Earthlings (2005)

Earthlings is a 2005 American documentary film about humankind’s total dependence on animals for economic purposes.  Presented in five chapters (pets, food, clothing, entertainment and scientific research) the film is narrated by Joaquin Phoenix, featuring music by Moby, and was written, produced and directed by Shaun Monson.”

How Not to Die describes the numerous health benefits of eating a plant-based diet. After reading through half the book, I watched Earthlings to see arguments from the animal rights activists for eliminating animal products from the dinner table. Personal health has always been my primary interest for minimizing meat consumption. But the message in this documentary is just as difficult to ignore as it is to watch.

There are some valid counter arguments to abandoning meat, which are listed in this reddit thread. The most compelling was that from an Indian man who argues he will not stop eating meat nor stop providing it for his family because he has genuine concern that his children my not survive due to malnutrition. Perhaps citizens of the more developed nations are the primary audience for this documentary.

I have watched a handful of anti-meat documentaries, and often they appeal to emotions such as shame, guilt, or anger. Earthlings takes a more objective role, showing film of industrial animal manufacturing in the United States. It was refreshing to be treated as a neutral observer, instead of being reprimanded. There are definite appeals to emotion, but the dialogue in the documentary is more calm than any I’ve seen before.

Earthlings has made me reconsider my current relationship with meat and animal products.  I imagine I have grown up with more livestock experience than many of my neighbors. I learned from my family to slaughter fish, chickens, turkeys, and rabbits for food. I attempted a pescatarian diet for several years in my twenties, but only for personal health reasons. This is the most cognizant I have been of my indirect participation in the massive consumption of animals, and what that actually means.

Three Stages of Truth

  1. Ridicule
  2. Violent Opposition
  3. Acceptance

Attributed to German Philosopher Arthur Schopenhauer (1788–1860)


Does Pure Nicotine Cause Cancer?

Cigarettes contain many chemicals that increase the risk of cancer. Polycyclic hydrocarbons and tobacco-specific N-nitrosamines are some of the more well-known carcinogens in this class.

But now, e-cigarettes appear to be isolating nicotine, and leaving behind many of the old toxins from cigarettes. This sounds like e-cigarettes may be “better” for the modern smoker. Are smokers of e-cigarettes increasing their chances of cancer later in their lives? If so, what is the risk of cancer from smoking pure nicotine?

For the sake of discussion, let’s ignore the possibility for novel cancer-inducing chemicals introduced from the various oils and heating mechanisms in e-cigarettes. Let’s assume it is possible to have a method of smoking that only exposes the smoker to nicotine and nothing else. Would this method of smoking still cause cancer?

This review of the literature on Nicotine from 2015 suggests the answer is “yes”. Nicotine alone still increases the risk of cancer for the smoker of pure nicotine.

“Several lines of evidence indicate that nicotine may contribute to the development of cancer.

“Evidence from experimental in vitro studies on cell cultures, in vivo studies on rodents as well as studies on humans inclusive of epidemiological studies indicate that nicotine itself, independent of other tobacco constituents, may stimulate a number of effects of importance in cancer development (5, 6).”


NCBI: Nicotine: Carcinogenicity and Effects on Response to Cancer Treatment – A Review

Physiatry in the Future

Before forecasting its future, there is likely merit in explaining what physiatry is.

What is Physiatry/PM&R?

“Physiatry, also known as pain management and rehabilitation (PM&R) is a branch of medicine that aims to enhance and restore functional ability and quality of life to those with physical impairments or disabilities.”

– Wikipedia

Medicine tends to be sterile. When the end goal is reduced to keeping the patient alive, or moving a lab value within its appropriate range, doctors can forget to be human. Resources are stretched thin in a county hospital in a large metropolitan area. Providers are only attending to biological issues because they are prioritizing scarce resources. They are not trained to deal with the more pressing, social issues. What is the point in treating a patient’s asthma, discharging them back to the streets, waiting for another exacerbation, and then rounding on them next week after they’ve been admitted once again from the ER? Patients like these need social work and preventive public health measures. Instead they get expensive medications once every few months. Medical care can feel calloused and at times even cruel.

On the other end of the spectrum, there are fields based entirely in human connection, but they lack teeth. Naturopathy and alternative medicines have either been shown to have no efficacy, or there is no incentive to research them because they are assumed to be entirely based on the placebo effect. Sometimes people need to be heard and feel connected with their provider. These fields take advantage of this, and patients may be happier, albeit less healthy.

