J Hope

January 11, 2021
by J Hope Leave a comment

COVID-19 FAQs

One of the main reasons I started this blog and have decided to continue posting is my simple yet strong belief that objectivity and truth are essential when both analyzing and discussing political or public health decisions. I have been thinking about writing this post for over a year and, unfortunately, there is still a lot of misinformation and lack of understanding regarding COVID-19 in the general public as the virus continues to rage in our country and the world at large.

For this post, I researched questions that are commonly asked about COVID-19 and provided a referenced summary of what I learned. Quick and simple answers to each question are provided at the top of each section followed by a deeper dive. If you have further questions please comment and I will do my best to respond with credible information.

Thank you for reading!

COVID-19 FAQs:

What is COVID-19?
Where did COVID-19 come from?
Isn’t COVID-19 like the flu?
Do masks and social distancing work?
Would a nation-wide shutdown help?
What happens if I get COVID-19?
Do COVID-19 tests work?
Are the vaccines safe?
What does the future look like?

Some Quick Definitions:

Virus: microscopic pathogens unable to replicate on their own, requiring the infection of host cells for replication and existence.
Viral Classification System: viruses follow the same taxonomic ranks as living organisms: domain, kingdom, phylum, class, order, family (there can be sub families as well), genus, and species, but some commonly used terms come up beyond the species level:
- Strain/Type/Variant: essentially all mean the same thing, but are used within different naming conventions – all refer to a virus with a genetic and/or phenotypic feature setting it apart from other viruses within the same species.
Genome & Genetics: the genome refers to the entirety of an organism’s genetic information. Genetics refers to the information encoded in nucleic acids (DNA & RNA).
Phenotype: the observable features of an organism, encoded by nucleic acids,
Antigens & Antibodies: antigens are foreign entities within the cell (produced by viruses or other infectious agents) which cause the immune system to create antibodies. Antibodies are proteins produced by the immune system that are engineered to target and ultimately rid the cell of a specific antigen, clearing out pathogens.

1. What is COVID-19?

COVID-19 is the disease caused by SARS-CoV-2, a new type of coronavirus that emerged in 2019. COVID-19 stands for “Corona Virus Disease 2019” and SARS-CoV-2 stands for “Severe Acute Respiratory Coronavirus 2”.

Although we are dealing with a novel species of coronavirus we are not dealing with a novel type of virus. In fact, there are hundreds of known coronaviruses; six were already known to infect humans before SARS-CoV-2, including the previous species to cause severe acute respiratory syndrome (SARS) in 2002¹.

Coronaviruses, or Coronaviridae, are a family of membrane-enveloped, positive-sense RNA viruses. Coronaviruses (CoVs) were first detected in humans in the 1960s, but most species can be found in animals ranging from domesticated livestock to wildlife². All coronaviruses share a similar outer cell membrane structure with spikes that resemble a corona, or “crown” (image 1). Within the family, coronaviruses are further categorized by uniquely shared genomic and phenotypic features into four genera: Alpha, Beta, Gamma, and Delta. SARS-CoV-2 and SARS-CoV are both Betacoronaviruses³.

This image has an empty alt attribute; its file name is coronavirus-structure.png — Image 1. General coronavirus structure
(source: https://www.biophysics.org/blog/coronavirus-structure-vaccine-and-therapy-development).

Including this most recent virus there are now seven coronavirus species that can infect humans (image 2) causing mild to severe respiratory illnesses ranging from the common cold to SARS and MERS, Middle East Respiratory Syndrome, both of which can be fatal⁴. All seven of the known species of human coronaviruses can be traced to animal reservoirs, meaning that certain animal species are known carriers of the viruses. These animal carriers are often asymptomatic and do not show any adverse effects themselves, but are able to readily spread the virus to new hosts.

This image has an empty alt attribute; its file name is JA7.png — Image 2. Seven species of coronaviruses that have infected humans (source: https://www.cebm.net/covid-19/coronaviruses-a-general introduction/).

Why is the virus called SARS-CoV-2 and what does COVID-19 stand for?

The coronavirus that caused the 2002 SARS outbreak in the Guangdong province of China was named SARS-CoV because it was the SARS-causing coronavirus. This new species responsible for the current pandemic is likewise titled SARS-CoV-2, because it is the second species to cause SARS in humans (“Second SARS-Causing Coronavirus”). COVID-19 is the name of the disease caused by SARS-CoV-2 and stands for “Corona Virus Disease 2019”.

What makes SARS-CoV-2 different from SARS-CoV?

Its exact genetic code has variations, or differences, within it that set it apart from all other known coronaviruses, including SARS-CoV. The genetic code, or sequence, of the new virus was identified once it was isolated from patients with the disease we now call COVID-19. Once the sequence was identified it could be compared to other coronavirus species, allowing us to see how closely related it is to others. SARS-CoV is the most closely related human coronavirus, but other coronaviruses found in animals, and more specifically bats, are also closely related. The relativity between virus species is used to determine where a virus originated from and how it crossed over to infect humans from animals.

2. Where did COVID-19 come from?

The exact origin of SARS-CoV-2 is still being determined, but all previous human coronaviruses have originated from animal hosts. Horseshoe bats are carriers of coronavirus species very similar to SARS-CoV-2 and the virus most likely originated from a bat carrier, though it is still being determined if there was an intermediate host between bats and humans.

Viruses are not considered living beings because they lack the ability to reproduce on their own – one of the seven characteristics of life (for a refresher on viruses and other microbes, please visit my previous post). Instead, viruses are essentially capsules containing genetic information, or what could be considered a viral genome, that can transport and spread this information from host to host and/or cell to cell. To “reproduce”, or replicate, a virus must insert its genetic information into a host’s cell, and the host’s own cells will assist with the replication of viral particles. As more viruses are created within the cell, it will eventually die and release viruses to neighboring cells. This is the basis for infection and disease caused by viruses within the host.

When inside a host cell, a virus’ genome can mutate either through a change in its own genetic code, or by “mixing” genetic information with another virus. This is a big oversimplification but the general ideas are that an error can occur during the replication process, leading to a change in the genetic code, or alternatively, if two or more viruses happen to co-exist within a cell for long enough they can recombine their genetic information during replication. Either process can result in functional changes for the virus – including the ability to infect a new type of species. When a virus is able to “jump” from an animal species into humans it’s considered a zoonotic spread and the disease it causes is a zoonotic disease.

Sometimes you will hear people describe a virus as “evolving”. This essentially means that the virus’ genome has changed, or mutated, to the point that they are considered a novel type of virus – they can still be classified by the group of viruses they are related to and evolved from, but they have unique genetic codes and characteristics that now set them apart. When a virus has changed enough that it can infect a new species, jumping from an animal to humans for example, it is generally said that the virus “evolved to infect humans”.

Some viruses evolve so rapidly that new strains are frequently created or co-exist within a population, leading to the need to continuously update vaccinations and treatments. This is the case with influenza, the cause of the common flu. Each year the flu vaccine is adjusted to fight against what is believed to be the most common flu strain that season. Sometimes a different strain is actually the most infectious, or a new mutation leads to the vaccine being less effective, so the flu vaccine doesn’t always get it right; it does, however, prevent millions of infections each year⁵ and medical professionals generally recommend getting the vaccine each flu season.

These “ever evolving” viruses will most likely indefinitely remain in the human population due to their ability to adapt to therapies, and viruses will continue to evolve to jump from animals to humans due to their continual genetic updates.

As mentioned before, all seven of the coronaviruses in humans can be traced to animal reservoirs, and most can be traced to the exact species that directly acted as the donor to human hosts⁶. Zoonotic spread of viruses usually occurs through the consumption of animal meat, though it can also happen from simply being in close proximity to animals, such as the conditions found in live animal markets or factory farms⁷.

We know zoonotic spread occurs because of each virus’ genetic similarities. We now have the ability to sequence, or read, the entire genome of viruses and compare them. The genome is mind-blowingly rich with information, or data. Through genomic data, we can determine if a virus is related to another and how closely they are related – this is an essential step for identifying the cause of a viral outbreak. The genome also contains information on how the virus spreads and infects human cells, helping us to further isolate the cause as well as formulate treatments.

The SARS-CoV outbreak in 2002 was traced back to Masked palm civets (Paguma larvata), or “racoon dogs”, in a live animal market. The genome of the coronavirus isolated from humans infected with SARS was almost identical to the genome of the coronavirus isolated from civets found in the market⁸. This led to the order to kill all the civets, shortly after which the outbreak ended, further suggesting that the zoonotic spread had ended with the civets (cruel) removal. However, all the animal species in the market were tested for antibodies against SARS-CoV, which if positive would suggest that they had at one point and most likely recently been infected with the virus. Antibodies were found in 80% of the different animals⁸.

Included in this antibody-positive group were Chinese horseshoe bats (Rhinolophus sinicus) which were found to contain a coronavirus very similar to SARS-CoV in humans⁸. In fact, bats have been identified as the main animal reservoir for all human coronaviruses⁹. A coronavirus isolated from horseshoe bats in the early 2000s shares 96.2% nucleotide sequence homology with SARS-CoV, meaning that 96.2% of their genomes match and suggests that the human virus originated from the bat virus.

