James B. Hanks

My life and why I think about what I think about

Family, early life, and primary education

I was born on the Upper West Side of Manhattan in 1981. My father was born and raised in Beaumont, Texas and my mother in Pittsburgh. They both moved to NYC in the early '60s and lived on the Upper West Side for almost all of that time.

My mother came to NYC to continue ballet studies that she had started at a young age. After an injury ended her ballet career, she did varied work related to fashion design and crafts in 1960's-70s NYC. In the '80s, she managed an artist collective gallery called Show of Hands on the Upper West Side.

My father was an accomplished tuba player who played and taught for many years before being forced into retirement from performance by a neuromuscular disorder called focal dystonia.

My father’s work brought our family to Chautauqua, NY for every summer of my youth. That county and the cultural institute it hosts will always have a special place in my heart.

I did not grow up in a particularly technology-oriented household. We did not own a TV until I was five years old, and that was a 5" black and white one, good enough to enjoy Sesame Street and Mr. Rogers. In the early 90's We got color TV, a VCR and cable. I think not having a TV in the house for my first years was a good choice on the part of my parents. I do not recall ever being bored.

My very first computing experiences (not counting Nintendo at friends houses) were at the local public library and at school. Carmen Sandiego, Oregon Trail, and all that.

The first computer in our house was a used Commodore 128 inherited from my cousin via my uncle. Actually, it was a Commodore 64 upgraded to a 128. That’s 64 and 128 Kb of RAM for those who don't remember. This was probably 1990. It came with a dot-matrix printer which made a nails-on-chalkboard sound that is forever burned into my mind. The 5.25” disk drive sounded like a woodpecker when it was reading.

I got my first up-to-date computer for Christmas, 1992. Technically, that Christmas Day I got a tree ornament of a computer and a couple issues of Macworld. But it represented the fact that I would be getting a computer. My mother (who had never touched a computer prior to this) had done some research and talked to my uncle (same uncle as gave me the Commodore). She knew that CD-ROM was going to be important and that we should get it. She wasn’t sure if we should get a PowerPC or not given that software was going to need to be re-released, and I was in no mood to wait.

It was a magical, hopeful time. I had enough awareness of world events at the age of eleven to know that momentous things were happening in the world. I sensed that there was both promise and danger in this technological post-Cold War world that I was about to grow up into.

On my first day with the new computer, I had a lot of fun messing around with the drawing and painting modules of ClarisWorks (precursor to AppleWorks, precursor to iWork) and fell in love with color gradients. Soon after, I got a demo of Infini-D, which sparked an interest in 3D rendering. My shop teacher Leo, an incredibly cool and knowledgeable guy, helped me a lot with my early interest in computer graphics.

When I first started playing with 3D, it was on the Performa, which meant a 68030 CPU and no floating point unit (FPU). Without an FPU it was so slow that it didn’t matter that the demo limited me to rendering at 320x240, It would take overnight to render a very simple scene. Adding in an FPU helped a lot. I loved rendering shiny balls and cones arranged on variously textured planes. A little later I convinced my parents to buy me KPT Bryce, and had even more fun with that.

In hindsight, I did not use this time as productively as I wish I had. I was really obsessed with Star Wars, and I engaged in a lot of fantasizing that limited my vision for what I could do with what was in front of me. For example I spent countless hours using Macromedia Director. But instead of doing something more creative, I made reproductions of the Death Star trench scene using cutouts from still images. Sure, I learned about keyframing and various other concepts, but I still feel that I stunted myself. Monomania is not necessarily harmful, but it can be very limiting.

My first programming experience was at school on their Macintosh LC-IIIs, in sixth grade if I am not mistaken. We learned LOGO, moving the "turtle" around the screen. I didn't see why anyone would bother with something like that. I was into graphics, but it was all a little too abstract for me. I couldn’t see how I could use it to do anything cool except draw obscene shapes or words and neither could my classmates. I love that school for the humanities education I got there, but technology was unfortunately not its strong point. They had their most competent computer person teaching shop and not administering their computers.

In retrospect, I realize that a fear of the command line held me back. It seemed reasonable at the time, everyone agreed that DOS was a piece of shit and GUIs were the future. And I was mostly into graphics, so Apple was the default choice. There was no compelling reason for me to do anything that I couldn’t do with a GUI. I knew there was also this UNIX thing that ran on machines that cost $10,000. I dreamed that perhaps someday I would own an SGI workstation and do 3D for the upcoming Star Wars movies.

I am grateful to have grown up on the Upper West Side and that my parents did not move us to the suburbs as they briefly contemplated. The high concentration of museums in Manhattan greatly enriched my childhood.

