Author and Research Scientist James Lyons-Weiler, PhD – Extended Biography

James Lyons-Weiler, research scientist and author of “Cures vs. Profits“, “Environmental and Genetic Causes of Autism“, and  “Ebola:An Evolving Story”, was born on July 4, 1967.

James grew up in Upstate New York as the youngest of three children.  On Valentine’s Day, 1973, his mom died of breast cancer.  Always a bright student, he sought refuge in school as a respite from stresses at home that sometimes come with a mixed family.  His favorite classes were biology, geometry, history, music, and creative writing.

He attended State University of New York College at Oswego, intending on becoming a high school biology teacher.  After a course genetics, and another human evolution, he was hooked on research.  In that semester, he immediately applied his problem-solving skills to an early flaw he recognized in DNA-DNA hybridization, a method being used at the time to estimate evolutionary relationship
jlwdecemberpics among species of birds.  He called an expert on the matter and offered a mathematical correction to the problem of the assumption of base composition homogeneity.  That expert was Dr. Vincent Sarich, at UC Berkeley.  His advisor, Dr. Peter Rosenbaum, counseled him to be a generalist in science – to learn everything he could, from anyone he could.  He carries this advice with him to this day.

A lifelong student, he developed a keen interest to the big questions in biology: how new species are formed, why is there so much species diversity in the tropics?  He studied Zoology and Paleoecology at Ohio State University, taking additional courses in Molecular Biology, Molecular Evolution, Plant Biology, Biogeography, and Paleontology, and Population Ecology, and Evolutionary Trends in Flowering Plants.  His research project brought him to the Cuyabeno Faunistic Reserve in lowland Amazonian Ecuador (South America), to study (with Dr. Paul Colinvaux) the effects of global climate change on the Amazonian rainforest ecosystem.  For those projects, he derived new computational methods for integrating species diversity patterns using ordination methods.  He proposed a dynamic environment hypothesis for species diversity in his Master’s Thesis (OSU Link, Google Books Link).

He studied for a while at The University of Connecticut in Storrs, CT.  His favorite experience there was a research study with Dr. David Wagner.  He honed his computational skills and studied Evolutionary Theory, Multivariate statistics and Plant Systematics.  From there, he traveled to Reno, NV to work on the distribution of rare species in the Intermountain West.  On the side, he developed a new field of inquiry in the area of computational statistics for phylogenetics – the science of estimating species’ evolutionary relationships.  It was well known that different algorithms for phylogenetic analysis could give different results given the same data.  He devised a test of the data set for suitability for phylogenetic inference.  He worked under the tutellage and advisorship of Dr. Guy Hoelzer and Dr. Robin Tausch.  He published twelve papers as a result of his PhD research, and quickly became recognized as a thought leader in the area of complex analysis in biological systems.  His favorite courses were in Classical and Molecular Cytogenetics, Conservation Biology, Population Genetics, Experimental Design.  As another side project, he derived a mathematical explanation for the so-called humped-shape pattern of species diversity across a productivity cline, and made a special visit to Arizona to share his findings with Dr. Michael Rosenzweig.  He was invited shortly thereafter to serve as the Associate Editor of Applied Bioinformatics.

During his graduate school years, James enjoyed teaching ecology, evolution, genetics, environmental biology, and population genetics.  He studied multivariate statistics, regression theory, and applied statistics.  His mind was always at work in wonder, looking at the world of nature at all scales, both as a biologist and as a graphical mathematician.  Often relating questions in biology, an observational and experimental field, to quantitative system, he could see solutions to complex problems first, only to have work backwards to study their correctness.  He excelled in the areas of permutation and resampling-based methods of hypothesis testing of big questions in science, developing new methods in this area, and new applications in molecular genetics.  His terminal degree is in Ecology, Evolution, and Conservation Biology.

His energy, drive and quantitative skills brought a fellowship from the Alfred P. Sloan Foundation, which he took to Penn State University.  While studying Molecular Evolutionary Genetics under Dr. Masatoshi Nei and Dr. Webb Miller at Penn State University during his postdoctoral years, James became a father.  He continued to study statistical properties of methods for studying molecular evolution, and also developed a new method for detecting purifying selection in evolving protein sequences.  He continued to study biological systems (proteins, biological pathways).  One day, Dr. Mark Boguski came to visit.  He presented data on cancer research using partial genome microarrays.  In these platforms, one can interrogate >40,000 genes in cancer, and, compared to tumors, determine which genes are turned on, and off, in cancer tissue relative to normal.  Because James had his own funding, he requested permission from Dr. Nei to move into the area of computational statistics for microarray data analysis.  James had recognized that, as in phylogenetics, people might derive arbitrary conclusions from these new, important ways of studying cancer.

