COVID-19: what is known and what do you need to know?

COVID-19: what is known and what do you need to know?


There’s a lot of information out there and justifiable anxiety even when looking at the facts. So what is it that we know about this disease, what causes it, where it came from, what we need to be aware of, and what we can do about it?

What is COVID-19?

COVID-19 is the disease caused by a novel coronavirus, SARS-CoV-2. The name stands for sudden acute respiratory syndrome, coronavirus 2. The disease, COVID-19, signifies a coronavirus disease that emerged in 2019. You may see other names that were used before the official naming, but these are the names used by the WHO and published by the International Committee on Taxonomy of Viruses in this manuscript. If the name looks familiar, that may be due to SARS and MERS both being coronaviruses that emerged in 2003 and 2012.

Where did this come from and why?

SARS-CoV-2 is believed to have originated in pangolins or bats. Being of non-human animal origin, this was a zoonotic disease. Zoonotic diseases are not uncommon, and arise when a pathogen, such as a virus, that normally exists in an animal population is transmitted to a human. The bigger problem arises when the pathogen is transmissible between humans and goes from being a zoonotic disease to being human disease. Zoonotic diseases such as anthrax, rabies, lyme disease and mosquito-borne illnesses are all familiar to us, but cannot be transmitted between people. Diseases such as the H1N1 and H5N1 influenza strains and SARS and COVID-19 are zoonotic in origin, but then began spreading between humans.

What do I need to know about COVID-19?

The first thing to know is how to kill it or prevent its spread. For this, we need to understand how this type of virus works. SARS-CoV-2 is enveloped; this means it has a membrane envelope surrounding the viral capsid. The details of the viral capsid, internal proteins, and RNA genome aren’t important here, but it is important to understand testing. Here’s what makes the envelope so important; envelopes are easily destroyed with soap!

Time for a quick biochemistry lesson… Envelopes are the outer layer of some viruses and are made up of lipids. Specifically, these are phospholipids, like a cellular membrane, which has proteins sticking out of it that work like a key that matches locks (receptors) on your cells. Fats and oils are made of lipids. Phospholipids are a little more complicated because they are amphiphilic, meaning they have both a hydrophobic and hydrophilic portion. Luckily, dissolving them still goes through the same process. Add a detergent, time, and agitation, and viola! You’ve destroyed the membrane. Remember how the viral membrane contains the proteins (keys) that tell your cells to let the virus in? No viral membrane means no infection. You’ll still be able to detect parts of the virus, like the RNA, but it’s dead, aka, noninfectious.

What can we do about it?

We’ve already talked about why soap is so effective, but other cleaners (not antibiotics!) are also helpful. Bleach will also disrupt the membrane, which is why it makes your skin feel slippery. Alcohol will also destroy it if applied in a proper concentration, usually 60-70%; too much and you’ll preserve many pathogens instead of killing them or it’ll just evaporate before it can work. But killing the particles is what you do if they are present. Whenever possible, the better thing to do is to avoid coming in contact. This can be done through self-quarantine, social distancing, avoiding public spaces, practicing good hygiene, and doing your part to protect both yourself and everyone you cannot avoid interacting with.


Testing, method of infection, treatments are also very important, but we’re just scratching the surface of part one here.


Stay home, stay safe, and trust science.

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GMO products and GMO labeling have been at the forefront of many people’s news feeds over the last few years. Some people have strong opinions one way or the other, but many people are unaware of what these terms mean or what their implications are. We’re going to delve into a little bit about why you should care about GMO foods and why discussions regarding their labeling are so important.

First, we need to be clear on terminology. All domesticated animals and crops have gone through some form of human modification. Many of them have been inbred over centuries and preferred traits are selected for future breeding. Historically, this is how we increased crop yields, the sweetness of a fruit, or the amount of milk a cow would produce. Crossbreeding to select for preferred traits is largely considered safe and acceptable, since these traits naturally occurred in other varieties or species of the same crop.Growing heirloom fruits and vegetables is a way to focus on the older varieties before as much crossbreeding was done, but even these are inbred for domestication. Even companies like Monsanto have streamlined crossbreeding and screening to develop new crop varieties based on these widely accepted techniques. Although all of these agricultural items are developed through a form of genetic selection and engineering, crossbreeding not not results in considering a plant or animal as as GMO or genetically modified organism.