Similar to SARS-CoV, a coronavirus isolated from Intermediate horseshoe bats (Rhinolophus affinis) shares 96% homology with the SARS-CoV-2 genome¹⁰. It has yet to be determined if the human virus jumped directly from bats to humans or if another animal acted as an intermediate host, but all evidence points to COVID-19 being a zoonotic disease. It has not been determined that the cause of the SARS-CoV-2 outbreak was the wet market in Wuhan, China, but the spike in spread and subsequent environmental testing suggests that there were infected animal hosts present¹¹.

How do we know it wasn’t engineered in a lab?

As described before, genetics is like data and those trained to understand that data can determine if there have been “man-made alterations” because it would leave behind telltale signs. When humans perform genetic engineering there are a very small number of tools that can be used, and each leaves it’s “mark” on the genome which can then be detected, usually by the presence of genetic sequences, or codes, that naturally should not exist at the number or location in which they do in a genetically modified genome. I recommend this article if you’d like to read more about the evidence against COVID-19 being a lab-engineered virus.

3. Isn’t COVID-19 like the flu?

No. COVID-19 and the flu are both respiratory illnesses that have some shared symptoms, but COVID-19 is more infectious, causes more severe symptoms, and has a higher mortality rate compared to the flu.

Beyond both causing respiratory illnesses, influenza viruses and coronaviruses are quite different, just as the flu and COVID-19 share some symptoms but are very different illnesses.

There are four influenza viruses, belonging to the Orthomyxoviridae family and Orthomyxovirus genus – influenza A, B, C, and D. Influenzas A & B both cause the seasonal flu, and influenza A was responsible for the Spanish flu pandemic. Differences in the flu virus structure, among other variations, lead to different mechanisms of entering host cells and replicating within the cell (figure 3) compared to coronaviruses, which is why COVID-19 and the flu infect people at different rates and with different effects.

Since the pandemic is ongoing the rate of spread, otherwise called the contagion or infection rate, and death rate are still being determined, but so far by looking across patients with COVID-19 and patients with the flu (both currently and historically) COVID-19 has a significantly higher rate of spread, and has a significantly higher death rate, along with showing signs of causing chronic diseases not associated with the flu¹². Previous to COVID-19, the biggest pandemic humans experienced was the Spanish Flu (1918-1920); it’s estimated that 500 million, or 1/3 of the world population, became infected and out of those infected 50 million died, including 675,000 Americans¹³. As of January 11, 2021 an estimated 90.4 million people have been infected by COVID-19 worldwide, with almost 2 million deaths, including nearly 375,000 Americans¹⁴.

The common flu generally leads to 30,000-40,000 US deaths per year or up to 650,000 globally and has a mortality rate of about 1% or less¹⁵. In striking contrast, the mortality rate of COVID-19 is as high as 29% in countries hit hardest and is about 2% in the United States¹⁶. The difference in country-specific mortality rates is due to a number of variables¹⁷:

Access to COVID testing: testing can prevent deaths by prompting those who test positive to get healthcare early on.
Access to proper healthcare: those that require medical attention need the ability to both get to the doctor and to also get the proper treatments.
Culture: cultures that already practice or are more willing to practice social distancing and wearing masks generally have lower rates of mortality.
Socioeconomics: countries with higher rates of poverty are generally experiencing higher mortality rates.
Demographics: countries with higher populations of those 65 and over are generally experiencing higher mortality rates than others; also populations that have a higher rate of comorbidities (cancer, heart disease, chronic respiratory disease, etc.) have higher rates of mortality. Air quality and higher rates of smoking are also linked to increased mortality rates.

Minority groups have generally been hit hardest by SARS-CoV-2, with higher rates of infection and mortality compared with white individuals in the same areas. Though there may be some ethnicity-based genetics that influence this, research has identified factors to be socioeconomics and due to cultural biases. Minorities are more likely to work in a position that puts them at risk of exposure, while also being less likely to receive proper medical care, often due to prejudices within healthcare, and on the other side fear of seeing doctors due to past discrimination. Chronic stress can also increase the risk of getting COVID-19 and of having a more severe reaction, and it has long been proven that minorities often endure chronic stress due to racism they experience¹⁸.

A comparison of the last two flu seasons and COVID-19 infection and mortality rates (source: https://www.goodrx.com/blog/flu-vs-coronavirus-mortality-and-death-rates-by-year/)

A study released in December 2020 looking at COVID-19 and flu patients within a French hospital found that almost twice as many people were admitted to the hospital with COVID-19 than the flu over a 2-month period when flu season occurs¹⁹. Of these hospitalizations, respiratory complications were more common in COVID-19 patients, who were twice as likely to end up in the ICU. More significantly, the in-hospital mortality of COVID-19 patients was three-times higher than those with the seasonal flu, and still significantly higher than the worst seasons of influenza the hospital had experienced in the past 5 years.

Evidence shows that SARS-CoV-2 is more infectious than influenza thus spreading through the population more quickly and when infected, COVID-19 causes more serious respiratory issues and has a significantly higher probability of being fatal when compared with the flu.

Fig. 1 — Figure 3. A high-level comparison of SARS-CoV-2 and Influenza A viral structures, phylogenies and replication mechanisms (source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217786/).

4. Do masks and social distancing work?

Yes. SARS-CoV-2 is spread through respiratory droplets – masks and social distancing reduce the likelihood of droplets coming into contact with your own respiratory system, preventing infection.

SARS-CoV-2 is a respiratory virus, meaning that it specifically infects cells within the respiratory system. Humans will secrete the virus in respiratory droplets – saliva or other secretions. No matter how hard we try, we release these respiratory droplets into the air around us; even more so when we are talking or eating. To be infected with SARS-CoV-2, you either come in physical contact with a person or surface where a virus-carrying respiratory droplet exists (contact transmission) or you breathe in a respiratory droplet from the air (droplet transmission). Thankfully SARS-CoV-2 cannot survive for long outside of host cells, so it’s not capable of airborne transmission and contact transmission from surfaces is relatively rare. Most SARS-CoV-2 transmission comes from breathing in respiratory droplets from a nearby person.

Social distancing helps lower the transmission rate significantly by reducing the likelihood someone will breathe in respiratory droplets from a SARS-CoV-2 carrying person. Previous studies have found that most droplet transmission occurs when people are within three feet (1 meter) of each other²⁰ and sneezes can cause droplets to travel 6 feet (2 meter) and beyond. This is why guidelines tell us to keep at least 6 feet away from each other – so you don’t breathe in infected droplets, but droplets can travel further than 6 feet so it’s best to keep as far away from others as possible during these times.

When social distancing is not possible, and even with the six foot rule can be followed, masks help to further reduce the transmission of SARS-CoV-2 by acting as a shield against the respiratory droplets. It’s true that the viruses are too small to be shielded by most masks, though some filters are efficient at removing these as wells, but the viruses are not entering the respiratory system alone. Instead, they have to hitch a ride in droplets, so if we can prevent them from entering the mouth or nose, the virus will also be blocked.

Surgical and cloth masks, like the ones worn by healthcare professionals and the variety of masks now available to the public, are efficient at blocking most droplets, especially larger ones (>10 um) – if worn properly (figure 4). Smaller droplets (<2.5 um) may still get through the masks; N95 masks are better are blocking these smaller droplets, but are not always 100% efficient – this is why both social distancing and masks are required to end transmission.

Masks and social distancing have proven to be effective when followed by a community. Studies have shown that when mask ordinances have been put in place on state or local levels, the COVID-19 infection rate dropped up to 2% per day²¹. To help put this in perspective, epidemiology guidelines dictate that a COVID-19 positive rate below 5% within a community for at least 2 weeks is considered the threshold under which businesses can open up fully. This is because the transmission rate is then manageable and population-wide outbreaks are not likely to occur²². Currently most US states are well above this 5% threshold and COVID-positive rates are reaching high double-digits, with the average across the US currently around 12%²³.

If a state is experiencing a 15% positivity rate, enforcing a mask mandate along with social distancing, including the temporary shutdown of in-person and non-essential businesses, could drop the positivity rate to below 5% potentially within one to two weeks. Following this, businesses could open back up without fear of further major outbreaks and repeated shutdowns. However, for these measures to work, everyone has to participate.

Groups of people protesting the social distancing rules, not wearing masks in public or reducing their in-person interactions are causing the pandemic to spread and continue to devastate the country; it is because of these actions that businesses cannot open fully. So if you want businesses to open and the economy to recover – promote the use of masks and following social distancing guidelines.

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Object name is heartjnl-2020-317104f01.jpg — Figure 4. Droplet transmission can be significantly reduced with the use of a mask; N95 masks are best, but surgical and cloth masks also work efficiently (source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246096/)

Could wearing a mask caused me to suffer loss of oxygen or cause any long-term negative effects?

Simply put, there is no evidence that masks cause depletion of oxygen or lower your oxygen levels, nor will they trap carbon dioxide when you breathe out. Masks have not been linked to causing any health disorders, including cancer. However, masks can cause disruptions in breathing patterns and you should only be using certain fabrics to be at your safest.

