For the last year, I've been self-learning synthetic biology by working to become one of the few people to have ever genetically modified fungi in a diy lab environment[1][2][3]. It occurred to me that genetic engineering is largely a process of hacking biosynthetic pathways; that is, we take heterologous genes from organisms which have evolved novel biochemical pathways and we put them into other organisms that are really good at biosynthesizing those compounds at-scale (like Saccharomyces cerevisiae aka yeast).<p>One thing I've observed is there seems to be no universal well-annotated structured database for biosynthetic pathways. Updates and additions to known pathways are published unstructured in papers, often in graphical form, presenting even more challenging for structuring the data.<p>Were this to exist, it would be possible to build an app that let you easily design DNA plasmids for testing all kinds of incredible biosynthesis experiments. For instance, it would be able to select an organism [E. coli], enter your starting substrate [glucose], select a desired metabolite [psilocybin] and out would come a DNA sequence for a plasmid that contains are the necessary parts, promoters, genes and terminators for transforming E. coli to produce psilocybin.<p>In my opinion, such a tool could profoundly impact science, industry and human well-being.<p>[1] <a href="http://everymanbio.com/" rel="nofollow">http://everymanbio.com/</a><p>[2] <a href="https://www.instagram.com/everymanbio/" rel="nofollow">https://www.instagram.com/everymanbio/</a><p>[3] <a href="https://youtube.com/everymanbio" rel="nofollow">https://youtube.com/everymanbio</a>
People sometimes ask me how come a biologist might end up programming (or vice versa).<p>Showing them a map like this tends to clear things up pretty quickly!
These maps are fun and fascinating, but can be misleading for the supplement enthusiasts.<p>In many cases you can trace pathways upstream until arriving at a supplement or nutrient that can be bought online. People erroneously assume that consuming that nutrient will achieve some downstream effects in certain pathways because all of the arrows connect. It's not that simple, though. For the most part our bodies are excellent at absorbing the nutrients we need and regulating everything as appropriate.
i had this poster on my wall (actually, the predecessor, which you could order for free by physical mail) my entire sophomore year while taking biochemistry. I used to joke to people that by the end, I would have memorized most of it, and that did actually turn out to be true. Even today, some 28 years later, I remember the hexose mannophoshate shunt.
Related discussion from about 6 months back (including where to find the PDF version).<p><a href="https://news.ycombinator.com/item?id=25158249" rel="nofollow">https://news.ycombinator.com/item?id=25158249</a>
Beautiful! And complex from start to finish.<p>I wonder what formalisms/representations are there to manage the complexity of metabolic pathways. For example, say that that figure is 100% accurate, and furthermore, "all metadata needed" in terms of reaction rates, etc. for each individual reaction is available. If one wants to stage an intervention (say, suppress the production of compound X without altering anything else significantly), what kind of program would be able to find a solution?
It’s cool to see this on HN. It’s a common activity in metabolic modeling & metabolic engineering circles to build new pathway visualization tools (I spent a chunk of my PhD on one called “Escher”). I keep waiting for a tool to come along that’s good enough to be sticky and win this little market. But it might be more like IDEs, where there are some classics (pathway tools = emacs?), and an endless supply of new entrants.
My friend who studied biochemistry in Turku University once had this kind of poster on his wall, but it had all the pathways overlaid on a human body. When I first saw it, I studied it for the better part of an hour.<p>I have been trying to find an image of this poster without success. The detail level was like on these Roche posters, but the style was more like in these:<p><a href="https://www.tocris.com/literature/life-science-posters" rel="nofollow">https://www.tocris.com/literature/life-science-posters</a>
I love these posters! I had them on my bedroom wall as a teenager. (I had very little idea about most of what it is describing, but I thought it looked cool and hey, it’s free!)
It’s amazing how these things happen in the volume of a cubic micrometer. There is however a big misleading element; Not all of these pathways operate in the same cell and not all of them are equally strong - the arrows are not of equal “thickness” if you like. That’s the big problem in molecular biology and biochemistry: all these arrows are always depicted as of equal strength.
On the commercial side of this is Elsevier Pathway studio [1]<p>[1] <a href="https://www.elsevier.com/solutions/pathway-studio-biological-research" rel="nofollow">https://www.elsevier.com/solutions/pathway-studio-biological...</a>
I remember reading someone doing the math on these and finding that statistics-wise, it was essentially impossible for these metabolic pathways to have evolved through randomness given the age of our planet.