2006-08-15

Visible science


Way back when, when I had the privilege of being taught medical engineering by leading physicians at various Stockholm hospitals, one of the things you would find in all medical research departments was a huge wall chart titled “Biochemical Pathways”. This showed the chemical interactions in living organisms (primarily humans, I assumed).

You may remember the Prime Radiant displaying the Seldon Plan in such a way that the equations themselves formed a visible representation of the plan, where it was heading, the deviations from the intended path and the corrections performed. This was much the impression I got of “Biochemical Pathways”.

I was proud and humbled by the effort that had gone into finding all this out, especially when I found the Citrate Cycle, that I had spent so much effort to learn and, superficially, understand, as a small area slightly right of centre, towards the bottom. I was also excited by the knowledge that this was work in progress, every year more information about biochemistry would be found out, adding to what was already there, making the map ever more complex. And in particular that this knowledge was there as a physical map you could look at and study, rather than just an abstract collection of research papers. (Not that I then fully understood the concept of research papers, but I did vaguely realise that research was somehow created and collected.)

I don't know if this wall chart actually was updated regularly and made available in new editions, or if it was a one-shot effort made at some specific time, but I've later found it was created by Roche Applied Science and, as far as I can tell, it is now long out of print. Maybe the sum total of our knowledge of biochemical pathways has grown so much that it no longer can be contained on a wall chart that will fit on the wall of a hospital research department.

It was thus with nostalgic joy I found that ExPASy have scanned the entire chart and put it online. Not only that, they have made all the enzymes clickable so that you can look them up in their ENZYME Data Bank to get references to papers referring to that enzyme, alternate designations, where it is expressed and other things I know too little of.

Probably ExPASy will not update the underlying graphics and network, but, oh, how I wish they or someone else would. Imagine putting that on a really big tiled display. And imagine that every new biochemistry Ph.D. would get to add their contribution to science to the Prime Radiant, so that they and others can see what they have done, and its relation to the vast expanse of what others have done before them.

2 comments:

Anonymous said...

I loved that chart. In college, I sent away for a copy from Boehringer Mannheim, which is now part of Roche, apparently. I had it mounted, and it graced my walls for many years. I don't know when or how I gave it up. I followed your link to the Roche website, and found the chart listed among printed materials available, and sent for one. I tried to include the link, but it was not allowed. https://www.roche-applied-science.com/techresources/publications_req.jsp Maybe this is what you did, and they'll tell me it's out of print, too. Thanks for pointing me to the exPASy site...though it's not quite the same

Andrew said...

Brilliant. I remember this from the BioChem labs at uni.

This would work well in some kind of "google maps" type interface. You could explore it at will.