Monthly Archives: February 2015

UPenn Webinar – ‘Mickey’s Got Measles’


Poor Mickey

Today, I attended the webinar, Mickey’s Got Measles, through the Live Faculty Lecture Series offered at the University of Pennsylvania. Today’s lecture focussed on the epidemiology of Measles, Herd Immunity, and Trends in Immunization was presented by Alison Buttenheim. Given the recent outbreak of Measles that puts 2015 well ahead of year-to-date infection numbers, it was very timely and an excellent lecture. If you have 50 minutes, I highly recommend that you check it out here.


Posted by on February 27, 2015 in Uncategorized


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Data say the Darndest Things

Apparently I’m late on the bandwagon for spotting this one, but twitter is atwitter with news that it’s cold in Washington D.C. right now. A propose of my last post, Chairman the Senate Environment and Social Works Committee and Amateur scientist, James Inhofe (R-OK), brought a snowball into the B-zSXewUIAATlKMSenate yesterday as data against the notion that Climate Change is occurring.  “We hear the perpetual headline that 2014 has been the warmest year on record,” he said.

Apparently he meant to say that climate can change, but that humans have no ability to effect this kind of change directly. As he states on his webpage:

“The climate is changing, as it always has been changing, and always will, there’s archeological evidence of that, there’s biblical evidence of that, there’s historic evidence of that, it will always change,”Inhofe said.

But more interesting to me is his data gathering.

datapoint 1: Snowball in Washington D.C. February 27

datapoint 2: “It’s very, very cold out.”

conclusion: It is unseasonably warm.

Senator Inhofe should spend some time with Darrell Huff. Huff’s classic text, How to Lie with Statistics is one of my favorite books. It’s a bit out of date with its examples, but still a fun, easy read. And more importantly, a good look at how data can be manipulated to appear to represent a picture different from reality.

CongressIt all comes down to data collection and interpretation. As Senator Inhofe did, I could easily gather some quick data from my immediate surroundings, ‘ 100% of the people I had breakfast with live in my house’ and derive a quick conclusion: ‘everyone in the world lives in my house.’

Or, I could go more subtly and use data closer to Sen Inhofe. Right down the hall in the other house of congress sit enough data to clearly demonstrate that employment numbers are climbing steadily with no sign of this so called ‘great recession.’ In fact, no sitting member of Congress has ever been unemployed while serving in congress.

Actually, the important point to make is that science can be done well, but it can also be done poorly. When it’s done poorly, it can be due to a number of reasons, such as poorly designed experiments, lack of appropriate controls, inaccurate data collection or poor choice of samples. All of these can happen without any intent to deceive, however, any experiment done with a conclusion already in hand is inherently partisan and is bound to produce unrepresentative results. Science should not be politicized, doing so generates flawed data and erodes public confidence in both our lawmakers and our scientists.

I have no problem with science being presented in congress, but I do think that it needs to be done responsibly and in careful consultation with those who understand the entire scientific process.

Does your congress member have a scientific advisor?

I’ve just written to my Senators and Representative to ask that question directly and I hope to hear back from them soon. I’ll be sure to post their answer here.

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Posted by on February 27, 2015 in Uncategorized


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Undisclosed Funding – or – How to Look Like You have Something to Hide

Apparently disclosure of funding sources does not seem to be a important to some researchers. In Paul Offit’s Autism’s False Prophets, Andrew Wakefield’s failure to disclose $800,000 given to him by Richard Barr’s law firm to link MMR vaccine to Autism is a major factor contributing to his decline and fall. In Wakefield’s case, he failed to disclose any conflicts of interest as required by the journal, The Lancet, where he published his work.

The Lancet’s Author Instructions state clearly what may constitute a conflict of interest and that anything giving the impression of a conflict should be reported to the editor.

A conflict of interest exists when professional judgement concerning a primary interest (such as patients’ welfare or validity of research) may be influenced by a secondary interest (such a financial gain). Financial relationships are easily identifiable … A conflict can be actual or potential, and full disclosure to the Editor is the safest course.

