It’s been a while since I was here. I was socially overwhelmed and something had to go. I could see places where I was crossing boundaries where it should have been obvious, as well as other signs of being overloaded. It’s useful to talk about though, and this post is for some of that as well as what I need to write about next.

I’ve become totally open about mental health and mental illness issues and their connection to me, and most of my anxiety involves how I might affect others. When I was last here I was coming out of a period of general anxiety induced unemployment and started some serious therapy work. High school teacher, and substitute teacher to make money, were poor choices and I got general anxiety out of it. I’m not ready to write about that yet, it’s not that I don’t want to, but it’s more like I’ve got other thoughts that would be more useful to constructively express.

I started mopping floors so that I would have the mental downtime to start functionally working on changes. It’s been useful with respect to learning more about myself. I’ve actually been depressed since graduate school a little over a decade ago and at the time I didn’t recognize it creeping on. The substitute teacher stuff layered a different trauma onto that. And then there’s the social avoidance since early childhood.

And there’s more. Little objectified pieces of myself that I’m learning to lock into place. Someone should have shown me how to do this mental work when I was a child, but I come from a very ignorant and incompetent culture. A white conservative protestant american military culture that didn’t know what to do with a social sensitive in general.

But my culture did have ideas about what to do with social aggression. One thing I did since my last post was to keep up the political aggression as much as I could for practice. I need control over all the bits related to my aggressive instincts. Culture and basic sensation like fear, anger and disgust. Overtly expressed, repeatedly when useful and possible. Practicing using strong negative feeling words when relevant and necessary. Ignorant, incompetent, irrational, illogical, bigoted, sexist, misogynist, racist, homophobe, transphobe…the more you practice using them the better you get.

Today I go to maybe 10-15 facebook posts a week. Posts that attract negative, often hostile attention. In retrospect it feels like I’ve been creating political dispositions, social attitudes towards behavior. I feel like I’ve tried to make my personality activist, concerned with changing basic social behavior around me in some fashion. And just a little while ago I found something that feels like it’s always been a part of my personality. Social gadfly. On that note posts no longer require pre-approval, I’ll get some rules posted on an actual rules page as problems manifest.

In addition to restarting blogging I’m trying to get back into academic research. I never lost my dream of working in a laboratory doing origin of life research. I think I stand a better chance of figuring out how I need to organize myself and assert my differences when needed. Unfortunately there are complications involving my diagnoses. My social senses are skewed in a way that I’m still figuring out. I have some sources of advice and eventually I’ll put something up here.

Before I do that though, have you ever had something in your mind that you just had to get out to make room for other things related to the thing? I’ve got one of those related to origin of life research and the reading and more I’ve been doing and I think if I get it out it will help me out in several areas.

While I mopped floors I refreshed my memory and memorized metabolic pathways by drawing them over and over. That’s a useful way to internalize information. I mean sustained motor and visual activity feels like it enhanced my ability to work with what I’m memorizing. And I think there’s this whole other aspect where when you mash as much information as possible into your visual field it helps in creative thinking. Let me give you an example of a drawing where I’m trying to find connections related to the origin of the molecules that make genomes and ribosomes.

I’ll do a little explaining but the majority later.

A PRPP centered view of metabolism.
Center left to center right: Purine (A, G bases) biosynthesis starting from Phospho-Ribo-Pyro-Phosphate as phosphate bound reaction intermeadiates from individual enzymatic reactions, and splitting at the end into ATP and GTP.
Top center: other metabolites that use PRPP. in their biosynthesis, the UCT bases, two amino acids, and an H+, e- dispenser. They attach at carbon 1.
Bottom center: columns that represent attachment points for amino acids in tRNA. Class 1 (carbon 2) and Class 2 (carbon 3) amino acyl transferases. I also included each amino acids codons in the genetic code.
Bottom right: the urea cycle focusing on a two step -NH2 addition by aspartate addition and fumerate ejection. There are two of these “2 step aspartate aminations” going from just before precursor IMP to AMP.
Left: the functional interactions of ribose through carbon 5 relative to AGCU metabolism wide. All donate phosphate to drive protein chemistry, but in different domains. A: cofactors (tools for proteins), G: U: carbohydrate trafficking, C: glycerophospholipid trafficking.

