The Evolution of DNA Profiles

Nearly forty years ago, a revolution that would alter our understanding of genetics began quietly in a lab at the University of Leicester (UK). A team of scientists headed by Dr. Alec Jeffreys had been studying highly variable regions of human DNA for several years. Sometimes during the DNA copying process, the enzyme responsible can slip on the template and "stutter". Jeffreys and his team noted that the resulting "minisatellites" - short regions of repetitive DNA - had a high amount of variability from person to person. They used a technique of cutting the DNA with different enzymes before running it on a gel to visualize this variability. In September of 1984, while analyzing the DNA of his technician and her parents, Jeffreys had a eureka moment and realized their approach had created the first DNA fingerprint or profile. 

The first time this technique was used in a forensic science capacity was in 1985. In November 1983, a 15-year-old girl Lynda Mann was found sexually assaulted and strangled to death in a field not far from her home in the village of Narborough in Leicestershire. A police officer who had heard about Jeffreys work at the University asked if it might be possible to create a DNA fingerprint from the semen left behind at the scene. Before long, another 15-year-old Dawn Ashworth was found sexually assaulted and murdered in a manner similar to Lynda in the neighboring village of Enderby. Jeffreys confirmed that the same individual was responsible for both attacks and eliminated the initial suspect. Police collected a DNA sample from all the men in the area to screen for the perpetrator. No one was a match, leaving investigators perplexed.

Finally in August of 1987 there was a break in the case. A coworker of Colin Pitchfork told other colleagues at a pub that he had provided a DNA sample for Colin because Colin told him he didn't want to be "harassed by the police over prior convictions for indecent exposure". One of the coworkers reported this admission to the police. Law enforcement promptly found the real Colin and got a DNA sample, which matched the semen found at both crime scenes. Colin Pitchfork was convicted and jailed in 1988 with a minimum sentence of 30 years. He was released in 2021, but returned to jail 2 months later for violating parole by approaching a lone woman. Just this week, the parole board has once again deemed Mr. Pitchfork suitable for release. There has been considerable public outcry in response to this decision.

While the basic tenet of Jeffreys approach to DNA profiling (exploitation of variable regions of DNA) has remained the same, the technique has evolved to focus on smaller segments of repetitive DNA known as short tandem repeats or STRs. Scientists amplify dozens of STRs scattered around the human genome to determine how many repeats are present for that loci or location. Rather than running the DNA mixture through a gel like Jeffreys did, the samples are now run through a very small capillary tube and the results are captured by software on the computer attached to the machine.

Remember that for each STR loci there will be two copies analyzed because each parent contributed one allele or version of the STR to their child. At present, the FBI recommends examining a minimum of 20 STR loci to create a DNA profile. Due to the number of loci analyzed, the likelihood of someone having the exact same pattern of repeats as another individual is so extremely small as to essentially be improbable. The exception to this, of course, is monozygotic or identical individuals. An example of what a modern DNA profile looks like is below (Source: NIST).

Once an STR profile has been generated, it can be compared against other STR profiles. CODIS is the FBI's software program that runs a variety of DNA databases. For example, there are separate databases that fall under the CODIS umbrella for criminal offenders and missing persons.  

DNA profiling has radically changed how we identify people over the past 40 years. It allowed for effective paternity (and maternity) testing and revolutionized forensic science. No doubt the methodology for developing a DNA profile will continue to be improved upon in the future. There are already rumblings that single nucleotide polymorphism (SNP) profiling may be the next wave. But one thing is certain - DNA profiles are here to stay.

New Year, New Me

Today is the first day of 2023. I have been thinking a lot lately about how much I have associated my identity with my employment over the course of my life. I will be turning 45 this year. For over 15 years now, I've been a high school science teacher. It took me quite a few years to get comfortable with saying that, after having spent over 8 years becoming a practicing bench scientist. 

In time, I became proud to say that I was a biology teacher. But in the past 5 years of my teaching career, I have spent very little time actually teaching biology. The bulk of my courses have been forensic science, a course which I volunteered to finish writing the curriculum for in 2012-2013 because the coworker who originally proposed it was planning a move into supervision. 

Teaching forensics has been a great creative challenge for me. I needed to learn more about chemistry, physics, psychology and criminal justice to do the subject justice (pun intended). But I will say that it also caused me to have an identity crisis. How could I call myself a biology teacher if I rarely taught the subject? How could I connect to the identity that helped me accept that I'd left the bench and was no longer a researcher? I had a conversation with my very supportive boss more than a year ago explaining this growing internal panic. I'm not ashamed to admit that I got teary eyed. It's not that I didn't want to teach forensics anymore. I just didn't want it to be the only thing I was teaching. 

My boss suggested I write a curriculum for a new course. And so I did. Last fall, I planned out three technically - either two half year courses or one full year course covering genetics, molecular biology and biotechnology in greater detail than Biology 1 or AP Bio could cover. Unfortunately, budget cuts and staff reduction seemed to temporarily derail any efforts to develop new courses. I was disappointed, but that disappointment was tempered by learning that I would be able to teach two sections of Biology 1 in the fall.

