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COVID-19 is causing silent epidemics — societal and medical crises

As the nation emerges in fits and starts from the lockdowns spurred by the first wave of COVID-19 illnesses, we’re beginning to appreciate the full impact of the pandemic, how tenacious it is, and that the sickness and death directly caused by the virus are only part of the picture.

The three-month-plus suspension of routine, non-emergency medical care has created secondary, silent epidemics of societal and medical problems that require the urgent focus of both our public health officials and the public themselves. In a survey by the Kaiser Family Foundation, 48% of adults responded that they or someone in their household either rescheduled or decided to entirely forego medical appointments during the previous three months because of COVID-19. Notably, 11% of adults overall said their own or a family member’s condition actually worsened as a result of postponing or skipping medical care due to the pandemic.

The effects were sometimes lethal. According to an analysis of federal data by the Washington Post, in New York City and five states hit hard by coronavirus infections, there were 8,300 more deaths from heart disease than would have been typical in March, April and May — an increase of roughly 27 percent over historical averages. Deaths from diabetes and Alzheimer’s disease also were up.

There’s more misery to come. Writing in the journal Science, National Cancer Institute Director Ned Sharpless expressed concern about marked declines in U.S. cancer diagnoses since the onset of the pandemic, attributing them to an estimated 75 to 90 percent decrease in mammograms and colonoscopies over the past few months.  Clarifying that “there is no reason to believe the actual incidence of cancer has dropped,” he offered what he termed a “conservative” estimate of more than an additional 10,000 deaths from breast and colorectal cancers over the next 10 years due to coronavirus-caused postponements in diagnosis and care.

Another significant threat to individuals’ health is the delay in routine, but essential, prophylactic dental care. On March 16, the Centers for Disease Control and Prevention advised dentists to suspend all routine examinations and limit treatment only to emergencies. While the measure was necessary to limit exposure and conserve personal protective equipment, myriad oral health conditions have now gone undiagnosed or untreated for more than two months. The resulting dental procedures will be more extensive, the outcomes worse and more expensive, and the backlog will not disappear immediately.

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Dental care has been neglected during the pandemic. Credit: Adam Berry/Getty Images

Patients’ overall health will likely suffer as well. Many chronic medical conditions are reflected by findings in the mouth and first discovered in routine visits to the dentist. Some of these are discussed below.

Periodontitis

Like the skin, stomach, and intestines, the mouth harbors large numbers and kinds of bacteria, which normally exist in a symbiotic relationship with the rest of the body. These bacteria are found in the pockets between the teeth and gums. If not cleaned by specialized tools, they feast on carbohydrate-rich food and multiply, causing inflammation in the gums and bleeding when the gum tissue is ruptured — a condition known as periodontitis. This in turn provides a gateway for the bacteria to contaminate the bloodstream, potentially leading to abscesses, heart valve infections, and in the worst case, sepsis—a life-threatening immune response to infection that can damage multiple organ systems.

Diabetes

Periodontitis and diabetes are also closely associated, each magnifying the severity of the other. Controlling gum disease can help improve blood glucose levels in diabetic patients, while high blood sugar levels worsen outcomes for periodontal disease. In well-controlled diabetics, the risk for periodontitis is not significantly increased, but it rises exponentially as blood sugar increases. Higher levels of blood sugar results in poor wound healing which, in turn, increases the likelihood of oral infections.

Pregnancy

Pregnancy makes periodontal disease especially worrisome due to the possible migration of bacteria and inflammation-related chemicals though the mother’s bloodstream to the uterus.

Similarly, a condition called “pregnancy gingivitis” afflicts 50-70 percent of pregnant women. Increased pregnancy-related hormone levels cause blood vessels in the gums to become more permeable, allowing bacteria in the mouth move to other parts of the body. Studies have shown an association between periodontitis and premature births, preeclampsia, and gestational diabetes. This is why, until the lockdowns, dental examinations were a routine part of medical care for mothers of the roughly 10,000 babies born in the United States every day.

Cardiovascular disease

According to the Centers for Disease Control and Prevention, atherosclerosis and cardiovascular disease account for nearly a quarter of all deaths in the United States, due to a build-up of inflammatory plaques that obstruct blood vessels. This disrupts the supply of oxygen to the body and can cause life-threatening events such as heart attacks and strokes.

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Although no direct connection between gum disease and cardiovascular disease has been identified, people with gum diseases appear to have two to three times higher likelihood of having a heart attack or other cardiovascular event. Ongoing research is investigating the relationship and assessing whether gum disease is an independent risk factor for heart disease. The hypothesis is that bacteria from periodontitis can gain access to the body’s circulatory system and penetrate the endothelial cells that line the inside of the blood vessels. One study found that around 40% of atherosclerotic lesions contained remnants of periodontal pathogens that normally are found only in the mouth.

Other Conditions

In addition to those discussed above, other findings during oral examinations may suggest a variety of medical problems:

  • Oral cancers are often detected during routine dental exams
  • Immunocompromised patients often have oral infections which are apparent to the dentist before the patient is aware of any abnormality
  • HIV/AIDS may present with non-healing ulcers or a black coating on the tongue
  • Bulimia — the frequent vomiting exposes the teeth to stomach acid that erodes the enamel of the backs of the teeth

Because dentists are often the first to detect a medical problem that requires diagnostic testing and treatment, in the absence of routine dental exams and cleaning during the pandemic, many oral conditions will be missed and treatment delayed.

This pandemic has real teeth; chalk up another way it threatens our health.

Dr. Shiv Sharma, a California dentist, owns Palo Alto Oral Health in California.

Henry I. Miller, a physician and molecular biologist, is a Senior Fellow in Healthcare at the Pacific Research Institute. He was the founding director of the Office of Biotechnology at the FDA. Please follow him on Twitter at @henryimiller

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Viewpoint: Pesticides on produce aren’t dangerous. Ignore the ‘Dirty Dozen’ and eat more fruits and veggies

Full disclosure: I buy organic fruits & veggies. I also buy conventional fruits & veggies. For me, it depends on the time of year, the way the produce looks, which grocer or market I’m visiting, and price (those two-for-one berry deals are no joke!). At D2D, we also believe that feeding a growing population requires all kinds of safe, sustainable growing methods. We should have a choice and not be unnecessarily fearful of the food at the grocery store.

What’s at Stake?

If I told you that I only buy organic produce, you’d probably assume that I had the Environmental Working Group’s (EWG) list of contaminated produce memorized for when I go shopping, right? And probably expound on the “horrors” of conventional farming, too. Some of you may not know what EWG is, but you’re probably familiar with their annual “Dirty Dozen” list showing which conventionally-farmed fruits & veggies have the most pesticide residue based on data from the USDA Pesticide Data Program. But should you really be afraid of these “Dirty Dozen” items?

EWG would give a big ‘yes’ to that one. But wouldn’t you do this, too, if your corporate donations came from Organic Valley, Earthbound Farms, Applegate Farms, and Stonyfield Farms? Hey, I kinda get it – they’d infuriate their stakeholders if they published information discouraging their products. But their report hurts our health and frankly, our sanity. And at a time when we need it most with COVID-19.

Sad State of Health

Did you know that only 10% of us eat the recommended amounts of fruits & veggies each day? I’m literally sneaking riced cauliflower and diced sweet potatoes into my oatmeal each morning and am barely scraping by in that department. There is no doubt about it: washing, chopping, and preparing five to nine servings of veggies for each family member every day takes a lot of time.

But what about those who can’t even shop for fresh produce? The USDA’s food desert map examines lower-income and lower-access locations where people live far from a supermarket. EWG’s message particularly preys on these shoppers. In a peer-reviewed study in the journal, Nutrition Today, researchers found that low-income participants preferred not to buy produce at all – neither organic nor conventional – when informed of specific fruits & veggies with pesticides, putting this group at greater risk of obesity, heart disease, and cancer. Kinda counter-productive to EWG’s mission, right?

“Messages naming specific fruits and vegetables with pesticides shifted [low-income shopper] participants toward ‘less likely’ to purchase any type of FV, regardless whether organically or conventionally grown.”
– Burton-Freeman et al., Nutrition Today

You’re Only as Good as Your Data

Though we’ve previously posted on how the USDA and EPA monitor and manage pesticide residues on produce, here are a few points about the margin of safety the EPA applies to our produce, the data gathered by the USDA that shows where produce falls within that spectrum, and how the EWG misrepresents the data to scare the daylights out of us.

Let’s first take a look at data collection and what it shows:

Organic and conventional crops: It’s not a level playing field

“The EPA requires synthetic pesticide manufacturers to conduct a whole battery of tests for initial and ongoing registration. The extensive and costly testing is conducted to determine toxicity on human health from dermal exposure, inhalation, and ingestion, and assesses human health outcomes related to reproduction, cancer, and organ systems.

On the other hand, “natural” organic pesticides are not required to be tested for toxicity and have never received this level of assessment.” 

– Susan Leaman, Toxicology Consultant, Vice President at IDS Decision Sciences

Have you heard of copper sulfate? It’s considered an organic pesticide and is frequently used on crops prone to fungus. It’s also one of the most toxic pesticides. Yes, even among synthetic ones.

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Fungicide copper sulfate is popular with organic farmers.

Toxicity Levels of Various Substances

Yes, there is pesticide residue on most produce – both conventional and organic. It’s also in our air. And water. And, our bodies can handle it. Time to move on.

  • Despite what you may hear on the interwebs, the USDA conducts very rigorous testing on thousands of produce samples for its Pesticide Data Program (EWG’s data source). The USDA then works with the EPA to develop tolerances for acceptable pesticide residue on produce.
  • This is how the EPA determines pesticide tolerance: they identify an allowable level of residue for no health risks based on exhaustive toxicological evaluations. If a residue is at or below the tolerated amount, it is safe by a factor of 100, which means the residue present is 100 times smaller than the smallest amount that would have a negative health effect. That’s a pretty plentiful safety cushion there.

“In reality, exposure to toxins like pesticides is not as simple as ‘this is good, that is bad’. Whether or not something is toxic depends on numerous factors, such as the substance’s form, the amount you are exposed to, how you are exposed, and your genetic make-up.”

– Susan Leaman, Toxicology Consultant, Vice President at IDS Decision Sciences

  • Still scared? Check out this page from Alliance for Food and Farming, which represents organic and conventional produce farmers, to see how much produce you’d need to eat to incur some ill effect from the residue, based on our gender and age range. As much as I love strawberries, I don’t think I can eat 453 berries in one day 😉

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EWG’s Dirty Data Habits

Look, we don’t need to go too far down this rabbit hole of EWG’s dubious research practices. Thankfully, plenty of researchers with lots of peer-reviewed studies to factually substantiate their claims have made a more compelling argument than I can to discredit EWG’s improper research methods and false claims.

But let’s take a quick look at how EWG takes advantage of omissions and manipulates data in favor of their stakeholders:

EWG’s desperate search for data to substantiate their position

EWG recycles practically all the same data as previous years and slaps the “2020” on Food Shoppers Guide to make it look meaningful

  • The USDA analyzes pesticide residues with dozens of rotating crops, so each year only select crops are re-analyzed. For instance, this year it was just three crops analyzed that fall under EWG’s coverage: asparagus, cabbages, and sweet peas. Yet they make a big stink about releasing a whole new report, instead of just giving an update on the 6% of data that may or may not have changed since last year!
  • To that end, we don’t know the current pesticide levels of pineapples and eggplants, which were last analyzed in 2002 and 2006, respectively. But both show up on EWG’s “Clean Fifteen” list, without really knowing levels within the last 14+ years.
  • As for raspberries, another delicately-skinned fruit like strawberries (notoriously #1 in the “Dirty Dozen”), they haven’t been analyzed since 2013 – a long time for those overly-concerned with these things.

And EWG only addresses COVID-19…

  • In a recent email touting their “COVID Tips”, EWG states that “organic vegetables…offer a great nutritional bang for your buck”. Ummmm…I’m pretty sure conventional produce is still the cheaper option. Also, nutrient density depends on the health of the soil, not whether it’s organic.
  • Even worse, EWG’s email also states “to reduce the risk of ingesting pesticides, wash all conventional produce by running it under the faucet”. Yeeesh…where were they on this one? We must wash ALL our produce. Pathogens like e. coli and salmonella don’t care if it’s organic or conventional…so always wash up!

…When it’s convenient for them

  • Suddenly they’re reporting on shelf-stable goods? Their report vilifies conventional raisins during a time when some of us don’t have access to fresh fruit. What kind of timing is that?
  • And as unemployment skyrockets, they send an email blast asking for money ☹ Sounds kinda culty, too, right? And, I don’t know, maybe directing at least SOME of those funds to a COVID relief fund would make this email seem a little less crude and more helpful at keeping people alive and healthy, perhaps?

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EWG Actually Knows Better

The most disheartening part about the EWG’s Dirty Dozen report? They know they’re causing unnecessary panic. Perhaps in light of the current pandemic, they stated in their press release that “…consumers should continue eating plenty of healthy fruits and vegetables, whether they are conventional or organic”. Doesn’t this seem contradictory to their entire report? So why cause more panic when we’re all already freaking out???

There’s no question that the benefits of eating fresh fruits and vegetables FAR outweigh any ill effects from pesticides – the vitamins, minerals, antioxidants, fiber, and other nutrients keep our bodies healthy. How else are we to build up our immune systems to help combat this virus?

Uniting for Health

Despite the mixed messages of the EWG report, there’s one common theme that unifies us all in our plight for overall and immune health: to eat more fruits and veggies, no matter the source. Whether explicitly said by nutritionists and doctors, or hidden between the lines in a press release, we all agree that eating more produce can positively affect our immunity against COVID, and beyond.

And if you are still concerned about pesticide residues and pathogens, just rigorously wash and prepare your produce.

Make sure to wash your produce thoroughly under cool running water BEFORE eating or preparing. It is important to rinse…to avoid transferring dirt or bacteria onto your knife, the flesh of the produce or your work surface. The FDA does not recommend washing your fruits and vegetables with soap…however, you may want to use a clean produce brush to scrub firm crops.”

