dr.ricky online

Tag: science

  • COVID-19 Tests

    COVID-19 Tests

    Coronavirus in Texas
    Snapshot from Texas Tribune tracking of coronavirus testing in Texas.

    Before May 14, 2020, Texas reporting of coronavirus test mixed results from two different kinds of tests: the PCR tests and the antibody tests. The PCR test looks for the presence of the genetic material of SARS-COV-2, it answers the question: “Is the patient infected and contagious?”

    The other kind, the antibody test, looks for the presence of early antibodies in the blood. It answers the question, “Has the patient been infected in the past?” At this time, we do not know if the presence of antibodies confers immunity to the virus. 

    Mixing the two results is highly problematic. It can make it appear that there are fewer infectious individuals, since antibody tests tend to come up negative more, and that inflates the denominator. Part of the reason why Gov Abbott proceeded with Phase 2 in reopening Texas activities is be attributed the increasing rate of detected infections to an increased number tests happening. However, that is not the case – much of this increase is due to mixing of the antibody tests. The rate of PCR tests is almost flat, but the rate of new infected cases continue to rise. 

  • Remdesivir Hopes

    Remdesivir Hopes

    • Remdesivir is an experimental antiviral drug made by the company Gilead. Designed to act against the RNA driven RNA polymerase enzyme in RNA viruses, it was initially tested on Ebola.
    • Since coronaviruses are also RNA viruses, Remdesivir is expected to work on them, too.
    • Published in The Lancet: Clinical trial of remdesivir in adults with severe COVID-19
      • Randomized, double-blinded
        • 237 patients
      • Placebo controlled
      • Multi-center
        • 10 hospitals in China
      • Bottom line
        • Any improvement was not statistically significant

  • Visualizing NCAA GPA data

    On 5 Sept 2018, the NCAA Research team tweeted out this chart  :

    It reports the average core high school grade point averages (GPA) among NCAA Division I freshman student athletes. So, a bit of a background – the National Collegiate Athletics Association governs just about all collegiate athletic programs in America, and the Division I schools devote the most money and resources to their athletic programs. A great deal of attention is thus focused on the Division I programs, almost to the detriment of the others (it goes all the way to Division III). The GPA is usually used as a measure of academic performance, though it may not reflect the difficulty of the coursework. But this chart is an egregious use of “infographics” to mislead rather than to bring insight to data:

    • Without a Y-axis to denote scale, the use of bar charts here visually make it appear that 3.77 is 7x higher than 3.07, when it’s actually far smaller in scale on standard 4.0 GPA scales (it tops out at 4).
    • The categorical use of the different sports makes it appear that it is the independent variable, and that GPA is what is being measured. But since the GPA was measured in high school, it actually precedes the sport.
    • Because of this switch in dependent and independent variables, a reader may interpret some form of causality – implying for example that choosing fencing will lead to better academic performance.

    Good data visualization should serve to bring new insight to the data that isn’t evident from just looking at the numbers. The GPAs considered here range between 3-4, which is letter grade B-A, quite above average academically, and that is unsurprising. These are the high school GPAs of student athletes recruited to Division I schools, arguably the most competitive programs. This is a measure of their past academic performance, but doesn’t say anything about how the sport chosen affects their current or future performance. The data, however, informs something about the sports programs themselves. Using the exact same data, I replotted the chart.

    High school GPA of males and females as recruited into NCAA Div 1 sports programs.

    The chart is in two parts – on the left is the section where a sport is available for both males and females, and on the right is a smaller section for sports that are gender specific. The axes go from 3.0 to 4.0, indicating the spread within this range. Sports are labeled accordingly.

    A linear relationship exists between enrolled female and male student athlete high school GPAs  – regardless of sport program. What this means is that at least within each sport, they apply their GPA criteria roughly with the same proportion to both genders. Which probably means that the sports programs recruit from the same communities for both men and women, that is fencing programs put a heavier emphasis on high GPAs for admission than basketball programs do, regardless of gender. But we see a stark difference in the GPA cutoffs between genders: almost all athletic programs recruit females with a GPA above 3.5, while more than half athletic programs enrolled male student athletes with GPAs below 3.5. In fact, all the male specific sport programs – baseball, wrestling and football – recruit with GPAs below 3.5. One cannot make definitive interpretations without further details on how the data is collected, but this implies that the barrier to entry to a collegiate athletic program, at least based on GPA, is significantly lower for males than for females. While some may think that this indicates superior academic performance among female student athletes, it could be an indicator for a systemic bias when recruiting for women across all sports programs.

