Category: Science

Issues on science.

A conversation with vaccine hesitancy

Excerpted.

[VaccineHesitantFriend]: I completely understand that. We are lucky to be here in the US. And I’m doing my part by not getting the vaccine, so those other countries can have it. Sorry I don’t put anything into my body without fully understanding it, and not going to start now. That’s my personal choice, not a privilege.

[me] I’ll be glad to help you understand the vaccines. Please feel free to post questions and I’ll do the underlying research. You may have a legitimate concern that we have missed and I’ll be glad to learn something from it. Scientists from the American Society for Virology have volunteered their time to have online town halls to help explain vaccination.

[VHF]: I really appreciate that. And a question I ask a lot of people is why can’t we put all this effort into curing cancer? Or getting rid of child slavery? Just seems interesting to me that all these scientist and government officials group together to cure a disease that other scientists created. Would really love to hear your answer on this. The only answer I ever get is… there’s just too much money being made.

[Me] Important distinction: a cure deals with people with a disease, and a vaccine is about preventing the disease in the first place. There’s no evidence that COVID19 was engineered or created by scientists – the genetic sequence of the virus available to the public (as is most of the publications), and we can check for tell tale marks of engineering. They aren’t there. But proving a negative is rather difficult, so as more evidence arises, we can follow up. The mRNA vaccines are actually partly developed to prevent cancer, and it just turns out that COVID-19 is the first wide application of the technology. More applications will come in the future. Note that this attached review is from 2018 – the mRNA vaccines have been in development for a while – https://www.nature.com/articles/nrd.2017.243

[VHF] Well this is where I part ways from the discussion. It was absolutely made in a lab. And your boy Fauci is a big fat liar. Thanks for the info and the responses.

There’s more to say about the question of money and the profit motive, but the issue was never really about vaccination, or the nature of the technology. Once a narrative is threatened, the conversation was shut down.

2021-06-24
COVID-19 Tests

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.

2020-05-25
Thelytoky in the honeybee
A Single Gene Causes Thelytokous Parthenogenesis, the Defining Feature of the Cape Honeybee Apis mellifera capensis, by Yagound et al, 2020
- That means virgin birth.
- A single gene controls the switch from sexual to asexual modes of reproduction
- The scientists used an impressive combination of classical backcrossing and genomic data to pinpoint the gene, and build of model of how virgin birth can happen.
- And it’s in bees.
- Just cool science.
2020-05-08
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
2020-05-01
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.

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.
2018-09-06
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.

2018-08-06
Becoming height neutral

The website Beachvolleyballspace covered the recent FIVB Gstaad Major with an article celebrating the winners, the currently top ranked Canadian team of Paredes and Pavan claiming the gold. The article title (Canadian women dominate Gstaad Major – Japan challenges top teams) makes special mention of the fifth place Japanese team of Murakami and Ishii. Why? Was it a remarkable breakthrough performance?

The whole latter half was spent mentioning how much shorter the team was relative to their opponents. That’s it. Beach volleyball culture venerates height so much that it’s often the first and only statistic mentioned for players. No mention that Murakami is a 7 year veteran of the FIVB circuit – it’s newsworthy because they were supposed to lose.

Height discrimination is so pervasive that coaches will refuse to consider athletes just for being too short. I’ve spoken with talented young women who have already given up the dream of playing beach volleyball for college because they’ve been told time and again that their genetics will simply not give them a chance. Players constantly pine about being taller, and taller players, regardless of experience, are always groomed. A metric this damning should be backed by extensive studies or data – yet every discussion I’ve had with coaches either point to anecdotal experience, or cherrypicked material. Saying that the best athletes in the world are always taller is flawed logic – they are the product of this pervasive bias, so of course the selection for taller players is evident. What’s more telling is that despite this, players of all sizes break through: Bruno Schmidt, Shelda Bede, Holly McPeak, Annie Martin. If the thesis is that height is always a beach volleyball advantage, these counterexamples are sufficient to discredit it.

The cultural baggage of height superiority is entrained from a young age, and repeated incessantly – thus, how height becomes an advantage stems from a psychological one. Taller players are simply given more opportunities to play, to explore, to make mistakes. Pay attention without bias next time, and see the language difference between how coaches treat taller and shorter players, and how they treat each other. A shorter team hands to the taller team an immediate advantage by simply expecting themselves to be at a disadvantage. The way out of this is to begin young, and to start instilling in them the confidence of height neutrality. Even among older athletes, we can unlock a richer vein of talent from our pool of players by simply opening our eyes beyond how tall they stand or how high they jump. The game is deeper and wider than the height of its tallest players.