After not teaching biology since the 2018-2019 school year, I was very excited for my 16th school year to begin. Redoing my Biology 1 course to reflect the sequencing and increased emphasis on NGSS pedagogy adopted by my colleagues over the past 5 years was a challenge I was looking forward to. And I will say that things were going pretty normally. Until late October. A short email changed everything.

It said "We got funding for the grant. Can you call me?"

For this to make sense, I need to go back about 2 years to the winter of 2021. I'd been trying without success to volunteer to do genetic genealogy for forensic cases since 2020. I applied to the DNA Doe Project and got no response. I attended many forensics webinars and asked the presenters about what to do but was met with vague non answers. I asked my sister (the forensic DNA analyst) if her lab worked with volunteers, but they field all of that kind of work out to Parabon. So as a last effort, I emailed the director of the county crime lab. We'd interacted several times before trying to make a forensics field trip work. 

She said that yes, they had just begun to use the technique on cold cases and were using outside contractors to do the genealogy. She was writing for a federal grant to get funding for these projects and said that she would be happy to work with me as a volunteer or independent contractor. She was hopeful they'd get an answer on the grant by the summer. That didn't happen. In October 2021, the director contacted me to say the grant application was rejected. But she said that she would try again and keep me updated.

Fast forward to the last week of October 2022. I finally call her on Friday after school to congratulate her about getting funding. She says, "Well, it's potentially good news, bad news. Good news is we have the funding. But the grant doesn't allow for volunteers or outside contractors. It's written with the expectation of a full time lab employee in house doing the work." I'm sure she could hear the disappointment in my voice when I said "Oh." She quickly said, "What I'm trying to say is that if you want the job, it's yours."

I will admit that the decision wasn't an easy one. And it may have resulted in quite a few tears being shed. But after a couple of weeks of weighing everything and discussing the topic with my immediate family ad nauseam, I accepted. The official print offer came just after Thanksgiving. I sent my resignation to the Superintendent on Monday December 5th, told my students and science colleagues what was happening on Thursday December 8th and my departure was announced at the Board of Ed meeting on Tuesday December 13th. My last day as a teacher at the school that's been home for over 15 years is February 3rd.

Come Monday February 6th, I will be working full time as a data analyst (aka genetic genealogist) for the Union County Prosecutor's Office Forensics Lab. I will be collaborating with the homicide detectives to identify victims and generate suspect leads in cold cases. 

I know that this is a once in a lifetime career opportunity. It's thrilling and bittersweet at the same time. It's made me fundamentally rethink who I am as a professional. I am a scientist, whether I am at a bench or not. I am an educator, whether I am in a classroom or not. I have made a career of being a public servant in so many different capacities. I am more than any job title I may hold. And now I'm excited to step into the unknown of 2023, fully authentically me.

Vaccines - what's in them and how do they work?

Vaccination against disease-causing pathogens like viruses and bacteria has been saving lives for hundreds of years. Vaccine comes from the Latin vacca (cow) because of Edward Jenner's late 1700s success at preventing often deadly smallpox (variola) by inoculating patients with a related virus, the unsightly but not deadly cowpox (vaccinia). Smallpox was eradicated globally in 1980.

Both boys exposed to smallpox - boy on the right had previous vaccination. Leicester England 1901

So how exactly do vaccines work then? Think back to when you were in school. If you had a big test or project, when did you earn the best grade? When you studied and prepared or when you just winged it? There may have been times you got lucky and did alright without extra prep because you had paid attention in class and had some prior knowledge, but imagine going into a class and being told you have a pop test on something you have never seen or heard about before in your life. How well do you think would you do then? Now imagine that doing poorly on this test decides whether or not you will have permanent disabilities or even if you live or die... You'd probably want to study for the test somehow, right? Think of vaccination like your immune system studying for that pop test rather than just winging it. 

If at first, you don't succeed, try try again. Science backs this up.

We never know exactly when we might get exposed to a new pathogen that could have serious consequences for our life. But for certain pathogens, we've been fortunate enough to develop a training strategy for our immune system - vaccines - so it isn't completely blind-sided if it comes up against them.

Your immune system has many specialized cells that scan your body for anything unusual (like cancerous cells) or foreign (like bacteria or viruses). Vaccines help those cells recognize potential threats and begin the process of making protective antibodies against them. They can contain weakened pathogens, "killed" pathogens or sometimes just a small portion of the pathogen called an antigen.

Vaccines stimulate the adaptive immune response.

Developing the ability to recognize and target a pathogen can take weeks to months after the immune system has its first exposure to the foreign agent. This is why people may say they came down with the flu shortly after they got vaccinated - it means they were exposed to an infectious virus before vaccination was able to help prime their immune system.

How the immune system responds to COVID infection

This shows the lag between exposure and antibody production.