PM&R is western medicine that focuses on the patient’s function and quality of life. Chronic pain patients have sifted through the medical system, frustrated by the lack of resolution to their pain. They’ve stumped doctors who cannot do anything for them because all of their lab values are correct and they seem healthy enough by the protocol standards. Surgeons will happily perform surgery, but it seems a drastic move exposing patients to serious risks, which can be minimized or ignored during the pre-op. Surgery may be the best option for some, but certainly not all of these patients. Physiatry can offer medical treatment, alongside physical therapy for a multidisciplinary approach to increasing patient health and quality of life.


But it turns out, not many procedures used by physiatrists have been supported by clinical evidence.

Dr. Braddom Predicts the Future of PM&R


Dr. Randall Braddom is a clinical professor of physiatry. While at Rutgers Medical School in 2014, he gave a 100-Slide PowerPoint presentation that concisely summarizes the field of PM&R and it’s future direction from his perspective. Dr. Braddom acknowledges how worthless predictions of the future often are, but an experienced physician creating a deep portrayal of their specialty is worth far more than SDN forums.

According to Dr. Braddom, the field of physiatry is placing more value on research. One of the reasons is that physiatric procedures have not been validated in randomized clinical trials, and insurance companies are eliminating reimbursements for procedures without scientific evidence supporting their efficacy. The large proportion of physiatrist in clinical practice may see large reductions in their financial reimbursement for some of their procedures, such as sacroiliac and Z-joint (zygapophysial) injections.  A whole field of doctors potentially not getting paid for their work may be a powerful force. It seems that clinical research opportunities in PM&R will likely thrive in the near future.

Below are select few slides from Dr. Braddom’s presentation.

PM&R Research will Boom Soon

Trend to Evidence Based Medicine

Evidence Basis of PM&R is Significantly limited due to:

  • Variability/complexity
  • Limited research
  • Distance from molecular biology
  • Clinical studies lack analytical rigor

Research is Critical for PM&R Practice

  • Outcome Studies are key to practice survival
  • Randomized controlled trials (RCT’s)
    • Almost no other kind of research is taken seriously
    • Uncontrolled research is only a pilot study, at best
  • Laboratory moving closer to the bedside
  • New emphasis on Evidence Based Medicine in Health Care Reform

Few Physiatrists Have Become High Quality Researchers


“It has also been generally agreed that Rehabilitation research has not done well in fulfilling its objective of providing a foundation of knowledge for rehabilitation practice.”

Lieberman (1993)

AAPMR LNA: 2004 Physiatric Effort Report

  • Outpatient 50%
  • Inpatient 23%
  • Administration 10%
  • Teaching/CME 4%
  • Research 3%
  • Miscellaneous 10%

What to Do After Residency

2014 ABPMR Subspecialty Exams for Physiatrists

  • Sports Medicine
  • Neuromuscular Medicine
  • Pain Medicine
  • Hospice and Palliative Medicine
  • Pediatric Rehabilitation Medicine
  • Spinal Cord Injury Medicine
  • Brain Injury Medicine
Braddom_-_Future_2014_handout (dragged).png

What Percentage of Residents Join Orthopedic Groups?

  • 22%
  • Range from 10-40%

On residents joining Orthopedic groups:

“This is a sin against humanity!”

– PM&R Chair

From reading forums, it sounds like being a physiatrists working in an orthopedic practice may be a horrible experience. Surgeons with large personalities shunt all their conservative preventive care to one physiatrist on the team because it is a waste of their time to do injections when there are more challenging surgeries to be performed.

I personally would not want to spend so much time in training to be looked down upon or taken advantage of financially during my day to day practice. I don’t see the allure to working in orthopedic groups that the 22% of survey respondents said they are doing.

PM&R is a Great Field

  • Patients appreciate what we do
  • Not limited by an organ
  • Jobs of all types available
  • Population demographics favor us
  • Good balance of procedure/E&M
  • Many academic opportunities
  • Good physiatric profile/nice people
  • Small (10,000)

PM&R is focused on patient outcomes and quality of life. There are a wide variety of procedures, subspecialties, and practice styles within physiatry. Dr. Braddom presented many trends in the field as of 2014, and where he expects it to head in the future. He underscores the growing research opportunities in PM&R, the breadth of fellowships for sub-specialization, and that working in an orthopedic group may be less than ideal. Regardless of his prophecies, as of now physiatry looks like a promising career path.


Wikipedia: Physiatry

The Atlantic: The Problem With Satisfied Patients

Doctor Voices: What is PM&R?

Doximity: Randall L. Braddom, M.D., M.S.

The California Society of Physical Medicine and Rehabilitation: The Future of PM&R From a PGY-46

NCBI: National Center for Medical Rehabilitation Research – K12 Grant

SDN: Work Under Orthopedic Surgery?