At the end of the text, under a subheading “Declaration of interests”, all authors must disclose any financial and personal relationships with other people or organisations that could inappropriately influence (bias) their work.

Wakefield’s failure to report the potential conflict of interest both to the journal and also to his collaborators. Unsurprisingly, both groups were upset when they learned about the money. Eventually, along with alleged ethical violations, Wakefield had his license to practice medicine revoked and his paper retracted.

524990main_FAQ10_fullOne would think that this would serve as a warning to those with similar perceived conflicts, suggesting the best course of action to be one of full disclosure. In the end, it is often easier to defend a potential conflict that the author puts forward him or herself, rather than having to retroactively explain why information was withheld and then try to demonstrate that any conflicts did not impact the quality or findings discovered.

Nevertheless, The New York Times has published an account of a very similar situation in climate science today. In their article, Deeper Ties to Corporate Cash for Doubtful Climate Researcher, the case of Wei-Hock Soon, a scientist at the Harvard-Smithsonian Center for Astrophysics who claims that variations in the sun’s energy can largely explain recent global warming is being investigated for the influence of cash on his findings.

The crux of the times article is that Soon…

… accepted more than $1.2 million in money from the fossil-fuel industry over the last decade while failing to disclose that conflict of interest in most of his scientific papers. At least 11 papers he has published since 2008 omitted such a disclosure, and in at least eight of those cases, he appears to have violated ethical guidelines of the journals that published his work.

The disclosure of Soon’s funding does not mean that his data were influenced by the money, however, keeping it hidden definitely leads to questions. Not the least of his problems comes from using terminology such as ‘deliverables’ to describe his papers and preparations for congressional testimony in communication with his supporters. The term ‘deliverable’ is defined by business as a “Report or item that must be completed and delivered under the terms of an agreement or contract.”

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Click here to see other great Calvin comics at go

Although these articles are not within the timeframe of the financial contributions alleged in the Times, these help to clarify Soon’s position on climate science. These publications include:

“Recent Warming is not Historically Unique”.  Callie Baliunas & Willie Soon (2001.04.17)Capitalism Magazine. In which he concludes “The facts are simple. The Little Optimum and Little Ice Age were real. They were also widespread over the globe. The twentieth century is not the least bit climatically unusual. So why the recent media hysteria that the twentieth century is the warmest of the last 1,000 years?”

“Variable solar irradiance as a plausible agent for multidecadal variations in the Arctic-wide surface air temperature record of the past 130 years” Volume 32, Issue 16. August 2005. Geophysical Research Letters. As the title suggests, this article attributes recent climate data to “features that are highly correlated with the Sun’s intrinsic magnetic variability especially on multidecadal time scales.”

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Posted by on February 25, 2015 in Uncategorized


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Pulmonary Anatomy and Physiology

Chapter 21 of Carol Porth’s Pathophysiology presents an introduction to respiratory anatomy and physiology. The following two chapters present pathologies that affect the system. I’ve outlined here the basics of lung A&P as notes from my reading of the chapter and I thought I would present that here as a guide for any of my students. I have yet to outline the second and third chapters, but there is a skeleton of conditions that we will cover. It is also worth noting that I expect my students to be able to recognize and identify the structural components of the respiratory system even though I did not include these elements in my outline …