Masks can cause us to actually breathe differently, often subconsciously, so what feels like the mask causing us to not get enough oxygen, is our reaction to the mask causing us to either hyperventilate – breathe too quickly – or hypoventilate – breathe too slowly²⁴. If you have a mask that feels like it’s “choking” you, the material or fit is most likely to blame. Cloth masks are recommended, specifically those with two layers, but even a single layer should be sufficient with proper social distancing; medical masks (surgical and N95) can also be used, though N95 masks require proper fitting and the CDC has recommended that N95 masks be reserved for healthcare workers²⁵. Masks should have a seal around the nose and mask, but it does not need to be so tight that it causes an imprint or feels restrictive.

There are rare respiratory conditions that may prevent someone from wearing a mask²⁶, however those with these conditions are also at a higher risk of contracting a severe form of SARS-CoV-2 and so should be practicing stay-at-home measures as strictly as possible for their safety.

5. Would a nation-wide shut down help?

It would help reduce the rate of new transmission significantly, helping hospitals deal with the recent influx of cases and preventing a number of deaths. However, at this stage we are most likely at such a high number of cases that it would not prevent future outbreaks from occurring, and we cannot “flatten the curve” without vaccinations.

A total shutdown, or “lockdown”, where everyone stays in their homes for a period of time, most likely 10-14 days for this virus, should greatly assist with reducing transmission rates and effectively flattening a virus’ transmission curve – meaning that further mass spread, or outbreak, is prevented²⁷.

This is because those who are infected with COVID-19 at the beginning of the lockdown cannot spread the virus to others and can receive treatment; and because new infections are not occurring, hospitals can more effectively treat these patients. Throughout the lockdown period new transmission should be near zero (essential work will still occur, so the possibility of continued transmission is still there but much lower), and those with long-term symptoms should be in treatment as well as remain quarantined after the shutdown has ended. This brings the total number of active cases down substantially.

Once the lockdown is lifted, masks and social distancing should be observed, but person-to-person transmission will begin again. However, the amount of people with infections should be low enough that the rate of transmission will be manageable, and outbreaks are prevented.

Unfortunately, shutdowns are only effective if everyone does them, so most measures taken by governments and businesses so far have largely been in vain. With the current number of infections in the United States, a lockdown may not reduce the transmission rate to one that is manageable, and mass spread is most likely only preventable with the introduction of vaccines. However, a lockdown would still assist with lowering the transmission rate and helping lower hospital capacity.

Currently, most states have over 75% of their ICU beds occupied, with many states reaching full capacity²⁸. This means that not only are those with COVID-19 in risk of not being able to get medical care when it is much needed, anyone with a medical emergency may need to be turned away. Prior to the pandemic, ICU capacity across the states averaged 68% and there had been no significant increase in this number during influenza season²⁹.

6. What happens if I get COVID-19?

The most likely symptoms are similar to the cold and flu, but in some cases you will require hospitalization, a stay in the ICU and potentially face death.

If you are infected with SARS-CoV-2 and get COVID-19, your symptoms will typically begin to occur 2-14 days after initial infection. Symptoms range from mild to severe and include fever, chills, coughing, difficulty breathing, muscle aches, fatigue, nausea, and diarrhea, among others³⁰. Most people with COVID-19, even those with mild symptoms, have reported a loss of taste or smell, and in some of these cases the loss can be long-term³¹. Thankfully, most COVID-19 cases do not require hospitalization, but if someone has an underlying condition, such as hypertension, diabetes, or cardiovascular disease their likelihood of having severe symptoms and requiring hospitalization is greatly increased³².

If you are unfortunate enough to have severe symptoms, your doctor may prescribe you Bamlanivimab, a new FDA-authorized therapy using monoclonal antibodies to help the immune system recognize the virus and respond effectively³³. If your symptoms are so severe that you require hospitalization, there are currently no 100% effective cures for COVID-19, meaning a treatment that will kill the virus directly and completely, so doctors mostly concentrate on fighting the symptoms and ensuring vital organs function properly. If you are having difficulty breathing, you may require a ventilator or a nasal cannula to deliver oxygen, and if you lose the ability to eat you’ll have nutrients delivered via an IV.

There are rare cases of COVID-19 as well that cause issues ranging from neurological problems to blood clots. Some patients have developed life-altering neurological disorders including seizures and psychosis³⁴. Other patients have had to have limbs and extremities, such as legs and hands, amputated due to blood clots formed from complications with COVID-19³⁵. Unfortunately, there will continue to be rare and potentially novel cases as each person’s immune response and viral infection are unique.

So far, the only COVID-19 specific treatment that has been administered within general hospitals is Remdesivir, an anti-viral medication made by Gilead Sciences that prevents SARS-CoV-2 from replicating. However, another treatment has just recently been granted FDA Emergency Use Authorization (EUA) – Regeneron’s REGN-COV2, which is an antibody treatment like Bamlanivimab, but is reserved for more severe cases. These antibody treatments deliver antibodies that will act like the cell’s own immune response, both recognizing and neutralizing SARS-CoV-2 antigens. Both antibody treatments have been largely unavailable to the general public, but should be available throughout the country by 2021.

Although the probability of having a severe reaction to COVID-19 is low if you are healthy and young, you may spread the virus to someone with a compromised immune system, such as someone dealing with cancer or a chronic illness, or those in an older age bracket, and these people could end up in the ICU or dead. It’s each of our responsibilities to care for those outside of ourselves, and prevent the virus from spreading.

7. Do COVID-19 tests work?

Yes, but they have their limitations. In general, trust positive results and confirm negative results. If you want to know if you currently have COVID-19, make sure you get a diagnostic test and not an antibody one.

There are two general types of testing for COVID-19: diagnostic and antibody testing. Diagnostic testing is looking for the virus itself, either through the detection of a genetic code unique to the virus or through the detection of a viral antigen, such as a protein, again unique to the virus. Antibody testing is looking for COVID-19 specific antibodies which we create as part of the immune response to the virus’ presence. Antibody testing may or may not tell you if you currently have COVID-19 since antibodies can take up to 1-3 weeks after initial infection occurs³⁶. Instead, antibody tests are meant to detect past infections.

There have been hopes that being infected by COVID-19 leads to temporary or indefinite immunity, due to the presence of antibodies, which have been detected up to 8 months after infection³⁷, however there is mixed evidence on antibodies always leading to immunity, and still nothing substantiating that once infected you can’t get re-infected; in fact several people have been re-infected within months of their initial infection³⁸.

Diagnostic tests are intended to check for current infection, and most of those created for COVID-19 are Real-Time (RT) PCR-based, which means that the tests are looking for a single or several unique genetic codes specific to SARS-CoV-2 through RT-PCR technology. Other tests are looking for SARS-CoV-2 specific proteins. These genetic codes or proteins are detected within a host’s sample, usually mucous from a nasal swab or saliva from a cheek swab.

Why do people get false positive or false negative results?

False positive results can occur when the specificity of the test is off and the test believes it has identified a viral gene or protein that is actually the host’s. This occurs because humans contain genetic codes that can be very similar to the virus’s, and our protein’s structures can also be closely related to viral ones, “tricking” the test into thinking what it detects is viral because it does not have a high enough degree of specificity to tell the difference. On the other hand, false negative results can occur when either the viral material within the given sample is in such a low amount that it cannot be detected or it happened to be not be captured in that sample at all; this is more common in people who are newly infected and still pre-symptomatic and those that remain asymptomatic. Technical errors with tests can also contribute to inaccurate results³⁹.

If you’ve been around someone with COVID-19 it’s best to quarantine and wait at least 48-72 hours before getting a diagnostic test to ensure the virus can be detected if present, and if the test is negative it’s recommended to get a second test 2-3 days later to confirm. Quarantining for 10-14 days after exposure should always occur regardless of the results to ensure the virus isn’t spread when people are asymptomatic.

8. Are the vaccines safe?

Yes. Some people will have allergic reactions, but these do not cause long-term effects.

There are two FDA-authorized vaccines currently available for SARS-CoV-2: Pfizer-BioNTech’s COVID-19 Vaccine (BNT162b2) and Moderna’s COVID-19 Vaccine (mRNA-1273), both of which are mRNA vaccines. In general, vaccines create immunity against a pathogen by causing a natural immune response within the body specific to that pathogen, in a safe manner – meaning that an inactive form or particle of the pathogen, in this case SARS-CoV-2, is introduced to the body, eliciting an immune response which creates antibodies against that virus, so if the pathogen does infect a cell, it is quickly recognized and destroyed via those “pre-made” antibodies.

The Central Dogma of genetics is the process of converting the information in DNA into proteins. You can think of RNA as the messenger in between DNA and proteins, which is where we get the name messenger RNA, or mRNA. DNA is converted into mRNA during a process called transcription, and the mRNA is then used to create proteins during a sequential process called translation.

With mRNA vaccines, an immune response is elicited by the introduction of mRNA strands which encode partial viral proteins, or antigens, that the body will produce antibodies against. When the mRNA is introduced into one’s cells, naturally-occurring translation will lead to the production of the protein the mRNA encodes for. Both the Pfizer-BioNTech and Moderna vaccines use mRNA that produce partial SARS-CoV-2 membrane spike proteins, acting as antigens and leading to an immune response and the production of antibodies that target those specific proteins. If SARS-CoV-2 infects you after being vaccinated, the body will readily recognize the virus by this protein and can destroy the virus before it can cause illness.