James then found a position at UMASS Lowell, where he founded one of the world’s first Centers for Bioinformatics.  He helped develop that institutions’ undergraduate and graduate studies curriculum in Bioinformatics.  He routinely had 20 or more students performing analyses for research projects, asking questions about the impact of algorithm selection on the biological inferences being made in many types of diseases.  He produced online software that implemented numerous methods of microarray data analysis – and that provided objective performance evaluation measures to aid in the selection of the optimal methods.  He studied gene expression in cancer, publishing a paper on overcoming experimental design flaws such as confounded controls.  He taught courses in biology, genetics, and bioinformatics, and set up a sequencing lab for the Department of Biological Sciences.

He was then invited to relocate to Pittsburgh, PA to work in the then-new Hillman Cancer Center and the University of Pittsburgh Cancer Institute, where Dr. Ronald Herberman was Director.  James worked with oncologists, surgeons, and other cancer researchers applied his methods of analysis to prostate cancer, ovarian cancer, renal cell carcinoma, astrocytoma, melanoma, and lung cancer.  There he met Dr. Sam Weiand, who took him under his wing and advised him on the use of matching methods for accrual of patients to randomized clinical trials.  He was selected to serve on numerous large grants, and managed a multi-institutional consortium focused on the optimization of laboratory and computational methods in proteomics.  He participated in the NCI’s Early Detection Research Network (EDRN) and their caBIG (Cancer Biomedical Informatics Grid) initiatives.  He served as the founding Editor-in-Chief of his brainchild journal, the open access, rigorously peer-reviewed journal, Cancer Informatics.  He published numerous papers on new ways of looking at cancer that have helped set the stage for research in individualized medicine. He taught two full courses a year, one on research design, and the other on the analysis of high dimensional genomic and proteomic data.

His favorite moment from these years was when five-time melanoma survivor Dr. Andy von Eschenbach, then Director of the National Cancer Institute, and future Commissioner of the Food and Drug Administration, gave him a hug at one of NCI’s meeting for creating the journal Cancer Informatics.

Throughout this time period, and to the present day,  he is a popular favorite speaker at many public speaking engagements.  Because he has a keen eye for important open questions in science, his presentations often draw crowds, and some make news.  As an advocate for the public trust in science, he has always kept a keen eye on translational potential in biomedical research.

Here Dr. Lyons-Weiler is seen at a national meeting in Philadelphia, PA, leading a discussion on whether existing information scores such as Phred and Phrap contain sufficient information to be used to assess confidence in Next Generation Sequencing applications. Photo Credit: Grace Innes
Here Dr. Lyons-Weiler is seen at a national meeting in Philadelphia, PA, leading a discussion on whether existing information scores such as Phred and Phrap contain sufficient information to be used to assess confidence in Next Generation Sequencing applications. Photo Credit: Grace Innes

Given the immense potential for knowledge from biomedical research to reduce human pain and suffering, he does not tolerate unethical or lazy practices in research, and believes that senior faculty members should see junior faculty not as competitors, but as their progeny: their legacy.  His popularity with students and researchers from all walks of biomedicine and biology allowed him to branch out from cancer to offer bioinformatics data analysis services to investigators across the campus.  Working closely with senior administrators Dr. Arthur S. Levine and Dr. Michelle Broido at the University of Pittsburgh, he founded the Bioinformatics Analysis Core as a three-year pilot project. His enthusiasm for translational research and his love of helping others helped the core project last for seven years, and he and his staff members provided data analysis and study design consultations to over 100 research projects.

His methodological research had continued over this time period, and he created improved methods for survivorship analysis, for identifying differentially expressed genes, for selected optimal methods for the normalization of high dimensional data, and for estimating the risk of false discovery.  He devised a novel statistical framework for modeling the incorporation of new biomarkers into existing clinical diagnostic workflows (Clinical Decision Modeling System, or CDMS software available from The University of Pittsburgh).

Dr. Lyons-Weiler breaks the news of the severity of the inherent bias in Fold-Change (Ratio) compared to Delta (Difference) to an audience in Boston, MA (2014).  He also introduced an application of the use of Boltzmann entropy to measure genotypic signal in Next Generation Sequence variant data to avoid spurious genotype calls.