Pulmonology Outline

  1. Structures and Functions (Chapter 21)
    1. Structures
      1. Upper Respiratory System
      2. Lower Respiratory System
  • Tissue and Cell types
    1. Ciliated columnar epithelial cells
    2. Goblet cells
  1. Alveoli – terminal air spaces in the lung & site of gas exchange
    1. Type I Alveolar Cells – this squamous cells making up ~95% of the alveolus
    2. Type II Alveolar Cells – secretory cells that produce surfactant, also serve as progenitors of Type I cells
    3. Alveolar Macrophages – responsible for removing organisms and debris that penetrated the lungs
  2. Pleura – a double layer of membrane lining the inner thoracic cavity and covering the lungs.
  1. Functions
    1. Conducting Airways
      1. Purpose: To deliver warm, moistened, cleaned air to Respiratory Tissue
    2. Respiratory Tissue: To perform gas exchange (O2 and CO2)
  • Gas Exchange
    1. Ventilation – Inspiration and Expiration
      1. Mechanically, ventilation depends upon the structure of chest cavity – i.e. it is entirely closed with the only opening to the exterior being the trachea
      2. Inspiration occurs as the diaphragm pulls down and opens the
    2. Perfusion – flow of blood through the alveolar capillary bed

Ventilation and Perfusion must be matched in order to optimally oxygenate blood in the lungs.

  1. Gas exchange (described by the Fick Law of Diffusion)
    1. V = [SA x KD (P1-P2)] / T
    2. Both O2 and CO2 are transported by blood
  2. Hb Dissociation Curve
  3. Partial Pressure – the pressure of some component of a gas. By definition, all partial pressures add up to the total pressure of a gas. (i.e. if a gas is comprised of O2 and CO2, then the partial pressures of O2 and CO2 must add up to the total pressure of the gas)
  4. The O2 / Hb dissociation Curve
    1. Measures the amount of O2 bound to Hb at any specific PO2
  5. Lung Volumes & Capacities (summarized in Table 21-1)
    1. Tidal Volume – volume of air going in and out of the lungs with each resting breath
    2. Total Lung Capacity (TLC) = tidal + inspiratory reserve + expiratory reserve + residual volumes
    3. Vital Capacity = tidal + inspiratory + expiratory reserve volumes
    4. Dead Air Space – Air in the lungs that does NOT participate in respiration


  1. Why is arterial (rather than venous) blood used to measure blood gases?
    1. What would venous blood gases measure?
  2. Using an O2 / Hb dissociation curve, show how Hb effectively carries O2 from the lung to the muscles, where it is released to myoglobin for use in respiration.


  1. General Issues
    1. Pleura effusions– are accumulations of fluid in the space between the pleural membranes around the lungs
    2. Infant Respiratory Distress Syndrome – alveolar collapse in young infants (esp prematures) due to lack of surfactant
    3. Dyspnea – general term for difficulty breathing. Can occur due to primary lung disease, heart disease, or neuromuscular disorders affecting the respiratory muscles
  2. Infections
    1. Pneumonia
    2. Influenza
    3. Fungal Infections
    4. Tuberculosis
  3. Congenital Problems
    1. CF
  4. Acquired Problems
    1. COPD
    2. Pulmonary Hypertension – causes and outcomes
  5. Respiratory Distress Syndrome
  6. Respiratory Failure
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Posted by on February 23, 2015 in Uncategorized


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The Hardest Working Organ of the Body

Like the James Brown of the Body

As I started grading the first Pathophysiology Exam on Cardiovascular Function in Health and Disease, the first material I saw was in answer to my questions about the flow of blood through the heart and to the rest of the body. I can’t say that I was happy with the results, but I want to emphasize that this is very basic material that we discussed and outlined in our class, but that I had also assumed was covered in Anatomy and Physiology last semester. After two passes through this material, it should be easily accessible in every student’s mind.

As a reminder of these functions and the flow of blood, here is Khan Academy’s summary of this material:

I believe that that is important foundational material, and you may have a pop quiz on it at any time.

stay on the scene

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Posted by on February 21, 2015 in Uncategorized


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Darned Veins

Admittedly, watching this video made my legs ache and become fidgety, but it does do a good job at providing a simple explanation for varicose veins and how they can be treated (removal). Since this is one of the topics covered in this unit that we did not discuss in class, I thought it made sense to post this here.

Sit back, elevate those legs and enjoy…


Posted by on February 18, 2015 in Uncategorized


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Mickey’s got Measles

A webinar from UPenn

I think this webinar is free and available to anyone.

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Posted by on February 15, 2015 in Uncategorized


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