Once they are raised, antibodies will bind to their targets, causing immune cells to slate them for destruction. As a result, a person with antibodies and primed T cells will typically either get a milder form of illness when exposed to a pathogen they've been vaccinated against or in many cases not even get sick at all. However, the reality is that no vaccine is 100% successful because people's immune system responses are variable and sometimes pathogens mutate (check out some success stats here). But the fewer potential hosts a pathogen has in a population, the better shot we have at controlling or eliminating the disease it causes.

There are legitimate reasons why some people cannot be vaccinated against certain diseases - sometimes they are too young or too old, other times they may have a specific allergy to a component of the vaccine or may be immunocompromised due to cancer treatments or organ transplantation. Those people rely on the rest of us with healthy fully functioning immune systems to get vaccinated to protect them by stopping the chain of disease transmission. The amount of people with immunity to a particular disease (either through infection or vaccination) needed for herd immunity to occur varies based on each disease (measles requires 95% of the population to have immunity for unvaccinated folks to be protected for example), but most diseases studied require greater than 80% of the population to have immunity.

Why is it so important to understand this concept? A large-scale study carried out on the blood of Americans last summer through September found that only about 10% of people showed evidence of antibodies against SARS-coV2/COVID. That's a far cry from what would be needed to abate this pandemic. This is why COVID vaccination is critical. Vaccine hesitancy affects us all. 

Quite frankly some of the rhetoric I've heard over the last year has me convinced that polio never would have been eradicated in the US if we'd had the same level of anti-science, anti-public health, anti-government sentiment back in the 1950s and 1960s as we do now. And that's a damn shame.

On A Safe Return To School Buildings

Post-script: I stopped writing about science in August because I felt frustrated that no one was listening to me, that no one cared what I had to say. I've struggled with feeling like I have a duty to educate people about science at the same time I need to protect my own sanity and not waste time and energy on fruitless endeavors. As COVID cases rise around the country, I've decided to share the letter I sent to the school district I am employed by. 

In-person school resumed in my district on Thursday September 10th. By Wednesday September 16th, the high school needed to switch to fully remote instruction because of six COVID positive students. We resumed in-person instruction on Thursday October 1st. On Sunday October 18th, staff were notified that 3 new students had tested positive for COVID and the district and health department were monitoring the situation. By Thursday October 22nd, we were fully remote again as another 3 students had tested positive. We were scheduled to resume in-person instruction on Monday November 9th, but got an email on Sunday night that we will continue to be remote until at least November 30th. 

There are at least 23 kids who have tested positive in the past two weeks, with no end in sight to cases. The town health officer is reporting that some families are saying they will not keep their COVID positive or COVID exposed children home. There are parents signing a petition to demand 5 day a week in-person instruction. About 150 students marched to the Board of Ed on Monday to protest the halt of the fall sports season. 

Meanwhile, the United States continues to post record numbers of COVID infections - over 100k a day. New Jersey has been reporting more than 2000 new cases a day for a couple of weeks - today we hit over 3800. Union County's case positivity rate is above 7% - the recommendation for opening schools was predicated on low case positivity rates. The last time NJ had that many positives was in April, during the peak of the first wave. This virus is not going to go away with people continuing to act like it doesn't exist or isn't a big deal. How many deaths and permanent health effects will be enough? 

                      

August 13, 2020

Dear Doctor Dolan and Board of Education members,

First, I would like to say that I appreciate the hard work that members of the Westfield School District community have put into trying to develop a plan to reopen the physical school buildings. I understand that this was a herculean task given the short amount of time between when Governor Murphy and the NJDOE released their “The Road Back” document and when tentative plans needed to be submitted to the state. However, I am writing to document my concerns about the Westfield School District plan, as it currently exists.

For those who do not know me well, I have been a teacher at Westfield High School for 13 years and I am the parent of two rising freshmen. A few words about my background: I have a B.S. in biology and a Ph.D. in biomedical science, during which time I took advanced course work in immunology. I spent 8 years working in labs before making the career switch to science communication and education. Therefore, I am looking at reopening through the lens of science. A safe return to physical buildings is predicated on extremely low community transmission (<1 case / 100,000 people) and a robust system to detect community spread¹. Multiple public health experts from around the globe have stated that community spread of SARS-coV2 (COVID-19) is inevitable without the ability to test, contact trace and isolate individuals who are sick and have been exposed^2,3.

In New Jersey and around the country, we have seen delays of a week or more in getting COVID19 test results. Governor Murphy recently opined that the delays may get worse in the near future^4,5. Contact tracing has also been problematic in NJ, with Governor Murphy reporting that only 63% of COVID positive folks responded to contract tracers and then about 45% of those folks refused to provide information about their close contacts^6,7. Throughout the summer, New Jersey has witnessed an increase in the effective reproductive rate of the virus (R_t)⁸. Much of this uptick has been associated with younger cohorts assembling for social gatherings during the summer^9,10. No doubt you are aware of the fact that Westfield made national news in July for a spike in COVID in the under 25 group.