– Maki Yazawa, RealSimple

My last point is for those who are still skeptical…

If you question the USDA and EPA data, just remember that between two stories may lie the truth. So, if you recall that the EPA’s pesticide residue tolerance scale for produce must be “100” at a bare minimum, and “1” is a serving of produce that has enough pesticide residue to cause an immediate ill health effect (as the EWG would like us to believe), that halfway point brings us to “50”. Even at a factor of 50, I would still encourage my family and friends to eat lots and lots of produce. Even then, 226 strawberries are still too many for me to eat at once 😉

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THE BOTTOM LINE

The EWG report negatively affects our shopping decisions with baseless information that preys on our fears. During these times, it’s even more important to make rational decisions about our health to protect ourselves and others by fortifying our immune systems. So when I see those strawberry packages that are on sale for “buy 2 get 1 free”, you better believe I’m stocking up, no matter how it’s farmed.

Hillary Kaufman covers food trends and technological advances in health for Dirt-to-Dinner, a site dedicated to helping you better understand how your food is grown

This article was originally published at Dirt to Dinner and has been republished here with permission. Follow Dirt To Dinner on Twitter @Dirt_To_Dinner.

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Viewpoint: Busting nutrition myths—Why you don’t have to cut potatoes out of your diet

“Stop cutting out white potatoes – they’re as healthy as sweet ones, dietitians say,” a recent headline in Insider urges us.

That gets a big hooray from me.

Forgive my conceit but I cook the best roast potatoes (a British culinary delight) just about anywhere on these shores. Ask my husband.

But the nutrition police don’t approve. According to an article darkly entitled “the problem with potatoes” on the Harvard T.H. Chan School of Public Health website, a cup of potatoes has a similar effect on blood sugar as a can of cola or a handful of jelly beans. Moreover they claim that “this roller-coaster-like effect on blood sugar and insulin can result in people feeling hungry again soon after eating, which may then lead to overeating.”

Wow, that’s quite the set of accusations, especially when sweet potatoes, which have almost identical levels of carbohydrates and calories are often lauded as exemplars of nutritional excellence.

The disdain for standard spuds hinges on the fact that they have a high glycemic index, or GI.

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GI measures how rapidly a food increases a person’s blood glucose. A global database of GI values is maintained by Sydney University Glycemic Index Research Services in Sydney, Australia. GI is measured relative to glucose (GI 100) under fixed conditions that  don’t relate very much to how we actually eat foods in mealtime combinations.

According to the above mentioned database, sweet potatoes have a GI of anywhere between 44 and 95 depending on the exact variety and method of preparation, whereas a serving of North America’s most popular potato, the Russet Burbank, registers GI values of between 56 and 111. As you can see, there’s not a whole lot of difference between the two.

GI and Hunger

There’s modest evidence that eating foods with a higher GI might leave you more vulnerable to snack attacks. For example it’s been shown that after a high glycemic index meal, there’s more activity in the area of the brain associated with craving and reward than after a low glycemic index meal.

When overweight, otherwise healthy, individuals consumed breakfasts with the same energy content but varying carbohydrate to fat ratios, people also felt hungrier after the higher carb meal, which correlated with an earlier and higher peak in blood glucose.

But though high GI is generally a rough proxy for a less nutritionally-dense source of carbohydrate, that’s not the case with potatoes.

To equate them with soda or candy is nonsense because, healthwise, they are very different.

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Different types of potatoes. Credit: Consumer Reports

A medium (285g) baked potato eaten with the skin has 265 calories, 7.1g protein,  60g carbohydrate, and 6.3g of fiber along with 1520mg potassium,  79.8 μg folate and 27.4mg vitamin C. These are really meaningful amounts of nutrients that have roles to play in maintaining a healthy digestive and immune system, as well as normal blood pressure. (For the record, sweet potatoes have more vitamin C, fiber, vitamin A and E, but less potassium and folate.)

Potatoes Are Satiating

The theory that a high GI makes potatoes poor at curbing hunger simply doesn’t stack up any way – far from it. In fact based on the Satiety Index, which rates foods based on how full people still feel two hours after eating them, boiled or baked potatoes are the most hunger-curbing of the lot. With a score of 323 they rate over three times more satiating than white bread, with a reference score of 100.

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In another study published in the Annals of Nutrition & Metabolism potato-based side dishes were more effective at blunting appetite than bread and pasta sides, though there were no differences in subsequent calorie intake at the next meal.

Pile High at Your Peril

On the not so bright side, a study in the journal Diabetes Care found that after adjustment for demographic, lifestyle and dietary factors, long term high intake of potatoes and French fries was linked to a greater risk of diabetes in women. Replacing  potatoes with whole grains, which as a general rule have a lower GI, lowered diabetes risk.

Common sense will tell you portion size, method of preparation and frequency of potato consumption is what matters. Regularly eating oversize quantities of any fried starchy carbohydrate  – which would include sweet potato as well as standard  fries – is almost certainly to have health downside.

But if you don’t eat them every day, and avoid super-sized portions, spuds are far from nutritional duds.

Which is why there will be some irresistibly crispy roast potatoes coming out my oven this Sunday.

Angela Dowden is a British award-winning health journalist and registered nutritionist with over twenty year’s experience. Follow her on Twitter @DietWrite

This article was originally published at the American Council on Science and Health and has been republished here with permission. Follow ACSH on Twitter @ACSHorg

ynews dna genome covid

In your genes? DNA holds clues about how you will fare when exposed to coronavirus

Although the spread of SARS-CoV2, the virus causing COVID-19, has slowed in many places that have successfully “flattened the curve”, cases are on the rise in certain areas, and the virus has only recently arrived in some countries. While enacting public health responses is key to responding to the expanding pandemic, scientists are beginning to analyze why some people might be asymptomatic carriers, as others end up in the ICU on a ventilator or, sadly, ultimately succumb to the disease.

Advanced age and pre-existing conditions are clearly major risk factors for the development of severe COVID-19, however there are also large numbers of younger and generally healthy people who develop serious symptoms, as well as patients of all ages who rapidly recover, or never shows signs of the disease to begin with.

The number of viral particles an individual is exposed to is certainly one variable that may determine disease trajectory, as are environmental considerations, as well as access to treatment. Nevertheless, numerous studies are currently seeking to determine how a person’s unique genome may influence the ultimate impact of the disease. It is important to remember that in contrast to some bacterial and fungal pathogens that produce toxins which directly impact the host, most viruses like SARS-CoV2 do not, and the symptoms and ultimate cause of death are generally produced by the inflammatory responses of our own immune system.

Thus, studying how human genetics impact disease progression could both lead to a predictive understanding of who might require strict isolation, as well as who could be spared the worst of the disease impacts. In addition, if we know specific genetic variants that cause bad outcomes, this could lead to the development of selectively targeted drugs that treat at-risk individuals.

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Woman in isolation. Credit: Riverside Health

Identification of individuals with genetic resistance to infection, or who may be protected from developing symptoms, could help us understand and exploit vulnerabilities at the interface between virus and host, and may have epidemiological implications. Isolating asymptomatic spreaders could significantly reduce the prevalence of the virus in a population, while genetic variants that protect from initial infection could lead to development of preventative therapeutics that block viral entry into host cells, as well as provide peace of mind to the resistant individuals.

Putting COVID in genetic context

Many of the broader medical issues we face have some genetic basis. However, rather than resulting from single catastrophic failures in function, such as running over a nail and getting a flat tire, human disease generally arises from numerous subtle genetic and environmental variables. Mutations with a large negative impact are generally not present at high rates within a population.

Most human diseases with a genetic component are like driving off-road in an aging car with worn out shocks and bald, under-inflated tires that are out of alignment; something will eventually go wrong due to the multiple potential sources of failure placed in the context of particular environmental stresses. While debilitating genetic diseases caused by individual catastrophic mutations certainly exist, and can tell us a great deal about how body systems work, in the vast majority of human diseases, a combination of subtle genetic and environmental factors is to blame, not a single mutation in one gene.

Much of human disease, and thus most genetics research, is based upon the two alternative arms of this apparent dichotomy: rare mutations with major direct impact, or common variants with subtle relevance placed in particular environmental context. In the search for understanding how human genetics plays a role in COVID-19 disease progression, each of these paradigms is being investigated.

One potential limitation to the search for individual genes that cause significant impact on COVID-19 when mutated, is previous experience with a so-called “candidate gene” approach. This involves taking the knowledge of a disease and the genes that might be involved, and then searching for variants in those genes within individuals who display the symptoms of the disease. This is akin to rounding up the “usual suspects”, and often equally as unproductive.

The problem that can often arise with a candidate gene approach is one of causality. As our genomes are full of differences that have no detectable functional impact, if you look at enough people you are likely to find some variations that exist in one population when compared to another. This correlation may be a statistical “red herring” that doesn’t provide any real insight into the disease.

An extreme example illustrating the potential limitations of a candidate gene approach would be to compare two very genetically distinct populations that are subject to very different environmental variables. In such a case a variant identified in a candidate gene could simply have arisen randomly and may correlate with a difference in a disease incidence or severity, but in actuality has no direct functional significance. Science is self-corrective and subsequent studies attempting to prove causation can certainly be performed, however these can be costly and time consuming, and especially during an ongoing pandemic, this type of candidate gene approach might not make sense.

While investigating the variants of an individual candidate gene might not be the best use of resources, new advances in DNA sequencing technologies allow the low-cost and high-speed analysis of entire genomes in large groups of people. Whole genome sequencing was once cost prohibitive and took years of painstaking work to complete, but can now be performed in hours, for about the price of a nice laptop.

Furthermore, studies focusing only on the expressed portion of the genome, the so-called exome, can be undertaken even more efficiently, and can increase the odds that any mutations identified might actually directly alter function. Thus, genetic variants potentially relevant to disease progression can be identified across large diverse populations with greater statistical certainty.

COVID whole genome mapping ‘moon shot’

The COVID Human Genetic Effort includes a worldwide group of research centers coordinated by Dr. Helen Su from the National Institute of Allergy and Infectious Disease, and Dr. Jean-Laurent Casanova of The Rockefeller University and Howard Hughes Medical Institute. The overall goal of this project is to perform whole genome and exome sequencing from COVID patients who are not elderly and don’t have clear pre-existing conditions to look for mutations that might be responsible for good or bad outcomes. In particular, the researchers are searching for monogenic variants that either increase immunity and are protective, or lead to particularly severe disease in individuals that might otherwise be spared the worst impacts of COVID-19.

Importantly, a key aspect of this work will be to biochemically characterize the candidate variants to look for potential mechanism of action, and weed out genetic variants that might be randomly associated with particular disease endpoints. This project will employ cutting-edge sequencing and analytical techniques to look at large populations with a high degree of sensitivity across the genome, and include follow-up functional studies to directly identify causative mutations and avoid potentially faulty conclusions based solely on statistical correlations.

While identifying genetic mutations with specific functional significance can drastically impact our understanding of a disease and the potential search for beneficial therapeutic interventions, correlative studies of subtle genetic variations can also be extremely important. The term single nucleotide polymorphism (SNPs) refers to individual variations in genomic DNA that can be found within particular populations. The locations of thousands of SNPs in the human genome that can exist in one form or another are known, and rapid, powerful analytical techniques can easily provide a fingerprint of any individual’s personal complement of SNPs. Although individual SNPs don’t confer any obvious functional significance, there is tremendous power in being able to assess which SNPs a person carries across the genome.

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Credit: Medium

SNPs are used to identify ancestry and personal genetic testing companies use panels which assess huge numbers of SNPs to determine one’s genetic background; for example, the part of the world from which a person’s family originated. Huge numbers of SNPs are looked at in concert across the whole genome and different patterns emerge which can then be correlated with the risk of developing particular diseases or pretty much any other characteristic with a genetic component. These analyses are broadly referred to as Genome-Wide Association Studies (GWAS).

The direct causative impact of any individual SNP is generally essentially zero, but the power is in the sheer magnitude of the numbers analyzed, both numbers of SNPs in one individual data set, and the combination across sometimes thousands of individuals. GWAS and similar types of analytical procedures can provide clues to the genetic basis of a particular disease process, and follow-up sequencing of genes harboring certain SNPs associated with a specific disease can provide further insight. Additionally, by treating a SNP signature associated with a particular condition as a “bio-marker”, predictive or diagnostic approaches can follow. In the context of COVID-19 this could mean identification of specific SNP patterns that might be associated with severity of disease or potential to respond to a particular therapeutic option.

Companies looking for genetic links to COVID susceptibility and recovery

The personal genetic testing company 23andMe, through the 23andMe COVID-19 Study, is currently conducting GWAS to look for associations between certain SNP patterns and COVID-19 infection, severity and recovery. PrecisionLife, a genetic analytics company based in Oxford, has announced the identification of 68 genes with SNP variants associated with severe COVID, including some that had been previously identified as playing a role in viral pathogenesis. PrecisionLife recently posted a pre-print on the website medRxiv which analyzed data obtained from the UK Biobank using an artificial intelligence genomic data analysis tool. The researchers stated that these results could have been obtained following traditional GWAS methods.

Whether through analysis of specific candidate genes, wholes genomes or exomes or GWAS with thousands of SNPs, a single study can only be so powerful, even if many individuals are included. Integrating numerous independent data sets into larger meta analyses can provide deeper and more meaningful understanding. This is where the COVID-19 Host Genetics Initiative hopes to make a significant impact.

Behind the scenes at the COVID-19 Host Genetics Initiative

Originally started by the Finnish Institute for Molecular Medicine, this multinational effort has been set up to share resources and data and organize multidisciplinary research activities. It includes clinicians, academic researchers and industry partners, such as DNA sequencing companies. One main aim is to create a series of agreed-upon phenotypic definitions and analytical procedures to harmonize data for meta analyses within an open science format in which results can be shared freely between partners. Although the potential for sharing data obtained with similar criteria and protocols holds tremendous potential power, international sharing of clinical data is very complicated and it will be interesting to see the results of this unprecedented effort—and extremely important in these unprecedented times.

