c0nc0rdance Profile picture
c0nc0rdance: arriving at the same conclusion by multiple lines of inquiry.
Jeffrey Rubinoff Profile picture 1 added to My Authors
29 Jul
In 1983, science fiction writer Isaac Asimov had triple bypass surgery at NYU Medical Center, during which he contracted HIV from transfusions. His doctors advised him not to disclose his status because of anti-AIDS sentiment.

He died 1992 from AIDS related complications.
His brother Stanley reported his cause of death as heart & kidney failure. The family was, yet again, advised to remain silent about his HIV diagnosis.

It was not until 2002 that his wife Janet revealed the full story in her autobiography. Many of his fans are still unaware.
Janet says they waited until after most of the treating physicians who advised them not to disclose Asimov's status had died, and couldn't be subject to criticism.

A sad story in the history of HIV/AIDS and our own intolerance to disease.
Read 3 tweets
19 Jul
Let's talk about the 'Concorde Fallacy'. (long thread)

The world's only supersonic passenger airplane (Mach 2.04) was co-developed by French & British aircraft manufacturers.
The project was begun in 1954, estimated to cost £70M. Airlines around the world put in large non-binding orders for >100, 1963-1967.
The first test flight was 1969.

By this point it was over budget by £80M & had to be bailed out by French & British governments.
Design flaws were discovered: metal at high speeds became soft, fuel failed to flow. Costs increased; French & British governments, invested in success, continue to bail out project. Development contract had large penalties for either government to pull out of ongoing support.
Read 10 tweets
20 Jun
As Trump supporters crowd into tight spaces without any masks it's a great time to talk about the temperature checks that are being used at the entrance.

Are they very effective at reducing exposures?

The answer is a resounding NO.
It's medical theater, diagnostic placebo.
If you look at COVID-19 patients being hospitalized, as in this JAMA study from April 2020, only ~30% are likely to even have fevers.

There's also the very dangerous pre-symptomatic phase of disease, where viral shedding can be at its highest.
CDC has no recommendation for temp checks. They're considered optional & only guidance offered is how to conduct scans safely... maintaining a 6 ft. distance & changing gloves if you come into contact with anyone.

For example, this is non-compliant by distance & glove change:
Read 3 tweets
19 Jun
I want to clarify a point of history that is constantly stated incorrectly:
Juneteenth *June 1865* wasn't the end of slavery in US.

It continued another 6 months in *Union* slave states.

100,000 slaves were freed by ratification of the 13th Amendment in *December 1865*
It's also worth noting that Kentucky ratified the 13th Amendment in 1976, Delaware in 1901, and Mississippi... *sigh*, in 2013.

Read 2 tweets
17 Jun
We should probably address a key distinction in research on SARS-CoV-2:
The METHOD used often changes the ANSWER we get.

viral RNA tests
viral antigen tests
infectious particle tests
host antibody tests
host clinical measures or biomarkers
The most sensitive test is a PCR based test for viral RNA. But not all viral RNA is going to be packaged in infectious viral particles.

It's also true that a single viral RNA may not result in successful infection of a patient. We might detect sub-infectious levels.
There is a test that only detects infectious viral particles (TCID50), but it's very low sensitivity and clunky to set up. We mostly use it to check assumptions.

So we have a too sensitive test and an insensitive test, and which one we use determines our answer in some cases.
Read 7 tweets
30 May
I need to share history from my hometown, Longview, TX. Long thread.

The population of Longview in 1919 was 5,700, of which 1/3rd were black. Before the Texas oil boom, it was a historical cotton town where slavery shaped the economy. In 1919, it erupted in a race riot.
The incident starts with a (possible) love story. Two white men from Kilgore object to "indecent advances" on their sister by Longview black man Lemuel Walters. Some accounts say they found him in her bedroom.

A lynch mob of 10 white men abduct and kill Lemuel on June 17th.
The lynching is reported in July 5th 'Chicago Defender', an African-American newspaper, along with commentary suggesting the woman he was "making advances on" deeply loved him & was distraught by his death.

Whites felt this cast aspersions on honor of local white women.
Read 17 tweets
8 Apr
Let's talk about *window period* and how it makes everything in diagnostics complicated and difficult.

Window period is the time between infection and when a diagnostic test becomes useful.

This is not Star Trek: our tests aren't perfect or comprehensive.
Typical viral infection:
1. Virus enters your tissues.
2. Virus starts spreading beyond local point.
3. You develop a local immune reaction (swelling, redness)
4. Local immune reaction prompts systemic reaction (fever, aches)
5. Your immune reaction overwhelms virus.
1 is too early to detect anything unless we biopsy the target tissue and have a perfect test.
Your symptoms don't show until 4 (maybe 3).