Although there has been no evidence that vaccines cause serious illness or adverse effects in the general population, mRNA vaccines are considered even safer than traditional vaccines because only a single viral protein or partial protein is introduced into the body and mRNA breaks down more rapidly than larger components within cells, removing it more quickly from cells and reducing the likelihood of any negative effects being triggered⁴⁰.

It may be a concern to have mRNA introduced into cells which encodes something viral, however mRNA does not have the ability to incorporate or interact with our DNA, causing no effects to our own genetics. Once mRNA is used to create a protein, the cell will degrade the mRNA, so it cannot be “re-used”⁴¹. The only effect on our cells will be the production of partial viral proteins, which have been proven to have no negative effect on people during clinical trials⁴². Both the Moderna and Pfizer-BioNTech vaccines provide doses of mRNA that lead to a relatively low amount of viral particles being made, so cells will not be overwhelmed while still able to elicit an immune response. Allergic reactions can occur in rare cases however.

Just as there will be different reactions to SARS-CoV-2 or the flu, there are different reactions to vaccinations. Some people’s bodies may respond strongly even to partial viral proteins, which can lead to inflammation and other symptoms that can be detrimental if they are too strong or persist for too long. The few severe allergic reactions to the COVID-19 vaccines so far have been in individuals with other strong allergies, suggesting that the body was sent into an “immune response overdrive” with the elicitation of a new immune response. The CDC recommends that those with severe allergies discuss these with their doctor prior to vaccination to determine if the risk is too high⁴³.

For those without allergies, you may still feel some short-term side effects following the vaccination. This is because the vaccine is causing an immune response, which can lead to side effects such as pain and swelling at the shot site, as well as fevers or chills, migraines, and fatigue⁴⁴. In general, vaccines produce a severe allergic reaction every 1 in 1-million doses⁴⁵. The rate of allergic reactions against the two mRNA vaccines are still being determined, but as of 250,000 doses, 6 allergic reactions had been reported which is a rate of 0.024%⁴⁶.

How many people need to be vaccinated before we have ‘herd immunity’?

In the case of SARS-CoV-2, its estimated that 75% of the population needs to acquire immunity to the virus before the rate of transmission is considered near zero, or halted⁴⁷, at this point it would be said that the population has “herd immunity” to the virus. Since there is still conflicting evidence that being infected with SARS-CoV-2 leads to long-term immunity, this essentially means that 75% of the population needs to be vaccinated before business can return to normal. Currently only about 0.9% of the population has been vaccinated as of December 31, 2020⁴⁸.

Will we need new vaccinations each year, like with the flu?

As mentioned before, the reason that the flu vaccine has to be updated each year is because the influenza virus mutates, or evolves into new types, rapidly – creating new ways to evade the immune response previously crafted against the virus, and effectively making a previous vaccine ineffective. The coronavirus similarly has several different strains, all most likely originating from a single one; this suggests that the virus will continue to evolve. Thankfully, the rate of change and ways in which the virus is changing do not seem significant enough to cause alarm with current vaccine effectiveness⁴⁹. It’s believed that both mRNA vaccines will be effective against all current SARS-CoV-2 strains, but it may be that these vaccines will also need to be updated overtime.

9. What does the future look like?

As bright as we make it.

The future is still very much to be determined, but there is a light at the end of the dark tunnel the pandemic has caused. Vaccinations are rolling out globally, treatments are still being discovered and improved, and people across the world are working tirelessly to help prevent further illness.

There should be specific appreciation shown to public health workers, frontline healthcare workers, scientists, teachers, essential food workers, and everyone else who is ensuring people are fed and cared for during these times.

There are still a lot of painful and hard months ahead that we must get through. Until vaccines have led to a high enough rate of immunity across populations, people will continue to get sick and die, and hospitals will continue to be overran when outbreaks occur. We must follow public safety measures including wearing masks and social distancing until we can call the virus defeated, and even after that we must stay vigilant and potentially continue to update our vaccines and treatments as the virus evolves.

We must also think beyond COVID-19. As much as we would like it to be, this will not be the last pandemic to sweep across the country or globe, so we must also continue to educate ourselves and promote measures that ensure public safety.

Thank you again for reading, and please keep each other safe.

Special thank you to Ryan Pierce for editing.

This scanning electron microscope image shows SARS-CoV-2 (yellow)—also known as 2019-nCoV, the virus that causes COVID-19—isolated from a patient in the U.S., emerging from the surface of cells (blue/pink) cultured in the lab. — Scanning electron microscope image of SARS-CoV-2 (yellow) emerging from the surface of cells (blue/pink) (Source: https://www.niaid.nih.gov/news-events/novel-coronavirus-sarscov2-images)

References:

August 29, 2019
by J Hope Leave a comment

Genetic Engineering Pt. III: Wanna Fight About It?

When most people consider genetic engineering, the first things that come to mind are genetically modified organisms (GMOs). Although GMOs are a hot topic of debate, they are not the only controversial topic involving genetic modification – for this post, I wanted to explore a few of these areas and take a look at why they are controversial.

We’ll begin with a look at GMOs, but will venture into the world of pure breeding our beloved pets, and the application of genetic engineering in human health.

These topics are shrouded in biases and false claims. I encourage everyone, regardless of their opinion, to have an open-mind and realize that most of life’s answers come in shades of gray that require patience, experimentation and collaboration to determine.

Genetically Modified Organisms – Are You Going to Eat That?

Are GMOs Safe to Eat?

GMOs can be thought of in two different ways: any organism (plant or animal) that has undergone genetic modification, which includes both artificially selected organisms and those that have been genetically engineered. When making this differentiation, some refer to the latter as genetically engineered organisms, or GEOs.

Since we began to develop agricultural practices and grow crops such as wheat, we’ve been eating artificially selected organisms and these have become the norm – we generally no longer question their safety.

For GEOs, the question of safety still exists. This stems mostly from worries that either our own genetics will be affected by eating GEOs or that genetic engineering changes the biochemistry of an organism in a way that will harm us when consumed. An interesting consequence of this is that t here are more studies being conducted on the safety of GMOs and GEOs then most other foods that we consume, including processed and packaged products – meaning that GMOs and GEOs may prove to be safer than many other foods we find in the market already (safer not necessarily meaning safe in all instances).

Flavr Savr Tomatoes were the first GEO product on the food market.

Currently, a controversial practice within the food industry is using the idea that GMOs are not safe in order to market non-GMO food and health products. However many of these products are still highly-processed through the hands of humans and not the most nutritionally valuable. So should the argument instead be are any processed foods safe? And should there be further standards for nutrition and safety for all food products we allow in the market, beyond those currently in place?

Many people do believe this is the fundamental argument and advocate for diets focused on unprocessed and organic foods. However, this is where we begin to enter into socioeconomic issues. Organic foods are often significantly more expensive than their processed or GMO/GEO counterparts, disallowing entire groups of people to purchase them.

In reality, the consumption of genetically modified food is not just a question of safety and nutrition, but is also a question of accessibility to alternatives and closing the division we have created in our society based on socioeconomic status. As of right now, we are experiencing a market where generally the more wealthy are able to purchase organic foods and those who are struggling financially can afford only conventionally raised and processed foods. However, many believe there is a tr ickle-down effect as more companies and restaurants compete in the organic market, driving down prices – so this may very well change overtime.

It should also be noted that many believe that through genetic engineering we can produce crops that can withstand harsh environmental conditions such as drought, and resist predators without the use of pesticides – allowing them to grow in developing countries who would otherwise not be able to grow crops for food or exporting.

With our growing populations and increasing environmental damage, if we don’t rely on GMOs and GEOs, we will need to find an alternative solution for maintaining food supplies and economic development (as we hopefully work to also reverse our environmental damage).

Isn’t Monsanto Evil?

There is evidence that companies like Monsanto are not genetically modifying crops so that they are better suited for feeding impoverished countries or resisting pests (Monsanto is also a world leader in pesticide production), but are instead producing traits that allow the crops to be patented, and essentially building a “crop monopoly”. However, Monsanto has also helped advance our understanding and application of genetic modification and contributes to research focused on environmental conservation.

Like any other major corporation, you can identify negative and positive impacts they have on the world, so it’s important to separate individual companies from the general goals and methods of an industry. There are hundreds to thousands of people involved in the GMO/GEO market and many are working towards modifying the type of crops that will help communities that are in need of economic boosts and nutritious food, and are working to produce plants that will help restore ecological integrity.

Genetically Engineered Animals – Frankenfish?

Recently, the first genetically engineered animal was approved to be introduced to the food market – the AquAdvantage® salmon. The salmon grows to adult size in half the time as wild-type salmon (those not genetically altered). The process to create the AquAdvantage salmon began over 20 years ago, and health and safety testing has been involved in this process since the beginning.

There should be some concerns however:

Will the fish be contained so that they don’t breed with wild-type salmon and introduce the modified genes into the wild population?
- Breeding with wild fish could introduce the new growth gene into the population, causing a disruption in the life and breeding cycles of wild salmon.
Are the fish okay?
- Studies have shown that fish do feel pain as well as suffering (meaning they are conscious of their pain). We should be concerned with the physiological effects on the fish as well as us.
Are we okay?
- Studies on the AquAdvantage salmon have shown that there are no negative health effects from consuming the salmon and they carry comparable nutritional values as their wild type, but many food products on the market lead to health problems in the long-term that we need to be aware of and mitigate if they become too serious (this is true of any food).