2018-07-18
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.

2018-06-20
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.
2018-06-07

The Texas Primary Elections: by the numbers

It’s the day after the Texas Primary Elections, which serves to narrow the field for the two major American political parties heading into the midterm elections in the fall. Here in Houston, which sits in Harris County, the results are posted online for the Republican Primaries and the Democratic Primaries as PDF files. A peculiar anomaly in the posting of the election results is how the totals are reported. At the top of each report is:

Republican: District Voters: 155,798 of 2,249,591 = 6.93%

Democratic: Number of District Voters: 167,396 of 2,249,591 = 3.72%

The total number of registered voters match up between the two reports, but while the Democratic numbers are slightly higher than the Republican numbers, the reported percentage is nearly half. Puzzling.

Most of the news have focused on the individual candidates vying for public office, but the party ballots also included a number of Propositions – statements which appear to reflect the party’s overall priorities and stances on certain issues. The primary election could also serve as a type of referendum on how party affiliated voters feel about them. The wording is distinctly different between the two parties. At least the Democratic Party used short subheadings to summarize each proposition. Voters in the Republican primary are more divided in the Propositions presented, with the topics involving abortion and replacing property taxes with consumption taxes both receiving over 30% against. Given that the wording is designed to appeal to tribal identity, this is pretty significant. There’s a glimmer of hope that even voters don’t want the abortion or “bathroom bill” to remain central to the Republican identity. Meanwhile, the loftier “Rights” wording of the Democrats seem to resonate fairly well with the electorate.

Stacked bar graph showing the heterogeneity of the results for the Republican propositions vs the relative homogeneity for the Democratic primary

Republican Propositions

Proposition	Description	For	Against	Total	%for	%against
1	Replace property tax with consumption tax	92,468	48,498	140,966	65.60%	34.40%
2	No governmental entity should ever construct or fund construction of toll roads without voter approval.	130,409	16,904	147,313	88.53%	11.47%
3	Republicans in the Texas House should select their Speaker nominee by secret ballot in a binding caucus without Democrat influence.	123,396	21,872	145,268	84.94%	15.06%
4	Texas should require employers to screen new hires through the free E-Verify system to protect jobs for legal workers.	132,206	14,896	147,102	89.87%	10.13%
5	Texas families should be empowered to choose from public, private, charter, or homeschool options for their children’s education, using tax credits or exemptions without government constraints or intrusion.	120,457	27,276	147,733	81.54%	18.46%
6	Texas should protect the privacy and safety of women and children in spaces such as bathrooms, locker rooms, and showers in all Texas schools and government buildings.	130,355	18,026	148,381	87.85%	12.15%
7	I believe abortion should be abolished in Texas.	91,786	53,209	144,995	63.30%	36.70%
8	Vote fraud should be a felony in Texas to help ensure fair elections.	139,556	9,248	148,804	93.79%	6.21%
9	Texas demands that Congress completely repeal Obamacare.	125,942	21,490	147,432	85.42%	14.58%
10	To slow the growth of property taxes, yearly revenue increases should be capped at 4%, with increases in excess of 4% requiring voter approval.	137,348	9,355	146,703	93.62%	6.38%
11	Tax dollars should not be used to fund the building of stadiums for professional or semi-professional sports teams.	129,860	18,179	148,039	87.72%	12.28%

Democratic Propositions

Proposition	Description	For	Against	Total	%for	%against
1	Right to a 21st Century Public Education	153,406	5,586	158,992	96.49%	3.51%
2	Student loan debt relief	147,747	10,830	158,577	93.17%	6.83%
3	Right to universal healthcare	153,461	6,138	159,599	96.15%	3.85%
4	Right to economic security	152,653	5,682	158,335	96.41%	3.59%
5	National jobs program	147,703	8,719	156,422	94.43%	5.57%
6	Right to Clean Air, Safe Water, and a Healthy Environment	157,466	1,821	159,287	98.86%	1.14%
7	Right to dignity and respect (antidiscrimination)	153,465	5,179	158,644	96.74%	3.26%
8	Right to housing	147,590	9,614	157,204	93.88%	6.12%
9	Right to vote	152,838	5,884	158,722	96.29%	3.71%
10	Right to a fair criminal justice system	154,559	3,864	158,423	97.56%	2.44%
11	Immigrant rights	151,231	7,310	158,541	95.39%	4.61%
12	Right to Fair Taxation	153,060	4,753	157,813	96.99%	3.01%

2018-03-07