Guides

What Will Your IndieBB Be?

IndieBB stands for “Indie Biotech Backbone”. When I started this blog, I had intended “Indie Biotech” to be a phrase that could be generally used, not a “trademark” for my own work, yet people sometimes still refer to my project/company as “Indie Biotech” (I do have a company for this, and it’s called “Glowbiotics”, not “Indie Biotech”!). With the same spirit in mind, I named my plasmid backbone “Indie Biotech Backbone” because I wanted it to be something that could be used by “indie” genetic engineers worldwide to make their own stuff.

Codon Optimisation: A Hidden Process Behind IndieBB

I’ve posted twice recently after a prolonged blogging absence, and here I am again. Perhaps I should always be running a crowdfunding campaign, so that I have a stake in blogging; I’d be far more prolific! I’m too principled (or, to some “dogmatic”) to include advertisement on this or any blog, and flattr revenue is far too thin to encourage more than the occasional post otherwise. In any case, today I’d like to share something with you all that I’ve been meaning to write up for ages anyway, but which becomes especially relevant in light of my IndieBB DIYbio/Biohacking/Teaching plasmid design project.

A Primer on Plasmid Design (For IndieBB)

So, in the preceding blogpost I introduced my current crowdfunding project, IndieBB: ..If you navigate to the “updates” panel on that crowdfunding page, I’ve been busy keeping things current. Among the promises I’ve made lately was to run through my workflow for total-plasmid-design as I plan to apply to IndieBB. So, here we go. Before clicking “more”, be aware that you do not need to understand any of the below to complete the IndieBB kit.

Performing Minipreps with Homebrew Buffers

The alkaline-lysis miniprep is a critical tool in the arsenal of a molecular biologist. It allows one to rapidly isolate only plasmid DNA from a bacterial cell by leveraging the increased resilience of this (usually supercoiled) form of DNA against highly basic conditions. Minipreps are routinely performed to isolate plasmids that serve as substrates for further assembly work, for PCR amplification of specific gene segments, for direct application in other species or strains, or simply for archival uses (DNA can be easier and cheaper to store than the cells containing it).

The Shortlist of Free-Speech Software For Our Newly Censored Ireland

So, our great and glorious Minister Sean Sherlock just signed SOPA into law in Ireland, despite a huge civil outcry. The poorly defined statutory instrument will allow anyone claiming “Copyright Infringement” to seek a court injunction against any website, without having to present evidence and without a consultation with the accused website. The form of the resulting censorship is unclear, but will probably require ISP-level DNS censorship of websites outside Ireland, or direct seizing of those within the Irish jurisdiction.

DIY Biosynthesis of Insulin and Thyroxine - Disaster Resilience and Personal Biotech

A twitter acquaintance asked me today about DIY thyroxine. As this acquaintance is a “collapsonomics” nerd, I took this question to be in the context of “what if the world’s supply chains freeze and I/we/my friends die?”. The question broadened to include insulin, another critical drug needed daily by those with a common condition, diabetes. That’s a fair question. After all, while one can grow food locally, and purify rainwater (when blessed by rainfall like we are in most of Europe), and tend to many other necessities of life locally in a total infrastructural breakdown scenario, pharmaceuticals are one of the few things that we can’t DIY easily.

Negligence and Coming-Soons

I’m a serial blog-abandoner, but I’m generally good for eventually returning to them and reviving them again for a while. Consider this an update since the last post, in which time much has happened and more is expected soon. Workshops The science gallery workshops went great, as far as I’m concerned. The (regrettably few) participants were great fun to work with, and I learned a lot about the unique requirements of a mobile or temporary lab.

Isolation and Culture of Bioluminescent Bacteria

Update: Keep your bacteria in the dark. I had been doing this without meaning to, and was confused to hear a fellow microbiologist growing a derivative of my cultures in her lab and getting no glow. When she grew them in the dark, they glowed again! Brief exposures have no effect. It’s the prevailing light conditions that seem to decide whether to stay active. This may be due to the light breaking down the little peptide the bacteria use to detect whether there are enough of them to glow meaningfully, or it might be a deliberate evolutionary adaptation.

Homebrew Bacterial Media for the Microbiology Hobbyist or DIYbio Enthusiast

Update: The links to these files have always been precarious, sorry.. I’ve just re-uploaded the two main files, and soon I’ll be reworking them into my “biohacking protocols” repository on Github in Markdown format with separate images. Enjoy! Life is, as ever these days, quite busy! I have two trips coming up, one to Ignite in Dublin and one to the Newcastle Maker Faire (where Brian Degger of Transitlab.org and I will be hosting a little workshop on a few DIYbio experiments and fun stuff).

Internet Security: Chapter 1

Well, I promised a post on Privacy and Security online, and it’s been long in coming. I’ll admit that’s because for all that I’d love to waffle on ad infinitum, I haven’t done enough research to know that everything I’m saying is up-to-date. So, to strike a nice middle ground I’ll split the post instead. In this installment, rather than offering “active” advice (such as what to install and how to browse), I’ll offer the groundwork and the basics of how to “passively” be more secure online and how to preserve your security.

Digital Privacy: An Upcoming How-To

I have a personal interest in my privacy both online and in the physical world. There’s no real reason behind it besides a knowledge that it is my right not to have my privacy invaded, and a feeling of insult that it is invaded anyway on probably a daily basis. Sources of this invasion include my ISP, Marketing Widgets on the internet, Possibly the odd hacker and the NSA, who are doubtless running programs that scan my email and monitor browsing statistics to identify them terrur-wrists at work on the internet.