This article does a good job at providing answers to these questions and the benefits of the AquAdvantage salmon.

AquAdvantage salmon compared to a hatchery raised wild-type salmon.

The fact is, any food, no matter where it comes from or how it’s produced, should be scrutinized for it’s effects on human health, animal health, and the health of the environment. And these effects should be tracked overtime to get an understanding of any long-term consequences. GMO/GEOs are no different, but they should also not be considered unsafe or unnatural simply due to being processed, as humans have created amazing things from nature, such as Aspirin, and genetic change does not necessitate harm.

Pure Breeding Animals – Are We Hurting Our Best Friends?

Pure breeding of domestic animals, mainly dogs and cats, began thousands of years ago. To the delight of the world, we’ve created pets and working animals that suite every personality and every lifestyle – from ranch dogs to teacup pets and luxurious breeds that are bred to be rare. Unfortunately, several of the breeds we have created through artificial selection now suffer from genetic disorders.

German Shepherds suffer from hip conditions, Bernese Mountain Dogs suffer from several disorders, including neoplasia in which tumors and abnormal growths cause health complications, and often do not live past 6 years. Brachycephalic breeds – those with flat faces such as bulldogs and persian cats – are not allowed to fly on most major airlines due their inability to breathe during the flight.

We’ve been creating breeds that are either aesthetically pleasing to us or complete a job for us, often without the consideration of the effects on the animal’s health. Pure breeds have a higher correlation with health complications than mixed breed counterparts and many studies have shown that mixed-breeds suffer from a lower level of genetic disorders and often have longer lifespans than pure breeds of similar size.

Thankfully, lovers of these breeds recognize the pain they are causing, and just as genetic issues have been inherited within breed lines, many of these issues can also be “bred out”. Depending on the severity of the disorder, it may be the best option for some breed lines. Finding parents that do not carry the genetic disorder and cross-breeding them leads to at least some, if not all offspring also not being carriers – and through generations, the breed can be rid of the disorder.

However, some conditions, such as the flat-faces of brachycephalic animals cannot be “out bred” without changing the physical appearance and essentially the breed. The question then becomes if we are willing to let certain breeds “go” and allow them to change overtime, either through random mixing or by selective breeding.

Old bulldog skull compared to the newer bulldog skull.

It should be noted that not all purebreds suffer from hereditary genetic disorders (those that are passed on through genetics) and mixed breeds can also suffer from genetic disorders.

It should also be noted that there are thousands of homeless pets in the world, and adopting one is a wonderful way to add to your family. Both mixed and pure breeds can be found through rescue and adoption organizations.

If you are concerned that your dog suffers from a genetic disorder, there are several genetic tests available. The most widely recognized and perhaps the most comprehensive is offered from Wisdom Health (this is not an ad and I have not used their products before). Before taking a test, speak to your vet about your concerns and how to interpret the test results.

Genetic Engineering & Human Health – The Fear of the Designer Baby

With the emergence of genetic sequencing and gene therapy in healthcare, there is a rising concern over how genetic information will be used. In a future post, I’ll dive further into genetic sequencing, but for this post I wanted to address the idea of genetic modification within humans for medical purposes.

Why Would We Change Our Genetics?

Genetics are the basis for a majority of our health concerns, including cancer, Alzheimer’s, Huntington’s Disease, and autism, just to name a few. Genetic sequencing has allowed us to identify exactly where in the genome mutations are occurring (changes in our genetic code that cause health abnormalities), and from there we can begin to identify ways to either address the consequences of that mutation – which can be as simple as giving someone an enzyme that they do not produce themselves (due to inherited disorders of metabolism) – or correct the genetic code itself.

Besides studies using in vitro methods (outside of the body), altering human genetics through techniques such as CRISPR-Cas9 is not practiced and generally not condoned in the scientific community until further standards around safety and application are determined. FDA-approved gene therapies are just beginning to emerge into the market now.

In vivo (within the body) techniques in practice utilize naturally occurring components of our cells to produce genetic responses. The initial sequencing allows us to determine a genetic cause of a health disorder, if the disorder is genetically-linked, and from there we can determine potential gene therapies, which would modify the patient’s genes in a way that stops or reverses a disorder. This is most commonly accomplished by introducing proteins or fragments of nucleic acid (RNA or DNA) into the targeted cells, though lipids and carbohydrates are also being studied. These gene therapy tools work to either:

Replace a mutated, inactive, or missing gene.
Silence an active gene, such as a mutated and cancer-causing gene.
Introduce a gene that will create a therapeutic protein (such as a protein necessary for our natural immune response to kick in).

Promising therapeutics are on the rise in numerous areas including, but not limited to cancer, neurological conditions, and pediatric disorders.

Will the Future Have Designer Babies?

An area of high concern regarding genetic modification is babies. The idea of changing a child’s genetics not to address a medical condition but instead alter them to carry a specific desirable trait is straight out of an episode of Star Trek. Although there have been some studies looking at genetically engineering within human embryos, with the only published work coming out of China, the science and safety behind these have been unsubstantiated and require significant work before they are considered ethically and medically sound, if they ever are.

On the other hand, non-invasive prenatal testing allows us to take a blood sample from a pregnant mother and separate the baby’s DNA from the mother’s. The baby’s DNA is then tested for abnormalities and if detected, expectant parents and their doctors are able to make more well-informed decisions on how to care for their child or in the least have an answer to why they experience miscarriages. Some conditions may be treatable through actions taken by the mother, such as diet changes or potential medications and gene therapies.

B’Elanna with her child (who she decided to not genetically alter) in “Lineage“, the 158th episode of the TV series Star Trek: Voyager

In the future, therapeutics may be available that directly change our genetic code, especially if it means preventing a miscarriage or pediatric disorder, but for now look at gene therapy as a rising industry and an area of optimistic development.

To learn more about non-invasive prenatal testing (NIPT), please follow this link.

Where Do We Go From Here?

We’re really just beginning to understand genetics, how they effect who we are, and how we can better control our futures with gene editing tools.

Many people who support genetic engineering envision a future where struggling communities and developing countries can grow their own food, and one where we’ve used our technology and knowledge to strengthen our environment and reverse ecological damage, including the causes and effects of climate change and species extinction.

Many people who do not support genetic engineering envision the same future, but through different means.

Maybe it’s time we stopped bashing each other for having differing opinions on the process, and begin to work together to find solutions and realistic compromises. The world truly takes all kinds, and we must work together to create the beautiful future so many of us have in mind.

Károly Markó, Árkádiában, 1830. [Hungarian National Gallery]

August 29, 2019
by J Hope 1 Comment

Genetic Engineering Pt. II: Tools of the Trade

As introduced in my previous post, this is the second of a 3-part series on genetic engineering. The first post was a brief overview and introduction to genetic engineering; while this one will focus on the tools used, and explain the difference between artificial selection and genetic modification. The third and final post will cover some of the more controversial topics, such as personalized medicine and genetically modified organisms (GMOs).

Artificial Selection: How We Created Man’s Best Friend

In order to explain the differences between genetic modification and artificial selection, it’s easiest to look at specific examples. A prominent example of artificial selection is the animal that has touched so many hearts it’s been named “man’s best friend”- dogs. Dogs are especially interesting because they are believed to be the first animal ever domesticated, occurring even before agricultural animals such as cattle, and there are now several studies suggesting that dogs were independently domesticated twice.

All dog breeds come from a common ancestor – the gray wolf. Genetic sequencing studies show how closely they are related. So how exactly did we get the chihuahua from the gray wolf? Through thousands of years of selective breeding, even as long as 30,000 years. Let’s start with the gray wolf meeting humans: it’s unknown whether humans sought out a relationship with wolves, if it was vise versa, or if it was a mutual “agreement”. However it happened, humans began to interact with wolves to the point where they were breeding them for specific qualities.

From the beginning of domestication, people recognized that if you cross two wolves that are docile than their offspring will have a high chance of being docile as well (versus breeding more aggressive wolves). If you continue this process, while also eliminating the aggressive wolves – let’s be honest, this occurred – than you would eventually, through several generations, have only docile wolves. If you continue this process while concentrating on a single characteristic at a time, such as size or coat-thickness, than eventually the wolves become so genetically different from their descendants that they became a new species: dogs.

For dogs, several characteristics were altered over thousands of years by repeatedly altering a trait at a time. In more modern times, such as with cattle and other agricultural animals, only a single trait or small set of traits is targeted for alteration, not allowing for speciation, or the separation of one species into two.

This same process is used for the domestication of plants. Although the exact date when wheat was first domesticated is still debated today, it is known that the wheat we consume today varies genetically from wild wheat due to years of selective breeding. Two traits in particular allowed humans to consume and to grow wheat: an increase in grain size and the development of non-shattering seeds. The former allows for easier cultivation of the seedlings and the latter prevents natural seed dispersal, so that humans can harvest the seeds at the optimal time. It’s believed that both of these traits occurred naturally, and humans took advantage of them by only selecting for plants with those qualities. Today, common wheat differs even greater from the wild ancestor through actual breeding programs. Wheat breeding programs around the world have artificially selected for traits that mostly confer a resistance to either a pest, disease or other environmental factor, creating a much more modern version of wheat.

