20 May 2018: What Do Scientists Do?

Progress Report
20 May 2018

What do scientists do? With many questioning the value of scientists regarding climate change, vaccinations and other matters, I thought it might be worthwhile to document my scientific life. Before I entered medical school, I had limited exposure to scientists in a social setting, and even now, talk to few people outside of my professional life who write papers or do research to advance scientific understanding.

Alas, I am not a typical scientist. I graduated medical school (University of Michigan 1983) and did a residency and fellowship in pathology (Wayne State University 2000). Most scientists work for a university or research institute, but I do not. I own a business which publishes a free online pathology textbook and am currently its Editor, although I recently hired a Deputy Editor who is much smarter than me and more attuned to the academic world.

Here are the projects / papers I am working on:

1. The Laws of Complexity and Self-organization: A Framework for Understanding Neoplasia (see natpernick.com/TheLawsJune2017.pdf).

This was my first complexity and cancer paper, initially published in 2011 and updated in 2017. I submitted it to several pathology conferences but it was repeatedly rejected. In fairness, it did not fit any of the categories for papers at the conferences, which logically suggests that the paper will not be well received.

This paper was accepted for presentation at the International Conference on Complex Systems in Boston in July 2018 (see http://www.necsi.edu/events/iccs2018/). I had to shrink the abstract (summary) to 250 words. I am starting my preparation for a 12 minute talk, which will be followed by 3 minutes of questions. The purpose of the talk is to get feedback, leading to new insights, corrections of errors and possibly new directions to study. The questions often are impossible to answer in that setting other than “I don’t know, I will follow up”. Sometimes, the questioner is really giving a speech about his/her own work.

I also submitted my complete paper for their published proceedings. Using their very wide margins my paper was 18 pages, which I have chopped to their limit of 10 pages.

2. How Cancer Arises Based on Complexity Theory (see natpernick.com/HowCancerArises.pdf)

A revised abstract of this paper (currently 37 pages) will be submitted to the 2019 ASCO conference (American Society of Clinical Oncology) in May 2019. I tried in 2018 but the hurdles were (a) I had to find an ASCO member to sponsor me and (b) I had previously posted the paper on my personal website and prior publication was prohibited. But I eventually found a sponsor and will revise the paper for 2019 based on the findings in the other papers I am working on, as described below. I will also try to find a medical center (Wayne State, University of Michigan, Oakland University) where I can give a talk about it, to get feedback.

3. How lung cancer arises based on complexity theory
I am writing papers on the  top 20 leading causes of cancer death in the US, beginning with lung cancer, applying the knowledge / theory derived from my first 2 cancer and complexity papers. This paper has been through many drafts, and is now complete. I submitted an abstract for this paper to a pathology conference for presentation, and they should accept or reject it this month for an October 2018 conference.

4. How colon cancer arises based on complexity theory (under development)
I am working on the first draft of this paper. The plan is to finish this paper by September 30, 2018, completing one paper every 3 months. At this rate, it will take 5 years to write papers on the top 20 causes of cancer death.

5. Preinvasive neoplasia
I published a Letter to the Editor (see http://www.archivesofpathology.org/doi/pdf/10.5858/arpa.2017-0581-LE) about how complexity theory suggests that tumors such as glioblastoma, which currently do not have a known premalignant condition, likely do have one. I suggested that although we have not identified microscopic features of premalignancy, there probably are molecular patterns.

This was my first Letter to the Editor of a scientific journal in many years. It is a quite complicated task compared to preparing a Facebook post. There is much back and forth with the editor over formatting and references. Sometimes their copy editor changes the text to make it more “readable”, although in my case they completely changed the meaning. Fortunately they corrected it.

That’s it for now.

10May18: Preinvasive cancer, update

I received this response to my prior post about Preinvasive Cancer, see https://natpernickhealth.blogspot.com/2018/:

Thanks Nat. What can you say about the implications of these ideas for treatment of cancer?

This was my response: 

Better understanding of how cancer arises suggests new treatment options. When I was a pathology resident (1995-2000), there was no known precursor lesion for ovarian cancer. Subsequently, by studying BRCA1/2 mutation carriers, it was discovered that there is a premalignant condition, but in the fallopian tubes (https://www.ncbi.nlm.nih.gov/pubmed/22706539), suggesting that their removal (salpingectomy) may reduce ovarian cancer risk (https://www.ncbi.nlm.nih.gov/pubmed/25628372). Similarly, identifying precursors for glioblastoma may suggest new therapies to prevent or treat this devastating disease.

