How Peptides Are Made

What does body building, anti-aging cream and Bleomycin (a cancer drug) have in common? Peptides of course! Peptides are large molecules that are vital to life. If you were to take a protein and break it into smaller pieces, each piece would be called a peptide. Just like proteins, peptides are made of amino acids linked together in a chain-like structure. Whenever you ingest a protein, your body breaks it down to its individual amino acids. It then puts those amino acids back together in a different order to make whatever peptide or protein your body needs. Insulin, for instance, is a peptide that is 51 amino acids long. Your body synthesizes insulin from the amino acids it gets from the proteins you eat.

Peptides and small proteins can be synthesized in a lab as well. Peptide synthesis is a huge market in the pharmaceutical and skin care industry. They’re also used, somewhat shadily, as a steroid substitute by serious athletes and body builders. In this article, we’re going to go over the basic steps of how to join amino acids together to make a peptide. The chemistry of peptide synthesis is complex and well beyond the scope of this article. But the basic steps of making a peptide are not as difficult as you might think. Join me after the break to gain a basic understanding of how peptides are synthesized in labs across the world, and to establish a good footing should you ever wish to delve deeper and make peptides on your own.

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The Enigma Enigma: How The Enigma Machine Worked

To many, the Enigma machine is an enigma. But it’s really quite simple. The following is a step-by-step explanation of how it works, from the basics to the full machine.

Possibly the greatest dedicated cipher machine in human history the Enigma machine is a typewriter-sized machine, with keyboard included, that the Germans used to encrypt and decrypt messages during World War II. It’s also one of the machines that the Polish Cipher Bureau and those at Britain’s Bletchley Park figured out how to decipher, or break. Most recently the story of how it was broken was the topic of the movie The Imitation Game.

Let’s start with the basics.

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Living Logic: Biological Circuits for the Electrically Minded

Did you know you can build fundamental circuits using biological methods? These aren’t your average circuits, but they work just like common electrical components. We talk alot about normal silicon and copper circuits ‘roud here, but it’s time to get our hands wet and see what we can do with the power of life!

In 1703, Gottfried Wilhelm Leibniz published his Explication de l’Arithmétique Binaire (translated). Inspired by the I Ching, an ancient Chinese classic, Leibniz established that the principles of arithmetic and logic could be combined and represented by just 1s and 0s. Two hundred years later in 1907, Lee De Forest’s “Audion” is used as an AND gate. Forty years later in 1947, Brattain and H. R. Moore demonstrate their “PNP point-contact germanium transistor” in Bell Labs (often given as the birth date of the transistor). Six years later in 1953, the world’s first transistor computer was created by the University of Manchester. Today, 13,086,801,423,016,741,282,5001 transistors have built a world of progressing connectivity, automation and analysis.

While we will never know how Fu Hsi, Leibniz, Forest or Moore felt as they lay the foundation of the digital world we know today, we’re not completely out of luck: we’re in the midst’s of our own growing revolution, but this one’s centered around biotechnology. In 1961, Jacob and Monod discovered the lac system: a biological analog to the PNP transistor presented in Bell Labs fourteen years earlier. In 2000, Gardner, Cantor, and Collins created a genetic toggle switch controlled by heat and a synthetic fluid bio-analog2. Today, AND, OR, NOR, NAND, and XOR gates (among others) have been successfully demonstrated in academic labs around the world.

But wait a moment. Revolution you say? Electrical transistors went from invention to computers in 6 years, and biological transistors went from invention to toggle button in 40? I’m going to get to the challenges facing biological circuits in time, but suffice it to say that working with living things that want to be fed and (seem to) like to die comes with its own set of challenges that aren’t relevant when working with inanimate and uncaring transistors. But, in the spirit of hacking, let’s dive right in.

My First BioCircuit™

Following the Composition Model (even though the Network Layer Model might be preferred), I’m going to go through the construction of a simple oscillator through electronic and biological methods. The goal is by the end you know a bit more about biological circuits, what they’re made of, what they can do and why they’re hard to make.

DNA/Physical Makeup

In electronics, we make our parts (for the most part) out of copper, silicon, and epoxy. In biology, the base parts are strands of DNA3. For this reason, if you need a quick refresher on DNA, take it. But, all you must know for this article is that DNA encodes genetic information.

Part List: Protein Expression Mediated Logic

For our oscillator, we’re going to need three inverting gates. In the electronics world, that’s pretty easy (like $0.06 easy). You can make electronic logic gates out of (almost) anything and there are countless resources detailing every… intricate… detail that any sane person would want to know.

The biological world has its fair share of logic gates, some of which we’ve already covered. We’re going to focus on the most common type: protein expression mediated logic. Through this method, protein concentrations are treated as signal and are used just like electrical signals are. Below is a genetic NOT gate, signal A (a specific protein for the Promoter or “input”) inhibits the output of signal B (the protein that the “Gene of Interest” codes for). This works just like a traditional NOT gate, if there is not signal A, then produce signal B. Well, it works almost the same way as a traditional NOT gate. This is where we find one of the great challenges that synthetic biology faces: orthogonality.