For a further understanding of artificial selection, check out these links:

Genetic Modification: The Simple-ish Version

As mentioned in my previous post, genetic engineering, or modification, has been in practice since the 1970’s, when Boyer and Cohen first successfully recombined DNA into E. coli. Although the procedure Boyer and Cohen used, known as recombinant DNA technology, is still used today along with several other methods, there is a current shift into using CRISPR technology as the main tool for genetic alteration. Since this shift is occurring and there has been a focus on CRISPR, both by those that support genetic engineering and those that don’t, the rest of this post will have a major emphasis on CRISPR technology.

CRISPR stands for Clustered Regularly Inter-spaced Short Palindromic Repeats. Palindromic repeats are prokaryotic DNA containing short repetitions of base sequences, and in between the sequences are short segments of non-coding DNA (“spacer DNA”). One of the main components of CRISPR technology are CRISPR associated proteins, or Cas proteins, which are endonuclease enzymes – enzymes that will cut double-stranded DNA (dsDNA) – that are guided by RNA. CRISPR and Cas proteins are naturally found in several species of bacteria, and work as mechanisms of immunity by cleaving the DNA of invading pathogens, such as viruses. Although there are multiple Cas proteins, the Cas9 endonuclease found in Streptococcus pyogenes is currently the most efficient Cas protein, thus the current technology is known as CRISPR/Cas9.

CRISPR/Cas9 technology is progressively getting more complicated with the addition of new information and modifications to the current methodology. However, the basic procedure that CRISPR/Cas9 performs remains the same. As mentioned, one of the main components of the technology is the Cas9 protein. The other component is a guiding RNA (gRNA). The gRNA is created so that it matches, or compliments, a DNA sequence within a genome. The gRNA will find that sequence and will hybridize to it. Next, the Cas9 protein uses that gRNA as a guide to find and bind to both the gRNA and to the DNA it’s hybridized to – binding to both strands of the DNA, not just the strand the gRNA is hybridized to. Finally, Cas9 will cleave both strands of the DNA. When the dsDNA is cleaved, the cell will detect there is a cut and when repairing the area, mutations will be introduced in a natural repair process. If the DNA encoded a gene, the introduction of a mutation will alter or silence the expression of that gene.

crspr_cas9

After gaining an idea of what the CRISPR/Cas9 system does, it makes sense that scientists are trying to use this tool as a way to silence and edit genes. The system can be modified to target specific genes by creating specific sequences of gRNA. Current studies are using the system in several new ways, including studying epigenetics – the study of how gene expression is effected by the environment, and the potential to target genes associated with cancer and Alzheimer’s, among other diseases. The first cancer-targeted CRISPR human trial has been green-lighted by the National Institute of Health, and may mark the beginning of a future where diseases are edited out of the genome.

Stick around for the next post, I’ll be covering further controversies associated with gene editing. And if you would like any further information on CRISPR/Cas9 technology, please check out the following links:

Author’s note: in an attempt to reach a wider audience, the processes of both artificial selection and genetic modification have been simplified. Before forming any opinions of either subject, I highly recommend doing further research on both topics. Thank you for reading.

August 29, 2019
by J Hope 1 Comment

Genetic Engineering: The Good, The Bad, and The Ugly

After the completion of the human genome project, the field of genetics began to gain popularity and intrigue with the general public. Genetics, as a field, has been explored since the early 19th century, beginning with Imre Festetics, a long forgotten predecessor to Gregor Mendel, but it wasn’t until recently that it became center stage in our everyday lives-everything from disease, ancestry, medicine, and personality are wrapped up in genetics. This makes sense when you view genes as personal codes: encoding what eye color we have, which hand we write with, and which diseases we are prone to getting. Our genes encode our existence in a very real way, so understanding genetics leads to a better understanding of what it means to be human and what it means to be us.

Genetics can be a daunting and even scary field to study, but now that genetic engineering and personalized medicine are being covered by media and discussed online, it’s time for the general public to have a solid understanding of what genetics is and especially how their own genetics affect them. This is the beginning of a 3-part series regarding genetics and genetic engineering. This first post will cover an overview of genetics and genetic engineering. The next two will discuss tools and techniques used for genetic engineering, such as CRISPR, and the more controversial side of genetics, such as “designer babies” and genetically modified organisms.

What is genetics?

Instead of repeating most of the information that is available online or in text books, I thought it would be more efficient to share some links that I believe cover the topic of genetics well. Understanding genetics is essential to understanding genetic engineering, so before proceeding to the next section I highly recommend checking out at least one of the following links:

Genetic Engineering: An Introduction

Genetic engineering may seem like a new 21st century technology, especially with its recent boom in media coverage and controversy, but the concept has been in the scientific community since the 70’s and is in fact a naturally occurring process. The technology used for genetic engineering began to form in 1973 when Herbert Boyer and Stanley N. Cohen performed the first successful genetic recombination experiment. Together they were were able to combine two separate plasmids-carriers of genes-and clone the new recombined plasmid into E. coli. The recombined plasmid was functional and provided the E. coli with genes resistant to both tetracycline and kanamycin, both antibiotics. This same process occurs naturally in bacteria, usually with the assistance of viruses (see my previous post for an explanation), and this is why we have “antibiotic resistant” strains of bacteria.

Speaking of naturally occurring cases of genetic engineering, there is the case of the sweet potato. Several studies, including one at the International Potato Center in Lima, Peru, have found that sweet potatoes were genetically modified by bacteria approximately 8,000 years ago. Bacteria, such as Agrobacterium, are present in soils and act like a virus by injecting plant cells with their genes. Once these genes are inside the plant cells, they produce proteins within the plant-effectively changing that plant. Researchers from Peru believe that the modifications caused from the bacterial genes helped make sweet potatoes more edible for humans. Today sweet potatoes are the 7th most important crop in the world according to the Agriculture Organization of the United Nations.

So, what is genetic engineering? And is it all the same? The simple answers are: modification of an organism by the insertion of a functional gene from a different organism, and no. But this isn’t a subject that can boiled down to black and white, or right and wrong, and one that not only requires, but deserves to be looked at in depth. So, with that being said, let’s begin by describing what genetic engineering is.

Defining Genetic Engineering:

Genetic engineering, or genetic modification, can be done using several different processes, but the basic purpose is the same: to alter an organism on the genetic level, by either inserting or removing a gene. The gene could come from the same type of organism (i.e. E. coli to E. coli) or from different organisms, such as the follow-up experiment done by Boyer and Cohen which consisted of taking a gene from the African clawed frog, Xenophs laevis, and inserting it into E. coli.

Genetic engineering is commonly divided into two categories: modification using biotechnology (traditional genetic engineering), or modification through selective breeding or other forms of artificial selection. The latter is often not considered genetic engineering at all, but on the genetic level, they are actually quite similar processes. This will be explained further in the next post.

In order to get a better understanding of genetic modification and the processes used to achieve it, some common terms need to be defined first. When genetic material, either RNA or DNA, is taken from two different organisms and combined together it is considered recombinant nucleic acid (DNA or RNA). When the recombinant nucleic acid is successfully inserted into an organism, that organism is either termed transgenic, if the material came from a different type of organism, or cisgenic, if the material came from the same type of organism. While transgenic and cisgenic are commonly used in the scientific community, the more popularized term for any genetically altered organism is genetically modified organism (GMO). Alternatively, organisms can have a gene “knocked out”, or made non-functional, through gene knockout techniques and these organisms are referred to simply as knockout organisms.

Final Note

Genetic engineering also has roots in stem cell and cell cloning science, but for the purpose of these posts I’ll be concentrating on the modification of plants and animals through traditional genetic modification and artificial selection. In the second post of this series, I’ll be discussing the tools and actual processes used to create modified organisms. Until then, brush up on your genetics, and enjoy some sweet potatoes.

To Be Continued..

August 29, 2019
by J Hope Leave a comment

My Top 6 Lessons From Science

I consider myself a “late-bloomer” when it comes to being a science-enthusiast. I didn’t grow up watching Bill Nye the Science Guy, I attended a high school where creationism was taught as an alternative to evolution, and I originally went to college to become an English teacher. Now, science is a huge part of my life and identity. I confidently believe that studying science and simply being exposed to scientific ideas has helped me to become a better person. So here’s the top 6 lessons that I’ve learned through science, I hope you find value in them as well.