  • Volleyball and Newton

    Volleyball and Newton

    I ignited a fierce debate a few months back by simply asking:

    “the higher you jump, the more force you land with, right? (Yes, it’s a trick question)”

    I posed the question shortly after the McKibbin Brothers released their video on dealing with knee pain, and a trainer was explaining that you could land with up to 5x body weight in force (about 45 seconds into the video) – which then rolls into this rabbit hole about the equivalent of elephants on your knees. Now how could this be?

    So, a lot of this comes from the incorrect use of the term “force”. Basic physics, which most people should know, force acting on an object is defined by it’s mass multiplied by its acceleration, or

    Force =mass x acceleration 

    In most cases, we are talking about the force of gravity, which imparts the same acceleration to objects regardless of their mass (which is why in a vacuum, a feather and a bowling ball will fall at the same rate). This is an appropriate situation, because for a jumping athlete, that impact with the ground is really the same question about falling from different heights. So, what is acceleration? Acceleration is a change in velocity over time. The higher up you are, the more time gravity has to affect you, and so by the time you get to the ground, your velocity is higher. But what happens on impact? The velocity changes, from whatever it is imparted by gravity, to zero. This, too is a type of acceleration, and it’s this acceleration where the force comes from. So, let’s look at this equation again:

    F=ma = m (starting velocity-ending velocity)/time

    if we rearrange it:

    F x time = mass x change in velocity 

    The missing element in this discussion is how much time is being taken to bring the falling athlete to rest. Since mass and the change in velocity aren’t changing, we need to look at the relationship between time and the amount of force applied. The assumption in all the landing measurements is that the athlete stops on contact with the ground – hence, time is set to be very small. Thus, the amount of force goes up to effect the same change in velocity (the term, I believe, is impulse). But if we are able to extend the amount of time landing, the force acting can go down.

    It’s like dropping your phone from various heights. But how can a protective case allow it to drop without as much damage? That’s because parts of the phone can continue to fall as the case deforms, increasing time, decreasing force, and protecting the phone itself. Likewise, the flaw in the force plate measurements is not considering that a body is an elastic object and can redistribute the energy of impact. It only measures the force based on a very short period of time, and that will bring the force measurement up.

    In sand, since falling time continues longer than on an inelastic force plate, the force will decrease. But there are still more things to do to dissipate that energy of impact. Now will those exercises actually help? That’s a discussion for another day.

  • Falsifiability

    Falsifiability

    In an earlier posting on detecting the signs of pseudoscience, I quoted an article which mentions unfalsifiability as a property. This is actually a pretty good early test for understanding if something is science-based, and attends to a common misunderstanding about the scientific process.

    Whenever the phrase “scientifically proven” is used, your critical thinking alarm bells should go off – because much of scientific progress is based on disproving things. Unambiguously proving a hypothesis is actually quite difficult and rare, but what happens more frequently is disproving the counter-hypothesis, because all you need is a simple break in the logic or a sample contrary to it. When a conjecture or concept withstands extensive attempts at disproof is when it enters the field as a major theory.

    Let’s try this out. Take the statement that “All cars have four wheels”. It’s kind of difficult to figure out how to prove this, but finding a single car that has three or five wheels is sufficient to disprove it. A single example of an object falling at a different acceleration rate would be sufficient to disprove what we know about gravity, or a single core sample of fossils forming at a different order would overturn evolution – but after hundreds of years of attempts, these theories have stood their ground. And good scientists continue to think about ways to show that something accepted as true may be false. Which is an important feature – falsifiability is key. And the failure of these tests add to our confidence in these major theories. If you cannot devise a test that will sufficiently disprove the statement, it’s likely outside of science, no matter what the trappings.