My primary education began at Manhattan Country School (MCS) when I was five years old. From that early age art and science both attracted me, and my environment fed those interests. I attended MCS until 8th grade, after which I attended Bronx High School of Science. MCS taught me solid values, good writing, and clear thinking. Bronx Science taught me about the world in the company of some incredible characters. As much as I loved New York City and the Northeast in general, when I finished high school I knew I needed a change of scenery.


I started college at Arizona State University in 2000. As an incoming freshman I intended to major in something related to computer graphics or multimedia. A lot of my art had what might colloquially be called “shamanic” themes, and I wanted to go deeper into my attraction to such things. This led me to take courses in anthropology and psychology, which both captured my imagination. However, I was bothered by the disconnect between these two disciplines.

I first dabbled with the command line in college because of OSX. Although I did not use it often I got used to using it on occasion to install things. If I recall correctly, my very first use was to install SuperShape and GNUPlot.

This was around the time when my studies shifted to science, putting art on the back burner (and thus many of the things I would have used coding for). I knew that there were cool things I could do if I could get good at the command line or learn programming. But at that point my studies focused on the wet lab as my focus on behavior neuroscience intensified.

The incompatibility of knowledge between disciplines only bothered me more the older I got. In my opinion psychology and psychiatry do not do enough to take culture into account. But anthropology often shies away from biological explanations of human behavior which I believe are critical to understanding humans. These are both problematic tendencies which I hope will be resolved in the future. I cannot say I am optimistic in the short term.

Although the scenery was stunning and the learning opportunities at ASU were amazing, I needed to get out of Arizona. The culture was difficult for me to adapt to, and even the constantly sunny weather got on my nerves. When I got back for my first summer vacation I reveled in a grey and rainy summer. The lesson from that was that I prefer variety in weather.

The events of 9/11 were also part of my desire to go back east. I wanted to be closer to my parents, and comparing the responses to the attacks by people in Arizona vs New York made me love my hometown all the more. I applied and was accepted to SUNY-Albany.

After I transferred to SUNY-Albany as an anthropology major, I added a psychology major. I knew that my main interest was neuroscience and found all aspects of psychology were fascinating, but I still loved anthropology. I tried to bring them together in an independent research course. This was a very enlightening experience, but not quite in the way I hoped. I came away highly doubtful (even scornful) of some of the theories which had at first appealed to me the most. While at SUNY-Albany I also took a part time job in a neurobiology lab, using NIH Image software to measure synaptic junctions in flies exposed to lead.

My first "independent" laboratory research project was for an honors thesis at SUNY Albany in a behavioral neuroscience lab that studied neurosteroids. My project was intended to study the effects on anxiety-like behavior of the testosterone metabolite and GABA-A receptor allosteric modulator 3-α-androstanediol. Unfortunately, as I did my write-up, disagreements arose about how to describe the methods used. Under a new arrangement, a different professor evaluated my thesis and I was able to write it in a way that I felt good about. Although the situation was resolved to my satisfaction, it made me shy about explaining my lab experience to prospective employers.

I completed my degree in 2004 with a double major in anthropology and psychology. Although my grades from college were good, I found it difficult to find a science job. I doubt most professors would take kindly to a student going over their head with the department, so I was hesitant to ask for letters of recommendation from the professor who oversaw my laboratory research. On the other hand, I worried that recommendations from people who had not personally overseen me in a wet lab would carry less weight.

Post-College and Graduate School

During the first couple of years after college, I lived with my parents and made money by street vending my art. I had a table display that I set up around NYC. I sold what I call "leaf lamps". These are back-lit collages made from preserved leaves. I had the idea one autumn day in Albany's Washington Park. I was struck by the beauty of the leaves back-lit by the sun, and I wanted to have that beauty in my room, so I started scheming about how. I still sometimes make them as gifts.

After a couple of years, I found my way to a job as a technician in the lab of Jay Gingrich at Columbia University.

The Gingrich lab uses behavioral pharmacology and genetics to study schizophrenia (the focus of my work there) and other psychiatric disorders. The projects I worked on focused on the mechanisms of action of hallucinogenic drugs at serotonin 5-HT2A receptors.

The countless hours I spent running mice and analyzing the behavioral data were the best professional experience of my life. This is in no small part because of my wonderful coworkers.

The discussions I had with my labmates were among the finest I have had in my life. It was an intellectually open environment and I never felt afraid of disagreeing with my supervisors. This was by far my best experience in the science world.

When I got an Intel Mac in 2008, it became practical for me to use more than one OS. I ran Windows and Ubuntu in Vmware Fusion, as dual-booting always seemed clunky to me. When it came time for my next computer however, I decided not to get a Mac. After having used several generations of Macs (030, 604e, G4, Nahelem), I’d had enough of Apple's overly expensive and specialized hardware. I built what was meant to be a hackintosh, but I ended up deciding that Windows 7 was good enough. Like with my previous computer, I kept Ubuntu running in a virtual machine and used it occasionally. Over time however, Windows began to annoy me. It became clear to me that I prefer the controllable annoyances of Linux the the arbitrarily imposed annoyances of Apple and Microsoft.