Observation is the key to discovery. Every great idea began as an observation. Most of us are familiar with the story of Isaac Newton sitting under an apple tree and seeing the apple fall, leading to the theory of gravity. Although this story is only a legend, it illustrates the point that the only way to discover something is to first make an observation. In order to do this, you must be aware of your surroundings; taking the time to see, hear, smell, taste, and feel the world around you. You must be present.
Knowledge knows no borders. Science is an international community. Every conference and lab I’ve attended or worked in has been a melting pot of cultures. People from every walk of life are drawn to science, as they are drawn to other interests as well, but science is unique in that we need people from all over the world to collaborate in order to make profound discoveries, and especially to have scientific innovations change the world for the better. There’s even an International Council for Science, which works to “strengthen international science for the benefit of society”. Of course no industry is without bias or prejudice, but in order for scientific discoveries to continue to be made, the scientific community must work together, regardless of location or politics-and that is a wondrous thing on its own.
We are a fundamentally connected to the universe. You may have heard the saying we are made of star stuff. While that may seem like a romantic notion, we are indeed connected to the universe through the elements that compose our bodies. Elements such as iron are believed to have originated from stars, in a process called nuclear fusion. When stars exhaust their supply of hydrogen (the building block for all other elements) they explode in what’s called a supernova. During a supernova, the material of the star, including elements like iron are scattered across the universe, providing the building blocks for all matter—including us. In fact, it’s believed that all of the atoms in the universe are connected by a single origin. As Carl Sagan said so eloquently during an episode of the original Cosmos, “We are a way for the universe to know itself. Some part of our being knows this is where we came from. We long to return. And we can, because the cosmos is also within us. We’re made of star stuff”.
I have not failed 1000 times, I have figured out 1000 ways how to not make a light bulb. Though this is a misquote, with the actual quote originating from a conversation with Thomas Edison in which he said “Results! Why, man, I have gotten a lot of results! I know several thousand things that won’t work”, this is still a powerful idea. Science embraces failure; without it nothing would have been discovered, no theories would have proven, and no laws would have been established. One must fail in order to succeed, and one usually must fail several times. Instead of being disheartened and allowing this to stop you, you observe your own mistakes, learn from them, and try again. Allow your failures to encourage you to grow rather than to give up—you will not regret it in the end.
Life is about creating and maintaining a balance. From physical forces like gravity keeping us in place, to chemical reactions occurring in our brains to allow us to think and type blog posts: life is about balance. There’s a word commonly used in biology—homeostasis—it describes a state of balance within a system; for example when we become too hot from external sources, our body works to maintain a core temperature by regulating internal conditions. In our own lives we can strive to maintain homeostasis. When external forces work to disturb our bodies or minds, we can in turn use internal forces to prevent that disturbance from effecting us (use the force). You can also think of “maintaining homeostasis” through keeping matters in your life balanced: work, family, friends, personal goals, etc. Finding and keeping a balance allows you to de-stress and enjoy more in life.
We are connected to all forms of life. When you look into a dog’s eyes your brain releases oxytocin, otherwise known as the love hormone, and maybe not-so-surprisingly, your dog’s brain releases the same hormone. When a baboon mother loses an infant, she shows psychological and physiological signs of the same grief human mothers feel at the loss of a child. These aren’t just coincidences of nature; instead they are signs of a deeper connection that we share with all other organisms—we are genetically linked. Our closest relatives are the chimpanzee and bonobo, sharing up to 98.8% of our genes. (For an explanation of how this is determined follow this link). But it may be surprising to some that we’re also closely related to animals such as mice, sharing nearly 90% of our genes with them—this is why mice are commonly used in biomedical research.To me, this is the most important lesson. Being connected to other organisms not just because we share this world and its resources, but because we are genetically related is profound. Other organisms besides us feel emotions, they feel pain and fear, love and compassion. Just because they speak a different language doesn’t mean that they do not feel or have thoughts, it only means that we must take the time to consider, respect, and appreciate other forms of life so that we can better understand them. No matter what religion or philosophy you believe in, having love and respect for other beings is one of the most important things you could ever do.

So there you have it, my top 6 lessons from science. There’s numerous more that I could go on to talk about, but they all relate to one of these 6 main ideas. So here’s the last piece of advice I’ll leave with you today: keep your curiosity.

Work Cited:

August 29, 2019
by J Hope 5 Comments

The Invisible World of Microorganisms

As humans, it’s difficult to imagine the world in a scale that is different than our own, especially when that difference is significant, such as the expanse of the universe or the workings of a cell. That’s what makes microorganisms so interesting. There is an entire world among us and in us that is invisible to the naked eye. Now, not only are we aware of these hidden communities, but we use microorganisms in a wide range of industries, and we also know that the bacterial communities living inside and on us help keep us healthy. With all of this unseen activity among us, learning about microorganisms opens up our eyes and minds to an once-invisible world.

What is a microorganism anyway?

The simplest definition of a microorganism, or microbe, is an organism that is too small to be seen by human vision, i.e. can only be seen with a microscope. Of course, microbes are much more complex and diverse than this definition implies. First off, microbes can be single-celled organisms or multicellular, and there are several categories of microbes: bacteria, archaea, fungi (includes yeasts, molds, and mushrooms), protista (algae and protozoa), and viruses.

Bacteria:

Escherichia coli

Archaea:

Pyrococcus furiosus

Fungi:

Zygomycota rhizopus

Protista:

Noctiluca scintillans
(Sea Sparkle; protozoa)

Viruses:

Orthomyxovirus (Influenza)

Viruses are especially interesting in that it has long been debated whether viruses are “living” organisms are not, since they lack one of the seven characteristics of life: the ability to reproduce on their own [1]. Viruses need cells from other organisms in order to replicate, or reproduce. That is also why they are considered such a threat to our health—they can move from cell to cell, replicating and usually killing the cells they inhabited along the way. As I’ll soon discuss though, viruses can also be used for good.

Microbes are actually everywhere

Microbes can be found in any type of environment, including the human body. Since they can be found virtually everywhere, I’m only going to describe the more extreme habitats. Microbes living in these conditions are known as extremophiles. To start with, microbes can be found in the deepest parts of the ocean. When divers first discovered hydrothermal vents at the bottom of the ocean, they were surprised to find thriving communities of life there [2]. It turns out that microbes, especially archaea, are adept at surviving in extreme conditions; in this case those conditions are extreme pressure, and temperatures up to 350°C (662°F)! Microbes can also be found in the freezing temperatures of the arctic. On February 6, 2013 scientists first reported bacteria found a half-mile deep under the ice of Antarctica. In fact, since the arctic isn’t hospitable to other forms of life, bacterial communities dominate the biodiversity [3].

Radiation is scary for humans even at very low doses, but there are microorganisms that can withstand extremely high levels. These microbes exhibit “radio-resistance”: resistant to ionizing radiation [4]. A lethal dose of radiation for humans is approximately 4-10 gray (Gy), while these organisms can survive radiation of at least 1000 (Gy) (100x more than humans!) The most extreme example is Thermococcus gammatolerans, rightly named after its ability to survive 30,000 (Gy)! [5]

And last, but certainly not least, there are astronaut microbes! When the unmanned lunar lander Surveyor 3 returned to earth, NASA scientists were surprised to find living Streptococcus mitis from Earth that had survived on the lander for 31 months in the vacuum of space [6]. Since then several microorganisms have been identified as having the ability to survive in space, and these include one of my favorite organisms (micro or macro): Tardigrades! Also known as “water bears”, because they literally look like little bears, these little guys are the ultimate extremophiles. Not only can they survive in space, they are also radio-resistant and can survive radiation levels up to 5,700 (Gy), as well as in temperatures below freezing and above boiling. To top it off, they can survive more than 10 years without food or water [7]. Basically, Tardigrades will outlive us all.

Some other not-so-common places that microbes are commonly found: bubbling tar, steam vents, boiling water, in soil and ice miles underground, and most likely in areas that humans have been unable to discover thus far [8].

Tardigrade (Water Bear)

Humans and Microbes: A love-hate relationship

The term “human microbiota” is becoming increasingly well-known as we learn more about our close interactions with microorganisms, but as a short description: the human microbiota, or microflora, is the collective of microbes that live on the surface and in layers of the skin, the saliva and oral mucosa, in the conjunctiva (lines the inside of the eyelids), in the gastrointestinal tract, in the respiratory system, and in the vagina [9]. The interactions between the human body, the microbiota, and the environment are so complex that I’m not even going to go there in this post. What I do want to discuss though, is how microbes are actually helping us!

Bacteria in our body play vital roles in keeping us healthy – they interact with and boost our immune systems and even combat pathogenic microbes (ones that cause disease). The bacteria on our skin act as an extra layer of protection against any bad guys getting in or on us. In a nut-shell, having these communities of good bacteria in and on our bodies helps prevent bad communities from moving in [10]. In fact, bacteria play such an important role in our health that there are more bacterial cells in our bodies than our own actual cells [11].

Microbes are also used to improve our health and combat diseases in more targeted ways. An example of this is the use of microbes as vehicles, or carriers, for medicine. Some bacterial strains are commonly used as “delivery capsules” for drugs that are normally toxic when taken alone. E. coli has been engineered to transport an enzyme specifically to cancer cells, without targeting and harming other cells [12].

Viruses are also being used to treat cancer, as a team from Massachusetts General Hospital and Harvard Medical School used engineered Herpes Simplex Virus Type 1 (HSV-1) as vectors for targeting cancer cells [13]. Using viruses or other microbes as vehicles could eliminate more dangerous types of treatment such as chemotherapy. Microorganisms can also be genetically engineered to target tumors and specific areas of the body that are under attack from disease.

Other ways that microbes are helping us range from food production to toxic cleanup. Yeasts are commonly used for bread and beer production and various bacteria are used for cheese production. Microbes are also exploited for the compounds they make: including enzymes, vitamins, and antibiotics. For example, penicillin was originally isolated from the fungi Penicillium, and lactic acid is used as a food preservative. Microbes are also essential to agriculture and nutrient recycling. Microbes living in the soil break down nutrients that are found in their environment, and provide things like nitrogen to plants in a process called mineralization [14] (side note: bacteria also break down nutrients in the GI tract to help humans digest them better). As mentioned, microbes are also used for cleaning up environmental toxins, including oil spills. Some microorganisms actually use oil as fuel, so that they can be released into a contaminated area and, given enough time, the oil will be removed [15]. This is a promising approach to cleaning up other toxins found in soil and water in a relatively safe and hands-off way.