Even more alarming, as summer camps and schools have begun to reopen, we are witnessing unprecedented numbers of infected children^{11,12,13,14,15}. According to the American Academy of Pediatrics, between July 9 and August 6th, 179,990 children around the country tested positive – a 90% increase over previous reports¹⁶. This is likely an undercount, as it is estimated that as many as 40% of infected individuals are asymptomatic¹⁷. We’ve already begun to see southern schools shut down in response to outbreaks less than a week after reopening. One district in Georgia opened on August 3^rd and has already had to quarantine almost 1200 students and staff.¹⁸ We may not have the same COVID numbers as Georgia right now, but New Jersey is not special – the virus is still circulating in our communities and we will see increases in infections if we give it the right environment.

To address specific questions of the feasibility of a safe return to Westfield school buildings in September, I have gone through the district plan and frequently asked questions document to identify areas that I believe need to be addressed before students and staff return.

·       HVAC systems have a fresh air component to their operation. All filters for air conditioning units are maintained as per manufacturers’ recommendations based on the type of equipment.

There is growing evidence that SARS-coV2 is spread through certain air conditioning systems and that SARS-coV2 is airborne^19,20. For example, a recent hospital study showed that infectious virus could be found as far away at 17 feet from sick patients – the room had six air changes per hour and was fitted with efficient filters, ultraviolet irradiation and other safety measures to inactivate the virus before the air was reintroduced into the room²¹. How do our current systems compare to that? Does your statement mean that the school building systems are fitted with MERV13 filters that are most effective at removing viral particles? If not, what other systems are being explored to keep air quality as safe as possible (UV lights, etc)? How will you be addressing the air quality in classrooms that may have few windows, difficult to open windows or lack central air conditioning for cooling?

·       Face coverings are required for staff and students while in the building, unless it will inhibit an individual’s health as documented by a physician.

Research shows that cloth masks predominantly work by preventing expulsion of large quantities of infectious droplets into the air; cloth masks are not particularly effective at preventing uptake of particles once they are in the air. How will students and staff be protected from individuals who are not wearing masks in the school buildings? Will face shields be mandatory for these individuals to help minimize their respiratory droplets in the air? Will students not wearing masks have something to identify that they are in compliance with district policy? Will staff be responsible for ensuring that students (other than those with exemptions) are wearing their masks properly? If a student refuses to wear a mask properly and does not have an exemption, what is the course of action?

 ·       Mask breaks will be provided.

How will this be accomplished? Removing masks indoors even for short periods of time defeats the purpose of masking in the first place. If you are proposing students be outside the buildings in large numbers, how are you addressing security? You also reference that students will be able to fill water bottles in school. Will mask removal for drinking be allowed anywhere in the building?

·       Student desks and seating in classrooms, cafeterias, multi-purpose rooms, and other spaces will be placed 6 feet apart. When social distancing is not possible, physical barriers and other measures will be utilized to maintain safety.

How will safety drills be accomplished according to these guidelines? Will there be no more active shooter drills? How will distances be maintained during fire drills?

·       Schedules will accommodate limited mixing or passing of students in common areas such as hallways and bathrooms; cafeterias and gymnasiums may be utilized by small student cohorts to aid in social distancing protocols.

How will social distancing be enforced in the hallways between classes in the upper grade levels? Even with half the WHS student body, there is not enough space to keep all students 6 feet apart in all directions when traveling. How will bathroom usage be regulated so that students are not overcrowding or socializing in there? How will you ensure that enough bathrooms are available for staff so that they may remain apart? Recent studies have shown that SARS-coV2 is present in human waste and flushing toilets creates a vortex of potentially viral containing particles in the air^22,23. How will you minimize the viral particles in the bathrooms? Will the toilets have lids or self-flushing mechanisms installed if they do not already have those features? Will all sink faucets and soap dispensers also be automatic?

·       Staff is encouraged to use telephones and intercoms for interactions with the main office and colleagues in other classes to minimize staff-to-staff interaction and maintaining social distancing.

How will staff access to the faculty lounge and main office (where photocopiers/scanners are located) be regulated such that distancing can be maintained? How often will these high traffic spaces be cleaned? If staff are encouraged not to congregate, where will staff work when they are not teaching in a classroom if it is not possible to keep 6 feet apart in office or faculty lounge spaces?

·       Parents/guardians will be required to take the temperature of their child(ren) each morning no more than one hour before the start of school. They will manually enter the temperature reading into a daily online form that will include a brief health questionnaire regarding COVID-19 symptoms.