One of the methods devised was a test for differentially expressed genes called the J5 test, which he then improved with the world’s first nonlinear thresholding method called G-thresholding.  He and his staff studied so many data sets that they noticed a serious bias in the commonly used fold-change measure (ratio).  Time and again his staff demonstrated that the J5 test, which he named after his mother, Joan, was less biased and more informative than fold-change.  J5 is a simple function of delta, a difference score, and is more reproducible in repeated studies than fold-change.  In 2013, he demonstrated that the widespread use of fold-change was an absolute bias that led to hundreds if not thousands of researchers throwing away significant portions of their high- and low-dimensional data.  He considers this unintentional practice more harmful to biomedical science than any fraud perpetuated to date, or any funding cut.  In the final year at the University (2014), he devised measures of genotypic signal, to identify sites in next generation sequencing data where different genotype calling algorithms are likely to disagree, and to provide measures of uncertainty for individual base calls.

When the core closed in 2014 due to state budget cuts, the Ebola outbreak in Guinea had become an epidemic, spreading to Liberia, Sierra Leone.  James decided to use his expertise to help society better understand the outbreak, so he began reading research papers, and interviewing experts to sort out the confusing mess of public policy.  During a drive through the hills of Western PA, it dawned on him that a powerful way to help shut down transmission was pre-symptomatic diagnosis.  He created the Ebola Rapid Assay Development Consortium, enlisting the help of colleagues from Penn State University (Dr. Costas Maranas), University of Illinois Urbana-Champaign (Prof. Klaus Schulten), The Scripps Research Institute (Dr. Erica Ollman-Sapphire), and University of California Santa Barbara (Dr. Kevin Plaxco).  The group focused on the computational development of anti-body like binding proteins able to bind to Ebola Gp1Gp2 protein complex on the viral coat.  The synthetic antibodies were also optimized to undergo a large conformational state change upon binding to facilitate use in a rapid colorimetric assay.

As the situation in Africa worsened, James felt that his cumulative research experience and knowledge could benefit those in the front lines, and the general public, if they had a better understood the virus, especially its modes of transmission.  He spoke with experts in epidemiology, public health, policy makers, evolutionary psychologists, emergency responders, truck drivers and every day people, and researchers at the very cutting edge of drug development targeting Ebola.  He wrote his first book “Ebola: An Evolving Story” (World Scientific) to not only inform people of the details of the outbreak and how it became an epidemic, but also to sort out how policy should be based on logic, science, and evidence, and not on fear, superstition, belief, or dogma.  His research on Ebola allowed him to discover and catalog a number of important new research directions and open questions surrounding Ebola.

In the process of his career, James got more than he bargained for.  Always looking to improve ways of doing science, he discovered numerous fundamental flaws in the methods for analyzing data.  He always strived to provide improved solutions to these problems.   Over the years, given his extensive knowledge of cutting-edge research in cancer and cancer treatments, James helped his sister, his uncle, his future father-in-law, and several close friends find optimal routes to treatment of their cancer.  Close friends and family would, on a regular basis, challenge him with statements like “They already have a cure for cancer.  They don’t want cures, they want treatments!”  While conducting research for “Ebola: An Evolving Story”, it became apparent to him that important and significant improvements could be made to FDA’s approach to gold standard randomized clinical trials.   To help sort out these perspectives, using the cumulative benefit of all of these experiences, he is now writing a second book “Cures vs. Profits: Success Stories in Translational Research”, published in May, 2016.

Today, James on a national tour with his latest book, “The Environmental and Genetic Causes of Autism“, directing analysis of studies of many types at the Institute for Pure and Applied Knowledge where scientists work to reduce human pain and suffering through knowledge without profit motive.

(For some photos of PA wildlife, scroll down…)

Connecting with Dr. Lyons-Weiler in Academia





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Books and Publications by James Lyons-Weiler

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  1. Dr. Lyons-Weiler,

    I’ve recently become aware of your work to restore truth and integrity to scientific study. Thank you for your efforts! I also live in Pittsburgh, and although I can’t speak to the situation in other places, the healthcare monopolies appear to run this town on multiple levels – not least of which is essentially thought control of their medical providers, (I’ve joked that it’s ironic that in a city swamped with doctors, to get a true second opinion, you’d need to leave town). I would not be surprised in the least if similar corruption exists in the type and direction of research conducted at the universities and medical centers here. The point being, from my perspective, your effort is more impressive because you’re working for change from within the lion’s den, (or one of them at least!)

    You’re right if you’re imagining I’m bitter – I can’t deny that. I won’t bore you with the events and circumstances that have caused those feelings. I only wanted to let you know, you remind me that there are still brave souls willing to fight for science in the hopes that research regains it’s promise, and with that foundation, mainstream medicine can one day provide true “healthcare”. For so many of us, that day can’t come soon enough.

