printer commands).  

Protein structures are very complex and require many scaffolds.  This makes printing them difficult.  The right image is the first few layers.  The many dots will be the scaffolding structure.  The left image is the final printed protein.  There are a lot of scaffolds inside the print.

Below is an image of the final protein.  On the top are beta sheets (the long flat structures).  On the bottom is an alpha helix (cork screw structure).  There is still some scaffolding left because the print messed up in a few places and if I remove the scaffold the protein will break.  Over all this was a fun project but next time I'll have to either scale the protein up to make the features bigger or slow the printer down to catch all the details.

Moss and Mycelium Update

The minimal surface, vertical moss garden is growing well!  I water it twice a day by pouring water on the top of the tower.  I'm keeping it covered with a glass to keep the humidity high.  After a day in the sunlight, condensation builds on the glass.  The pencils leave a small gap to allow some air exchange.  The moss at the bottom of the surface (closest to the water) are growing much better than the suspended moss.  I think this is because the bottom is wetter.  I've added plant food for acid loving plants to the water to provide the moss with nutrients.


There is growth in both mycelium cultures.  The one in the bottle is growing much better.  The culture does not look like a solid mass yet.  I'll wait a little longer to see if it grows denser.  The culture in the cup is not really growing.  This may be because I seeded the culture with mushrooms instead of spores.  This culture also has a small mold contamination (green spot in upper right corner).  I didn't plan ahead and think about how to bake these to get a nice solid, sterile mycelium brick.  Neither container will do well in the oven.  Maybe I'll cut the containers away and transfer the mycelium/coffee grounds into a ramekin.

Mycelium Bricks

Ecovative has a very interesting way to design materials.  They grow mycelium (part of the mushroom lifecycle) and dry the mycelium to replace packaging material, surfboards, insulation, and other application.  I want to try this process out my self to get a better understanding of the material properties of mycelium.  Ecovative grows mycelium on agricultural waste (like corn stalks), but I am starting out with something easier, coffee grounds.  Mushrooms grow by breaking down nutrients in biomass (corn stalks or coffee grounds).  Microorganisms can also grow on biomass and compete with the mycelium.  This would ruin the experiment.  So, any biomass used for mushroom food needs to be sterilized.  Cornstalks would need to be autoclaved.  Luckily, coffee grounds are saturated with boiling water, so they are sterile just after use.


I looked around my backyard for different kinds of mushrooms.  I haven't identified the species, and I do not know which species produce the strongest mycelium.  We'll find out.  I found two species, one growing on a log and one that looks like a pile of spores.  I placed the mushrooms and spores in fresh coffee grounds (I shook the spores in the bottle to distribute them.  I used an empty plastic water bottle and an old plastic container covered with plastic wrap.  Both environments are moist, but have holes for air flow.  I've placed both containers in a warm dark place (the laundry room).  Now we have to wait a few weeks for the mycelium to grow.  Hopefully a white fuzz grows throughout the coffee grounds!


Minimal Surface Vertical Garden

minimal surface tower.png

This weekend I thought it would be fun to grow moss on a minimal surface.  Moss is an interesting living addition to many surfaces (e.g. moss graffiti).  Minimal surfaces are the minimal surface needed to connect given boundary conditions (like soap bubbles forming inside a ring of wire or a circus tent draped on poles.  The wire and poles are the boundary conditions and the shape of the bubble and tent is the minimal surface).  Minimal surfaces are also recognized as having high surface area to volume ratios and being good substrates for cell growth.  Minimal surfaces have attracted the attention of architects who use them to minimize weight and materials.  Because of their high surface area to volume ratio (and thus minimal material requirements) minimal surfaces are an interesting way to explore efficient vertical farming.  

I chose to use a 1/2 scale, 1/4 resolution model of the Voronoi Tower by Dizingof (modified by RichRaf).  Here is the STL file.  This model resembles an organic tower.  My sister kindly printed the tower on her Ultimaker.  

 

I selected what I hope are two different types of moss, one Acrocarp and one Pleurocarp.  Acrocarps have upright growth, branch a lot, and are slower growing.

Pleurocarps grow as a carpet, they grow faster, and and they attach to hard surfaces better.  Additionally (and more challengingly) pleurocarps can tolerate constant moisture while acrocarps cannot.  

