The Transfer Problem

There is a dramatic difference between full automation and partial automation. When I was automating protocols with the OT2 robots, I quickly realized that I could only manage a few robots at a time (in my case, 3 robots). There was actually a lot of work adjacent to my protocols that I did not realize really existed: labeling plates took a long time, sealing plates took even longer, and loading/unloading pipette tips took more time than I thought it would.

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The Seqhash Algorithm

What is Seqhash? There is a big problem with current sequence databases - they all use different identifiers and accession numbers. This means cross-referencing databases is a complicated exercise, especially as the quantity of databases increases, or if you need to compare “wild” DNA sequences. Seqhash is a simple algorithm to produce consistent identifiers for any genetic sequence. The basic premise of the Seqhash algorithm is to hash sequences with the hash being a robust cross-database identifier.

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Plants, Progress, and Production

Humanity has a core dependency, one that we have never been able to shake ourselves from: Plants. I don’t need to go over their importance, because I’m assuming humans are reading this, and you have probably eaten the product of a plant today. From the dawn of our civilization, we’ve been entirely dependent on these organisms to produce what is necessary to sustain us. Agriculture is what allows humans to prosper today, even if it is so removed from our daily lives that it is invisible.

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DNA assembly is not obsolete

When I talk about my dream of building the best DNA assembly system ever created, the most common response is to ask “won’t that be obsolete once DNA synthesis gets good enough?” It is a fair question, but I also think it is rather lazy if you try to think about the relationship of DNA synthesis to DNA assembly. Those 2 do not directly compete with each other - DNA assembly is important and will continue to be important for a couple of reasons.

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Liberty through Innovation

“Liberty through innovation and innovation through liberty” Lately, I thought of this statement as a concise way to summarize my beliefs. Basically, I believe that innovation and technological progress is an enabler of liberty. Throughout time, ownership of the means of production has been synonymous for freedom. If you have the means to provide for yourself, you can’t be oppressed by any mechanism except explicit force - if you have a terrible boss/leader, you can simply leave your job/country.

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Approximately Engineers

The entire field of biological “engineering” is built on a pretty self-delusional (though useful) foundation - that we can engineer biological systems. For the most part, we can’t do reliable genetic engineering, but instead we do what I like to call “approximate engineering”. While engineering is built off of a premise of reliable parts that can be composed to achieve a goal, approximate engineering is built off of a premise of there being a combination of parts that can achieve a goal.

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Plasmids per Person per Year

There is something deceptive about many metrics in biotechnology. Everyone’s favorite little graph is the plot of DNA synthesis and DNA sequencing costs dropping faster than Moore’s law, which to everyone is source of great excitement! How things have improved! However, those advancements are both unevenly distributed and may be partially explained by alternative statistics. For example, let’s consider if we wanted to measure if the average productivity has increased of a bioengineer has increased.

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The Computer Lab

There is a core concept in the land of silicon that is especially interesting when applied to biology: the idea of a generic processor. While you can have chips that are good specifically for a single task, you also have processors which execute a small number of different commands that can be chained together in arbitrary ways. These generic processors allowed for programmable computers to become widespread and commonplace. Right now, biology labs are very much like chips.

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The Sporenet Protocol

If we look back on the emergence and rise of the internet, there was and still is a fundamental conflict: Information is valuable, and information wants to be free. Education is the great equalizer, and the internet has enabled people without access to traditional educational systems to educate themselves. In biotechnology, this idea still applies, but in a slightly different way. The Human Genome Project can easily be summed up in 6 words - “Bought the book; hard to read” (Eric Lander).

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How to make DNA affordable

Everyone should have the opportunity to make beautiful things with biology, and that means we need to get better at giving people the opportunity to work with DNA tools. There are two methods that are typically used to get interesting DNA right now: people email their buddies, or they get the DNA from plasmid repositories. Those plasmid repositories have a big problem: they are exclusive to academics, both in property rights and in price.

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Liberate DNA

Information is power. But like all power, there are those who want to keep it for themselves. The academic-industrial system of biotechnology wants you to believe that giving access to genetic material to normal people would be dangerous. Physical genetic information is being locked up, for safety, for the exclusive use and benefit of the powerful. We are in beginning of a culture conflict within the discipline of bioengineering. Synthetic DNA is freeing people from the monopoly of material lineages that universities and companies once had.

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