In electrical logic, we don’t usually need to worry about orthogonality, as we can connect the output of a NOT gate to what we want (and only what we want) with wires and/or traces. In biology, we don’t usually have this luxury as we’re working in prokaryotes (cells without nuclei) which can be effectively thought of as bags of chemicals4 So, instead of having direct connections from one gate to another, we only have one signal “net” as part of our network.

Computers have this figured out with identifiers like MAC addresses. For example, if Bob wants to send a message to Sue, he might broadcast something like “FOR: SUE, MESSAGE: HI”. This works out great for computers: they craft their own receivers and transmitters. In code and hardware, it can be trivial (that’s part of the reason why we have so many electronics communication standards ) but, in biology protein engineering is hard, and it takes time, ingenuity and labor.

Imagine that you could only use one type of transistor in each project. As an example, consider that if you used two 2N3904s, you turn both on or off, but never one off and one on. Now, pretend that for each transistor, you had to corner a computer in the wild, disassemble it and hand remove all of its components in the hopes of finding a new type of transistor. Surely, that would make creating a computer with 30 billion transistors, in one word, difficult.

As such, practically all of the promoters5 (input sites, coded in DNA) that are used today were originally discovered in nature and have been adapted for synthetic use. And, we’ve been pretty successful at this, with enough usable promoters that we need a catalog to sort them all out6.

Device Built with NOT Gates

Now, ever forward. Let’s try to build a device with our NOT gates. And, as we’re really just here to learn concepts, I’m going to show you how to create a ring-oscillator. If you’re a bit rusty on your terminology, or you’ve been too busy to bother with a 100 level circuits class, no worries. A ring-oscillator is really simple, which is why it was one of the first bio-oscillators made. Ring-oscillators are made by placing an odd number of inverters (usually greater than 1) in a cycle (ring). See below for a very cool gif™ that hopefully should clear up any doubts about how it works. But, if things aren’t crystal clear, Enrique from MITx has your back.

Now for the bio part. We already have our NOT gates, so surely we can string three identical NOT gates together and end up with an oscillator, right? Well, as we covered earlier, we’ll need to use three different gates, so things look like three NOT gates in parallel, rather than in series. But, even with three different NOT gates, we might have another problem: death.

After all, all our logic is taking place in a cell using up resources and producing a “useless” protein. And, by the very nature of cells, there’s a limit to the number of resources a cell has. We can try to improve our cell’s effective throughput, but at some point, we need to realize that the cell, as greedy as it is, must take care of the basic requirements of life. However, fear not. Our three gate oscillator should be sustainable7. But, if we were to try seven or even nine gate oscillators we might need to start worrying.

Anyway, enough dilly dallying. We’ve put our DNA sequences together, introduced them into a cell and now we wait for them to grow8. We’ve used GFP (a Green Fluorescent Protein) as one of our “signals” so we can visualize our signal (just like one would use an LED to view a digital signal).

And… nothing. At first. After about 160 minutes our cells start to glow. Just like electronic ring-oscillators, our frequency depends on the delay time of each NOT gate. In electrical contexts, this gives us frequencies commonly in/above the kHz range. In biology, we’re working at a blazing fast 1×10[-4] Hz with a period of ~160 minutes. Again, another stark difference between biological and electrical circuits.

In Practice / Why You Should Care

Okay, I know how it seems. Biological Logic is underdeveloped, slow and constrained by life. But, there is a harmony! What biology lacks, it makes up for in immeasurable ways. After all, we’re made of cells, not silicon.

From regulating transgene expression for regenerative medicine to a tunable dual-promoter integrator for targeting of cancer cells, cellular logic has the opportunity to change the way we think about how medicine should work, what we think life is and whether or not plant’s should glow. You should care because it’s cool it’s new and it has the potential to help lots of people. We’re hackers. We’ve always been at the forefront of technology, and just because this one’s squishy things don’t need to change. So, let’s get hacking!

I really enjoy writing about synthetic biology, as you might have guessed, so let me know if there are any topics that y’all would like to hear about. Would a few “Getting Started” articles on, well, getting started in synthetic biology with actionable procedures be a good place to start?

Notes

[1] Calculated using the figures from the Forbes Article “How Many Transistors Have Ever Shipped?”. While I have little confidence in this article, I am willing to believe that the figure presented is accurate to at least a few orders of magnitude. Regardless, the exact number is less important than the overall impression that many transistors surround us today.

[2] Specifically, the E. Coli was controlled by Isopropyl β-D-1-thiogalactopyranoside (IPTG) which is a molecular mimic of allolactose, a lactose metabolite. IPTG is used because, unlike allolactose, IPTG is not hydrolysable by β-galactosidase, so its concentration remains constant as it’s not broken down as readily.

[3] Okay, yes: DNA is made of nucleotides but copper is made of atoms and we have to stop somewhere. In our context today, it makes sense to stop at DNA, but in other contexts, such as DNA synthesis, DNA clearly isn’t the base unit.