Now we have to consider what we're testing for.
Read 12 tweets
23 Feb
"Everyone talks about the weather, but nobody ever does anything about it." Until now, muhahahaha!

Okay, actual story of Cold War Doomsday Weather Programs here:
Some highlights: Soviet plans to build Bering Strait nuclear super-dams to alter the flow of the Pacific causing heat waves in New York & London.

Soviet ✓
nuclear ✓
super-something ✓
bizarre and terrifying consequences ✓

It warms an Evil Genius's heart to imagine it.
Better images to illustrate how Arkady Borisovich Markin's Bering Strait Nuclear Super-Dam would have worked.

The "muhahahaha" is implied in the image.
Read 4 tweets
5 Dec 19
Step 1 in adopting rational skepticism in practice is examining your own biased thought processes, and I think you can never really stop revisiting this step.

Being skeptical means trying to see the world as it is, and not as you want it to be.
Step 2 is learning to withhold judgment as a reflex. It's about truly internalizing that there is a state between "proved" and "disproved" called "unproven" and every new assertion must start with a presumption of uncertain knowledge until it can be tested.
Step 3 is deciding in advance of examination where the burden of proof lies, and what that burden is. Deciding on what constitutes proof after observations are mentally logged invalidates the conclusions you can draw.
Read 6 tweets
6 Oct 19
The population of the US (327 million) own 393 million firearms, about 46% of all firearms on Earth, and a per capita ownership of 1.2 firearms per man, woman and child.

There are about 268 million automobiles in the US, so there are 1.5 firearms for every automobile in the US.
Just another comparison:
In 2000 (the most recent date I can find a figure), there were an estimated 170 million personal computers.

In the same year, there were 270 million firearms, or 1.6 firearms for every personal computer in the US.
Pricing is definitely a factor. You can buy a shotgun and pistol combo for less than the cost of a computer capable of running the latest generation first person shooter.
Read 4 tweets
18 Feb 19
Fantastic image from @TracesofTexas
November 1905: President Teddy Roosevelt (who I've circled in red) speaks to a crowd in front of Alamo, San Antonio, TX.

Teddy visited SA 3 times:
- 1892 to hunt javelinas
- 1898 to train the Rough Riders
- 1905 as President
Love this image.
This is the Presidential procession, by horseback and buggy, through a sea of men and women wearing hats.

The event was a Rough Rider reunion, so I imagine he was surrounded by his former fellow soldiers.
If I ever get my time machine working, I'm setting the dials to 1905 and listening to his speech.
Read 3 tweets
14 Feb 19
I'm just going to admit it:
I miss the days in primary school when we prepared dozens of these little cards with attached candy and dropped them in shoeboxes on everyone's desk.

Thinking of doing same for my lab staff, but with cryoboxes.
Honestly, the dorkier the message, the more authentic it will feel.
*touches earpiece*
I am being told that many of these constitute workplace harassment now.
Read 3 tweets
12 Feb 19
What's interesting about El Paso, TX (El Paso del Norte) in Texas history is that it wasn't part of Texas.

Texas was born from the MX state of "Coahuila y Tejas", while El Paso was in the state of Chihuahua. No paseños were involved in the Texas Revolution...
... which took place hundreds of miles away in a different state entirely. The new nation, Republic of Texas, made no claims on El Paso.

The city got thrown in at the 1845 annexation of Texas as a US state, which was a big surprise to the actual Texans!
All of these contested territorial claims by the US (claiming half the MX state of Chihuahua) led to disputes that gave rise to the Mexican-American War.

The US ultimately invaded Mexico, occupied their capital, and forced the government to sign a surrender at gunpoint.
Read 4 tweets
11 Feb 19
CW: biology x theology.
Can you be a Christian and accept evolution?
I certainly hope so (I know many who are), but I also understand *why* they are in conflict.
1. Original sin:
If Adam & Eve brought sin into God's perfect world, then Jesus' sacrifice is necessary. If we challenge this notion, then sin was either built into the world, or Jesus died for political theater.
2. Humans as animals:
Biologists will tell you humans are animals, taxonomically, but the Bible is clear on humans being special and capable. Is Heaven filled with, at a minimum, high IQ dolphins, ravens and horses? Smart protohumans? Chimps?
Read 5 tweets
10 Feb 19
Full confession: 98% of science is boring to read about, even to scientists.
I have spent entire conferences on cancer research not learning anything worth telling anyone about.
It's like reading about someone's business trip to Toledo, OH; or their recent IRS audit.
It must be an eternal struggle for those in #scicomm. How do you reduce the boring bits without losing the integrity of the message?