Public health officials have cautioned that temperature checks will not avert all community spread, as there are plenty of people who can be infected and not have a fever^24,25,26. However, asking parents and staff to check temperatures daily and report it using the honor system alone is foolhardy. It relies on everyone in the community acting responsibly and being considerate of others. However, we continue to see people all around the state (including Westfield) disregarding public health advice to use masks, keep socially distant and not have large gatherings. We know that students often come to school ill so that they do not miss days. How can we rely on the accuracy of these reports? If a parent does not enter a response for a particular student, how will the staff be alerted to this fact to prevent entrance of that student to the school building? Will students be expected to wait in a socially distanced lines to have staff check if their name is on the digital temperature form?

·       If a student or staff member is suspected to have COVID-19, the district will comply with the CDC and New Jersey Department of Health recommendations that the classroom and work areas where the student or staff member was located should be closed off for at least 24 hours prior to being cleaned, sanitized, and disinfected.

Where will instruction occur for classes whose classrooms need to be shut down for this process? In the upper grade levels (6-12), where an infected student or staff member may have moved through 4+ classrooms, how will this be feasible to find replacement rooms? Does that mean that all those classes must be taught 100% remote until the classroom is cleared?

·       If a student or staff member is exposed to COVID-19 at home and/or outside of the school building, they should self-quarantine and monitor symptoms for fourteen (14) days from the last date of exposure. Exposure is defined as being within 6 feet of a COVID-19 positive person for 10 minutes with or without wearing a mask.

There is no clear policy on how school community members (students and staff) who may have been exposed to someone who is COVID-19 positive at school will be notified of their risk nor how quarantining will be achieved. This is asking for community spread in our schools.

·       Each building will be cleaned, sanitized, and disinfected on a daily basis.

This was the practice pre-COVID. How will you address the fact that students and teachers in many of the school buildings change rooms multiple times throughout the day? How will classroom spaces be cleaned in between periods, if passing times are 10 minutes or less? If there is not enough custodial staff to sanitize each room between classes, do you believe it is appropriate to expect students or staff to clean work surfaces? Will there be any legal ramifications to staff if a student contracts COVID from a space they are assigned to clean?

·       Families will have the option to choose the A/B Hybrid Model or All Remote Learning.

I applaud Governor Murphy and the NJDOE for making the decision to allow families the flexibility to safeguard their children as they feel is necessary. One of my sons is asthmatic, as well as my husband, so I am grateful to be able to lower their risk of contracting COVID by having my boys do their instruction 100% remotely. However, I have serious concerns about the fact that the same consideration is not being afforded by the Governor to all the staff of school buildings. I am also concerned about educational equity between students who are engaged in hybrid instruction and fully remote instruction. What safeguards will be in place to ensure that equity is achieved between these two groups?

·       Teachers will broadcast live lessons during each of their assigned periods for students to take part in synchronous learning activities.

Teachers will be wearing facemasks at a minimum and potentially other PPE like face shields that could impair the quality of their enunciation for recordings. We have not yet tested the district’s servers’ ability to allow for livestreaming from every classroom. Last spring, there were problems with video quality when streaming through WebEx when we were not requiring every course to be synchronous. What has changed to fix this problem?

·       Per the New Jersey Department of Education, all school districts in New Jersey must resume some form of in-person instruction for September 2020.

This is not what “The Road Back” document states. Instead, it says “Accordingly, absent a shift in the public health data, school buildings will open in some capacity for in-person instruction and operations in the Fall.” It does not say that all students must be inside the buildings, nor does it say that in person instruction must resume in September. Today’s press conference gave further clarification on that point – if all safety guidelines cannot be met by September, districts do not need to open their doors to everyone. Many other districts are following public health authorities lead on this issue and are either remaining entirely remote for all students until later in the fall or opening the doors only to the youngest or most vulnerable students.

This will be my 14^th school year with the Westfield district. I have come to see Westfield as my home away from home and my colleagues as my extended family. I am incredibly proud of the students I have taught over the past 13 years. I have always looked forward to the start of the school year and meeting my next group of students. But this year, I want to keep everyone safe – my colleagues, all the students of Westfield, the families of our school community members – so that we may grow together for many years to come. Right now, I believe that means opening schools with 100% remote instruction in the fall.

Sincerely, 

Dana Philipps

Citations

1.     https://globalepidemics.org/wp-content/uploads/2020/07/pandemic_resilient_schools_briefing_72020.pdf

2.     https://www.who.int/news-room/commentaries/detail/transmission-of-sars-cov-2-implications-for-infection-prevention-precautions

3.     https://www.sciencemag.org/news/2020/07/school-openings-across-globe-suggest-ways-keep-coronavirus-bay-despite-outbreaks

4.     https://www.nj.com/coronavirus/2020/08/coronavirus-testing-delay-already-sucks-according-to-murphy-it-could-get-worse.html

5.     https://www.roi-nj.com/2020/07/22/healthcare/lagging-turnaround-times-on-tests-becoming-n-j-s-biggest-problem/

6.     https://www.nj.com/coronavirus/2020/08/most-nj-covid-19-patients-arent-giving-contact-tracers-the-information-they-need.html

7.     https://www.nj.com/coronavirus/2020/07/more-people-are-refusing-to-cooperate-with-coronavirus-contact-tracers-heres-why-that-could-spell-disaster.html