Newer technologies allow for the direct manipulation of genes. Instead of waiting to crossbreed an insect resistant strain of wheat with a drought resistant strain of wheat, the genes can be directly inserted into the gametes to produce the desired outcome without having to wait for several generations of crossbreeding. This form of manipulation also allows for the insertion of traits that may not exist in other closely related strains or species. Perhaps a population suffers from a vitamin A deficiency or someone wants to make pink or reddish rice; a gene could be inserted into a strain of rice so that it makes beta-carotene. While the reddish color would be a clear indication that something is different about this rice, many modifications are less obvious. Any manipulation of an organism by directly modifying the DNA results in a GMO.

Basically, all domesticated plants and animals have been genetically modified by humans, but only the modifications performed in a lab by directly adding, removing, or altering genes result in a GMO.

So what?

Any genetic modification, whether crossbreeding on a farm or DNA manipulation in a lab, has the potential to be good or bad. Allowing a sweet and hot pepper plant to grow near each other will lead to peppers that are no longer only sweet nor extremely hot. A hypoallergenic plant may be crossed with the traditional strain resulting in a plant that could send someone into anaphylactic shock. The introduction of a pesticide gene into a crop may decimate a local insect population that feeds on that plant; similarly, a pesticide resistance gene may result in the overuse of pesticides, leaving the plants unharmed, but ravaging the local environment. While positive change is always the goal, the ramifications are often not immediately clear. The fact that an organism has been modified, either on a farm or in a lab, is no indication of its potential benefit or harm to the environment, industry, or consumers.

Aren’t these unknowns reason enough to ensure proper labeling of GMOs?

“Proper” labeling is a tricky point. Since not all modifications are created equal, simply labeling “GMO” is akin to saying “this cow sat down during inclement weather”. Was this cow ill or did it just prefer to sit down from time to time? One answer means you should not be consuming any part of it while the other is completely innocuous. The only way to discern the value of a modification would be to know what was changed and how. Would it be best to require plan labeling with additional details via the company’s website? Perhaps this would easily allow consumers to know that something was changed and find out for themselves what it was. However, the push against all GMOs makes it clear that many consumers view GMOs are inherently bad. In this case, a plain “GMO” label serves to stigmatize a product containing an innocuous modification. This would be like requiring labeling a food because a family of whooping cranes lives on a lake at the farm. Some consumers would think it is wonderful that the farm is supporting whooping cranes, but it would also raise questions as to why they are required to disclose this information. Do the cranes contaminate the water on the farm? Is there some unknown risk of cranes near foodcrops? Simply forcing such a disclosure says nothing about what the statement means. Furthermore, there is already some disclosure of GMO products through the USDA’s organic labeling. According to the USDA, “[t]he use of genetic engineering, or genetically modified organisms (GMOs), is prohibited in organic products”; although a GMO does not need to be labeled, an organic label already denotes a non-GMO product.

This is the danger of forced GMO labeling. Without knowing what, why, or how of a modification, the only thing accomplished by such labeling is applying a stigma. If the purpose of forced labeling is disclosure, then we should advocate for disclose. State what has been altered in any modified organism, e.g., “this soy has been bred to resist drought”, “neonicotinoid resistance has been inserted into this strawberry”, or “these apples lack the gene for browning.”

Let’s accept that large corporations on both sides of this issue are pouring money into the fight and focus on the science and what this means for the rest of us as consumers. Too often these discussions devolve into accusations that someone is being paid by one side or the other instead of focusing on the issues at hand and the vast majority of us who have nothing to gain but everything to lose if we fail to engage in useful discussions of this topic. The majority of people who care about these topics are not connected to any of the big agricultural corporations on either side (do you really think they are paying tens of thousands of people just to rant on Facebook?). It’s okay to be frightened when you don’t know what the impact of something is, but it is not ok to lash out at people because you don’t want to know. As Neil deGrasse Tyson said, “[t]he good thing about science is that it’s true whether or not you believe in it”.

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Communicating Science: Part 2

This is the continuation of talks on communicating science and confronting pseudoscience  at IFT16, a massive conference of food scientists. Part 1 can be found here.

We continue with a short summary of Ben Goldcare’s talk, “Telling the Story of Science in an Age of Misunderstanding”

Next up was Ben Goldcare of the University of Oxford’s Center for Evidence-Based Medicine. His background is as a physician, epidemiologist, and science writer. His talk went more toward proper communication of science. He used to write a weekly column, Bad Science, which ran for nearly a decade in The Guardian.