6 May 2018: Preinvasive cancer

I recently published a Letter to the Editor, entitled Focusing on Preinvasive Neoplasia, that may be of interest. Neoplasia is the abnormal growth of tissue due to uncontrolled division by one or more cells. It includes cancer as well as benign tumors. Preinvasive neoplasia means growths that have not yet demonstrated the ability to infiltrate adjacent tissue, a property relatively specific for cancer.

To understand cancer, it is helpful to think about how life arose. According to Kauffman, life is the emergent collective property of a modestly complex mix of biomolecules (DNA, RNA, proteins and others), confined to a closed space, which catalyze each other’s formation (The Origins of Order 1993). Networks of biomolecules with this property are relatively resistant to change from internal or external stressors (The Laws of Complexity 2017). In addition, natural selection has added additional control features that make deviations less likely. As a result, a cell cannot quickly change from normal to malignant. I previously proposed that most cancers are caused, typically over decades, by nine chronic stressors (chronic inflammation, carcinogen exposure, reproductive hormones, Western diet, aging, radiation, immune system dysfunction, germ line changes and random chronic stress / bad luck), acting together and in the appropriate context (How Cancer Arises Based on Complexity Theory 2017).

Cancer arises through stepwise progression. Although intuitively it might seem that the microscopic appearance would be slightly different at each step, this may not be true. For example, glioblastoma and Hodgkin lymphoma have no known intermediate or premalignant states based on microscopic examination. However, the Letter to the Editor suggested that intermediate states may be identified based on analysis of molecular patterns. They are also predicted by complexity theory, which discusses the requirement for stable intermediate states for cancer to develop.

4 April 2018: Living without a Car in the Suburbs

Living without a Car in Huntington Woods
4 April 2018
By Nat Pernick

It has been almost one year since I gave up my car to ensure my daughter had reliable transportation to take to her summer job in Alaska. This essay describes the advantages and disadvantages:

Here are the advantages:

1. I have a better life, albeit a slightly different one. I still go to work, shop, have a social and family life. I am part of the resistance, and doing something about climate change. I am not going back.

2. Most people have concerns that don't apply to me including shoveling the driveway after a big snow, clearing off the car, warming up the car, driving in bad weather, bad traffic, bad drivers, parking, car maintenance, car insurance, tickets, accidents, stolen cars and getting a new car.

3. I can relax when traveling - read, sleep, talk to the driver or do nothing.

4. There is less running around, because I just don't do things unless important. I shop online and do grocery shopping after another activity, or when I know I will have a driver anyway. I sometimes use Uber / Lyft for deliveries (I pay by credit card and have them pick up the product and deliver it to me).

5. I have a much healthier life. I bicycle more (April to November), walk to / from the bus and anywhere within a mile (sometimes longer). I don't miss driving because I don't view it as an option.

6. I have a more interesting life. I talk to Uber / Lyft drivers about their lives - most want to talk.

7. This life may be cheaper - no car payment, gas, maintenance, insurance or parking. It costs more in the winter because I do not bike and dislike waiting for the bus or walking in the cold.

Here are the disadvantages:

1. Waiting for the bus, particularly in the cold, is not pleasant. I wear up to 7 layers - T shirt, long underwear shirt, regular shirt, sweatshirt, 2 sweaters, winter coat plus light neon yellow jacket to be seen; double socks + boots, hat, balaclava, 2 scarves, long underwear pants and regular pants. The SMART bus has an app with a tracker that tells where the bus is, which usually works. The bus is usually on time. Lyft / Uber is my backup.

2. I may wait 15-20 minutes for Uber / Lyft drivers in West Bloomfield, but elsewhere the wait is usually 10 minutes or less. I can see how far away the driver is on the app. Rides can be scheduled in advance, such as airport runs. Drivers may arrive early, particularly at 5am, but they will wait for me to come out at the designated time.

3. The “surge” for Uber / Lyft can be frustrating. Costs can vary dramatically within a few minutes. A few months ago, the cost for a weekday afternoon trip from Ann Arbor to Southfield moved wildly from $75 to $200 before I snagged it at $50. Booking in advance may avoid this problem.

4. Taking people out to eat is different. It's not hard - it helps to know the ultimate destination, then program the first pickup and the restaurant, but it takes a little getting used to.

5. Shopping requires more planning. I don't want to use Uber / Lyft all the time, so I mentally divide shopping into trips where I can walk or bicycle (and don’t buy more than I can carry) and those that in which I will have a driver (and load up). If possible, when I am going to be at a restaurant and use Uber / Lyft to get back, I try to shop nearby before I head back.

6. You must be willing to be different to do this; most of your friends and family will consider you odd or a little crazy. Dating is more difficult - women do not like that I do not have a car. Some people consider me a burden, even though I have a reliable driver that can pick me up in 10-15 minutes, but that’s how they feel.