8.     https://www.nj.com/coronavirus/2020/08/njs-coronavirus-rate-of-transmission-is-rising-heres-how-its-calculated.html

9.     https://www.nj.com/coronavirus/2020/08/murphy-reverses-indoor-gathering-rules-in-nj-after-a-spike-in-the-spread-of-coronavirus.html

10.  https://www.nytimes.com/2020/07/30/nyregion/coronavirus-cases-nj.html

11.  https://www.wired.com/story/a-summer-camp-covid-19-outbreak-offers-back-to-school-lessons/

12.  https://www.businessinsider.com/covid-broke-out-at-our-kids-camp-this-is-what-school-will-look-like-2020-7

13.  https://www.nytimes.com/2020/08/04/world/middleeast/coronavirus-israel-schools-reopen.html

14.  https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.29.2001352

15.  https://www.wired.com/story/some-countries-reopened-schools-what-did-they-learn-about-kids-and-covid/

16.  https://services.aap.org/en/pages/2019-novel-coronavirus-covid-19-infections/children-and-covid-19-state-level-data-report/

17.  https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html

18.  https://www.nytimes.com/2020/08/12/us/georgia-school-coronavirus.html

19.  https://wwwnc.cdc.gov/eid/article/26/7/20-0764_article

20.  https://news.harvard.edu/gazette/story/2020/06/air-conditioning-may-be-factor-in-covid-19-spread-in-the-south/

21.  https://www.nytimes.com/2020/08/11/health/coronavirus-aerosols-indoors.html

22.  https://www.nytimes.com/2020/06/16/health/coronavirus-toilets-flushing.html

23.  https://www.nationalgeographic.com/science/2020/06/could-flushing-public-toilet-plume-spread-coronavirus-cvd/#close

24.  https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/non-contact-temperature-assessment-devices-during-covid-19-pandemic

25.  https://www.statnews.com/2020/07/02/smell-tests-temperature-checks-covid19/

26.  https://www.businessinsider.com/temperature-checks-flawed-coronavirus-cases-asymptomatic-no-fever-2020-5

Calculating and Interpreting R Values

https://www.nature.com/articles/d41586-020-02009-w

https://www.cebm.net/covid-19/when-will-it-be-over-an-introduction-to-viral-reproduction-numbers-r0-and-re/

Airborne SARS-coV2 and Ventilation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182754/

https://jamanetwork.com/journals/jama/fullarticle/2766821

https://www.epa.gov/coronavirus/indoor-air-and-coronavirus-covid-19

https://www.wbur.org/hereandnow/2020/07/15/coronavirus-indoor-air-conditioning

https://www.forbes.com/sites/brucelee/2020/05/14/here-is-more-evidence-for-face-mask-use-with-covid-19-coronavirus/#4e6233671060

https://www.ashrae.org/technical-resources/reopening-of-schools-and-universities

https://www.epa.gov/coronavirus/air-cleaners-hvac-filters-and-coronavirus-covid-19

https://www.energyvanguard.com/blog/can-your-hvac-system-filter-out-coronavirus

COVID19 in Children

https://www.cdc.gov/mmwr/volumes/69/wr/mm6932e3.htm?s

On Loss, Personal and Collective

Written May 7, 2020

Separation 

by W.S. Merwin

Your absence has gone through me 

Like thread through a needle. 

Everything I do is stitched with its color. 

Let me preface this post: I won't pretend to be a mental health expert. I'm merely speaking as someone who spends a great deal of time observing the world and has had direct personal experience with both loss and mental illness. 

On March 12th of last year, just around 1 AM, my mother in law's courageous 20+ year-long battle with breast cancer ended. I was 8.5 months pregnant with my youngest son, the grandchild she first asked me about on my wedding day. The baby we were anxiously awaiting after 3 miscarriages in a row. For two years straight, my personal life was tinged with death. When Griffin arrived on March 30th of last year, my husband and I were still deeply mourning the loss of Mom, but we finally felt there was something to look forward to after so much sadness. Fast forward to this March. We were planning a celebration of Griffin's first birthday - the first time we'd see many of our large extended family since Mom's funeral. The pandemic threw a monkey wrench in those plans.

The scale of collective loss is something we haven't experienced in my lifetime. Over 70,000 Americans dead in a month, over 8000 in New Jersey alone. We've been fortunate thus far. No one we love has died. We still have enough income to pay our mortgage and food bills - I can work from home, though my husband has to go to work where he is risking exposure to the virus weekly. So far we are healthy. I know that not everyone has been so lucky. My heart breaks a little more with each death I read about and each family thrown into chaos by loss. I also worry for the small business owners like my father and employees who have been let go and can't find work or get enough unemployment to pay bills like my eldest son. It's easy to get sucked into a spiral of anxiety and depression.