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The first results from these studies are starting to trickle in, and already there are examples of differential COVID-19 outcomes dependent on human genetics. People with blood group A seem more likely to develop severe COVID-19 with respiratory failure, while blood group O appears to confer a protective effect. A paper reporting these observations was recently published in the New England Journal of Medicine by the Severe Covid-19 GWAS Group. The study identified the ABO blood group locus and a cluster of genes on chromosome 3, including a region known to contain genes involved in immune cell function, associated with worse outcomes after analyzing ~1,600 patients in Spain and Italy with respiratory failure caused by COVID-19. However, another recent study in the journal Annals of Hematology found no association between ABO blood type and the severity of COVID-19 disease.

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Determining blood type in the ABO group system. Credit: Getty Images

Hopefully, more results such as these will soon be published, and insights into how human genetics might impact COVID-19 severity will become evident. That could well lead to epidemiological actions and drive the development and deployment of therapeutic interventions. Until then, the more patients studied, and the deeper the analyses, the closer we will hopefully come to reigning in this terrible pandemic.

Joshua Z. Rappoport, Ph.D., is the executive director, Research Infrastructure at Boston College, and the author of the newly published Mapping Humanity: How Modern Genetics Is Changing Criminal Justice, Personalized Medicine, and Our Identities. Follow him on LinkedIn

vaccines editorial

Re-energized anti-vaccine activism is growing on the right and winning the social media battle to discredit coming coronavirus treatments

What does an antivaxxer and a far-right activist have in common? If the thought of someone who opposes vaccines brings to mind tie-dye shirts and tree hugging, your answer may be “nothing.” But clearly, some do have a commonality: protesting the COVID-19 lockdowns. Coverage from these protests often show people holding signs slapped with antivaccine rhetoric next to pro-militia activists and white supremacists. This phenomenon can also be seen among homeschoolers according to Anne Borden, a pro-vaccine homeschooler who fights against phony autism cures.

“The first antivaxxers I ever met were left-leaning unschoolers when I was an unschooled teenager. They were very much a part of the early efforts to ‘stop the Food and Drug Administration’ from regulating alternative medicine. What has happened in recent years is that this demographic of homeschooling is being now recruited by the radical right on social media, and some are turning right. And this is very concerning.”

This may leave you wondering just what is happening to the anti-vaccine movement in 2020.

Distrust of establishment medicine

The central dogma of the anti-vaccine ideology is that vaccines cause autism and other bad health effects, and that governments and the pharmaceutical industry knowingly suppress this information. This tenet, we easily imagine, is tightly wedded to the political left. It’s a hippy-dippy attitude, we often think, borne out of an irrational fear of chemicals, and there are indeed prominent spokespeople for the movement who fit this sketch. Joe Mercola made his fortune selling natural health products and has contributed more than $2.9 million to the National Vaccine Information Center in the U.S., an anti-vaccine advocacy group. There is Robert F. Kennedy, Jr., a Democrat and environmentalist, who is a major public figure on the anti-vaccination scene as the chairman of the Children’s Health Defense.

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This branch of the movement shows a distrust of pharmaceutical companies and a pursuit of purity. Their wrongful idea that nature is inherently good ends up framing their thinking, which is why in the age of COVID we read about their “natural immunity theory”: that barriers to germs, like physical distancing and masks, weaken our immune system. Vaccines are just one more synthetic loaded gun aimed at our immune system, they say. The embedding of antivaxx sentiment within this nature worship is familiar to many of us. But there is a segment of the anti-vaccination movement on the far right, drawn to its libertarian streak of distrusting the government, and there exists at least one prominent bridge between leftist antivaxxers and the political right in the United States: Donald Trump.

Before associating with the Republicans and as far back as 2007, Trump had publicly expressed the erroneous belief that vaccines cause autism. He has helped raise money over the years for his friend Bob Wright, who founded the charity Autism Speaks whose stance on vaccines has been deemed “controversial.” And Trump himself invited Robert F. Kennedy, Jr., to chair a commission on vaccine safety (which ended up dying on the vine). Trump, it should be pointed out, is the first American president to be on the record as having anti-vaccine views, an influence that cannot be ignored.

A survey involving Americans who voted in the 2016 presidential election revealed that Trump voters expressed more vaccine concern (specifically about the MMR vaccine, wrongly linked to autism) than non-Trump voters,screen shot at pm
a result which the authors conclude was explained by their conspiracist ideation. This association between the current right-wing of American politics and questioning the value and safety of vaccines can also be seen in Gallup polls. For the years 2001, 2015 and 2019, the percentage of Democrats who say it is either extremely or very important for parents to vaccinate their children has moved from 97% to 88% to 92%. For the same time points, Republicans went from 93% to 82% to 79%.

Beyond political affiliation, researchers can shed some additional light on who an antivaxxer tends to be and how they think. Interviews with Australian parents who reject vaccines revealed they see themselves as virtuous but oppressed, and vaccinators are perceived as an “Unhealthy Other”. Those who reject vaccines may have a skewed perception of the risks posed by them and the diseases they prevent, with some evidence showing that Internet searches may increase the perception that childhood vaccines are risky. And a large investigation into the anti-vaccination phenomenon, conducted in 24 countries by a team at the University of Queensland, revealed a strong pattern: people who reported more conspiratorial beliefs tended to be more anti-vaccine. This association was particularly strong in Western imagesnations, like Canada and the U.S. Next in line was the link between anti-vaccination attitudes and the resistance to having their freedom taken away from them. The authors report that “more conservative participants also had stronger antivaccination attitudes.” What was not linked to antivaxx beliefs was education.

The prototypical antivaxxer described above, though, does not exist in a vacuum. The people who espouse these views can find each other quite easily because of the existence of an important conduit that allows their claims, anxieties and incitements to spread: social media. Even though social media giants have said they would crack down on vaccine misinformation, anti-vaccine communities quickly adapt to the new rules, like a guided virus mutating with a purpose. For example, the word “vaccine” disappears in the name of their group, replaced by “medical freedom.” And according to a recent massive analysis of 100 million Facebook users worldwide, online supporters of anti-vaccine views have been more successful by some measures than those of us publicly supporting vaccines. They are smaller numerically but occupy a more central position in the network; they are heavily involved with clusters of Facebook users who haven’t made up their mind about vaccines; and they
offer a wide variety of “potentially attractive” stories (about safety concerns, about government conspiracies, about natural immunity) that can attract a greater diversity of people compared to pro-vaccine messaging which tends to be one-note.

This diversity is also encouraged by social media companies. Platforms like Facebook and YouTube want to hold onto your eyeballs so they recommend other content. Renee DiResta, a security researcher, told BuzzFeed News that as she joined more anti-vaccine parenting groups on Facebook for the purpose of investigating them, the platform recommended more and more conspiracist groups: about chemtrails, about the flat Earth, about the Pizzagate conspiracy theory. She called this phenomenon “radicalization via the recommendation engine.” And as Anne Borden was telling me, there is active cross-pollination happening on social media with the far right. “Right-wing movements have deeply infiltrated the social media spaces of the antivaxx and vaccine-hesitant homeschoolers and alt-schoolers. They recruit in antivaxx and Facebook groups related to complementary and alternative medicine.”

What these concerns and conspiracy theories may mean for the future

When we pull at this big ball of conspiracy theories and pro-freedom sentiment, we can find some genuine concerns buried inside. Jon Perry, the founder of the Stated Clearly science communication project, pointed me in the direction of a Facebook meme declaring that its poster would not be “vaccinated (chipped) for the coronavirus.” “The meme,” he told me, “is a mixed bag of legitimate concerns about tracking devices, a justifiable mistrust of billionaires and large organizations, common knowledge that most large nations dabble (or have dabbled) in bio-weapons research, a far less warranted (but not totally baseless) fear of new vaccines, and many more, all combined with a horrible confusion about medical patents and virus naming structures.”

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A project like ID2020, aimed at providing everyone with a secure digital identification, can be twisted by a distrustful, pattern-seeking mind into a cover for Bill Gates’ nefarious plan to monitor every human being. The fact that multiple coronavirus vaccines use the virus’ RNA can be misinterpreted into the fear that vaccines will mutate our own DNA. Justified worries are fed by misunderstandings and further amplified by a conspiracist mindset in online communities cross-pollinated by radical political actors, leading to progressive vaccine-hesitant parents holding hands with the anti-lockdown movement. Like a big ball of colourful rubber bands, these disparate-looking actors share an underlying property and end up sticking together.original

While this big wobbly ball looks overwhelming, there are discreet actions pro-vaccine people and organizations can take to minimize the damage caused by anti-vaccine attitudes, and
because these attitudes tend to be tied to the belief in a grand conspiracy, the recent publication of the Conspiracy Theory Handbook can be of help. When addressing members of the public unlikely to endorse conspiracy theories, the Handbook recommends empowering people with facts, uncovering the bad logic in the initial argument, linking to fact-checking websites, and exposing the lack of credibility of the sources of these theories. Trying to reach extremists, on the other hand, is usually a fool’s errand; personally, I’d rather address the people on the fence and we have preliminary evidence that empathy and really listening to the concerns of vaccine-hesitant parents can improve their attitudes toward vaccines.

If safe and effective vaccines against the new coronavirus end up being approved (which is not a guarantee, though over 90 experimental vaccines are at various testing stages), I wonder how much public confidence will have been eroded by this reenergized anti-vaccine movement and their radical allies. In the past decade, the United States has seen a 10% overall decline in the number of parents who feel it’s extremely or very important to vaccinate their children (from 94% in 2001 to 84% in 2019), with 11% saying they think vaccines are more dangerous than the disease they are meant to prevent. Meanwhile, in 2015, almost two in five respondents to a Canadian survey agreed that the science on vaccinations isn’t quite clear. What these numbers capture is not just antivaxxers, however. Their movement is a small and vocal minority, but its fear-based messaging reaches a larger segment of the population: the vaccine hesitant. And people on the fence about vaccines are now being served an incredible buffet of prickly anxieties: from genuine concerns that a coronavirus vaccine may be rushed to the loud cries of “my body, my temple”, all the way to stories of Bill Gates’ evil plan to depopulate the world, with the occasional viral video like Plandemic fuelling this unease with a veneer of respectability. How much damage this ever-growing ball will cause on its way down the slope is anyone’s guess, but we have genuine reason to be worried.

Jonathan Jarry is a biological scientist who once worked for the U.S. Armed Forces, using the power of DNA technology to identify really old American soldiers. His passion for critical science communication has resulted in a nascent blogging and podcasting career, most notably with Dr. Christopher Labos on The Body of Evidence, a website that takes a skeptical eye at health claims. Find Jonathan on Twitter @crackedscience 

A version of this article was originally posted at the McGill Office for Science and Society website and has been republished here with permission. The McGill Office for Science and Society can be found on Twitter @McGillOSS

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Viewpoint: Are synthetic food additives dangerous? Here’s the science anti-chemical activists ignore

It’s more of the same from the Environmental Working Group (EWG)—cleverly designed but scientifically nonsensical scares. Organic: The Original Clean Food is a magnificent body of work, that is if your goal is to scare and manipulate people into doing something that will provide no benefit other than lightening your wallet. EWG is trying to solve a non-problem—making our already-safe food safe. As usual, the science of their article is ghastly and this is no accident. Here are the authors and their credentials, such as they are.

  • Dawn Undurraga –  Nutritionist
  • Nneka Leiba – Zoology and public health
  • Melanie Benesh – Lawyer
  • Scott Faber – Another lawyer

Now there’s a fine group of people to be writing about chemicals and toxicity. It is not clear whether any of them ever took a chemistry class, let alone, have any expertise whatsoever. And it shows. Let’s dive in.

Americans are increasingly seeking “clean” foods that are free from artificial colors, flavors and preservatives.

That’s true; they are being frightened into doing so by silly scare tactics such as those used in this article.

No artificial preservatives, colors or flavors are ever allowed in organic food.

This statement is based on a fallacy—that there is a difference between a chemical that is obtained from natural sources and the same chemical made in a lab or factory. (See my book Natural And Artificial Flavors: What’s The Difference?). But it’s even worse. Let’s say that you take beta-carotene—a vitamin A precursor that is used to give foods yellow/orange colors—and extract it from carrots or spinach. According to EWG if you make the stuff in a factory it’s less healthy than the beta-carotene from the carrot. Wrong.

Worse still, if you take the extract, which is “natural,” and add it to a different food as a colorant, it becomes an artificial flavor. Pretty crazy, no? Even crazier: if you take the extract and add it back to the same carrots from which it was extracted it becomes an artificial color and the carrots cannot be organic.

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Image: Shutterstock

What’s more, many consumers are unaware that food companies don’t need government approval for most of the chemicals added to conventional packaged foods.

Here’s a cute half-truth. Food companies don’t need government for most of the “chemicals” added to food because these awful chemicals have GRAS (generally accepted as safe) status from the FDA. EGW is lying when they say that a food company can just start chucking new chemicals or ingredients into a food product. New additives must be evaluated for safety using methods that are similar, but less rigorous than those required for new drugs.

By contrast, only flavors derived from natural, non-synthetic substances can be used in organic packaged food and, beginning in December 2019, natural flavors cannot be used if organic flavors are commercially available.

This rule is magnificently stupid. “Natural, non-synthetic substances,” as I mentioned above, are identical to their synthetic counterparts. No instrument can tell the difference. Your body can’t tell them apart. But it’s OK to use them anyhow if you can’t buy the natural version. Talk about hypocrisy. EWG is implying that the natural substances are safer (they aren’t) but it’s OK for organic food companies to subject consumers to these monstrous chemical assassins if you can’t buy the “real” stuff.

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If organic food companies are so concerned about these synthetic chemicals then it should simply not sell any product containing the chemical in question. Instead, the use is dependent on commercial availability. How dare they put consumers and their children at risk!

Some “flavors” in conventional foods can actually be made up of more than 100 chemicals that do not have to be labeled on the package.

They finally got something right, albeit by accident. One hundred chemicals in conventional foods? Oh, the humanity. A banana, whether is it organic or not, contains 42 chemicals that are responsible for its scent alone and a whole bunch more that are in it just for the hell of it. There’s about 100 right there. Shall we start labeling bananas, or maybe banning them?