In 2010, I began a Ph.D. program in neuroscience at Mount Sinai School of Medicine (now Icahn School of Medicine at Mount Sinai). Graduate school was a difficult experience for me, but I was involved in some truly cutting-edge research and learned a lot. In the seven years I spent there, I went through three three advisors. Most of the advisors I chose at Sinai did not have the same tolerance for devil’s advocacy that I had become accustomed to in the Gingrich lab. I don’t think Sinai (now Icahn School of Medicine) is a bad institution, but I did make poor choices about where to put my energy and did not get the support I believe I should have gotten. In retrospect, I believe that I could have done much better had I advocated for myself more effectively.

The first lab I settled down in after lab rotations was in a lab studying the neurobiology of schizophrenia. There I conducted research with both mouse behavior and cell culture models, as well as overseeing two high school students. My work there focused on investigating the mechanisms of action of current and prospective antipsychotic drugs.

I was excited about my project but had trouble replicating a finding which was central to the rationale of my project. This became a problem when in a thesis committee meeting, I stated that I did not think the assumptions on which my project was based were as solid as I had initially understood. This was my unavoidable conclusion after looking at the raw data from the experiment that was previously published by the lab. The sample size apparently had been doubled by running the same mice twice, which was not stated in the published paper and was not made clear to me when I was taking on the project.

After that committee meeting, everyone decided it was best if I find a new lab. In hindsight I probably should have filed a formal complaint, as it would have given me a basis to argue that my lost years be given back. At the time though I felt I had done my duty by stating my observations in front of my committee.

The next lab I went to studied autism both in humans and using genetic models in mice and rats. I had a very interesting project looking at the role of vasopressin in social behavior in mice.

Unfortunately, it proved to be a problem that this project required direct injection of vasopressin into the cerebral ventricles. I was unable to implant cannulae into brains of mice without killing most of the them, even after much training and practice. This led me to wonder about my physical fitness for the work. In the past, I had been handling the behavior side of experiments, which requires much less physical finesse than surgery. However if I were to be a behavioral neuroscientist, I could not avoid such tasks forever. I had never been especially coordinated, but this was the first time in my life where I hit what felt like a hard limit to my abilities.

I consulted a neurologist, got an MRI, and learned that I have something called a Chiari Malformation. It is a cerebellar abnormality, and while it wasn't clear that it was causing the problem, it seemed plausible to me. My then-adviser took a dim view of my attempts to seek medical advice regarding my difficulties. The man even accused me of “threatening” him when I said that I was looking into whether I might have some sort of coordination disability. There were also instances when expensive things disappeared from my desk and freezer space, which did not make me look good and which I could not explain except to insist that I had not moved them, which I had not.

I realized too late that I have issues with fine motor coordination and angle perception which limited me throughout my scientific career. Sadly, I was slow to recognize that practice was unlikely to get those skills up to the level necessary (or at least not as fast as necessary). Because of those issues, I moved away from the wet lab and towards the computational. While still doing behavior work, I started using R to analyze my data and write simple python scripts to clean or reformat data.

Around this time, the focus of my learning turned (back) to computing. As Linux slowly grew on me, I used it for more and more things. I finally put Ubuntu on a laptop around 2012 and started using it for most of my work. I started using R instead of SPSS to do statistics. At first it was just to make beautiful plots, but being able to script my analyses grew on me. Pointing and clicking in SPSS is so much less reproducible than running a script. My PI did not think much of using open-source software for "serious" things, but did not prohibit me. In hindsight, I think my failure to take the hint might have annoyed him.

My difficulties in the wet lab (such as doing surgeries on mice) made me seek work where split-second mistakes could be rolled back. "Undo" is a great boon to clumsy people. Eventually I left this second lab and went to one that did more in-silico work. However not having done much coding other than some fairly trivial shell/sed/awk tasks, it was a steep learning curve for me.

In the new lab, I was still learning core computational skills while also trying to use them. On the whole, this third lab was not a bad experience. The PI is a brilliant man and I understand why I tried his patience. I learned a great deal and participated in the incredible Common Mind Consortium project. Despite the difficulty I had catching up my knowledge, I knew this kind of work (data science and especially bioinformatics) was something I wanted to do more of.

In particular, making the transition from working on the desktop to scheduling jobs on an HPC cluster was challenging for me. I ran a lot of failed jobs, to the great annoyance of my PI (and myself). Eventually I got the hang of it, and started writing my own analysis pipelines. Most of what I worked on there was RNA-seq data from postmortem brains of schizophrenia patients and controls.