He presented several examples of misleading representations of data, ranging from inverted y-axes, uniquely scaled y-axes, and various graphs where the diagrams were not proportional to the values. (Stocks are almost always shown with a cropped y-axis so that even the smallest variations are visible on a graph.)

He goes on to point out that the Daily Mail (a British newspaper) has run headlines on almost everything both preventing and causing cancer. You can find references on the internet of many foods and ingredients both causing and preventing cancer. Since consumers cannot be expected to decipher all of these sources, some level of responsibility must be placed on the journalists. However, very few journalists are scientists, so they determine the impact of something by the press release. When press releases contain inaccuracies and exaggerations, the 58-86% of the news articles also contained exaggerate claims. For press releases that did not contain exaggerations, only 10-17% of the related news articles created such claims.

Goldcare also spoke about pulses. This was mostly interesting due to the way he said the word “pulses” and educated the audience about pulses, the dried seeds of legumes.

He also discussed the issue of multiple studies on the same topic with disparate results. With the amount and accessibility of data, the ability now exists to perform systematic reviews where data is weighted and considered as a whole. This sounded similar, and less complicated, than the way that FiveThirtyEight weighs polling data in building a model for election predictions in the USA. Skip down to around the 18th paragraph and Nate Silver starts talking about weighting polling averages ( He did get into some details of funnel plots in systematic reviews; suffice it to say, there are statistical analyses to help determine the validity of systematic reviews.

The last point we’ll make from Golcare’s talk is to direct you to a study on medical advice from doctors with daytime TV shows. (Spoiler alert: most of the advice is not good)

“Taming Dragons in the Age of Pseudoscience”

The last speaker on this topic was Bev Postma of Food Industry Asia. She had the honor of being front and center in Brussels when the European Commission was analyzing the previous 15 years of GMO use. For those unaware, GMOs have been used for over 30 years.

Despite 15 years of successful and safe GMO use in Europe, discussion turned negative as people were swept up in fear and confusion. The pseudoscientists and celebrities were referred to as dragons, mythical creatures striking fear into the populace. The inability of the scientific community to respond was a wake-up call to be effective communicators and always be accurate and consistent if there is any hope of a unified voice of science against an onslaught of fear and misunderstanding.


We leave you with a lovely Marie Curie quote used in Postma’s presentation:

Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less.

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Communicating Science: Part 1

This site was created to be good citizens of the scientific community and to help communicate scientific knowledge and understanding to our family, friends, and anyone else who wanted to listen. I recently attended the Institute of Food Technologists conference (with over 24,000 other people!) and was impressed by how prominent they made the topic of identifying and communicating accurate science. The largest conference room had three entire seminars on the topic; the topic was pervasive enough that it managed to surface in some of the scientific sessions as well. As this topic becomes a larger and more prominent discussion among scientists, expect to see more voices explaining similar concepts with similar messages. Scientists tend to have a hard time connecting with normal people; the scientific community is still figuring out how to talk to people like real people and how to navigate social media. The prevailing theme seemed to be that knowledge and information that has been properly vetted needs to be communicated accurately and consistently, especially when confronted with inaccuracies and emotion.

These two posts (it’s a lot for a single post) will be a little bit different than our others in that they will mostly be summaries of concepts conveyed during these talks and less original material with references. References for specific points will still be necessary but, unless the presentations are made public by the speakers or the conference, we won’t be able to share the slides in their entirety. The three sessions devoted to this topic were by Jacques Rousseau, Ben Goldcare, and Bev Postma. We’ll give the titles of each of their talks when we get there, but our take on the topics come down to the philosophy of knowledge, the dissemination and analysis of science, and the impact of pseudoscience.

We’ll lead off with Jacques Rousseau’s talk: “Science Versus Sensationalism and Soundbites: How Can Consumers Make More Informed Choices?”

Jacques Rousseau is the founder of the Free Society Institute which is a non-profit out of South Africa promoting, among other things, scientific reasoning. He is very direct and does not mince words when it comes to established science.

He points out that knowledge is not a democratic process. There is no popular vote on what is fact. It is decided by experts in a field who painstakingly gather data and share it with other experts in the same field until there is a consensus on what is known.