[4] To say that cells are just “bags of chemicals” is a gross oversimplification analogous to calling our bodies just “skin with stuff inside”. Technically true, but not very descriptive. What I’m trying to get across here is that cells are (1) bound by a membrane, that they are (2) one system of transmitters and receivers and that (3) they have a limited rate at which they can absorb/deport things. This metaphor makes it easy to visualize these attributes, so I have chosen it in the spirit of Upaya (where something may not be ultimately “true” in the highest sense, but it may still be an expedient practice). For a more accurate representation of cells, check out this award winning book: Cells, Gels and the Engines of Life.

[5] Throughout this article, I use Promoter as a broad phrase, to refer to Repressors and Promoters for two reasons: simplicity and to avoid the constant use of promoters/repressors throughout the article, promoter is already a long enough word.

[6] Granted most, if not all of these promoters are only characterized for E. Coli. But, with E. Coli being the workhorse of synthetic biology, this usually isn’t an issue.

[7] By sustainable, I mean that the cell shouldn’t die from expressing the proteins that we need for our circuit. I, however, did not mean that the output would be sustainable over extended periods of time. As time progresses, our system will break down we’ll eventually get weak expression of all 3 proteins in our system. Oh well, that’s life in the city.

[8] I dislike the fact that I fast forwarded past this process. The process of getting DNA ready (not to mention preparing/designing the DNA) and coercing the cells to express your DNA is a whole ‘nother bucket of worms. Could easily be another article (or set of articles). (Wink wink)

Monoprice Mini Delta Review

For the last year or so, Monoprice has been teasing their follow-up to the fantastic $200 MP Select Mini. This is the $150 mini delta printer. We got a look at it last January at CES, it was on display at the Bay Area Maker Faire last May. Now there’s one on the Hackaday review desk.

Over the last few years, 3D printing has settled down into what most of us expected way back in 2010. No, not everyone wants, or arguably needs, a 3D printer on their desks. This is a far cry from the hype of a few years ago, leaving us with what we have today. 3D printers are just tools, much like a drill press or a laser cutter.

With that said, there still are some fantastic advances in 3D printing coming down from on high. Prusa will be shipping the 4-color multi-extruder add-on for the i3 Mk 2 shortly, and somehow or another we have infinite build volume printers. Still, there’s space to democratize 3D printing, and an opportunity for someone to release a very cheap, very good printer.

Monoprice was kind enough to send me a review unit of the MP Mini Delta before it officially hit their website. This is one of the first off the production line, alongside the few hundred pre ordered on an Indiegogo campaign earlier this year.  Does this printer live up to expectations? It sure does, and that’s not just because it’s a $150 printer.

This would be an excellent printer at three times the price, and evidence enough that 3D printing is changing from a weird hobbyist thing to a proper tool.

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Living on Mars: the Stuff You Never Thought About

In The Martian we saw what kind of hacking was needed to stay alive for a relatively short while on Mars, but what if you were trying to live there permanently? Mars’ hostile environment would affect your house, your transportation, even how you communicate. So here’s a fun thought experiment about how you’d live on Mars as part of a larger community.

Not Your Normal House

Mars One living units under regolith
Mars One living units under regolith, Source video

Radiation on Mars comes from solar particle events (SPE) and galactic cosmic radiation (GCR). Mars One, the organization planning one-way trips to Mars talks about covering their habitats in several meters of regolith, a fancy word for the miscellaneous rocky material covering the bedrock. Five meters provides the same protection as the Earth’s atmosphere — around 1,000 g/cm2 of shielding. A paper from the NASA Langley Research Center says that the largest reduction comes from the top 15 to 20 cm of regolith. And so our Mars house will have an underlying structure but the radiation protection will come from somewhere between 20 cm to a few meters of regolith. Effectively, people will be living underground.

On Earth, producing water and air for your house is not something you think of doing, let alone disposing of exhaled CO2. But Mars houses will need systems for this and more.

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Product Development and Avoiding Stock Problems

You’ve spent months developing your product, your Kickstarter just finished successfully, and now you’re ready to order all the parts. Unfortunately, your main component, an ATmega328P, is out of stock everywhere with a manufacturer lead time of 16 weeks. Now what?

When manufacturing things in large volumes, acquiring enough stock at the right time can be tricky. There can be seasonal shortages with companies trying to get products manufactured and available for Christmas. There can be natural disasters like floods of hard drive factories, or politically-related availability problems like tantalum for capacitors, or maybe new markets open up that increase demand or a new product sucks up all the available supply. The result is all the same; you have a harder time getting what you need. Fortunately, there are some ways to avoid this problem, or at least mitigate it.

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Hands On With The SHACamp 2017 Badge

The badge has become one of the defining features of a modern hacker camp, a wearable electronic device that serves as both event computer and platform for some mild software and hardware hacking. Some events have had astoundingly sophisticated badges while others are more simple affairs, and the phenomenon has even spawned an ecosystem of unofficial badges which have nothing to do with the event in question.

The SHACamp 2017 badge is the latest to come the way of a Hackaday writer, and certainly contains enough to be taken as representative of the state of hacker camp badges in 2017. It doesn’t have a star turn like CCCCamp 2015’s software defined radio, instead it’s an extremely handy little computer in its own right.

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