As an example of how far I’m going to find information to integrate, that center row going left to right consists of reaction intermeadiates that don’t leave the protein. The image below are the reactants and products placed between the proteins for the pathway producing Purines (DNA/RNA bases A and G). Places where there is a split (PurN vs. PurT) are where bacteria, archaea, and/or eukarya have differences.

From Structural biology of the purine biosynthetic pathway: this paper shows the biosynthetic pathway for the precursor to the A and G bases, Inosine Monophosphate. From IMP the molecule can be turned into AMP or GMP.

And I can still think of things I can add to that drawing, as well as making it look better. The 2 carbon is where a Dehydroxy ribonucleic acid is made. The 3 carbon to 5 carbon are the end points for polymerization. The 3 carbon is where a metabolic distinction is made between anabolic (building) and catabolic (dismantling) H+/e- addition and subtraction through the addition of a phosphate for anabolic NADP…

So my next several posts will be about patterns in abiogenesis research because it’s going to help me make room in my mind. I’ll do the best I can to make it general interest but I’m still getting a feel for the audience so I’ll probably be somewhat disorganized somewhere. I’m happy to answer questions and explain things differently in comments.

And now I’ve got this thing in my mind that I want to organize. The pathway suggests how it evolved and what our pre-cellular ancestors might be like. I think I can see metabolic modules coming with each purine or pyrimidine base. Carbohydrate organization with U, membrane organization with C, organizing sets of molecular tools called organic molecule cofactors with G and A that dispense molecules and organize synthesis.

One more drawing. This image transformed from a linear presentation of physical data of the earth focusing on it’s first billion or so years, to information about LUCA, to maybe hadean crust data, to something about archaea monolayer membranes I wanted to memorize in comparison with the bilayer membranes.

And finally I want to leave something related to political conflicts despite my misgivings. I’ll end this with something I think of as “strangling them in the social contract”. Technical language means something and I think that fixing society will require people overtly critisizing others using technical language badly.

I’m tired of seeing people abuse mental health and mental illness language. Technical terms they haven’t the competence to use, but use anyway. Often in politics. So I’ve decided to interrogate the use of mental health language and science and medical language more broadly. People blaming shootings on “mental illness”. People dismissing rape accusations because of “mental illness”. There’s so many. Even the insults “idiot”, “stupid”, “moron” and the like are in the general territory though I challenge those a bit differently. Most recently it’s people who seem upset that transgender isn’t a disorder anymore.

For people who appear to be politically abusing such language I put varying levels of pressure to demonstrate that they are using the language competently. For the people upset with transgender not being a disorder anymore I demand they define the disorder they think applies and they have to use the same professional guidelines. Otherwise casually diagnosing people is rude at best. For the word disorder I demand something like:

  1. The name and type of disorder.
  2. The specific diagnostic criteria.
  3. Actual quoted or videotaped examples of the behavior in question that are rationally and logically tied to number 2 and any specific political points and claims they are making.

Now this runs some risks (and if anyone sees any I don’t please speak up) but I think they are manageable and we want a society more competent at these things. One risk is giving a bigot a platform to display disgusting views but as long as they keep showing any lack of objective criteria for attaching medical terms you can do a lot of things to take advantage of and point out their incompetence. It’s a respect to society to make sure people use these words right. I’m sure there are other risks and if any occur to me I’ll point them out in the comments.

And you can call people out and have them explain in technical terms of you don’t know what they mean. You can write it down and see for yourself. Anyone who actually cares about a political issue would want to give you something you can look up on your own. It’s their connections, they should be giving you ways find out for yourself. This goes for legitimate professionals too. You should learn to explain yourself to the people around you. It’s a skill.