This leads into another point, reasserting the primacy of subject experts. It may seem obvious that the subject experts determine what we know about a subject, but their expertise is being undermined by outsiders without sufficient background to analyze data within the field.

Given that this was a conference of food scientists, the topic of genetic modifications and GMOs came up. Rousseau pointed out the wide discrepancy between the public and scientists on the relative safety of consuming genetically modified foods. This survey is not limited to food scientists and is based on the American Association for the Advancement of Science (AAAS) members covering a range of scientific disciplines. The vast majority (88%) of scientists said that GM foods were safe to eat, while only 37% of the general population agreed with that statement. The survey can be found here with a more detailed description including how they defined “scientists” here.

How do we address the lack of faith in experts as people place their faith in outside advocates for a cause? How did interpretation and determination of knowledge become a cause in the first place?

One of the most apropos lessons from Rousseau was his discussion of rules of argument put forth by game theorist Anatol Rapaport and summarized by Daniel Dennett.

We’ve noticed the conversations are much more fruitful when loosely following these rules; you may see some similarities in how we approached vaccines. There is no discussion if one party begins on the defensive and closed off to outside views.

How to compose a successful critical commentary:

1. Attempt to re-express your target’s position so clearly, vividly and fairly that your target says: “Thanks, I wish I’d thought of putting it that way.”

2. List any points of agreement (especially if they are not matters of general or widespread agreement).

3. Mention anything you have learned from your target.

4. Only then are you permitted to say so much as a word of rebuttal or criticism.

Roughly, you attempt to express your opponent’s viewpoint, identify common ground, express something new that you have learned from your opponent, then, and only then, you begin to introduce counterpoints or criticism. We were particularly intrigued by this formula and hope to refine our own discussions based on it.

If anyone has experience with engaging opposing viewpoints and stimulating discussion, please share. This is an ongoing process and, just like science, it can always be critiqued and improved upon.


To be continued here.

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So you think you can pH

Cells contain small membrane-bound compartments called vesicles. These vesicles can be so small that you can’t even see them in your typical light microscope. They are used for all sorts of things, from transporting compounds around the cell to deconstructing compounds or digesting bacteria. Some of these digesting vesicles, called lysosomes, use acid (low pH) and enzymes to tear apart molecules or entire bacteria. Since acidity is expressed in pH, a measure of how many hydrogen ions (H+ or protons) are floating around in solution, I started thinking…

Molecules are usually talked about in numbers too large to count — millions, quadrillions, or 1023 — but this is a small space, a really small space. In a space so incredibly small, how few free protons are there? (I can submit my own questions, right?)

In case you can’t tell from the question, this is going to get into some technical details pretty quickly, so if you have an aversion to mathematics, you may want to skip to the summary.

The vesicles in a cell can be as small as 20 nm across, which would have a volume of roughly 4.189×10-21 L ((4/3)πr3). At pH 5, the proton concentration is 10 mM or 10-5 M (pH=-log([H+])). This would mean that a 20 nm vesicle with a pH of 5 contains approximately 4.2×10-26 mol of H+ or 0.026 free protons per vesicle (6.022×1023 molecules/mol). Since you can’t have a fraction of a subatomic particle (yes, a proton can be divided into its three quarks, but they aren’t ever observed alone anyway), there must be something more to this simple definition of pH.

A common mistake is to forget that altering the proton concentration by a small amount (<10-7 M) does not contribute significantly to the proton concentration of water at neutral pH (pH 7). Although we’re talking about very small numbers of protons in these vesicles, the concentration is still well above that cutoff at 10-5 M. The other point to consider is that pH is a balance between the forces of acids and bases. Lowering the amount of basic ions (which is how a Lewis acid functions) relative to acidic ions would also make a solution more acidic. At pH 5, there should be 10000× more H+ than OH (water’s basic half). If the concentration of OH could be raised to 10-3 M (~2 molecules/vesicle), then H+ would have to be 10 M (~20000/vesicle) to obtain the desired pH. At least now we would be talking about whole molecules, this would also require lowering the concentration of H2O relative to H+ and OH can be lowered. This is where the dissociation constant of water becomes an issue. The typical concentration of dissociated water molecules is 10-14 M, but if the environment was under such tight constraints that the normal equilibrium of H+ + OH ⇌ HOH was shifted to the left, then the previously described hypothesis may hold true. The dissociation constant of water is affected by temperature, but such dramatic alterations of the dissociative properties of water in a controlled microenvironment is quickly escaping out capacity, so we’re hopeful for a simpler solution.