Full Poem Source: Jay Hulme

I've heard several people say "The cure can't be worse than the disease", as though repealing shelter in place orders will fix what is ailing us. I've heard people claim that more people will die due to alcohol and drug addictions or suicide because of the shelter in place than will die because of the virus. As a person who has dealt with suicidal ideations since childhood, I reject both of these statements.

Hardship is not worse than death. Hardship is temporary, death is permanent. Suicide doesn't end pain; it simply transfers it.

Source: VailDaily

I'm not naive. There certainly will be people who die from addiction and suicide because the pandemic has impacted their mental health - the 1918 pandemic taught us that. Some tragic stories like that of Dr. Lorna Breen have already been reported. However, we now have tools to help people cope with their demons. We can be proactive to minimize risk. 

Need a lifeline? Call 1 800 273 8255.

So what do the mental health experts say we should do? A consortium of psychiatrists and other mental health professionals developed a short position paper about the steps we can take.

Lancet: Strategies for Mitigating Suicide Risk

They recommend that we implement universal interventions that will support individuals not previously known to have mental health challenges at the same time we are applying specific, selective interventions for people known to be facing a crisis. The general interventions recommended...

1. Government provided safety nets to help deal with pandemic related financial stressors
2. Government provided support for individuals needing to escape domestic violence
3. Public health education about alcohol consumption 
4. Find creative ways for community members to remain engaged with each other when person to person contact is not possible
5. Monitoring access to means and reporting suspicious behavior
6. Reinforce guidelines on responsible media reporting, in order to not encourage suicidal behavior

I understand the desire to return to "normal". But right now, that's not possible. I understand grieving for what we've lost and what we are missing. Now is the time to think outside the box, to figure out new ways of doing the business of being human, in order to keep as many people healthy as possible. If we take away nothing else from this global crisis, it should be that people need other people (even if that means keeping apart) and that both individuals and society as a whole are better when we work together. So let's be careful out there...

Why Facts Should Matter But They Often Don't

Note: I wrote this post on May 15, 2020, but forgot to share it. In light of everything that has happened in the past few weeks, I think it is still timely.

We, humans, take for granted our ability to reason - that is to make sense of the world in a logical fashion, to easily separate fact from fiction - and erroneously believe that we are correct in our beliefs most of the time. Cognitive scientists and evolutionary biologists suspect this ability to accept false beliefs begins around the age of 4 to 5 and helped our species survive.

Since we are hardwired to look for patterns that match with the mental maps that formed during our own development, we often seek out information that appears to reinforce our pre-existing beliefs about how things work. This is known as confirmation bias (*NOTE: there are many other kinds of bias).

More than four decades ago, researchers at Stanford found that even when people were told they were intentionally misled about their ability to assess information, those people's initial impressions about how accurate they were at the task remained. In other words, if the research subjects thought they were better than average at a task, they continued to believe that even when provided evidence that they were not.

This is why in large part giving someone with an erroneous false belief the evidence necessary to reject their thinking, they often don't change their minds. And this is why conspiracy theories are also hugely popular.

So how can you help convince someone to reexamine strongly held beliefs? The first thing to do is to identify the other person's major concerns and shared values. People are more likely to consider what you have to say if they believe you have some common ground. 

It's important to be aware of these brain tendencies because if we aren't and we act irrationally, we can make mistakes that have significant, long-lasting impacts on society. Like rushing to pull NIH funding from EcoHealth Alliance, a leader in surveillance of zoonotic diseases including coronaviruses in the middle of a global pandemic because of a conspiracy narrative...

More videos on these topics:

12 Cognitive Biases Explained

Why You Think You're Right - Even If You Are Wrong

How You Can Change Someone's Mind

Science 101 or How to Spot A Grifter

Right now there's a barrage of conflicting information regarding SARS-coV2 swirling about the internet.  It can make it challenging for people without a solid science education to know how to interpret what's out there. I will admit, typically when I read pseudoscience conspiracy theory mumbo jumbo, I roll my eyes and ignore it. I even think to myself "How ridiculous!" Or more pointedly "How farcking stupid can you get?" It's easy if you have the tools to interpret scientific BS to get frustrated and overwhelmed by the ignorance and charlatanism that is freely propagated on the web and dismiss it offhand. But now that it's misinformation about a deadly infectious disease, I feel some sort of obligation to speak out. 

So let's start at the beginning - the nature of science. This is the first unit I do with my Biology 1 students each year because I really do see teaching them scientific literacy my primary goal - all the cool facts about how life works we talk about are just icing on the cake. Science comes from the Latin word scientia meaning "to know". It is a process of inquiry designed to help us understand how the natural world works. It is cumulative in nature, meaning that scientists are constantly revising their explanations of how and why things happen as they gain new knowledge. I always tell my students changing your mind in science isn't "flip-flopping" - it's good science. If you refuse to change your understanding of a phenomenon when presented with multiple lines of evidence showing you that your original idea was incorrect, you've failed. 