Acrocarp

Acrocarp

Pleurocarp

Pleurocarp

 

I arranged bits of moss on the tower, preferentially placing the pleurocarp on the top and the acrocarp toward the bottom.  To grow the two different types of moss on the same tower I am halfway covering the structure with a glass to retain moisture at the top and allow airflow at the bottom.  If this does not work I expect one of the mosses to take over.  (I may keep it covered more because it looks cooler).  I will report on new growth in a few weeks.

Cell-free Protein Synthesis

In the Central Dogma of molecular biology, DNA encodes blueprints, RNA transcribes the blueprints and carries them outside the nucleus, and proteins are build from blueprints.  This general format is found in all life.  For this process to occur, a few more molecules are needed.  Specifically, RNA polymerase is needed to convert DNA to RNA, ribosomes are needed to convert RNA to protein, 4 ribonucleotides are needed as the building blocks of RNA, 20 amino acids are needed as the building blocks of protein, tRNA are needed to translate RNA to protein, and all these machines need ATP as an energy source.  Aside from those components, no other part of a cell is needed to create protein from DNA.  Removing the rest of the cell creates a simplified environment ideal for studying transcription (DNA to RNA) and translation (RNA to protein).  In the image DNA is being transcribed by a polymerase.  The resulting mRNA is being translated by a ribosome into protein (green chain).  This is all happening in vitro.

Cell-free systems were first used in the 1960s by Alfred Tissieres to study ribosomes and by Marshall Nirenberg and Heinrich Matthaei to break the amino acid code.  These systems were raw extracts.  Cells (usually E. coli) are broken open, lysed, by high pressure, chemicals, or sonication.  The resulting slurry is centrifuged to remove large pieces of the membrane and chromosome, and the extract is ready.  

The benefits of CFPS are greater control over the system, quicker design cycle times, and the ability to produce chemicals that may be toxic to cells.  Now, CFPS research focuses on improving its weaknesses including increasing reaction times (up to 100 hours), increasing protein yields (up to 2.3 mg/mL), increasing reaction scale (up to 100L), lowering the cost of the energy source (14 times cheaper), and studying fundamental questions like incorporating unnatural amino acids (Michael Jewett Lab), testing genetic circuit designs (Richard Murray Lab), and studying noise in transcription and translation (my lab!).  

Noisy Genes

Gene expression is inherently noisy.  This means there is variability in the gene's response to an input.  Say a population of genetically identical cells all receive the same input signal (e.g. concentration of an inducer like IPTG, light, or a stressor like heat).  If you measure the response of each cell to the input, their responses will vary across the population.  Some will respond too much, some too little.  This variability is called noise.  Some of the noise is Poissonian and is a result of the discrete nature of reactions in cells.  

Cells typically only have a single copy of a gene.  So, when an input signal arrives, the gene will start making mRNA which will be translated into protein.  Because there is only one gene, mRNA must be made one at a time (discretely).  The Poissonian description of this noise means these independent, uncorrelated, discrete events are spaced in time according to an exponential distribution.  

This variation was explored by Michael Elowitz et al. in the 2002 paper Stochastic Gene Expression in a Single Cell.  This important paper was one of the first to study noise in gene expression.  Elowitz et al. wanted to understand how much variation in gene expression was intrinsic (specific to a particular gene) and how much was extrinsic (variations in global assets like polymerase and ribosomes).  So, the authors crated a plasmid (injectable sequence of DNA) with cyan fluorescent protein (CFP, on the green channel) on one side and yellow fluorescent protein (YFP, on the red channel) on the other.  These genes are nearly identical, and in this plasmid they are controlled by the same promoter.  Any variations in both colors indicates a global variation or extrinsic noise.  Any variation in a single color over the other indicates noise particular to that gene, intrinsic noise.

As can be seen in the image, many cells are yellow (low intrinsic noise and high extrinsic noise), but some are more red or more green (high intrinsic noise and low extrinsic noise).  The authors tune the level of expression and find noise increases as expression decreases.  That is, as an input gets smaller the response is less fine tuned because proteins are made in discrete numbers.  Additionally, notice how varied the response of an individual cell is to the average of the population.  Even though these cells are growing right next to each other in the same media with the same inputs their protein expressions vary widely.