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Some chemicals are not allowed to be in organic foods because they may be harmful to the environment.

OK, although it’s hard to see how a billionth of a gram of ammonium hydroxide (a form of ammonia) is going to heat up the planet, by all means, let’s keep it out of organic food. But this makes the following a little hard to explain:

“Synthetic ingredients allowed in organic food include ingredients that act as leavening agents, such as ammonium carbonate…”

Apparently, these guys aren’t such great chefs either, since the purpose of a leavening agent is to make dough rise. It does so via the following chemical reaction:

(NH4)2CO3 + HEAT ———> CO2   +  NH3 (ammonia)

There is so much more and it’s just as ridiculous, so you really need to take chemical advice from EWG with a grain of salt. Or not. Salt is inorganic.

Josh Bloom joined the American Council on Science and Health in 2010 as Director of Chemical and Pharmaceutical Sciences, and has published 40 op-eds in numerous periodicals, including The Wall Street Journal, Forbes and The Chicago Tribune. Follow him on Twitter @JoshBloomACSH

A version of this article originally appeared on the GLP on July 10, 2019.

This article was originally published at the American Council on Science and Health and has been republished here with permission. The American Council on Science and Health can be found on Twitter @ACSHorg

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Podcast: Doctors have to think about sex; AI text generators spread ‘fake news’? Coffee can indeed make you poop

An ER physician says doctors have to consider biological sex to properly care for their patients. Coffee can send some people to the bathroom—but probably not for the reason we’ve been led to believe. AI-powered text generators can write realistic news stories, fueling concerns that the technology will encourage the spread of misinformation online.

Join geneticist Kevin Folta and GLP editor Cameron English on this episode of Science Facts and Fallacies as they break down these latest news stories:

When physicians don’t properly consider biological sex, patients are prescribed incorrect treatments and suffer entirely preventable consequences, says Alyson McGregor, an Associate Professor of Emergency Medicine at The Warren Alpert Medical School of Brown University.

The problem runs through our health care system, affecting millions of patients, and stems from the fact that doctors often prescribe multiple medications to female patients without recognizing “female sex as an independent risk factor for serious drug interactions,” McGregor notes. This occurs because women are more likely to have multiple physicians prescribing medications, each possibly unaware of all the relevant drugs unless the patient reports them.

Is there a way to correct the situation and prevent needless suffering?

Scientists and educators spend a considerable amount of time combating the spread of misinformation online, and their jobs may get much harder in the coming years as text generators powered by artificial intelligence become more widely used. These applications can perform word association, answer questions and, perhaps most importantly, comprehend related concepts.

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The latest iteration of the technology developed by OpenAI was able to write 200-500 word sample news articles that were difficult to distinguish from news reports written by humans. There are some inherent risks in the technology, but AI-powered text generators are also poised to do a lot of good.

It’s a common joke you’ve probably heard in your favorite movie or TV show: that first morning cup of coffee makes you poop. While it may not be as universal as implied by pop culture, this reaction to coffee is real. Caffeine might be one of the culprits. However, multiple (albeit small) studies show that coffee stimulates several physiological responses that can send you to the bathroom in short order.

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Kevin M. Folta is a professor in the Horticultural Sciences Department at the University of Florida. Follow Professor Folta on Twitter @kevinfolta

Cameron J. English is the GLP’s managing editor. BIO. Follow him on Twitter @camjenglish

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Rare genetic disorder homocystinuria can cause strokes, seizures and death. A ‘genetic glitch’ in blind cavefish offers hope for a treatment

The discovery of a gene behind the absence of eyes in Mexican cavefish may suggest a new way to treat a rare but debilitating disease in humans– homocystinuria.

In homocystinuria, deficiency of an enzyme (cystathionine beta-synthase a, or CBS), blocks the breakdown of two protein building blocks, the amino acids methionine and serine, while a third, cysteine, diminishes. An array of signs and symptoms result.

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Lens dislocation in homocystinuria (National Eye Institute)

Young children may have slow weight gain and growth, learning disabilities, scoliosis, developmental delay, and behavior and emotional problems. Later symptoms include osteoporosis, chest deformities (a protrusion or caved-in breastbone), and severe nearsightedness and dislocation of the lenses, which can lead to blindness.

Some symptoms of homocystinuria are more serious, including blood clots (increasing the risk for stroke, heart attack, pulmonary embolism, and blocked veins), seizures, hemorrhage, and aneurysm (burst arteries). Premature death is a possibility.

People with homocystinuria tend to be tall and thin with pale hair and skin and long, skinny arms, legs, and fingers. It is a single-gene condition inherited from parents who are carriers. The gene encoding cystathionine ß-synthase a is cbsa.

Mutations in four other genes can also cause the condition, but the subtype due to abnormal CBS is the most common. Still, homocystinuria due to CBS deficiency is rare, affecting from 1 in 200,000 to 1 in 300,000 people in the US. It’s more common in Norway, where 1 in about 6400 people has it, and in Qatar, where it affects about 1 in 1800 people.

A rare fish

Mexican cavefish have long been a mystery. Some populations live in surface waters and have eyes, like any other bony fish. Yet at least 30 other populations live in cave waters, and the eyes of those fish mysteriously stop developing when embryos become larvae.

In the fish, members of Astyanax mexicanus, paired retinas and lenses begin to form but the cells die and the fledgling structures recede, becoming covered with skin and scar tissue. The tiny shrunken eyes are vestigial organs, like the hindlimb buds of pythons and wing nubs in flightless birds and insects.

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Blind mysid shrimp live in caves in the Canary islands

Other animals that dwell in caves have shed their eyes over evolutionary time. The no- or tiny-eyed include moles, spiders, beetles, lobsters, crabs, lizards, crickets, worms, shrimp, crayfish, snakes, and other fish. The subterranean naked mole rats lose their eyes after birth. Species that have lost the sense of sight are called troglobites.

When one sense is impaired or absent, others tend to compensate, and that’s true for troglobites. These animals of the darkness also share lower metabolic requirements, and that’s the key to why the seemingly negative trait of sightlessness persists.

Without eyes, the fish shave off about 15% of their energy use compared to their sighted cousins swimming in surface waters. Natural selection favors characteristics that benefit an organism. Fish with lower energy requirements are more likely to survive to reproduce, thereby passing on the trait. 

But the blind cavefish don’t lack eyes simply because they don’t “need” them and somehow willed them away. The trait “may confer an evolutionary benefit for cavefish by eliminating the high energetic cost of maintaining eyes, as vision is useless in the dark cave environment,” the researchers wrote.

It’s the ability to lower energy needs, and exactly how the blindness unfolds in the fish, that may have implications for homocystinuria in people.

 

Zeroing in on one gene

Pachón cavefish, named for the caves that are their homes in Mexico, are the best genetically studied blind fish, but picking out what’s important among the just-under-a-billion DNA bases of the genome is a challenge.

“We know that genes controlling eye degeneration are scattered all over the Mexican cavefish genome,” said William Jeffery, a professor of biology at the University of Maryland in College Park, co-author of a study published in Nature Communications. “There may be 10 to 20 different genes involved, and this is the first time we’ve been able to pin down one specific gene and show the mechanism at work.”

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A naked mole rat enjoys a snack

The team, including collaborators from the National Institutes of Health and Stanford University, identified four genes whose expression changes – producing more or less of the protein – during the time in development when the eyes begin to fade away in the fish destined for blindness. Only one was mutant in all of the populations of blind cavefish but not in the sighted populations on the surface. The gene encodes the aforementioned enzyme, CBS.

The researchers used a classic genetic technique: obliterate the function of a gene and observe what goes wrong. They used the gene-editing tool CRISPR-Cas9 and another knockout technology to remove normal copies of the gene in eggs from sighted fish that live in surface waters.

Sure enough, the eggs with the gene knocked out developed into adults that had tiny eyes or none at all. Other experiments added working copies of the gene into cavefish embryos, and they went on to develop eyes.

Focusing in on the function of the implicated gene, and how the symptoms unfold, is what may provide information important to the human disease that results from the same genetic glitch.

Blocked blood flow

The shriveled visual vestiges of the Mexican cavefish arise from blocked blood flow to primordial eyes in embryos and larvae. Without blood, the delicate organs are deprived of nutrients, growth factors, and oxygen and therefore energy. Development halts.

Like any clogged pipe, though, the blockage leads to a range of problems stemming from the compromised circulatory system: leaky blood vessels, hemorrhages in the eyes, and aneurysms (ballooning and bursting arteries). But the problems are confined to the visual system – the adult fish are otherwise healthy.

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It’s good to know, from the cavefish, that the primary defect appears to be in blood flow, rather than an inherent weakness in an artery that might make it burst.

“Mexican cavefish are not only surviving with homocystinuria, they’re thriving,” Jeffery said. “One thing we might be able to understand is how these fish recover from hemorrhages in the eye, which could provide insight into treatments for the disease in humans,” he added.

A hint to the hardiness of the adult blind fish may lie in the fact that the species’ genome includes a second gene that encodes the enzyme, which maintains blood flow outside the eye.

Gene duplication is a well-known evolutionary phenomenon that arises from a misalignment of chromosome pairs during cell division, so that one resulting chromosome gets two copies of the gene and the other has none. Having two copies enables one to “test out” a mutation because the other copy maintains health. Sometimes the second copy mutates itself into inactivity, and is then called a pseudogene. This may be what happened to cbsa, the gene encoding CBS.

The human genome also has two copies of parts of the cbsa gene, neighbors on chromosome 21. Would it be possible to boost activity of the second copy in people? That’s the basis of a novel treatment for another genetic disease, spinal muscular atrophy. The strategy of deploying a second gene is a little like opening a second browser.

A new treatment for homocystinuria could be implemented early because the inborn error is part of standard newborn screening.

A blood spot detects buildup of homocysteine from methionine. Normally the enzyme converts the toxic homocysteine to cystathionine, which in turn is broken down into the amino acid cysteine. The buildup of homocysteine damages blood vessels and the brain. The pathway requires vitamin B6.

About half of patients respond to prescription-strength B6 supplements, which must be taken for life. If that doesn’t help, a diet very low in protein may dampen symptoms – otherwise, the risk of a blood clot is 25% before age 16 years and 50% by age 30 years. Supplements that may help are betaine (which flushes some of the built-up homocysteine from the blood), folic acid, vitamin B12, and the amino acid L-cysteine.

The bigger picture to the cavefish/homocystinuria story is a reminder that the common phrase “humans and animals” isn’t correct – we’re animals too! And we can learn from the oddities of other species.

Ricki Lewis has a PhD in genetics and is a genetics counselor, science writer and author of Human Genetics: The Basics. Follow her at her website or Twitter @rickilewis.

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Viewpoint: Fish farming has a sustainability problem and genetic engineering might be the solution

As the world endures the impacts of a rapidly changing climate—sea level rise, extreme weather events, warming and acidifying oceans (among many others)—policy makers and the public should critically examine how food production contributes to these worrying trends. Animal agriculture may be the best place to start since, many scientists argue, it’s the single biggest cause of biodiversity loss and a significant source of greenhouse gas emissions.

Over a quarter of the world’s land surface is currently dedicated to raising animals for food, but that practice can be exceptionally wasteful. Despite taking up almost 80 percent of global agricultural land, livestock represents less than 20 percent of the world’s calories. Proper stewardship of the land, which absorbs nearly one-third of global greenhouse gas emissions, is critical in our fight against climate change, but human activities degrade roughly a quarter of it, and livestock production is perhaps the primary culprit.

To help combat these growing environmental challenges, concerned citizens around the world are eating more sustainable and arguably healthier diets that partially or entirely replace meat with fish, crustaceans, and other aquatic animals. Fish production generally has a lower environmental impact than land animal farming, owing to the fact that fish require less feed. Most fish are “poikilotherms,” which means they don’t use energy to heat their bodies. And unlike most land animals (homeotherms), fish don’t need to constantly maintain their body temperatures, which tend to fluctuate with their external environment. Moreover, the density of water carries the weight of the fish, eliminating the requirement for heavy bones.

Despite its lower environmental footprint, global fish production — which includes wild capture and aquaculture (fish farming) — has its own sustainability issues. Around one-third of the world’s marine fish stocks have reached unsustainable levels due to overfishing. Simultaneously, the global demand for fish and nutritional oils containing omega-3 fatty acids is increasing rapidly as more consumers recognize that consuming them is linked to reduced cardiovascular disease risk. Saturation in capture fishing since the early 1990s means aquaculture is filling consumer demand for fish. But without significant changes, aquaculture isn’t a long-term solution.

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Fortunately, a valuable but misunderstood tool can help the industry become more sustainable. Of course, I’m talking about biotechnology. Genetic engineering has sped up the production of fish, and enabled the development of sustainable fish feed sources and nutritional oils. All three innovations are marching toward commercialization, and the evidence indicates their collective impact will be enormous.

While commercial fish farms have greatly improved their production systems over the years, feeding fish with fish (primarily fishmeal and oils) still poses a significant sustainability threat. In 2018, global fish production reached around 179 million tons, and humans ate about 88 percent of the produce (156 million tons) while about 10 percent (18 million tons) went towards producing fishmeal and fish oils. Finding alternative feed sources would slash the environmental footprint of aquaculture and contribute to global food security goals.

Breeding better fish

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AquaBounty GMO salmon

Fish maturity is based on physical features such as shape and size. The faster fish grow, the lower their environmental impact, so innovators have targeted faster growth rates as a solution to the industry’s sustainability problem. In 2015, the Food and Drug Administration (FDA) approved a bioengineered Atlantic salmon for consumption after decades of rigorous scientific review. The FDA concluded that the genetically engineered AquAdvantage salmon “is as safe to eat as any non-genetically engineered Atlantic, and also as nutritious.” This salmon is approved for sale in Canada and is slated for commercialization in the US.

