Ammon Hennacy: Questions and Answers

This post is a continuation of the "Heroes in Their Own Words" theme that started with a translation of the Zamenhof's Declaration of Homaranism. Basically what I'm doing is finding and posting texts in which people who I consider to be heroes briefly describe their core beliefs. Ammon Hennacy was a self-described "Christian Anarchist". He spent 18 months in solitary confinement for resisting the draft during WWI, and was arrested over 30 times for picketing and tax evasion. Like Zamenhof, Hennacy lived a life that demonstrated a high degree of moral courage. He lived a life consistent with his ideals, and constantly propagandized against war even when it was obvious that his propaganda was incapable of effecting any major changes in the world. For this post I transcribed chapter 19 of Hennacy's autobiography, "The Book of Ammon" (pdf link). The book appears to be self-published and contains no copyright notice, and it is almost certain that Hennacy would not object to my transcribing and posting it. The chapter, called "Questions and Answers," is basically an FAQ of Hennacy's opinions in the period from 1950 to 1964. I don't agree with all of Hennacy's positions, but I think they are all well worth reading and contemplating. There's nothing in the world as valuable as passionate people speaking on topics they're passionate about. What follows are not my words, but those of Hennacy (there are some spelling mistakes in the original that I have corrected without note, hopefully without introducing too many new ones at the same time):

Poetry as a force of destruction

This is an essay about the limitations of poetry and the potential for the poetic process to destroy the information it intends to preserve. I think the ideas could also be applied to other forms of art. I wrote it in January of 2011, and revised it just now. I don't think this is by any means the last word on this subject (it's barely even the first word), and I welcome discussion.

Hunting and eating the wild Ginkgo

There are a bunch of Ginkgo trees in various places around the WSU campus. When, staring up into one of them, I noticed that it was a fruit bearing female, I was pretty excited. Like with some other plants, there are male and female ginkgos. Most of the time people only plant male ginkgos for decorative purposes because the fruit produced by the females is kind of stinky and messy. However, inside the stinky fruit is a seed rumored to be delicious when cooked. I'd never tried one, and was eager to get the chance.

By a train window (a translation by me of an Esperanto poem by Julio Baghy)

I like translating stuff from Esperanto. Here's a translation  (followed by the original) of a poem that I encountered in the book "Vojaĝo en Esperanto Lando" edited by Boris Kolker, which is a collection of a wide range of different kinds of writings. I got bored with that book and quit about 2/3 of the way through, but I liked the poetry. This isn't quite a literal translation, but it's pretty close (for better or worse).

An improved tempe incubator and more lupin tempe

It's been a while since I've posted about cooking with lupins, making tempe, or the impending Dennis Moore memorial dinner. Rest assured, the lupin project is advancing at characteristic pace for a project of mine (that is, not very fast...) .In this post I discuss an improved heater setup for the incubation. Then I talk about making tempe from lupin grits, and whole california white sweet lupins. I've also figured out how to make lupin icecream, but I'll save talking about that for later this winter when I get a chance to make a big batch of it.

International Chemical Identifers (InChIs): You should use them!

One easy and increasingly common way to increase the make metabolite data more useful is to associate compounds with their corresponding InChI  International Chemical Identifier (InChI) (Heller et al., 2013). An InChI is a unique, standardized text representation of the structure of an organic molecule. Inclusion of InChIs in database records facilitates cross-referencing among databases. The InChI system has a number of advantages over other kinds of identifiers. Some chemical identifiers, such as PubChem IDs, Chemical Abstracts Service (CAS) numbers, and ChemSpider IDs, are database-specific accession numbers with no direct relation to the structure of the molecule they describe, this means that a molecule must have been indexed by one of these services to have an identifier. An InChI, by contrast, is a database-independent structure description, so it can be generated for a molecule regardless of whether the molecule has been indexed by a major database. An InChI can be generated for a novel natural product structure, whereas the other IDs cannot. InChI also has advantages over other linear text representations of molecule structure, such as SMILES. Unlike for SMILES, there is a single open source implementation of the InChI generation algorithm, so while a single structure may have multiple valid SMILES representations, it will only have one Standard InChI representation (Heller et al., 2013). A fixed length compressed version of an InChI, an InChIKey, can be generated from any InChI. InChIKeys are more compatible than InChIs with web search engines such as Google (google.com) (Southan, 2013), however, multiple distinct structure may have, and have been observed to have, the same InChIKey (http://www.chemconnector.com/2011/09/01/an-inchikey-collision-is-discovered-and-not-based-on-stereochemistry/), so InChIKeys should not be used as a basis for cross-referencing. When unambiguous identification of a molecule is the priority, InChI should be preferred. When ease of indexing and searchability is the priority, InChIKey should be preferred. When possible, both identifiers should be listed. By listing InChIs and InChIKeys in websites, databases, and publications (Coles et al., 2005), chemists can enhance the ability of their data to be indexed, searched, and cross-referenced. Free and easy to use software for generating InChIs and InChIKeys are the InChI software available from the InChI Trust (http://www.inchi-trust.org), and MolConverter available from ChemAxon (http://www.chemaxon.com).

Of course, even with the use of InChIs, inconsistencies can still arise in cross referencing. Galgonek and Vondrášek provide an excellent (and Open Access) analysis of the kinds of inconsistencies that can arise, and their sources.

I originally wrote this as part of a draft of the manuscript that eventually became this review article. It's a bit out of the scope of that article, so we dropped it. But I posted it here because I still think it's a good analysis.

References:
Heller et al. 2013 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599061/
Coles et al. 2005 http://www.ncbi.nlm.nih.gov/pubmed/15889163
Southan 2013 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598674/ 

What kinds of problems can (mathematical) models (of biochemical systems) solve?

I think the useful applications of computer modeling to biochemistry are in the following kind of situation: You have identified a phenotype of interest, you want to know what the molecular basis is for that phenotype, you know the form of the hypothesis (“a change in the concentration of substance X causes decreased activity of enzyme Y”), but there are too many possible instantiations of the hypothesis to test all of them experimentally (there may be 100 possibilities for “substance X” and 1000 possibilities for “enzyme Y”, giving 100,000 possible hypotheses). If you have some idea of how the system works, enough to make some kind of mathematical model of the system, and some experimental data (for example omics data comparing the condition displaying the phenotype to the condition not displaying the phenotype), you can use the computer to answer questions like: What instantiations of my hypothesis are most likely to be true, based on this dataset (or based on all available datasets)?