(C) Daily Kos This story was originally published by Daily Kos and is unaltered. . . . . . . . . . . Science protection racket [1] ['This Content Is Not Subject To Review Daily Kos Staff Prior To Publication.', 'Backgroundurl Avatar_Large', 'Nickname', 'Joined', 'Created_At', 'Story Count', 'N_Stories', 'Comment Count', 'N_Comments', 'Popular Tags'] Date: 2023-04-16 One of my ignored ideas came in attempts to tell fellow researchers that complexity in ecosystems must follow thermodynamic distributions. They had other research priorities. Thanks to my Ph.D. advisor Jonathan Lynch for recruiting me out of Missouri before job and candidate searching was so easy, and for affording me the opportunity to travel internationally where I have experienced the highest honor of all in meeting the love who inexplicably married and sticks with me over 23 years later. It practically makes up for the career changing academic constraints enforced by the aforementioned graduate advisor. As I left Missouri a quarter century ago, so too did my chances to lead independent research. Among the lessons learned in MO were that a horse is a community, of course, as are soybean, common bean, thale cress, and every other animal or plant. Instrumental to progress were scientific conversations with my great nematologist M.S. adviser Terry Niblack covering a wide range of agrosystem subjects, such as whether ecosystems are influenced more by bottom up or top down processes. Eventually, I gained degrees in biochemistry and plant pathology from the University of Missouri, along with a decade of field and lab experience. Turn of the millenium graduate studies in plant physiology at Penn State promised to be personally and professionally rewarding. I was called to do plant biology and was awarded fellowships from the National Science Foundation and NASA that were meant to promote collaborative research in root biology among a handful of PA researchers. In graduate studies at Penn State, I learned the latest models and science in hands on collaboration among multiple departments working with plants, culturing, microscopy, molecular biology, ecophysiolgoy, and electrophysiology. It could have been the perfect place to build upon on my field, greenhouse and lab experience to launch decades of agricultural and ecosystem research at the dawn of the omics era. Conversations with the adviser never got very far in PA, though I tried and tried and tried for the first two years until my research proposal was signed, and even some after that. I suggested topics such as how do root morphology and underground biotic interactions combine to impact plant nutrition and productivity. The advisor said that would be too complicated and, besides, they already did mycorrhiza experiments that showed root architecture is paramount to plant nutrition, so there was no need for me to do more. It was wrong, yet pointless to argue without independent arbitration backed by funding enforcement. I'd move on to asking about molecular biology of root architecture and whether we could leverage NSF funding and Penn State microarray facilities to look for key root morphology genes. Nope, fractals and computer science without computer science would be preferable to reductionist gene jockey work. I did get to do inexpensive gravitropism work with plants and time lapse imaging that was never submitted for peer review. I was also offered QTL analysis, if I bred common bean populations along with doing the fractal and computer science work, and possibly gravitropism work, as I recall. I passed on those added years to my program. Extracting transcripts from contrasting genotypes for microarray analysis was out of the question. Much of my research funding ended up going to buy laboratory supplies for the advisor's various projects at the end of the fiscal year. Whatever the justifications or negotiations, fractals should not have been in the conversation. Nobody in their right mind would think fractals beats molecular biology, especially for one with my experience and stated interests. Computer science without computer science was strange at the time, indefensible in hindsight, yet, as I have learned, not unexpected among scientists running protection rackets. My ideas were mostly panned. Molecular biology of root architecture was inferior to fractal research and programming root simulations, according to the advisor. Despite my lack of experience in computer programming, I could see the utility and potential and was willing to take that on. OK, when could I take classes and look to make my research also count towards a computer science degree? No, no, no, I was advised the best way for me to do computer science in his lab was without computer science, but rather by sitting in an office to learn from another plant scientist who was also trying to figure out programming, had little command of English, and even less time to train me in computer science. I ended up spending a lot of time in bookstores during those pre-stackoverflow graduate salary early internet days. My lab partners shared little or none of my excitement in discovering Dietel and Dietel among so many programming for dummies softcover books. If the advisor bought the goods he sold in our meetings, that made one of us. I knew he was mistaken at best, and possibly misusing me for his own ends. I talked to a few other plant physiology faculty. I wanted to leave his lab. The choices were to see it throough for the fellowship and degree, switch