Scientists at the biotech firm AquaBounty introduced two different bits of genetic information from other fish species into a bioengineered salmon: a growth hormone gene from the fast-growing Chinook salmon controlled by a DNA switch (promoter) from the ocean pout. Because the Chinook growth hormone gene works overtime, AquaBounty’s salmon grows to full size in about half the time required by conventional salmon—and consumes 25 percent less feed as a result.

Faster growth means the energy and carbon emissions required to produce the fish are lower. And since AquaBounty’s land-based aquaculture facilities are located in Canada and the US, transporting these fish to market generates lower carbon emission than delivering conventional salmon by air or ship. Additionally, the expansion of genetically engineered fish production could significantly reduce overfishing, since some of salmon feed comes from other wild fish.

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Some environmentalists have voiced concerns about the consequences of bioengineered fish escaping into the wild. In theory, genetically engineered fish may flee to the wild , breed with their wild relatives  and create a hybrid that could out-compete other fish in the marine ecosystem. Quite rightly, these are serious concerns that require proper attention and strong mitigation plans.

Considering the trade-off between hypothetical risks and the demonstrated benefits of biotechnology in fish production helps us evaluate the situation. AquAdvantage salmon are produced in land-based facilities and are sterile. Regulators at the FDA have therefore concluded it’s “extremely unlikely that the fish could escape and establish themselves in the wild.”

Shorter production time and lower feed and energy requirements clearly outweigh the low risk of fish escaping into the wild. And we get all these without compromising the nutritional value of the fish itself. AquaBounty is scheduled  to begin producing its bioengineered salmon in the US before the end of 2020, making it the first genetically engineered food animal to hit US markets. As COVID-19 continues to put pressure on food supplies, the introduction of genetically engineered salmon helps illustrate how biotechnology can help solve critical problems.

Alternative fish feeds and fish oils

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Bioengineered fish is an important step in the right direction, but it doesn’t fully address aquaculture’s sustainability issues. The industry has developed non-fish based feeds, cutting use of fishmeal and fish oil from 30 million tons in 1994 to about 18 million tons in 2018. But there are concerns that fish products grown on alternative feeds aren’t providing the same nutritional value as those fed real fish, which is high in omega-3 oils. To understand why, we need to look at the chemistry of these fatty acids.

Omega-3 oils are long-chain polyunsaturated fatty acids existing mainly in three types: α-linolenic acid (ALA); eicosapentaenoic acid (EPA); and docosahexaenoic acid (DHA). Plant oils contain ALA, which is the shorter version of EPA and DHA omega-3 fatty acids, typically found in marine organisms like microalgae and phytoplankton.

Our bodies can’t make omega-3, so we mostly get it from eating fish, which incidentally also can’t make omega-3 but accumulate it by eating microalgae and phytoplankton. As vegetable oils replace fish oil in aquafeeds, the level of beneficial fatty acids, EPA and DHA, have also declined considerably, reducing the nutritional value that fish offer. Therefore, the aquaculture industry needs to identify aquafeeds that are derived from alternative sources and provide the same level of nutrition.

Algae are a promising source to replace fish oil, but extracting algal oil is more expensive than producing fish oil and fishmeal, though the extraction technology is rapidly developing. Additionally, algae cultivation for aquafeed is sometimes limited to species that only produce DHA fatty acids, which means the algae-fed fish lack EPA, compromising their final nutritional value.

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Again, scientists have turned to biotechnology to address this problem. Research teams have engineered plants like camelina and canola that contain high levels of EPA and DHA in their seed oil. These plants naturally produce the shorter version of omega-3, ALA, and scientists introduced microalgal genes that convert ALA into EPA and DHA omega-3 fatty acids typically found in fish. Research shows that fish fed with seed oil from these camelina plants show good growth, maintain feed efficiency and don’t lose nutritional value—indicating that genetically engineered plants can provide a sustainable substitute for fish oil feeds.

Now innovators are aiming to produce omega-3 oils from camelina for aquafeeds and nutritional supplements. Biotech startup Yield10 Bioscience has fused artificial intelligence with synthetic biology to create a technology that identifies trait targets to produce better plants. Using their technology platform and genome editing, they have generated camelina plants that produce double seed yields with a high content of both EPA and DHA omega-3 oils. The company has recently launched field trials of their genome-edited seeds. They are scaling seed production, aiming to plant thousands of acres of camelina to produce plant-based omega-3 oil products for fish feed and human nutrition soon. Crucially, the USDA announced in January 2020 that it won’t regulate gene-edited camelina, accelerating development of this sustainable omega-3 oil source.

Biotechnology is already accelerating production of environmentally friendly salmon, and is poised to provide more sustainable fish feed and nutritional oils in the coming years. It could also bring aquaculture production costs down, reducing incentives to overfish our oceans, which will no doubt be better for the marine ecosystem.

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Surging fish demand will only be met by sustainable, low-cost solutions, enabled in key instances by biotechnology. Technical details aside, the benefits of broader biotechnology adoption in aquaculture will extend beyond the developed world to improve the lives of those most in need—impoverished people in the developing world.

Rupesh Paudyal holds a PhD in plant science and covers agriculture and the environment as a freelance writer. Visit his website and follow him on Twitter @TalkPlant

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Self medication: Blocked from drugs by the medical establishment, many transgender people resort to black-market hormones

For the first 10 months of Christine’s gender transition, a progressive LGBT health clinic in Boston made getting on hormones easy. But after a year or so on estrogen and a testosterone-blocker, she found herself in financial trouble. She had just recently moved to the city, where she was unable to find a job, and her savings were starting to wear thin.

Finding employment as a transgender person, she says, was overwhelmingly difficult: “I was turned down for more jobs than I can count — 20 or 40 different positions in a couple of months.” She would land an interview, then wouldn’t hear back, she says, which she suspects happened because the company noticed she was “not like their other potential hires.”

Christine, a transgender woman, had been enrolled in the state’s Medicaid program, MassHealth, for four months, and her copay for hormone therapy was only $5. But without a job, she found herself torn between food, rent, and medication. For a while, she juggled all three expenses with donations from friends. But after several months, she felt guilty about asking for help and stopped treatment. (Undark has agreed to use only Christine’s chosen name because she said she feared both online and in-person harassment for sharing her story.)

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Christine joins a rally holding the trans flag.

At first, Christine didn’t mind being off hormones. She marched in political protests alongside older trans people who assured her that starting and stopping hormones was a normal part of the trans experience. But eventually, Christine felt her body reverting back to the way it had been before her transition; her chest flattened and her fat moved from her hips to her stomach. She stopped wearing dresses and makeup.

“I wasn’t looking at myself in the mirror anymore,” she says. “I existed for 10 months, and then I was gone.”

People who are visibly transgender often have trouble finding a job. Nearly a third live in poverty. Many don’t have health insurance, and those who do may have a plan that doesn’t cover hormones. Although testosterone and estrogen only cost $5 to $30 a month for patients with an insurance plan (and typically less than $100 per month for the uninsured), doctors often require consistent therapy and blood work, which ratchets up the cost. Even when trans people have the money, finding doctors willing to treat them can prove impossible. Trans people are also likely to have had bad experiences with the health care system and want to avoid it altogether.

Without access to quality medical care, trans people around the world are seeking hormones from friends or through illegal online markets, even when the cost exceeds what it would through insurance. Although rare, others are resorting to self-surgery by cutting off their own penis and testicles or breasts.

Even with a doctor’s oversight, the health risks of transgender hormone therapy remain unclear, but without formal medical care, the do-it-yourself transition may be downright dangerous. To minimize these risks, some experts suggest health care reforms such as making it easier for primary care physicians to assess trans patients and prescribe hormones or creating specialized clinics where doctors prescribe hormones on demand.

But those solutions aren’t available to most people who are seeking DIY treatments right now. Many doctors aren’t even aware that DIY transitioning exists, although the few experts who are following the community aren’t surprised. Self-treatment is “the reality for most trans people in the world,” says Ayden Scheim, an epidemiologist focusing on transgender health at Drexel University who is trans himself.

In one respect, Christine was lucky. She lived in Boston with access to a local LGBT clinic — Fenway Health’s Sidney Borum, Jr. Health Center, which is geared toward youth who may not feel comfortable seeking medical care in a traditional setting — and she was able to continue her appointments even when she struggled to find work. But then money got too tight and she moved to Cape Cod to live with her parents. Because of the distance, Christine’s state insurance wouldn’t cover the appointments at Fenway, she says.

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After Christine posted about her frustrations on Facebook, a trans friend offered a connection to a store in China that illicitly ships hormones to the United States. Christine didn’t follow up, not wanting to take the legal risk. But as time ticked by and job opportunities came and went, her mind started to change.

“I’m ready to throw all of this away and reach out to anyone — any underground black-market means — of getting what I need,” she thought after moving to the Cape. “If these systems put in place to help me have failed me over and over again, why would I go back to them?”

Transgender is an umbrella term that refers to a person who identifies with a gender that doesn’t match the one they were assigned at birth. For example, someone who has male written on their birth certificate, but who identifies as a woman, is a transgender woman. Many trans people experience distress over how their bodies relate to their gender identity, called gender dysphoria. But gender identity is deeply personal. A five o’clock shadow can spur an intense reaction in some trans women, for instance, while others may be fine with it.

To treat gender dysphoria, some trans people take sex hormones, spurring a sort of second puberty. Trans women — as well as people like Christine, who also identifies as nonbinary, meaning she doesn’t exclusively identify as being either a man or a woman — usually take estrogen with the testosterone-blocker spironolactone. Estrogen comes as a daily pill, by injection, or as a patch (recommended for women above the age of 40). The medications redistribute body fat, spur breast growth, decrease muscle mass, slow body hair growth, and shrink the testicles.

Transgender men and non-binary people who want to appear more traditionally masculine use testosterone, usually in the form of injections, which can be taken weekly, biweekly, or every three months depending on the medication. Others use a daily cream, gel, or patch applied to the skin. Testosterone therapy can redistribute body fat, increase strength, boost body hair growth, deepen the voice, stop menstruation, increase libido, and make the clitoris larger.

Depending on which parts of the body give a transgender person dysphoria, they may choose to undergo surgery, with or without hormone therapy — removing breasts, for example, or reconstructing genitalia, called top and bottom surgery, respectively.

Some family members — especially those who are cisgender, which means their gender identity matches what they were assigned at birth — worry that people who are confused about their gender will begin hormones and accumulate permanent bodily changes before they realize they’re actually cisgender.

But many of the changes from taking hormones are reversible, and regret appears to be uncommon. Out of a group of nearly 3,400 trans people in the United Kingdom, only 16 regretted their gender transition, according to research presented at the 2019 biennial conference of the European Professional Association for Transgender Health. And although research on surgical transition is sparse, there are some hints that those who choose it are ultimately happy with the decision. According to a small 2018 study in Istanbul, post-operative trans people report a higher quality of life and fewer concerns about gender discrimination compared to those with dysphoria who haven’t had surgery.

And for trans people with dysphoria, hormones can be medically necessary. The treatments aren’t just cosmetic — transitioning literally saves lives, according to the American Academy of Pediatrics. In a 2019 review paper, researchers from the University of San Francisco found that hormone therapy is also linked to a higher quality of life and reduced anxiety and depression.

Despite the growing evidence that medical intervention can help, some trans people are wary of the health care system. According to the 2015 U.S. Transgender Survey, a third of trans people who saw a health care provider experienced mistreatment — from having to educate their doctor about transgender issues to being refused medical treatment to verbal abuse — and 23 percent avoided the doctor’s office because they feared mistreatment.

The health care system has a history of stigmatizing trans identity. Until recently, the World Health Organization and the American Psychiatric Association even considered it a mental disorder. And according to a 2015 study from researchers at the Lesbian, Gay, Bisexual, and Transgender Medical Education Research Group at the Stanford University School of Medicine, less than 35 percent of medical schools teach coursework related to transgender hormone therapy and surgery.

On June 12, the administration of President Donald J. Trump finalized a rule removing protections that had been put in place in 2016 to bar discrimination against transgender people by health care providers. Just three days later, the U.S. Supreme Court decided that the 1964 law that bans discrimination in the workplace based on sex, race, national origin, and religion also applies to sexual orientation and gender identity. While not directly touching on the new health care rule, some experts think the Supreme Court’s decision may make legal challenges to it more likely to succeed.

Trans-friendly health care providers are rare, and booking an appointment can stretch out over many weeks. In England, for example, the average wait time from the referral to the first appointment is 18 months, according to an investigation by the BBC. Even those with hormone prescriptions face hurdles to get them filled. Scheim, who lived in Canada until recently, knows this firsthand. “As someone who just moved to the U.S., I’m keenly aware of the hoops one has to jump through,” he says.

“Even if it’s theoretically possible to get a hormone prescription, and get it filled, and get it paid for, at a certain point people are going to want to go outside the system,” Scheim says. Navigating bureaucracy, being incorrectly identified — or misgendered — and facing outright transphobia from health care providers, he adds, “can just become too much for folks.”

Many of the health care barriers trans people face are amplified when it comes to surgery. Bottom surgery for trans feminine people, for example, costs about $25,000 and isn’t covered by most insurance plans in the U.S.

There are some signs that at least parts of the medical community have been rethinking their stance on transgender patients. “Clearly the medical professionals didn’t do the right thing. But things are changing now,” says Antonio Metastasio, a psychiatrist at the Camden and Islington NHS Foundation Trust in the U.K.

The Association of American Medical Colleges, for example, released their first curriculum guidelines for treating LGBT patients in 2014. In 2018, the American Academy of Pediatrics released a policy statement on transgender youth, encouraging gender-affirming models of treatment. And in 2019, the American College of Physicians released guidelines for primary care physicians on serving transgender patients.

Some hospitals, like Mount Sinai in New York and Saint Francis Memorial Hospital in San Francisco, now require transgender health education for medical employees. Others may soon join them: In February, experts from Harvard University, Fenway Health, and the Fenway Institute published the first peer-reviewed guidelines for creating primary care transgender health programs.