Writing the Introduction to an Epidemiology Paper

This is some brief guidance from my advisor on how to write the introduction section of an epidemiology scientific paper. When addressing previous papers in the introduction, do so only briefly. Generally, save the thorough literature review for the discussion.

Paragraph 1

What is the public health or clinical importance of the topic? What is the primary problem that will be addressed? How many people will be affected? What level of impact does this problem have? Statistics from the World Health Organization are often cited here.

Paragraph 2

What is currently known about the problem?

For example, what has been published on health related quality of life (HRQOL) in type 2 diabetes mellitus (T2DM) patients?

Briefly describe a variety of primary literature papers on the topic. State the lacking knowledge that will be addressed by the rest of the paper.

There is much known about HRQOL in T2DM in populations of White Americans, but there have been no studies to date describing HRQOL in Pacific Islanders diagnosed with T2DM.

Address challenges unique to this study.

Are there variations in HRQOL perceptions among different cultures?

Paragraph 3

Clearly and concisely state the primary aim of this study.

For example, in the current analysis we will study the impact of T2DM on HRQOL in a population of Pacific Islanders living in Oahu, Hawaii.

Say something specific about the population being studied.

The Pacific Islander Cohort of Hawaiians is a longitudinal, population-based cohort that has been ongoing since 1999, with followup every 4 years.

Explain why this study is novel. Tell what you are going to show.

 Hemoglobin A1c (HbA1c) is a validated clinical measure of T2DM severity (citation here), and the SF-36 is a validated health questionnaire measuring HRQOL (citation here). To the extent of our knowledge, this is the first study to study a potential quantitative association between HbA1c and the SF-36 in a population-based cohort of Pacific Islanders.

Mendeley Reference Management

Mendeley is a convenient, free research resource that allows you to manage primary literature references. Mendeley’s Citation Plugin allows easy citations in Microsoft Word while drafting scientific papers from your library.

Online Population-Based Cohort Study

An Internet Survey in a Population-Based Cohort Study

Consumption of ultra-processed foods and cancer risk: results from NutriNet-Santé prospective cohort is a web-based survey looking at the association of cancer risk and consuming ultra-processed foods in people in France who responded to a survey. Population-based cohort studies were previously done by calling people’s landlines, asking them to fill out surveys, and requesting that they drive to the clinic for a health examination.

Perhaps further epidemiological studies will be done primarily using online surveys, as the authors did in this paper. It would make epidemiological studies much less expensive and more readily available. But the validity of the results have not yet been verified.

Using the internet selects for younger people responding to the survey. This may not be representative of the larger population. But as these generations age, using the internet for data collection may be a useful tool.

The internet is an anonymous place, and it is difficult to understand the population that is being studied when using the World Wide Web as the only data collection vehicle. This may be a worth-while sacrifice for the convenience of bypassing what has historically been the most arduous part of studying the public’s health.


NCBI: Consumption of ultra-processed foods and cancer risk: results from NutriNet-Santé prospective cohort

Epidemiology Postdoctoral Position – 1 Year – Spanish-Speaking Country – Paid

Primary Aim: 1 Year Position for Epidemiology Postdoc

I am looking for a paid epidemiology position as a recent PhD graduate from May 2020 to April 2021 in a Spanish-speaking country.

I have experience working with large population-based cohort studies focused on chronic diseases. I am familiar with a variety of statistical software including R, SAS, and Stata. I have taken coursework on the statistical methods, regulation, and design of clinical trials. I have completed the first two years of medical school and passed the first medical boards examination.

Secondary Aim: Speak Fluent Spanish

One of my career goals is to speak fluent Spanish. I have lived in Mexico for weeks and Peru for months at a time, and I have an intermediate Spanish proficiency. I am interested in working no more than 40 hours per week, to study Spanish while being immersed in the language.

Tertiary Aim: Pay Student Loan Debt

I require enough compensation to afford cost-of-living while making student loan payments. I am aiming to make entry level wages similar to what I might find in the US for an epidemiology postdoctoral position. Otherwise I cannot justify taking an entire year off school while interest accrues on my six-figure student loans.


I am expecting to graduate from an epidemiology PhD program with a concentration in clinical trials in May of 2020. I am looking for a one year postdoctoral or private position before returning to medical school in May of 2021 to complete the final two years of clinical rotations.

International Epidemiology Job Resources

I’m amassing resources to identify international positions in clinical research at the MPH and PhD levels. Below is a list of job boards and international research funding mechanisms.