It's also important to note that scientists who are being ethical don't speak in absolutes. They don't tell you they are 100% certain of anything because they are smart enough to realize it's impossible to know everything we don't know and it's impossible to avoid making mistakes. To be a scientist or at least think like one, you need to be open to critically evaluate all information you come across and be aware that we all have biases that color our interpretations. And most importantly, it's OK to say "I don't know" and be willing to ask for help to find an answer to a question you have.

Source: Berkeley's Understanding Science

In the process of doing science, we ask questions about the world around us and we develop hypotheses - that is testable solutions or answers to our questions. In order for something to be a scientific hypothesis, it must be testable and those results must be replicable by others, in order to verify whether we should support or reject the hypothesis. Science is a collaborative effort and communication between researchers is critical to developing solid understanding. Typically, scientists work in relatively small group collaborations - a lab group - focused on a small subset of scientific questions or problems. They become a sort of expert unit - all discussing and sharing knowledge of the topic they are examining. The reality is that research is expensive and that solving big questions requires different perspectives and talents. So labs that are interested in the same topics often work together to share resources and sometimes they compete. 

When a sufficient amount of work has been completed to make a cogent argument about what the data means, scientists will write up their findings and submit them to scientific journals or professional meetings. Usually, to have work published means that research has been subjected to peer review - meaning other folks with the training to allow them to evaluate the claims being made by the authors have already critiqued the paper before it was published. And the peer review process doesn't stop once a paper is published - other scientists will try to replicate and verify the results based on the reagents and methodologies presented in the paper. If other labs cannot independently verify the claims, the paper is retracted. So is this process of vetting perfect? Absolutely not. Scientists are human after all - they make mistakes. But generally, bullshit is eventually detected and routed out.

Source: Berkeley's Understanding Science

Because of the seriousness of the COVID19 pandemic, non-scientists are getting to watch the process of science in real-time in a way they haven't before. Results are being released without traditional peer review (see my previous blog post for more details). Scientists who aren't accustomed to presenting data to the general public are finding themselves thrust onto the media. I'm sure this can make it look like scientists don't know what they are doing. But the truth is, you're just witnessing the sausage being made, rather than just enjoying how it tastes in the end. 

Another rather disturbing trend that has been going on for a while is the disregard of expertise. That's not to say that authority reigns supreme in science - paradigm shifts can be generated by up and comers and established scientists can be shown to be wrong. But everyone seems to think that their 20 minutes of Google "research" is equivalent to entire professional lives dedicated to the careful study of something. Isaac Asimov, the great biochemist and author, was quoted in 1980 as saying:

The availability of information on the internet, the ease with which people can make a source look reputable, the staggering amounts of money people can make by sharing their modern snake oil... It's a toxic mix. 

The latest malarkey I've seen shared by multiple friends, acquaintances and community members is a video claiming Anthony Fauci and others in infectious disease masterminded this pandemic. No, I'm not sharing the video nor am I wasting my time to individually break down each false claim it purports. Not because I'm a corporate shill (I have no connection to any pharmaceutical company) or because I'm a sheeple (pretty sure my PhD level education has actually taught me to be more critical than the average bear). But because I refuse to be a part of the misinformation machine that contributes to people's deaths. I will, however, call out the disgraced scientist who features prominently in it. Because people like Judy Mikovits are arguably the worst - people who earn degrees in science and medicine and then use that degree to grift others. Mikovits is not some hero or influential researcher; she was a mid-level scientist whose own decisions tanked her career (after her work on chronic fatigue was disproved she was fired from a private lab in 2011 and arrested for stealing intellectual property) and now makes a living off of writing books and pushing conspiracy theories. She's a shameless self-promoter. F*ck Judy Mikovits and others of her ilk.

So what's an average Joe or Jane to do? First, if it sounds too good to be true, it's probably not true. Recognize that the "I'm just fighting the establishment on your behalf" narrative is just that - a narrative to elevate someone's importance and gain your trust. Avoid sensational headlines - they are designed to capture attention and generate revenue. If you must read or watch something that seems like it is dancing into pseudoscience or conspiracy territory, do so with a healthy level of skepticism and critical thinking. I teach my students that if they make a claim, they must support their claim with verifiable evidence and be able to clearly explain their reasoning - in other words can you show the link between that particular evidence supporting your claims? Astronomer Carl Sagan is oft-quoted about the need for evidence:

Click here to hear Sagan speak on this in 1995.

Perhaps the most important thing you can do is to NOT SHARE INFORMATION THAT HASN'T BEEN FACT CHECKED. You cannot control the deluge of preliminary or shaky science, alternative facts, and fake news. But you CAN and should prevent the spread of misinformation. Remember the old Smoky the Bear campaign - only you can prevent forest fires? Well, folks, only you can prevent misinformation dumpster fires. You can quote me on that.

For more information on pseudoscience, battling bunk and why people believe weird stuff: here, here, here, and here. You should also probably check out the two infographics below:

Source: Compound Interest

Source: The Skeptical Cardiologist