The World Professional Association for Transgender Health (WPATH) — the international authority on transgender health care, according to a summary of clinical evidence on gender reassignment surgery prepared for the Centers for Medicare and Medicaid Services — has also changed its Standards of Care to make access to hormones easier. Previously, WPATH recommended that before a person could receive hormone treatment, they had to have “persistent, well-documented gender dysphoria,” as well as documented, real-life experiences covering at least three months. The newest guidelines, published in 2012, nix these stringent requirements, although they still strongly recommend mental health evaluations before allowing trans people to access gender-affirming medical care and require a referral letter from a mental health professional.

But the shift hasn’t stopped trans people from seeking DIY treatments.

Before Christine moved to Cape Cod, she secured about two weeks of estrogen from a trans friend. But she soon decided to end the DIY treatment and went off hormones for good. “I can only accept help for something like that for so long before I start to feel bad about it,” she says. “At that point, it was just like I gave up.”

But she didn’t give up for long. After the move, Christine tried to get back on hormones through a legitimate health care provider. First, she considered visiting a Planned Parenthood, but the closest one she could find was at least two hours away and she worried her old car couldn’t make the journey. Then she visited a local women’s health clinic. But she says they turned her away, refused to recognize her gender, and wouldn’t direct her to another provider or clinic. Instead of advice, Christine says, “I got ‘no, goodbye.’”

Left with few options and not wanting to take the risks of further DIY treatment, Christine accepted that she would be off hormones for the foreseeable future.

Many trans folks, however, start or extend their hormone use by turning to drugs that aren’t meant for transitioning, like birth control pills. Others buy hormones online, skirting the law to order from overseas pharmacies without a prescription. To figure out how best to take the drugs, people determine dosages from research online — they read academic literature, technical standards written for health care providers, or advice in blog posts and public forums like Reddit.

Then, they medicate themselves.

Metastasio is one of the few scientists who have studied the practice. He learned about it in 2014, when one of his transgender patients admitted they were taking non-prescribed hormones. Metastasio asked his colleagues if they’d heard similar stories, but none had. So he started asking all his trans patients about DIY hormones and tracked those who were involved in the practice, ultimately publishing a report of seven case studies in 2018.

While there isn’t a lot of other existing research on DIY hormone treatment, and some of it may be outdated, the available studies suggest it is fairly common and researchers may in fact be underestimating the prevalence of DIY hormone use because they miss people who avoid the medical system completely. In 2014, researchers in the U.K. found that at the time of their first gender clinic visit, 17 percent of transgender people were already taking hormones that they had bought online or from a friend. In Canada, a quarter of trans people on hormones had self-medicated, according to a 2013 study in the American Journal of Public Health. And in a survey of trans people in Washington, D.C. in 2000, 58 percent said they used non-prescribed hormones.

People cite all sorts of reasons for ordering the drugs online or acquiring them by other means. In addition to distrust of doctors and a lack of insurance or access to health care, some simply don’t want to endure long waits for medications. That’s the case for Emma, a trans woman in college in the Netherlands, where it can take two to three years to receive a physician prescription. (Emma is only using her first name to avoid online harassment, which she says she’s experienced in the past.)

Law enforcement doesn’t seem to pay much attention to the international black market shipments. Once, customs agents searched a package containing Emma’s non-prescribed estrogen and ultimately let the drugs through without any issues. That has also been the experience of Charley from Virginia, who identifies as non-binary or genderqueer and who requested to use only his nickname because he isn’t publicly out about his gender identity. Charley orders estrogen online and isn’t too worried about getting caught. “I happen to be a lawyer. I know I’m breaking the law,” he says. “Who’s going to chase me down, really? Is the FBI going to come and knock on my door? Or the county police?”

As for surgery, far fewer people turn to DIY versions compared to those who try hormones. A 2012 study in the Journal of Sexual Medicine reported that only 109 cases of self-castration or self-mutilation of the genitals appear in the scientific literature, and not all are related to gender identity. “But one is too many,” Scheim says. “No one should be in a position where they feel like they need to do that.”

The individual cases reveal a practice that is dangerous and devastating. In Hangzhou, China, a 30-year-old transgender woman feared rejection from her family, so she hid her true gender, according to a 2019 Amnesty International report. She also tried to transition in secret. At first, the woman tried putting ice on her genitals to stop them from functioning. When that didn’t work, she booked an appointment with a black-market surgeon, but the doctor was arrested before her session. She attempted surgery on herself, the report says, and after losing a profuse amount of blood, hailed a taxi to the emergency room. There, she asked the doctor to tell her family she had been in an accident.

When it comes to self-surgery, the dangers of DIY transitioning are obvious. The dangers of DIY hormones are more far-ranging, from “not ideal to serious,” Scheim says. Some DIY users take a more-is-better approach, but taking too much testosterone too quickly can fry the vocal cords. Even buying hormones from an online pharmacy is risky. In 2010, more than half of all treatments from illicit websites — not only of hormones, but of any drug — were counterfeit, according to a bulletin from the World Health Organization.

Still, Charley isn’t worried about the legitimacy of the drugs he’s taking. The packaging his estrogen comes in matches what he would get from a pharmacy with a doctor’s prescription, he says. He’s also unconcerned about the side effects. “I just did a metric century” — a 100-kilometer bike ride — “in under four hours and walked away from it feeling great. I’m healthy,” he says. “So, yeah, there might be a few side effects. But I know where the local hospital is.”

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Prescription estrogen tablets that Charley buys online.

Yet waiting to see if a seemingly minor side effect leads to a health emergency may mean a patient gets help too late. “I don’t want to say that the risks are incredibly high and there is a high mortality,” Metastasio says. “I am saying, though, that this is a procedure best to be monitored.” Metastasio and others recommend seeing a doctor regularly to catch any health issues that arise as quickly as possible.

But even when doctors prescribe the drugs, the risks are unclear because of a lack of research on trans health, says Scheim: “There’s so much we don’t know about hormone use.”

Researchers do know a little bit, though. Even when a doctor weighs in on the proper dosages, there is an increased risk of heart attack. Taking testosterone increases the chances of developing acne, headaches and migraines, and anger and irritability, according to the Trans Care Project, a program of the Transcend Transgender Support and Education Society and Vancouver Coastal Health’s Transgender Health Program in Canada. Testosterone also increases the risk of having abnormally high levels of red blood cells, or polycythemia, which thickens the blood and can lead to clotting. Meanwhile, studies suggest estrogen can up the risk for breast cancer, stroke, blood clots, gallstones, and a range of heart issues. And the most common testosterone-blocker, spironolactone, can cause dehydration and weaken the kidneys.

All of these risks make it especially important for trans people to have the support of a medical provider, Metastasio says. Specialists are in short supply, but general practitioners and family doctors should be able to fill the gap. After all, they already sign off on the hormone medications for cisgender people for birth control and conditions such as menopause and male pattern baldness — which come with similar side effects and warnings as when trans people use them.

Some doctors have already realized the connection. “People can increasingly get hormone therapy from their pre-existing family doctor,” Scheim says, “which is really ideal because people should be able to have a sort of continuity of health care.”

Zil Goldstein, associate medical director for transgender and gender non-binary health at the Callen-Lorde Community Health Center in New York City, would like to see more of this. Treating gender dysphoria, she says, should be just like treating a patient for any other condition. “It wouldn’t be acceptable for someone to come into a primary care provider’s office with diabetes” and for the doctor to say “‘I can’t actually treat you. Please leave,’” she says. Primary care providers need to see transgender care, she adds, “as a regular part of their practice.”

Another way to increase access to hormones is through informed consent, a system which received a green light from the newest WPATH guidelines. That’s how Christine received her hormones from Fenway Health before she moved from Boston to Cape Cod. Under informed consent, if someone has a blood test to assess personal health risks of treatment, they can receive a diagnosis of gender dysphoria, sign off on knowing the risks and benefits of hormone therapy, and get a prescription — all in one day.

The short process can be a lifeline for trans people who need quick access to a prescription. In 2016, Entropy, a non-binary trans woman who lives in Nashville, Tennessee, considered illegally buying hormones online. (Entropy is using her chosen name because she doesn’t identify with her given first or last name.) But she was only 16 at the time and, worried that her conservative family would search her mail, she scrapped the plan. She waited until she turned 18, then visited a doctor at Vanderbilt University Medical Center working under an informed consent basis. “I got the prescription that day,” she says. “It was incredibly efficient.”

And Jaime Lynn Gilmour, a trans woman using the full name she chose to match her gender identity, turned to informed consent after struggling to find DIY hormones. In 2017, Jaime realized she was trans while serving in the military, and says she felt she had to keep her gender a secret. When her service ended, she was ready to start taking hormones right away. So she tried to find them online, but her order wouldn’t go through on three different websites. Instead, she visited a Planned Parenthood clinic. After blood work and a few questions, she walked out with three months of estrogen and spironolactone.

But Goldstein says even informed consent doesn’t go far enough: “If I have someone who’s diabetic, I don’t make them sign a document eliciting their informed consent before starting insulin.”

For trans people, hormone treatments “are life-saving therapies,” Goldstein adds, “and we shouldn’t delay or stigmatize.”

For now, Christine still lives with her parents in Cape Cod. She’s also still off hormones. But she found a job. After she stashes a bit more cash in the bank, she plans to move closer to Boston and find a physician.

Despite the positive shifts in her life, it’s been a difficult few months. After moving to Cape Cod, Christine lost most of her social life and support system — particularly since her parents don’t understand or accept her gender identity. Though she has reconnected with a few friends in the past several weeks, she says she’s in a tough place emotionally. In public, she typically dresses and styles herself to look more masculine to avoid rude stares, and she is experiencing self-hatred that she fears won’t go away when she restarts treatment. Transitioning again isn’t going to be easy, as she explained to Undark in a private message on Facebook: “I’ve been beaten down enough that now I don’t wanna get back up most of the time.”

Even worse is the fear that she might not be able to restart treatment at all. Earlier this year, Christine suffered two health emergencies within the span of a week, in which she says her blood pressure spiked, potentially causing organ damage. Christine has had one similar episode in the past and her family has a history of heart issues.

Christine may not be able to get back on estrogen despite the hard work she’s done to be able to afford it, she says, since it can increase the risk of heart attack and stroke. Because she has so far resisted trying DIY treatments again, she may have saved herself from additional health problems.

But Christine doesn’t see it that way. “Even if it was unsafe, even if I risked health concerns making myself a guinea pig, I wish I followed through,” she wrote. “Being off hormones is hell. And now that I face potentially never taking them again, I wish I had.”

Tara Santora is a science journalist based out of Denver. They have written for Psychology Today, Live Science, Fatherly, Audubon, and more. Tara can be found on Twitter @Tara_Santora

A version of this article was originally published on Undark and has been republished here with permission. Undark can be found on Twitter @undarkmag

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Viewpoint: Organic food represents a ‘reactionary’ ideology that doesn’t support health or sustainable farming⁠—and should not be subsidized

With worldwide sales of almost $97 billion in 2017, “organic” products have won the hearts and plates of many consumers and are indicative of legitimate food concerns. However, the health and environmental benefits it claims are based on shaky scientific foundations. The very philosophy of “organic” is questionable from a methodological point of view.

An analysis of the scientific literature does not demonstrate the superiority of organic agriculture (OA) over conventional agriculture (CA), looking at it on the basis of health, nutrition or sensory appeal.

Pesticides are a necessary evil and OA cannot avoid them, despite normal assumptions to the contrary. The health consequences of “natural” pesticides can prove equally dramatic. For example, rotenone, a molecule extracted from tropical plants, poses an increased risk to those working with it of developing Parkinson’s disease. This “organic” pesticide was banned in 2011. Despite what people may think, pesticides are increasingly being monitored, evaluated and controlled. Just like medicine, pesticides are still essential but should not be used incorrectly.  Instances of pesticide traces in food do not pose a major health risk according to the European Food Safety Authority.

Environmentally, OA and CA come in neck and neck when compared on a per unit produced basis.  In fact, while it is recognized that under equivalent soil and climate conditions, OA tends to be more environmentally friendly per hectare, it is another matter when we take into account the additional area required for “organic” farming, which is much less productive.

“Organic” does not comply in practice with its anti-pesticide and anti-GMO doctrine. OA cannot do without plant protection products, like, for example, copper sulphate, which are “natural” only in name and could even be more toxic than other, synthetic, products. If “organic” producers really refused to grow plants whose genetic material has been artificially altered by humans, they would have to abandon many crops, such as Renan wheat or Camargue rice.

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OA is a philosophy rooted in a reactionary and anti-modernist ideology, which was taken up in the 1970s by anti-capitalist and ecological movements. The proponents of “organic” worship all things natural in opposition to anything synthetic, which they consider as inherently bad. This systemic approach is not founded on a scientific approach and becomes incomprehensible, even totally incoherent, when you consider that GMOs are an excellent means of reducing the amounts of plant protection products required.

Despite its agronomic underperformance and well-founded doubts about its benefits, OA receives state subsidies in many countries, particularly in Europe.

In fact, OA operations receive additional subsidies compared to CA. Aid for conversion and maintenance of the common agricultural policy (CAP) and a raft of local subsidies provide a windfall for conversion. While CA is often subsidized, OA is even more so. For example, in its recent report on OA, the Institute for Economic and Fiscal Research calculated that in France, one liter of “organic” milk is subsidized 50% more than conventional milk.

Other countries are less interventionist. The U.S. government offers far fewer subsidies. Across the pond, only 0.6% of agricultural land has been converted, compared with 5.7% in the EU, although the US is the leading consumer market for organic products, ahead of the EU. This significant difference shows that European “organic” production is being kept alive hooked up to a drip of taxpayers’ money.

With resources like this, it would probably have been more relevant to invest in agricultural progress like biotechnology or precision agriculture, which involves using artificial intelligence to prevent plant or animal diseases and optimize input requirements.  These are techniques that offer real ecological and economic solutions, helping to ensure a decent income for producers.

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Another form of interventionism are the OA official labels.  Thanks to these, producers can draw on the state’s moral support to boast the so-called virtues of “organic.” This marketing of the appeal to nature and health is based on an intellectual monopoly: the appropriation of the word “organic.” Etymologically, “organic” comes from biology, that is, relating to or derived from living matter – originally from Greek organikos “of or pertaining to an organ,” and taking on the meaning “from organized living beings” in the eighteenth century. But agriculture is a process based on living matter. So it can only ever be considered organic. This would make CA is no less “organic” than OA.