Stepping back for a moment, even with the tiny size of a vesicle, there are even smaller spaces in which we assume there is a maintained pH. Within and around proteins, there are microenvironments containing only a handful (if you had very small hands) of atoms and molecules. How can you claim such a small space has any particular pH when only five molecules are present?!


If the amino acid residues of a protein are sufficient to maintain a pH of 5, then surely a 20nm wide vesicle can maintain a pH of 5 without the need of impossibly small numbers of free protons. Much more likely is that pH really has nothing to do with the actual number of acid or alkaline ions at a given time; instead these numbers represent averages. If you spend an hour a day in your car, on average, your car would contain 0.04 people. This would not sound right, and you’re more likely to say that, 1/24 of the time, there is a person in your car. A molecule is considered more acidic if it has a proton that spends more time away from the molecule as it spends bound to it. Now let’s pretend that you are that proton and your car is a side-chain on a protein where the proton spends a small portion of its time. To get .026 free protons, the proton could be bound 97.4% of the time and free the other 2.6%.

Sometimes things in science seem confusing or impossible simply because science is not described in the same way that we speak and communicate. Even when the answer seems hard to find, translating science into terms we can all understand makes some things so much simpler.

Note: The back-of-the-envelope calculations were verified using Wolfram|Alpha, although I welcome any corrections.

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Citizens Hip in Science!

Today we give thanks to those citizens of the world who we consider to be hip in science.

Citizens Hip in Science

They’re with it. They’re hip.

Science wasn’t always hip. Science history is riddled with boring experiments ranging from watching planets and stars meander around the universe to bird watching while drifting around on the ocean with a beagle. However, our generation grew up watching Huey Lewis on the News talking about how it was hip to be square — the irony of being both interesting and bland at the same time. How could it be done? Scientists, in their white lab coats and monotone labs… what could be more square? How could they be hip?

Continue reading

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How I learned to stop worrying and love my bacteria (Part 2: The bad and the ugly)

In part one, we talked about the benefits of bacteria we live with every day. As you are likely aware, not all bacteria are friendly. In fact, there are plenty of bacteria that we never want to encounter. Nonpathogenic bacteria are the ones that are either necessary for survival, or simply not harmful; however, pathogenic bacteria are the ones that cause infections and disease. These are the ones we hear about when there is contamination of our food supply, a drug-resistant outbreak at a hospital, or when you get food poisoning. One of the most dangerous bacteria doesn’t even have to infect us at all. The toxins produced by Clostridium botulinum and its brethren are some of the most potent toxins known. Food contamination by these bacteria is sometimes noticed as those telltale bulges in canned food gone bad.

Continue reading

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How I learned to stop worrying and love my bacteria (Part 1: The good)

In our post on the origins of life in your refrigerator, we strayed into the area of friendly bacteria. Since this is the time of year when everyone seems to be sick, it seems like a good time to cover this topic.

Bacteria are often thought of as dirty, dangerous, denizens of the world, but we share our bodies with many of them. In fact, we are likely home to more bacterial cells than human cells! Continue reading

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State of Science

The National Science Foundation releases a rather extensive analysis of science and technology in the US every two years. This is a nonpartisan report that the National Science Board (NSB) uses to advise the government (both the president and Congress). Since the NSB holds such an important advisory role, it is worth seeing what sort of information they are basing their advice on. This year’s report, Science and Engineering Indicators 2014 was just released and we focused our attention on Chapter 7, Science and Technology: Public Attitudes and Understanding.

The splash that this report has made is based on some compiled survey data, although the public views toward science are worth noting as well. Continue reading

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Vaccines: Beyond Hype and Hyperbole


Warning: contents may elicit emotional response

With the ongoing debate raging between science and the right of parents to make medical decisions for their children, I have thought long and hard about how to approach this issue. Several people have asked me to write about it, but what is there to say that hasn’t already been said? Everyone who has bothered to research this area knows that vaccines are not linked to autism and other childhood diseases and that there are rare instances of allergic reactions and flu-like symptoms in children after getting vaccines. Everyone knows someone who has either gotten a fever from a vaccine or contracted a disease even though they received a preventative vaccine. Continue reading

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