I could honestly go on and on about the wonders and curiosities of microorganisms, but for the sake of keeping at least some readers I’m going to stop here. I hope you enjoyed reading about these amazing organisms, and have a new-found or refreshed appreciation for the invisible world of microbes. Now I dare you to look at anything around you, even in the mirror, and not think about how many microorganisms are there…good luck, and welcome to my world.

Work Cited:

Further Links:

Wikipedia: Microorganisms https://en.wikipedia.org/wiki/Microorganism

Fungi Information http://www.ucmp.berkeley.edu/fungi/fungi.html

Archaea Information https://en.wikipedia.org/wiki/Archaea#Morphology

Protista Information http://www.microbeworld.org/types-of-microbes/protista

Virus Information http://www.ucmp.berkeley.edu/alllife/virus.html

Tardigrade Information http://tardigrades.bio.unc.edu/

August 29, 2019
by J Hope Leave a comment

What Do You Mean: Finding Correct Information in a World Full of Disinformation

Let’s admit it, we occasionally find ourselves quoting a study or something we saw on the internet as truth without doing much or any background research to find out if the validity holds. I’m guilty of this, and as a scientist and a writer I should probably be the first to admit it. So—what do we do about it? In other words, how do we curb our opinions and statements to better represent the truth?

I believe that everyone, no matter age or education level (let’s ignore babies for this post), has the ability to discern fact from fiction and to be a critical thinker. When it comes to being a critical thinker online, where there is a plethora of disinformation, it’s important to have some ground rules for yourself. Today I am going to share my personal ground rules, but first let’s go over certain words that are used in both common and scientific language, but that have separate meanings (e.g. theory), and how they are used to “de-bunk” science

Trust me, you have a conspiracy hypothesis.

As an English major gone Biologist, the use of the word “theory” is a source of great frustration. Theory, like many other words, has a separate meaning when used in common language versus used in scientific work.

Common use of theory: used when one has an idea or is guessing at something “my theory is…”, while often these are based on simple observations or opinion, and not on experimental data (as is done in science). I used the word conspiracy for the heading because I’m sure most people have heard of conspiracy theories. These “theories” are examples of non-scientific ideas: ones that cannot be tested repeatedly and upheld or dismissed based on experimental data. Simply, in this context, a theory is a guess.

Scientific use of theory: “A well-substantiated explanation of some aspect of the natural world that is acquired through the scientific method and confirmed through observation and experimentation” [1]. Took the words right out of my mouth, but in simpler terms the word theory used in scientific terms means an idea that was tested repeatedly and by multiple, independent parties and consistently upheld by the results. So, in this context, a theory is much more than a guess. A theory may be altered overtime with new supporting evidence, but it always has a strong basis of truth attached to it.

Side Note: The theory of evolution is often attacked as being “just a theory”, but it has stood the test of time and repeated experimentation. Here are some other theories that have done the same: the theory of plate tectonics, the theories of special relativity and general relativity (Einstein ring a bell?), and Heliocentrism: the theory that the Earth revolves around the sun. The beautiful thing about science, and also the thing that makes it vulnerable to nay-sayers, is that nothing can be completely proven (i.e. there must always be room for growth and change)—meaning that we, as humans, are part of this world and universe and as such, we cannot see how the it all works from the outside.

An analogy of this: you are living in a house without the blueprints. You don’t know how the house was made, but by observing and testing various components of it you come up with a theory of how it was built. As you continue to collect more information, this theory may change, but without the blueprints you will never know for certain that you are right.

So there must always be room for doubt in science, but that also means room for new knowledge and growth.

Hypothesis vs. Theory vs. Law

Briefly, I wanted to define the other terms used in science as well.

Hypothesis: you can think of a hypothesis as an educated guess (which is what most people mean when they say they have a theory). When one observes something in nature, they make a hypothesis. Example: you are walking along and notice that a moth has the same coloring as the tree it is on, so thinking about camouflage you make the following hypothesis: “the moth has the same coloring as the tree in order to hide from predators”. Now you can begin to test this hypothesis by using the scientific method. (http://www.sciencemadesimple.com/scientific_method.html)

Law: this term can be the most confusing, but I think this is a good explanation: a law is “the description of an observed phenomenon. It doesn’t explain why the phenomenon exists or what causes it” [2]. In relation to this, a theory would be the explanation of the phenomenon. Newton’s Laws of Physics are probably the most well-known laws, which describe the world around us.
(http://www.physicsclassroom.com/Physics-Tutorial/Newton-s-Laws)

How to Navigate Through the Internet

The internet can be a wonderful place for connecting to others, sharing stories, and finding useful information, but it can also be an overwhelming place full of propaganda and false information. So here are my tips for navigating to useful and correct info.

Collect information from multiple sources. This is my number one tip, and even after following the next two I encourage everyone to always keep this in mind. Getting a consensus from independent sources is a way of ensuring that there is an agreement that the information is true. I usually check at least 4-5 different sources, which are not related to one another, before I feel comfortable believing the information.
Avoid getting information from sources that would benefit from the info being true. This can be pretty hard, and sometimes the information is right but I would take it with a grain of salt. Some examples of this would be sites that promote ideas which backup their existence. (e.g. a site that promotes the use of a certain drug, but that site is connected to the pharmaceutical industry). The main reason to not trust the information is that it is most likely biased. The best type of info, and really the only type of information that I think anyone should want, is objective. If you are having trouble finding sites that don’t have some sort of connection to the information that is being provided, go back to tip 1 and find several independent sources.
Look for studies that include evidence supporting the information. There are studies on almost everything out there, from nutritional needs to socio-economic issues. Finding studies, especially primary literature (http://www.lib.umd.edu/tl/guides/primary-sources) can be extremely useful for figuring out a question or gaining insight into an issue since studies provide evidence that supports a conclusion, or idea, and do not simply state an opinion.

Here are my favorite sources for finding articles:

https://scholar.google.com/ (multidisciplinary)
https://doaj.org/ (multidisciplinary)
http://www.jurn.org/#gsc.tab=0 (multidisciplinary)
https://www.econbiz.de/ (economics)
http://www.ncbi.nlm.nih.gov/pubmed (biology/medicine)
http://eric.ed.gov/ (education)

So there you have it folks! The internet can be a daunting and confusing place, but with the right tools and frame of mind you can use it as a source for valuable and trustworthy information.

Final (Cheesy) Note

If we can have a society and a world that is better at critical thinking, forming opinions based on evidence, and fact-checking on their own then I think that we can promote a brighter future in all areas: environmental, educational, economic, social, etc.

And one of the major components of being a critical thinker is having the ability to admit that we are only human and that we can be mistaken or mislead, so that when new evidence presents itself we have the ability to form our opinions on what is true and not on what we want to be true.

Final, Final Note

Right before I posted this I came across this article from IFLScience and I thought it would a great piece to share since it very much falls under the same theme. The article is titled “How Misinformation Spreads on the Internet”. Enjoy! http://www.iflscience.com/technology/facebook-echo-chambers-help-spread-and-reinforce-misinformation

Thank you for reading and, as always, keep questioning!

	COVID-19 FAQs \| The… on The Invisible World of Mi…
	COVID-19 FAQs \| The… on The Invisible World of Mi…
	NR on Genetic Engineering Pt. II: To…
	Genetic Engineering… on Genetic Engineering: The Good,…
	Genetic Engineering:… on The Invisible World of Mi…

1. What is COVID-19?

2. Where did COVID-19 come from?

3. Isn’t COVID-19 like the flu?

4. Do masks and social distancing work?

5. Would a nation-wide shut down help?

6. What happens if I get COVID-19?

7. Do COVID-19 tests work?

8. Are the vaccines safe?

9. What does the future look like?

Artificial Selection: How We Created Man’s Best Friend

Genetic Modification: The Simple-ish Version

What is a microorganism anyway?

Bacteria: Escherichia coli

Archaea: Pyrococcus furiosus

Fungi: Zygomycota rhizopus

Protista: Noctiluca scintillans (Sea Sparkle; protozoa)

Viruses: Orthomyxovirus (Influenza)

Microbes are actually everywhere

Tardigrade (Water Bear)

Humans and Microbes: A love-hate relationship

Further Links:

Wikipedia: Microorganisms https://en.wikipedia.org/wiki/Microorganism

Fungi Information http://www.ucmp.berkeley.edu/fungi/fungi.html

Archaea Information https://en.wikipedia.org/wiki/Archaea#Morphology

Protista Information http://www.microbeworld.org/types-of-microbes/protista

Virus Information http://www.ucmp.berkeley.edu/alllife/virus.html

Tardigrade Information http://tardigrades.bio.unc.edu/

Hypothesis vs. Theory vs. Law

How to Navigate Through the Internet

Final (Cheesy) Note

Final, Final Note

Work Cited:

Bacteria:

Escherichia coli

Archaea:

Pyrococcus furiosus

Fungi:

Zygomycota rhizopus

Protista:

Noctiluca scintillans
(Sea Sparkle; protozoa)

Viruses:

Orthomyxovirus (Influenza)