Proponents of “organic” insidiously suggest that CA is inorganic, non-biological, non-living, “chemical” and dead. With a state-sanctioned monopoly on the use of the word “organic,” OA covers itself in the glory of a monopoly of the living and the good, and possesses a powerful anti-competitive instrument that is not based on any coherent scientific consideration.

With everyone free to produce or consume what they want, interventionism in favor of “organic” offers a legal and subsidized income.  In order to restore consumer freedom, it is essential to abolish subsidies specific to “organic,” to privatize the OA labels and abolish the intellectual monopoly on the word “organic.”

The agricultural issue should be depoliticized so that competition, responsibility and innovation can provide consumers with the best possible diet, whether they choose to eat “organic” or not.

This article was previously published on June 25, 2020 on the Genetic Literacy Project. 

Laurent Pahpy is an analyst for the Institut de Economic and Fiscal Research (IREF). He writes about economics, technology, agriculture and law. Follow him on Twitter @LaurentPahpy

This article originally ran at European Scientist and has been republished here with permission. European Scientist can be found on Twitter @EuropeScientist

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Does our perception of the world reflect reality? Solving the problem of consciousness

When I see red, it’s the most religious experience. Seeing red just results from photons of a certain frequency hitting the retina of my eye, which cascades electrical and biochemical pulses through my brain, in the same way a PC runs. But nothing happening in my eye or brain actually is the red colour I experience, nor are the photons or pulses. This is seemingly outside this world. Some say my brain is just fooling me, but I don’t accept that as I actually experience the red. But then, how can something out of this world be in our world? 

-Andrew Kaye, 52, London.

What’s going on in your head right now? Presumably you’re having a visual experience of these words in front of you. Maybe you can hear the sound of traffic in the distance or a baby crying in the flat next door. Perhaps you’re feeling a bit tired and distracted, struggling to focus on the words on the page. Or maybe you’re feeling elated at the prospect of an enlightening read. Take a moment to attend to what it’s like to be you right now. This is what’s going on inside your head.

Or is it? There’s another, quite different story. According to neuroscience, the contents of your head are comprised of 86 billion neurons, each one linked to 10,000 others, yielding trillions of connections.

A neuron communicates with its neighbour by converting an electrical signal into a chemical signal (a neurotransmitter), which then passes across the gap in between the neurons (a synapse) to bind to a receptor in the neighbouring neuron, before being converted back into an electrical signal. From these basic building blocks, huge networks of electro-chemical communication are built up.

These two stories of what’s going on inside your head seem very different. How can they both be true at the same time? How do we reconcile what we know about ourselves from the inside with what science tells us about our body and brain from the outside? This is what philosophers have traditionally called the mind-body problem. And there are solutions to it that don’t require you to accept that there are separate worlds.

Ghost in the machine?

Probably the most popular solution to the mind-body problem historically is dualism: the belief that the human mind is non-physical, outside of the physical workings of the body and the brain. According to this view, your feelings and experiences aren’t strictly speaking in your head at all – rather they exist inside an immaterial soul, distinct from, although closely connected to, your brain.

The relationship between you and your body, according to dualism, is a little bit like the relationship between a drone pilot and his drone. You control your body, and receive information from its sensors, but you and your body are not the same thing.

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Dualism in a nutshell. Credit: Halfpoint/Shutterstock

Dualism allows for the possibility of life after death: we know the body and the brain decay, but perhaps the soul lives on when the body dies, just as a drone pilot lives on if his drone is shot down. It is also perhaps the most natural way for human beings to think about the body-mind relationship. The psychologist Paul Bloom has argued that dualism is hardwired into us, and that from a very early age infants start to distinguish “mental things” from “physical things”. Reflecting this, most cultures and religions throughout history seem to have adopted some kind of dualism.

The trouble is that dualism does not fit well with the findings of modern science. Although dualists think the mind and the brain are distinct, they believe there is an intimate causal relationship between the two. If the soul makes a decision to raise an arm, this somehow manages to influence the brain and thereby set off a causal chain which will result in the arm going up.

Rene Descartes, the most famous dualist in history, hypothesised that the soul communicated with the brain through the pineal gland, a small, pea-shaped gland located near the centre of the brain. But modern neuroscience has cast doubt on the idea that there is a single, special location in the brain where the mind interacts with the brain.

Perhaps a dualist could maintain that the soul operates at several places in the brain. Still, you’d think we’d be able to observe these incoming signals arriving in the brain from the immaterial soul, just as we can observe in a drone where the radio signals sent by the pilot arrive. Unfortunately, this is not what we find. Rather, scientific investigation seems to show that everything that happens in a brain has a physical cause within the brain itself.

Imagine we found what we thought was a drone, but upon subsequent examination we discovered that everything the drone did was caused by processes within it. We would conclude that this was not being controlled by some external “puppeteer” but by the physical processes within it. In other words, we would have discovered not a drone but a robot. Many philosophers and scientists are inclined to draw the same conclusions about the human brain.

Am I my brain?

Among contemporary scientists and philosophers, the most popular solution to the mind-body problem is probably materialism. Materialists aspire to explain feelings and experiences in terms of the chemistry of the brain. It is broadly agreed that nobody has the slightest clue as yet how to do it, but many are confident that we one day will.

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This confidence probably arises from the sense that materialism is the scientifically kosher option. The success of science in the past 500 years is after all mind-blowing. This gives people confidence that we just need to plug away with our standard methods of investigating the brain, and one day we’ll solve the riddle.

The trouble with this common viewpoint, as I argue in my book Galileo’s Error: Foundations for a New Science of Consciousness, is that our standard scientific approach was designed to exclude consciousness.

Galileo was the first person to demand that science should be mathematical. But Galileo understood quite well that human experience cannot be captured in these terms. That’s because human experience involves qualities – the redness of a red experience, the euphoria of love – and these kinds of qualities cannot be captured in the purely quantitative language of mathematics.

Galileo got around this problem by adopting a form of dualism, according to which the qualities of consciousness existed only in the incorporeal “animation” of the body, rather than in the basic matter that is the proper focus of physical science. Only once Galileo had located consciousness outside of the realm of science, was mathematical science possible.

In other words, our current scientific approach is premised on Galileo’s separation of the quantitative physical world from the qualitative reality of consciousness. If we now want to bring consciousness into our scientific story, we need to bring these two domains back together.

Is consciousness fundamental?

Materialists try to reduce consciousness to matter. We have explored some problems with that approach. What about doing it the other way around – can matter be reduced to consciousness? This brings us to the third option: idealism. Idealists believe that consciousness is all that exists at the fundamental level of reality. Historically, many forms of idealism held that the physical world is some kind of illusion, or a construction generated from our own minds.

Idealism is not without its problems either. Materialists put matter at the basis of everything, and then have a challenge understanding where consciousness comes from. Idealists put consciousness at the basis of everything, but then have a challenge explaining where matter comes from.

But a new – or rather rediscovered – way of building matter from consciousness has recently been garnering a great deal of attention among scientists and philosophers. The approach starts from the observation that physical science is confined to telling us about the behaviour of matter and what it does. Physics, for example, is basically just a mathematical tool for telling us how particles and fields interact. It tells us what matter does, not what it is.

If physics doesn’t tell us what fields and particles are, then this opens up the possibility that they might be forms of consciousness. This approach, known as panpsychism, allows us to hold that both physical matter and consciousness are fundamental. This is because, according to panpsychism, particles and fields simply are forms of consciousness.

At the level of basic physics, we find very simple forms of consciousness. Perhaps quarks, fundamental particles that help make up the atomic nucleus, have some degree of consciousness. These very simple forms of consciousness could then combine to form very complex forms of consciousness, including the consciousness enjoyed by humans and other animals.

So, according to panpsychism, your experience of red and the corresponding brain process don’t take place in separate worlds. Whereas Galileo separated out the qualitative reality of a red experience from the quantitative brain process, panpsychism offers us a way of bringing them together in a single, unified worldview. There is only one world, and it’s made of consciousness. Matter is what consciousness does.

Panpsychism is quite a radical rethink of our picture of the universe. But it does seem to achieve what other solutions cannot. It offers us a way to combine what we know about ourselves from the inside and what science tells us about our bodies and the brains from the outside, a way of understanding matter and consciousness as two sides of the same coin.

Can panpsychism be tested? In a sense it can, because all of the other options fail to account for important data. Dualism fails to account for the data of neuroscience. And materialism fails to account for the reality of consciousness itself. As Sherlock Holmes famously said: “Once we have ruled out the impossible, what remains, no matter how improbable, must be the truth.” Given the deep problems that plague both dualism and materialism, panpsychism looks to me to be the best solution to the mind-body problem.

Even if we can solve the mind-body problem, this can never dispel the wonder of human consciousness. On such matters, the philosopher is no match for the poet.

The Brain is wider than the Sky

For, put them side by side,

The one the other will contain

With ease, and you beside.

The Brain is deeper than the sea

For, hold them, Blue to Blue,

The one the other will absorb,

As sponges, Buckets do.

The Brain is just the weight of God

For, Heft them, Pound for Pound

And they will differ, if they do,

As Syllable from Sound.

-Emily Dickinson, c. 1862

Philip Goff is an Assistant Professor of Philosophy at Durham University. His research focuses on how to integrate consciousness into our scientific worldview. Find Philip on Twitter @philip_goff

A version of this article was originally published at the Conversation and has been republished here with permission. The Conversation can be found on Twitter @ConversationUS

crispr babies

Podcast: Beepocalypse debunked; Ban CRISPR babies? Anti-science views slow COVID-19 herd immunity

Some experts are calling for a ban on embryo gene editing after a “disaster” experiment resulted in potentially dangerous and unintended genetic changes. Rapidly spreading anti-science views may be slowing our ability to achieve herd immunity for COVID-19 and needlessly extending the pandemic. Are bees responsible for 1/3 of the food we reproduce, and are they in jeopardy thanks to pesticides?

Join geneticist Kevin Folta and GLP editor Cameron English on this episode of Science Facts and Fallacies as they break down these latest news stories:

human embryo editing

A botched experiment to edit the DNA of human embryos has prompted calls for researchers to “stay the living daylights away from embryo editing.” Using donated embryos and CRISPR gene editing, scientists at the Francis Crick Institute in London deleted a gene to better understand its role in early human develop, then compared the edited embryos to their unedited counterparts. The experiment worked, sort of. Embryos with the targeted edit also displayed unexpected mutations that could have led to birth defects and even cancer later in life, had they been used to start a pregnancy.

The concerning results have intensified calls to restrict embryo gene-editing research from some experts, who say the technology is nowhere near ready to be used safely. The situation raises difficult questions bioethicists, scientists and the public have to answer. If we overregulate embryo gene-editing research, will the technology ever be ready for commercial use, for example to correct inherited disorders? And if it eventually can be used safely, would we be able to stop governments and rogue scientists from using germline editing without proper oversight?

protest ap er hpmain x
Credit: Elaine Thompson/AP

A June CNN poll found that roughly 1/3 of Americans won’t get a COVID-19 vaccine if and when it becomes available. Anthony Fauci, the director of the National Institute of Allergy and Infectious Diseases, attributed the skepticism to widespread “anti-science, anti-authority, anti-vaccine feeling” in the US, perpetuated by a well-organized vaccine skepticism movement. Critics may push back, pointing to the  constantly changing information governments and scientists have released about the novel coronavirus.  Are the skeptics justified in denying the safety and efficacy of a COVID-19 vaccine?

Bees pollinate 1/3 of the food produced today, but their populations are rapidly declining due to the use of dangerous pesticides in agriculture. The mainstream press and environmental activist groups have made such pronouncements about bees for many years now. Fortunately, claims about an imminent bee apocalypse, and thus the instability of our food supply, are not supported by the science.

Subscribe to the Science Facts and Fallacies Podcast on iTunes and Spotify.

Kevin M. Folta is a professor in the Horticultural Sciences Department at the University of Florida. Follow Professor Folta on Twitter @kevinfolta

Cameron J. English is the GLP’s senior agricultural genetics and special projects editor. BIO. Follow him on Twitter @camjenglish

natural remedies

Viewpoint: Anti-GMO groups push ‘natural’ COVID cures, deny pandemic-fighting biotech solutions

One of the primary arguments hurled at proponents of genetic engineering is that the crops, medicines and vaccines produced using GE technology are not natural and therefore inherently dangerous. Genetic engineering, they claim, is tinkering with mother nature at the risk of unleashing possibly disastrous consequences. They conjure up fears of a runaway technology that breeds deadly Frankenfoods and uncontrollable diseases we are too stubborn to see coming.

Summarizing these dramatic concerns, Ronnie Cummins, founder and director of the Organic Consumers Association, warns of the bleak future that awaits us thanks to unregulated GE technology:

Genetic engineering allows global biotechnology companies to create and legally own new forms of plants and animals. These new GE products are unpredictable and could be a threat to humans, animals, and the environment. GE foods, for example, have been found to contain toxins, some of them deadly and others cancer-causing.

In addition, GE foods could harm people with allergies by exposing them to proteins spliced into common food products. And GE crops can offer less nutrition, lead to antibiotic resistance, and often contain as many or even more toxic pesticides than non-GE crops. GE crops also pose a threat to traditional and organic methods of farming. GE technology must be banned.

Toronto Clinical Homeopathic Medicine

To prevent such horrific outcomes, many opponents of genetic engineering say, we should take a “naturalistic” approach to growing our food and treating serious diseases, a strategy that works in “harmony” with nature, not against it. This inevitably leads to a world in which we rely on organic farming to feed 7.8 billion people and treat serious illness with herbs, homeopathic remedies and even food and vitamins.

It’s a lovely idea except for one critical detail: nature is anything but benign. The world we evolved in is quite dangerous, filled with a variety of natural hazards that regularly threaten to kill humans by the thousands or millions. COVID-19 is just the latest example.