I am happy to answer your questions at NatPernick@gmail.com.

4 January 2018: Even NBA Players are going vegan

The most common response I hear to my veganism is "where do you get your protein?" This is not surprising - we were brought up to believe that every meal should be centered on protein. However, we now know this is false; as the American Heart Association says "You don't need to eat foods from animals to have enough protein in your diet", link.

However, stronger evidence for some may be recent stories of National Basketball Association stars who have switched to a vegan diet, and feel healthier, lighter and faster.  For example, Kyrie Irving said "So my energy is up, my body feels amazing. Just understanding what the diet is like for me and what’s beneficial for me for having the highest energy out here and being able to sustain it at a very high level.” link. If these athletes do well with a vegan diet, the rest of us should also.

My concern is about the danger of the Western diet (high fat, low vegetables, low fruit), which is one of the chronic pressures that  I believe causes cancer (Pernick: How Cancer Arises Based on Complexity Theory, 2017), as well as heart disease and other chronic diseases.

The world has severe problems. To adequate respond, each of us needs to be our best, which means we should be as healthy as possible. The evidence is clear - our diets should focus on vegetables, fruits and whole grains (Pernick, The Good, The Bad and The Ugly, 2017)

27 December 2017: Food: The Good, The Bad and The Ugly

Food: The Good, The Bad and The Ugly

or Stop Eating Empty Calories

By Nat Pernick, M.D.

27 December 2017

This time of year we focus much of our time and energy on eating, so it is important to think about what we are eating and how it affects our health. All food is not created equal. In my recent paper, How Cancer Arises Based on Complexity Theory, I describe the Western diet (high fat, low fiber, low consumption of vegetables and fruit) as one of nine “chronic pressures” that cause most cancer cases. With apologies to Sergio Leone, in this paper I divide food into The Good, The Bad and The Ugly.

Most Americans can now easily get enough calories with all required nutritional components through a balanced diet. High quality food, not contaminated by microorganisms, parasites or toxins, is relatively inexpensive and available 24/7. Thus, we need not worry about eating to survive. Instead we should focus on eating to maximize our health.

The “good” foods are not controversial: vegetables, fruit and whole grains. This is the recommendation of US governmental agencies (Health and Human Services, USDA), the American Cancer Society and the American Heart Association. Each meal should be centered on eating vegetables, fruit and whole grains - they should not be an afterthought. This is a complete reversal of how we were taught to eat, in which protein must dominate a meal, and then we throw in some vegetables and fruit. It necessitates a major shift in our thinking and behavior that will require time to implement but is important for our optimal health.

Some foods are “bad” because they are simply empty calories. They don’t provide the anti-cancer, anti-heart disease factors found in vegetables, fruit and whole grains. Most people are obsessed with protein; their meals must be centered around meat, poultry, fish, eggs or dairy. But as the American Heart Association notes, “You don't need to eat foods from animals to have enough protein in your diet. Plant proteins alone can provide enough of the essential and non-essential amino acids, as long as sources of dietary protein are varied and caloric intake is high enough to meet energy needs.”

Foods are “ugly” that statistically have been found to contribute to cancer, heart disease or other serious diseases. They include foods high in fat, sugar, refined grains or that are highly processed. Many of these ugly foods are considered to be “proinflammatory” according to The University of South Carolina Cancer Prevention and Control Program, which developed the dietary inflammatory index (Shivappa 2014a). A proinflammatory diet is associated with a higher death rate due primarily to digestive cancer, cardiovascular disease and chronic obstructive pulmonary disease. Food groups associated in one study with the highest inflammatory index were butter, beer, coffee, fried food, liquor, high sugar beverages and french fries; those with the lowest inflammatory index were vegetables other than potatoes, low fat dairy, fish, fruit (not juice) and nuts (see Table 2).

Eating healthy is a continuous process of behavior change that takes years to optimize. We should choose more healthy foods, limit empty calories, stop eating when 70% full, resign from the “clean plate” club, avoid processed food, not eat for psychologic reasons, avoid unhealthy food even if easily available and monitor our caloric intake to maintain a body mass index (BMI) of 18.5 to 24.9.

Let’s start today!

26 November 2017: How Cancer Arises Based on Complexity Theory

I have written a new paper, How Cancer Arises Based on Complexity Theory, that I have been working on for many years. It is 37 pages and technical, but there is an Executive Summary that is easier to read. See http://www.natpernick.com/HowCancerArises.pdf.

Send comments to NatPernick@gmail.com (but unfortunately I cannot give personal advice on an individual's medical problems).