    Let’s look at an example of something which is unfalsifiable. This is taken directly from the product description page of VitaminShoppe, a prominent sponsor for the AVP (US domestic pro beach volleyball tour):

    Naturally detoxifies and boosts your immune system

    Can you think of a test that will falsify this statement? What kind of trial could be done to definitively show that something does not “boost the immune system” or “naturally detoxify”? Near as I can tell, this falls into the category of unfalsifiable, sort of like the claim that a machine detects ghosts. When evaluating promises made through coaching advice, improve your critical thinking skills by asking how you can falsify a statement. And this is how we progressively increase confidence in practice.

  • Recognizing Sports Pseudoscience

    Recognizing Sports Pseudoscience

    In a recent discussion with BJ Leroy of USA Volleyball, I encountered a paper by Bailey et al (2018) published in the open access journal Frontiers in Psychology, titled  “The Prevalence of Pseudoscientific Ideas and Neuromyths Among Sports Coaches“. Since the journal is open access, the paper is readily available to download and read. The paper is basically a study on the pervasiveness of pseudoscience among sports coaches, even with ideas that have been long established to be untrue. Dr. Ed Couglin wrote a layperson friendly (albeit Irish-centric) interpretation of the paper.

    Suffice it to say, pseudoscience is rampant in sports culture, and pervasive in beach volleyball. I’d say much of the sponsor economy is built around pseudoscientific beliefs, but I’ll address those specific examples in future articles. What I’d like to share here is an excerpt from the Bailey paper, that outlines some properties of pseudoscience which will help you identify it. Bear in mind, this also applies to how people may argue their points online.

    • Unfalsifiability
    • Absence of self-correction
    • Overuse of ad hoc immunizing tactics designed to protect theories from refutation
    • Absence of connectivity with other domains of knowledge
    • Use of unnecessarily unclear language
    • Over-reliance on anecdotes and testimonials at the expense of systematic evidence
    • Evasion of genuine peer review
    • Emphasis on confirmation rather than refutation.
  • How extinction shaped the Australian outback

    How extinction shaped the Australian outback

    The story in the Atlantic.

    When extinction is spoken about, it’s almost exclusively in terms of land based vertebrates, usually mammals, which form a tiny portion of the biodiversity of the planet. And even that attention is heavily skewed towards “charismatic megafauna” – animals that are cute and big enough to be visible. But it’s the extinction of the small and spineless that can shape how the world works. The very oxygen rich atmosphere of the planet is possible in part due to the extinction of anaerobic microbes, and how the extinction of oysters in the Hudson River changed the lives of New Yorkers.

  • BCAAs

    BCAAs

    Most people obsessed with BCAAs don’t even know what an amino acid is.

    FYI: BCAA = branched chain amino acid

  • Vaccination Exemptions in the USA

    Vaccination Exemptions in the USA

    Vaccination Exemptions in the USA

    The United States Centers for Disease Control (CDC) publishes a Morbidity and Mortality Weekly Report, and in it they track the vaccination rates in different states for children enrolled in kindergarten, and an interesting table is the report on the rate of exemptions from vaccinations, as well as the reason behind it. Granted, different states have varying laws with regards to vaccination requirements, and some allow separation of the exception reasons between medical, religious and other philosophical reasons, which makes getting consistent data problematic. But we do have good data for the 2015–2016 enrollment, and the 2016–2017 enrollment.

    The reports themselves are straight tables, but data visualization helps in teasing out the meaning there.

    2016_2017_CDC
    Summarizing the CDC reports between 2015-2016 and 2016-2017 school years for the rate of vaccine exemptions among kindergarten students, divided by state. A number of states are excluded. Blue dots are for the earlier year, red dots for the data a year later. Note that for herd immunity, the general consensus is about 95% of the population should be vaccinated. The Y-axis displays the ratio between medical and non medical reasons given for the exemption. Note that with the exception of DC, all states have ratios below 1, which means that more people are seeking exemptions for religious or philosophical reasons than for medical ones. 

    This data is dense, but highlights some problematic states, like Oregon, which has an unusually high rate of vaccine exemptions, and most of them for non medical reasons. Let’s look at the trend from year to year.