The 7 Deadly Sins of Data Analysis

In her final lecture, my statistics professor described the “7 deadly sins” of statistics in cartoon form. Enjoy

1. Correlation ≠ Causation


xkcd: Correlation


Dilbert: Correlation

2. Displaying Data Badly


xkcd: Convincing

Further reading on displaying data badly

The American Statistician: How to Display Data Badly by Howard Wainer

Johns Hopkins Bloomberg School of Public Health: How to Display Data Badly by Karl Broman

3. Failing to Assess Model Assumptions

FailingModelAssumptions.png Statistics Cartoons by Ben Shabad

4. Over-Reliance on Hypothesis Testing

Null Hypothesis

xkcd: Null Hypothesis

While we’re on the topic of hypothesis testing, don’t forget…

We can fail to reject the null hypothesis.

But we never accept the null hypothesis.

5. Drawing Inference from Biased Samples


Dilbert: Inferences

6. Data Dredging

If you try hard enough, eventually you can build a model that fits your data set.


Steve Moore: Got one

The key is to test the model on a new set of data, called a validation set. This can be done by splitting your data before building the model. Build the model using 80% of your original data, called a training set. Validate the model on the last 20% that you set aside at the beginning. Compare how the model performs on each of the two sets.

For example, let’s say you built a regression model on your training set (80% of the original data). Maybe it produces an R-squared value of 0.50, suggesting that your model predicts 50% of the variation observed in the training set. In other words, the R-squared value is a way to assess how “good” the model is at describing the data, and at 50% it’s not that great.

Then, lets say you try the model on the validation set (20% of the original data), and it produces an R-squared value of 0.25, suggesting your model predicts 25% of the variation observed in the validation set. The predictive ability of the model seems to depend on which data set is used; on the training set (R-squared 50%) it is better than on the validation set (R-squared 25%). This is called overfitting of the model to the training set. It gives off the impression that the model is more accurate than it really is. The true ability of the model can only be assessed once it has been validated on new data.

7. Extrapolating Beyond Range of Data


xkcd: Extrapolating

Similar Ideas Elsewhere

Columbia: “Lies, damned lies, and statistics”: the seven deadly sins

Child Neuropsychology: Statistical practices: the seven deadly sins

Annals of Plastic Surgery: The seven deadly sins of statistical analysis

Statistics done wrong


xkcd: Correlation

Dilbert: Correlation

xkcd: Convincing

The American Statistician: How to Display Data Badly by Howard Wainer

Johns Hopkins Bloomberg School of Public Health: How to Display Data Badly by Karl Broman Statistics Cartoons by Ben Shabad

xkcd: Null Hypothesis

Dilbert: Inferences

Steve Moore: Got one

Wiki: Overfitting

xkcd: Extrapolating

Columbia: “Lies, damned lies, and statistics”: the seven deadly sins

Child Neuropsychology: Statistical practices: the seven deadly sins

Annals of Plastic Surgery: The seven deadly sins of statistical analysis

Statistics done wrong

Fixed Effects vs Random Effects Models

What is a fixed effects model? What is a random effects model? What is the difference between them? Many people around me have been using these terms over and over in the past few weeks. I finally compiled several 5-10 min videos of people answering these questions well online.


If I had to answer the question of what fixed and random effects models are in one image, I would choose this one from the Indian Journal of Dermatology. Watch the videos and come back to this image for a quick reminder of these concepts.

Motivating Example: Meta-Analysis of Bieber Fever

This silly example is a simplistic demonstration of when fixed and random effects models should be used in designing a meta-analysis. This video is for the medical student.

Summary of Fixed and Random Effects Models

This summary video is a bit more technical and is aimed at a student of epidemiology or biostatistics.

What is Heterogeneity?

The concept of heterogeneity kept coming up in these videos. How is it different from random chance? This is a clear explanation of the difference that defines concepts alluded to in the previous videos.


Indian Journal of Dermatology: Understanding and evaluating systematic reviews and meta-analyses

Brian Cohn: Fixed and Random Effects Models and Bieber Fever

Terry Shaneyfelt: Fixed Effects and Random Effects Models

Terry Shaneyfelt: What is Heterogeneity?

Inigo Montoya & Openintro Statistics

I do not think it means what you think it means.

After reading Statistics Done Wrong, there were a couple of resources mentioned in the end of the book. One was a journal article written by a sassy pediatric orthopedist who quotes Inigo Montoya, challenging people to understand p values and to apply and interpret them correctly. The other was an free, open source introductory textbook on statistics, thus allowing people to learn about p values and other statistical concepts.


Statistics Done Wrong


OpenIntro Statistics

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