    With much gratitude,


  2. Pam, I second your thanks to James Lyons-Weiler. Big Pharma is so greedy, so powerful, so bullying that many voices of reason remain quiet so as not to lose their credibility, their careers, their family and friends. James, you have my full support. I am now referring to your work when I am in need of supporting my minority views about Big Pharma in regard to the vaccine industry in particular.

  3. HERO…without a cape 🙂
    Thank you for hooking up with Del, Bobby and the Gang, and shining the light of truth.
    God Bless You and yours.

    1. I am just an objective scientist. I would not care to be considered a hero. I find moms who spend everyday dealing with the fallout of vaccine injury in their child or children to be the real heros.

      1. Great point James, but all of those mammmmas need a good uncle to support them in such a professional 🦠🔬🧪🛠 to be heard.

  4. Dear Dr. Lyons-Weiler,

    Amazing Polly mentioned you on her most recent video on Bitchute as someone fighting the lies and speaking the truth in the medical research field, especially about the dangers of vaccination and the disinformation the public have been given regarding this current psyop/fraud being perpetrated upon the people of the entire world. Thank you for that! I’m wondering if you can direct me to a study, have had any experience in, or know anyone who has, regarding the the Tdap vaccine causing serious auto-immune response, in my case, severe Graves’ disease (hyperthyroidism) almost immediately after receiving it.

    There is a very interesting aside to my case – I’m a 65-yr old “Downwinder” from Operation Teapot (wiki has a comprehensive timeline) where 14 test nukes were detonated from March to May of 1955 at the Nevada Proving Grounds AKA Nevada Test Site. The fallout was Radioactive Iodine-131. Downwinders were/are victims of mostly thyroid cancers as iodine is stored in the thyroid; the childrens’ cancers were from drinking cow’s milk from cows grazing as far away as five surrounding states. I was born in October of 1955 about 60 miles downwind from the Proving Grounds (and was even named after one of the bombs – ouch), so I was nuked 14 times in utero from approx. month two to month four of gestation. To date I have had six organs removed, the last one last year – my thyroid.

    I received the Tdap vaccine in June of 2018 as a ridiculous condition to see my first grandchild in the hospital when he was born the next month. I immediately began developing symptoms of Graves’ disease, was diagnosed and began medication after a few months. I was allergic to the medication and my Graves’ symptoms were becoming quite severe (nearly killed me), so my only options were, and this is where it gets interesting, RAI therapy which is Radioactive Iodine-131 – I’m not kidding – to kill my thyroid (this was when it all came together for me), or surgery to remove it. Of course I declined the RAI therapy, I had had enough exposure to RAI-131 as a fetus, so I opted for total thyroidectomy which I had done in May of 2019, after 11 months of pure hell with Graves I barely survived and 11 months after the Tdap vaccine.

    I read your bio so this probably isn’t something you would apply that huge brain of yours into researching or conducting a study to correlate these two events as causation yourself, but am wondering if you know of anyone who would, or has done, or of any studies about this as I’m sure I’m not an isolated case and the ‘coincidence’, especially under my peculiar circumstances, are compelling. It’s a timely and important topic that should be investigated as I have yet to find any study, or even any mention or interest of Graves’ being triggered by Tdap (or any vaccine).

    The RAI-131 fallout exposure from Operation Teapot of 1955 proves they were actively performing, without informed consent, medical experimentation on American citizens by test-nuking us with Radioactive Iodine-131 and currently use this exact thing to “medically” kill an overactive thyroid. This is never even mentioned nor has anyone ever investigated it to my knowledge. As you know they’ve been doing medical experiments on us all along (Tuskegee – ended in ’72; St. Louis – ’53-’54 and ’63-’65; San Francisco – ’50; and Nevada ’51-’92 are only a few examples), all post-Nuremberg Code drafted in ’47, and my main point is, they’re doing it again on us right now – the CV-19 vaccine trials will not end until 2022, so everyone who takes it will be participating in medical experimentation without informed consent and with unknown risks. This is yet another serious war crime against us, their own people, and it needs to find a voice in public again before it’s too late.

    Best regards, thank you for reading, thanks for all you do, and thanks for any consideration to these issues, especially the medical experimentation issue because people need to be informed about it before it’s too late for them.

    ~Linda, Also in the Commonwealth of PA

  5. James I’ve learned about you on Covid Revealed. I am no longer working as a teacher because I refuse to be vaccinated with experimental drugs. I am now living off my savings. You are doing us a great favour to speak out with expertise on why it is disgusting that vaccines on trial are actually a human subject study. How dare they!? Thank you

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