Unfortunately I was having severe sleep problems which made it hard for me to work on the schedule that my adviser wanted me to. I also found the "open office" physical environment highly unpleasant. I begged to be allowed to work at home most of the time, but my PI did not like it. For a variety of reasons, I was unable to finish my projects in that lab (and thus also my PhD). I hope to get back into that type of research at some point.

When I received a diagnosis of Autism Spectrum Disorder, I felt it explained a lot, but it was too late to save my Ph.D. Even then, my PI made it clear that he would not consider speaking with the disability coordinator about possible accommodations a good use of his time. I did not press the matter.

My inability to get my advisors to understand or sympathize with my issues hindered my efforts to work around them. I believe that there were low-cost accommodations that could have been made (such as letting me work from home as much as possible or making use of the robotic pipetting equipment available), but not until the very end did I have a diagnosis to back me up and by then my time had run out.

Although ASD most likely harmed my social interactions, I do not believe I was mistaken on the big issues that I stood firm on. If anyone felt that I conducted myself inappropriately or unethically in any of these or other situations, nobody said so to me. ASD was probably most harmful to me in that I failed to detect warning signs of incompatibility with certain people. It most likely impaired my attempts to communicate my intentions and values, and in general my efficacy in advocating for myself.

In the years since my ASD diagnosis, through genetic screening I have found that I do not have a (known) genetic load that would predispose me to ASD. I am pretty agnostic on if I “have” ASD or if ASD is even a real thing and not category for distinct things that have similar phenotypes. One of my big take-home messages from my years involved in psychiatric research is that ASD and other "disorders" are really just extremes of psychological characteristics that everyone has to some extent. Similar phenotypes can have diverse biological causes. Psychiatrists often disagree about what diagnosis is most appropriate. Maybe a different clinician would have diagnose me with ADHD, I don't know and I'm only mildly curious.

What I do feel confident saying is that I have always been different, in some ways that helped and in other ways that have hurt me. I feel that I have a gift to perceive beauty in the world in a way that most people cannot. It can also be distracting. Intense interests are similarly a blessing and a curse. My social instincts have never worked quite right, social signals that are obvious vast majority of people are sometimes not at all obvious to me. I seem to need to consciously process what is instinctive for most people. This hasn't been entirely bad though. It has forced me to think more about how people interact and notice things that other people don't. In general, I don't think "normals" communicate nearly as well as they think they do. So much social knowledge comes through implication and assumption, and if your instincts in this regard work most of the time, it can be easy to fail to notice when they are not working.

After Graduate School

Near the end of my time in graduate school, I started building my own computers and went on a quest to create one workstation to rule them all. I got interested in ZFS (an advanced filesystem) and its advantages in terms of data integrity and performance. I was also using virtualization more and more. I had several virtual machines go bad both under Virtualbox and VMware and suspected that data corruption was the reason, so the redundancy and bitrot protection offered by ZFS were appealing.

When it was time for my next (and current) build I wanted to have Linux as my main OS, but the fact that Adobe does not support Linux was a problem. I love the FOSS options such as GIMP, but there is a good reason why Adobe can charge what it does. They make a truly superior product.

It was hard for me to decide which OS I wanted to be my main OS and which one to virtualize. I wanted to have all my computer needs in one box, running at as close to bare-metal speed as possible. My split OS preferences got me interested in KVM (Kernel-based Virtual Machine) and PCI passthrough, which would allow me to use GPUs and other hardware natively in a VM.

My solution was to set up a multi-seat workstation with dedicated a dedicated keyboard, mouse, and displays for Linux and Windows chairs. I just swivel my chair to move between OSs. Doing this project taught me about Linux administration and devops. It's nice to have a separation of concerns in my physical workspace (with the Windows side used for Adobe apps and consuming media, the Linux side for coding and development). I like working this way even though a setup like that is probably too extra for your average cubicle job.

The 2020's

My most recent formal employment was doing tech support and on-site service with a company that provides and manages information systems for valet parking garages. Although the valet parking industry was never part of my "Where do you see yourself in twenty years?" plan, it was a welcome respite from the complexities and pitfalls of academia and academic personalities.

Working there taught me about networking, Internet of Things, Linux administration, and devops. It was a remote-friendly job, which was a godsend during the pandemic. Not least, it allowed me to spend extended periods with my elderly parents in Western NY. Due to various health issues my parents have had, I spent 2020-23 mainly acting as a co-caregiver to my father and after he passed away, to my mother.

I love science as much as I always have and would like to get back in the game. But I am also open to going in new directions as opportunities present themselves.

The only thing I am certain of now is that I want to forge a career path which unites as many of my skills and interests as possible. I am open-minded about what form that might take, but it must be with good people. Currently, I spend free time on art projects, development projects, cooking, and listening to history podcasts.