    Change year
    The arrows point in the direction which portend better public health trends: a drop in the rate of exemptions, and an increase in ratio of medical to non-medical reasons. California and Vermont seem to be on the right track, but most of the country is actually inching in the wrong direction, with Nevada and Wisconsin leading the way. 

    Sadly, the antivaccinationist movement seems to be permeating the mindshare, just by manipulating doubt and exploiting parental concern. Non medical exemptions are a key to this degradation of our public health system.

  • The mythical 300 jumps

    The mythical 300 jumps

    This article has moved to a new location.

    Wilson, the sporting goods company, posted an ad on Instagram declaring

    DURING A MATCH, VOLLEYBALL PLAYERS ON AVERAGE JUMP 300 TIMES.

    The ad is accompanied by an illustration that depicts female beach volleyball players, which implies that this number applies to beach volleyball specifically. This number appears unusually high, so I inquired as to the source of the number.

    https://instagram.com/p/BedVH6rAMp0/

    Michelle Magsamen checked with the marketing department of Wilson, and provided three links that are the alleged source of this figure:

    1. From Redbull.com – 8 stats that show why beach volleyball is the best

    A beach ’baller jumps on average 300 times per game.

    In this article, the author Jonno Turner reports an average of 300 jumps per game – not per match as reported by the advertisement.

    1. From Schoolgamesfinals.org – this is an article written to encourage people to watch indoor volleyball at the school games of Loughborough University. The stat is reported at 300 times per match, but with indoor volleyball, there are up to five games per match, unlike the three set maximum for beach volleyball.
    2. A contributing article in Volleywood.net – written as “10 fun facts about volleyball”, it is a direct reprint from an article Ten fun facts about Volleyball from the website 10-facts-about.com. Fact 4 is listed as:

    Most volleyball players jump about 300 times a match.

    In all likelihood, this last link is the main source of this number, and was continually misinterpreted by the other writers to fit their current narratives. I tracked 10-facts-about.com to a company in Sweden called NanOak Technologies, appears to be a “content farm” – they produce these sites and brands like 10-facts-about and Wisefacts – ostensibly pouring out random interesting “facts” to attract page views, and therefore sell advertising. There is no verifiable vetting of this information, but they are cherrypicked to most likely to appeal to confirmation bias.

    In effect, this is fake news – unvetted information that is twisted just to profit from the misinformation. Though Wilson may have citations, those sources are ultimately unreliable at best.

    So what is the real number?

    Is there real data on the number of times beach volleyball athletes jump on average in a match? Much more peer reviewed data studies the indoor game, but there are some data on beach volleyball.

    1. Loren Anderson of Rise Volleyball Academy did some research on this during a discussion on the Facebook group Beach Volleyball Coaches. He tracked the all the jumps during the gold medal match at the FIVB 4-star beach tournament in the Hague between USA and Brazil. He counted 201 total jumps for all players, averaging 50 jumps per player over the match (~25 jumps per set).
    2. Loren also found a 2009 report from Slovenia (Turpin et al, 2009) that tracked the number and types of jumps during four matches of elite beach volleyball players during a tournament in 2006. They report a total average of 167.5 jumps per match (with a very large variance of 38.5), which comes down to about 40 jumps per player per match, or 20 per set.
    3. Perhaps most useful is that the FIVB report The Picture of the Game, last produced to statistically analyze 12 men’s and 12 women’s matches, and provides some pretty detailed stats and heat maps of defense. On page 37, it reports an average of 405.8 jumps per match (162.3 per set) for women, and 396.8 jumps per match (158.7 per set) for men. Dividing between the four athletes on the court, that comes down to ~40 jumps per set – which is consistent with the Turpin et al report.

    Granted, these are for elite volleyball players playing in high stakes tournaments, but it’s still nowhere near the 300 jumps per match average per player. In fact, only if you account for the jumping of all players on both teams in beach volleyball can you come close to this average number.

    Based on this research, the average number of jumps per player per match in beach volleyball seems to be between 40–80.

    Follow on Twitter and Instagram as @volleysensei