Cell and gene therapy is amazing stuff, but 98% of the published work on it is about donor sequence optimization, which is not exciting.
My actual work is boring as hell. We alter one variable at a time b/c that's good experimental design. The end result is a test that incrementally improves on what already exists.

The reality of discovery and product development is nothing like the "Eureka" moment.
Read 6 tweets
9 Feb 19
Searching for publications by Intelligent Design Creationist Michael Behe gives three hits:
1. A 2004 paper on protein evolution.
2. A 2005 letter acknowledging flaws in the 2004 paper.
3. A 2009 correction to his 2008 paper that used the wrong values for fixation rates.
I'm always struck not by how controversial or challenging intelligent design creationism is, but how *unproductive* it has been. They even started their own journal and can't seem to get many papers out even when they are author, reviewer, editor and publisher in one.
If a creationist wanted to convince me, they wouldn't wave Paley's Watch arguments in front of me. They'd apply a creation paradigm to intractable research problems and show that those paradigms were productive.

They have scientists, funding, a journal... what's stopping them?
Read 3 tweets
9 Feb 19
It has been my experience that people in science are promoted on the basis of their research, not leadership or administrative skill.

The result is often a Principal Investigator / Research Lead who hates their job (grant / report writing) & makes everyone in the lab miserable.
This is where I think industry has the advantage: different paths exist for exceptional scientists to either go administrative routes or remain at the bench and still be compensated according to productivity.
Academia has the post-doc and the research fellow, but there's a narrow path to full professor, and not enough emphasis on leadership, management and administrative ability.
Read 4 tweets
30 Jan 19
"Cure for cancer" is so poorly defined and misinterpreted.

- Cancer isn't like influenza; it's your cells, just behaving badly.
- It's not one disease; melanoma is as different from glioma as your elbow is from your brain.
- Cancer is built into our biology.
The better our cancer testing gets, the fuzzier the line between pre-cancer and cancer. Our cells are constantly moving on a continuum between normal and cancerous, being destroyed by internal or external regulation, and sometimes just failing to lead to tumors.
So "Cure for Cancer" has the same sense to me as:
"Cure for Crime" or
"Cure for Car Failure" or
"Cure for Poverty".

We could have highly effective therapies (and we do), but I would always hesitate to call them "cures" unless we can agree to what that word means.
Read 3 tweets
26 Jan 19
Dried blood spots are used to collect and archive proteins and DNA on filter paper for small volumes of blood, like those used in newborn screening.

Every time we think "surely we can improve on this" result = more expensive, complicated, less stable
...& don't call me Shirley.
The first step in extraction from DBS (dried blood spots) is the highly sophisticated tool called a "Hole" "Punch".

Again, not a lot of room for innovation, although there are automated and sterile hole punch devices.
My only real complaint is scale-up. It takes a few hours (3-4) for a recent punch collection to dry enough for handling/shipping/archiving, so for high throughput operations, there's value in having a drying area with lots of square footage.
Read 4 tweets
1 Dec 18
I want to talk about this image.

These are migrants in Mexico with numbers on their arms, awaiting their chance to cross the border and apply for asylum.

It's reminiscent of Jews in concentration camps, but let's be careful and fully informed before reacting!
The numbers are being drawn on in Sharpie by Casa del Migrante, a non-profit civil association that provides services to displaced migrants: shelter, food, safe storage. It's a shelter run on charitable donations, since 1987 helping 250,000 migrants.
So why are they writing numbers on arms?
Well, the US CBP are denying free access to border crossings. So Mexican charities/NGOs are providing transportation in small busloads to accessible ports of entry. Those numbers are the migrant's place in line.
Read 7 tweets
18 Sep 18
#Texas political affiliation, according to 2014 Pew Survey.

Top level: Texas is a preponderance Democrat state run almost entirely by Republicans. In some areas, the only challenger to Republican candidate is a Libertarian.

Let's drill down one level...
A mystery starts to unravel. Texans who are strongly Republican. Latinos are mixed/lean Democrat, and blacks are Democrat.

This makes voting rights and gerrymandering issues extremely important to how a Republican minority dominates elections in a state with equal D & R.
Correction: Texans who are *white are strongly Republican.
Read 4 tweets