labs with unsecured funding, or drop out. I discussed the situation over the phone with the spouse who was waiting 18 months for emigration approval. More than one faculty member said I could find places to do what I want after I got the degree. I chose to stay in the lab. Decades, thousands of applications, and several jobs later, it turns out opportunities to participate in research I sought have not appeared, though I have been able to assist others in similar research pursuits, often in China. Proof that I was misadvised comes in perusing the advisor’s own publications and finding that fractal work has fallen off as molecular and ecological bandwagons have been mounted. My mistake in PA was being too quiet. I should have raised hell with the funding agencies and department heads that my Ph.D. was being wasted by stupid choices of fractals and computer science without computer science over molecular biology of root architecture. The Ph.D. program was instrumental in changing me from a root guy into an unfocused tech worker lacking relevant degrees and certifications in a gig economy. In my last job, I said I was a plant scientist acting like a computer guy doing public health. There was no leverage when managers hid behind anti-worker at will contract clauses to say that me and my bike were no longer welcome with them after a few short months of service. Here are a few anecdotes before finishing. After speeding up the soil exploration component of root simulations ~1000 fold with a simple loop, the advisor did not talk about copywriting or any other attribution, but rather asked when the next 1000 fold improvement would be forthcoming. In the early aughts, I saw that the NFL was working on 3D imaging with some assistance from researchers at Carnegie Mellon in Pittsburgh. I arranged and paid for my own visit there to explore 3D imaging of plants, including root systems. I returned to Penn State and grew a plant or two on a semitransparent gel in a big glass container in the lab of a committee member. It was likely that with some tweaking of the gel we could grow plants, and potential collaborators were available. It went nowhere when the advisor declined to support the work. I remembered it well a decade later when I was helping a young PI get established in his new job based on 3D imaging of plant roots growing in semitransparent gel. Years after graduating, the advisor did offer another opportunity to work for him in a simulation project based out of Jülich, Germany. As much as I would have loved to work at the research center, I first had to inquire about doing the computer work remotely, with travel, of course, before considering taking the family to Europe for another American egomaniac. They said I needed to live there. OK. I said, I could do that if a quarter of my time could be devoted to helping work with the data coming from their high throughput phenotyping operation. The advisor vetoed that idea. I was told that I would have to focus on the simulations. Was the advisor laying another dead end trap in the midst of modern opportunity? I couldn't take the bait with my family. I declined. Could have been a mistake, but I'm not regretting the decision. After a seminar at the job interview in Jülich, an audience member stated that the advisor told a good story, but they still would not buy a used car from him. That is as good a summation of the advisor as I have heard. At this later stage in my career, each night I go to bed knowing that the next day I will lose time to depression. I can look lazy and unreliable, but I am proud of each time I get up and do something. Lest the advisor let this go to his head, it took more than one idiotic science egomaniac to bring me down. And, thanks to my patient, savvy spouse and our adorable children, we do have a nice home. My sorrow arises from my own hopes and expectations anyway. Learning about and working with plants and technology have been tremendously enjoyable during the time I have had. Still, it amazes and sickens me to this day, fractals over molecular biology. Really? Seriously? What do I tell my kids after misadventures such as mine? Follow your passion so that it can be used against you? Find mentors so you can labor for their goals and have your visions cast aside? Work hard and learn a lot so that managers who can’t program a growth chamber or a fizzbuzz challenge can take your work, dump you, and grab credit for themselves? Stay away from science? Go into real estate? What I do tell them is that as long as trees grow, opportunities exist, the more you learn, the better your chances, and I’m not ready to shut up and do as I’m told just yet. Thanks for reading. Thanks to the internet gods and Daily Kos proprietors for this forum. I think there is enough science and public funding discussed to make it relevant. I am not sure if I want anybody to read this. There will be no reward, recognition or reconciliation coming from this. There should be apologies to myself, NSF and NASA for the poor advice given in my Ph.D. program. I should get millions in lost wages and damages. None of that will happen. Nor will I advise students, teach with decent pay or direct research. As much as anything, this is me finally admitting that my science career is over outside of underpaid teaching and editing. I will move on and die. In the end, I wrote this simply for my sanity and look forward to writing anything enjoyable once again. 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