For this reason, man has had to conquer nature in order to survive. Had we not modified our environment to meet our needs, we would never have endured as a species.

Our naturally toxic world

Nature can be very dangerous to humans. Some of the most toxic substances are, in fact, natural. The list includes hemlock, cyanide, botulinum toxin, ricin, strychnine, anthrax, aflatoxin and arsenic. Measles, smallpox, cholera, typhus, dysentery, whooping cough, HIV/ AIDs, Ebola, Guinea worm, bubonic plague, dengue fever, influenza, leprosy, Lyme disease, malaria, shingles, yellow fever, malaria and syphilis are natural and in many instances are deadly to humans.

bubonic plague
Outbreak of bubonic plague. Credit: Chicago Reader

The bubonic plague in the 14th century killed between 75 million and 200 million people. The Spanish influenza pandemic of 1918-1919 was responsible for the death at least 50 million people. HIV/AIDS has killed about 32 million people since the disease was identified. According to the CDC, the seasonal flu killed 61,000 people in 2017/2018.

But that’s not all. Among the many naturally toxic plants are foxglove, hydrangea, lily of the valley, monkshood, white baneberry, oleander, narcissus and chrysanthemum. Eating the roots and other parts of the elderberry tree (excluding the flowers) can cause severe stomach problems, and consuming rhubarb leaves can cause breathing troubles, seizures, kidney problems and even coma. There are many poisonous mushrooms, too. Consuming about half a death cap mushroom, for instance, can be deadly.

Debunking natural disease cures: The COVID example

Perhaps nothing illustrates how destructive nature can be than the ongoing COVID-19 pandemic. Spread by a virus, SARS-COV-2, which is believed to have originated in bats in China, COVID-19 has killed hundreds of thousands of people globally and caused severe economic damage.

Against this tragic backdrop, natural product peddlers, who have long maintained that diseases from cancer to AIDS can be ‘cured’ using natural remedies, push equally dubious treatments for COVID-19. Most aggressive among them is Joe Mercola, an osteopath and vocal critic of GMOs and vaccines. In a recent article for the Organic Consumers Association, he argued that vitamins C and D could be used to treat COVID-19.

vitamin c

That’s a hopelessly ineffective treatment, say mainstream scientists. Dr. William Schaffner, the medical director for the National Foundation for Infectious Disease and a professor at Vanderbilt University School of Medicine said he wished Vitamin C and D were treatments for COVID-19, but “there’s no evidence to support either of those vitamins being an preventive or treatment in any dose ….”

Despite what the proponents of alternative medicine believe, there is no natural cure for COVID-19. According to the National Center for Complementary and Integrative Medicine, a division of the US Department of Health and Human Services established to evaluate alternative medical claims:

The media has reported that some people are seeking alternative remedies to prevent or to treat COVID-19. Some of these purported remedies include herbal therapies, teas, essential oils, tinctures, and silver products such as colloidal silver. There is no scientific evidence that any of these alternative remedies can prevent or cure COVID-19. In fact, some of them may not be safe to consume. It’s important to understand that although many herbal or dietary supplements (and some prescription drugs) come from natural sources, natural does not always mean that it’s a safer or better option for your health.

By labeling genetic engineering “unnatural,” critics are attempting to weaponize doubt and raise questions about the safety of the technology. Why take the risk if it might lead to unintended consequences?” they ask. Because the real danger lies in not using a technology that has already proved useful against other infectious diseases, and holds great potential against COVID-19.

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GE vaccines have be used successfully to prevent infection by Hepatitis B, Rotavirus, Ebola and the Human Papillomavirus virus (HPV). Likewise, genetic engineering is the key to developing a vaccine to immunize people against COVID-19 and thus enable a return to normal life. As I noted in a recent story for the GLP:

The COVID-19 virus highlights just how vulnerable humankind is to the natural world, which periodically produces pandemics such as the Spanish flu, the Bubonic plague, Polio and Asian flu that have the ability to kill many millions of people. Despite the inevitable challenges and trade-offs we face, the new tools of genetic engineering offer us the best chance of controlling, and possibly eliminating, the outbreak of future pandemics.

Genetic engineering is not to be feared because it is “unnatural.” Its supposed dangers, whether applied to food or medicine, have not been borne out. The technology has not created Frankenfoods or Frankenanimals, and it has yet to unleash some unanticipated disease on the world. As always, nature remains a threat and technology our best chance at neutralizing it.

Steven E. Cerier is a freelance international economist and a frequent contributor to the Genetic Literacy Project  

three stooges

The Three Stooges illustrate why coronavirus-fighting ‘antibody cocktails’ could help contain the virus well before a vaccine

“You imbecile!” bellowed Moe Howard as he stuck a finger up the nose of Curly. Moe the bully would often flick his hand across an unsuspecting face or deliver a two-pronged eye poke to distract from a simultaneous, more serious blow, elsewhere.

Moe, Larry, and Shemp/Curly/Joe were the various incarnations of The Three Stooges, the famed comedy team, with roots in vaudeville, who made films and TV shows from 1922 until 1970. Many of us growing up in the sixties loved them, while many of our parents didn’t. The 2012 film didn’t do the original three idiots justice.

An image of Moe poking Curly popped into my head while reading two new papers in Science that report teaming antibodies to tackle SARS-CoV-2, the virus behind COVID-19.

The papers describe the basis of two clinical trials that biotech company Regeneron is conducting to assess a pair of antibodies that work together, binding the viral spike protein where it contacts the human receptor (ACE2) and gains entry into our cells, but at different sites within the “receptor-binding domain.” One antibody is a distractor of sorts, like Moe’s finger-up-the-nose.

The key to the technology is in the coupling. “Our work inventing novel antibodies has shown that individual antibodies, no matter how good, are likely not enough against the devastating virus that causes COVID-19 and the ways it seeks to ‘escape’ being neutralized,” said George D. Yancopoulos, MD, PhD, Co-Founder, President and Chief Scientific Officer at Regeneron.

An antibody cocktail – pitched as “antibody medicine” – provides short-term, passive immunity, as opposed to the lasting active immunity of a vaccine, in which the body learns to manufacture its own antibodies. The Chinese proverb “Give a man a fish and you feed him for a day. Teach a man to fish and you feed him for a lifetime” makes the distinction: an antibody cocktail is a fish, a vaccine the ability to fish. Both are needed desperately right now. Antibody protection would last weeks or months.

Viral Resistance is a Natural Consequence of Evolution

The immune system of a host organism, like us, normally produces many different antibodies against a particular infecting pathogen – a “polyclonal” antibody response. Each type of antibody fits into the localized topography of the pathogen’s surface, like keys fitting into different locks.

Not all of the antibodies that an infection elicits destroy, or neutralize, the pathogen. Some antibodies do nothing, while others may actually enhance the infection. But identifying and scaling up neutralizing antibodies isn’t enough, because evolution can get in the way – microevolution, the natural changes in DNA or RNA sequences that happen as these genetic materials replicate. That’s mutation. Then natural selection acts on the new genetic variants that arise by mutation – a nanoscale survival of the fittest.

If a mutation enables a virus to infect and take over a human cell by sneaking into ACE2 by some other route, like a side entrance to a theater, it will soon take over – it has a selective advantage. Teaming antibodies into “cocktails” bypasses evolution by blocking “virus escape mutants” that spread the infection – like Moe distracting Curly or Larry with a hand swipe or eye poke and then walloping him with a clanging frying pan.

Power in Pairs

In one report in Science, Regeneron researchers describe how the virus mutates around four types of neutralizing antibodies – when the antibodies are given individually. Pairs of antibodies don’t stop the escape mutants if the targets overlap in space, partially-shared nooks and crannies. But when pairs of antibodies dock at physically separate parts of ACE2, escape mutants aren’t seen.

Regeneron has already gotten promising results in a clinical trial of a triple-antibody cocktail (REGN-EB3) to treat Ebola virus disease. And viral escape mutants proved a challenge in developing anti-retroviral drugs against HIV.

The second Science paper describes the sources of the antibodies: humanized mice (which have the genes encoding human immune system proteins) and B cells (white blood cells that produce antibodies) from three patients who’d recovered from COVID-19.

The researchers isolated thousands of human antibodies offering varying abilities to bind the receptor on human cells and to neutralize the virus. Then, like a dating app, they looked for good matches.

“We selected pairs of highly-potent individual antibodies that simultaneously bind the receptor-binding domain of the spike protein, providing ideal partners for a therapeutic antibody cocktail that aims to decrease the potential for virus escape mutants that might arise in response to selective pressure from a single antibody treatment,” they write.

Here’s an infographic that shows how the “antibody medicines” work. I’d at first thought that name a bit too dumbed down, but it’s necessary to distinguish the approach from antibody testing as well as from the mixed bag of convalescent plasma.

Regeneron is now conducting two clinical trials of the antibody pair, “REGN10933+REGN10987 combination therapy,” aka the “REGN-COV2 cocktail,” administered in a single intravenous infusion. Both trials are placebo-controlled, accelerate the three clinical trial phases, and assess clinical improvement, adverse effects, allergic reaction, and change in viral shedding in the nose and throat, as well as in saliva.

One trial is enrolling 1,054 ambulatory patients with COVID-19 and expects to have results by the end of November 21, and the other began enrolling 1,860 hospitalized patients this June and expects completion by March 2021. These sicker patients are being considered by the severity of their illness: those on low-flow oxygen, high oxygen, and mechanical ventilation, which should help pinpoint when the antibody cocktail is most helpful.

More Than a Treatment

An antibody cocktail may do much more than help people who are already sick– it also may be used to prevent infection, especially in high-risk environments like prisons and nursing homes when initial cases appear. The strategy may also help people who may not respond well to a vaccine, such as the immunocompromised and the elderly.

Meanwhile, antibody medicines can also provide a bridge until vaccines are available. And researchers can use bioinformatics to induce antibodies against other coronaviruses, even ones predicted to be possible to exist based on genome diversity information, which might enable the creation of a stockpile from which to draw when novel viruses emerge in the future. Precision preparedness.

Summed up Dr. Yancopoulos, “REGN-COV2 could have a major impact on public health by slowing spread of the virus and providing a needed treatment for those already sick – and could be available much sooner than a vaccine. Ultimately, the world needs multiple solutions for COVID-19, and the innovative biopharma industry is collectively working hard to help as many people as possible with a variety of complementary approaches.”

I mean no disrespect by comparing the dual antibody approach to The Three Stooges. I think both are brilliant!

Ricki Lewis is a senior contributing columnist for the GLP. A science writer with a PhD in genetics, Lewis is the author of several several fiction and nonfiction books and textbooks, and thousands of articles in scientific, medical and consumer publications. She can be found on Twitter @rickilewis

A version of this article was originally published at PLOS Blogs and has been republished here with permission. PLOS Blogs can be found on Twitter @PLOSBlogs

eye

Podcast: Let the light shine—Tackling eye disease with gene therapy

In this episode, supported by the UK Medical Research Council, geneticist Kat Arney and reporter Georgia Mills explore how researchers are letting the light shine in, literally, by uncovering the underlying genetic faults that cause eye diseases and developing game-changing  gene therapies to save sight.

Mills speaks with sight loss charity campaigner and fundraiser Ken Reid about his experiences of living with the genetic eye condition Retinitis Pigmentosa (RP)—a hereditary disease that causes the gradual degeneration of light-sensitive cells in the back of the eye. He first realized that something was wrong with his sight when he was a party-going teenager in the 1970s.

Ken Reid
Sight loss charity campaigner and fundraiser Ken Reid

I always had very poor eyesight and couldn’t understand how people could do things in the dark,” he says. “Most people probably don’t remember what discos in the ’70s were like, but they were just dark. You had this lovely interaction where it was very noisy, it was very dark and there were some flashing lights. I could see nothing and trying to find somebody to dance with was a real torment. I didn’t know how people managed it!

At the MRC Human Genetics Unit in Edinburgh, Chloe Stanton is searching for the gene faults that underpin RP and other hereditary eye diseases, with more than 100 RP genes identified so far. To find out more about what all these genes actually do, her colleague Roly Megaw is growing tiny ‘mini-eyes’ in the lab from reprogrammed stem cells originally derived from skin samples – including one from Reid himself. 

Finally, Robin Ali at King’s College London is running clinical trials of gene therapy for inherited eye disorders. There’s been impressive progress in recent years, and Ali is hopeful that treatments will come through for people like Reid.

In the 25 years I’ve been working on developing gene therapy for retinal degeneration, we’ve seen huge advances. I think we couldn’t imagine how far we could come. I remember when I first started, we were working out ways to deliver genes to the retina and we were pleased if we saw just one or two cells that had taken up a virus and maybe expressing a gene for a couple of weeks. We are now able to rescue dozens of different animal models highly effectively. It’s just a matter of time until this technology can be applied as effectively to humans.

Full transcript, links and references available online at GeneticsUnzipped.com

Genetics Unzipped is the podcast from the UK Genetics Society, presented by award-winning science communicator and biologist Kat Arney and produced by First Create the Media.  Follow Kat on Twitter @Kat_Arney, Genetics Unzipped @geneticsunzip, and the Genetics Society at @GenSocUK

Listen to Genetics Unzipped on Apple Podcasts (iTunes) Google Play, Spotify, or wherever you get your podcasts

im

Podcast: Bayer’s $10.9 billion glyphosate settlement a mistake? Vaccines from mosquito spit; CRISPR cures sickle cell disease?

Chemical giant Bayer just settled roughly 95,000 lawsuits alleging its Roundup weedkiller causes cancer. Has the company given its anti-GMO critics a gift by giving up the legal battle? A protein found in mosquito saliva could yield vaccines for dozens of deadly diseases, and CRISPR gene editing has effectively cured two inherited disorders that require lifelong treatment.

Join geneticist Kevin Folta and GLP editor Cameron English on this episode of Science Facts and Fallacies as they break down these latest news stories:

Bayer’s effort to defend its Roundup herbicide in court has ended in a $10.9 billion settlement. The company says settling was the financially reasonable decision and “will return the discussion about the safety and utility of glyphosate-based herbicides …. to the scientific and regulatory arena and to the full body of science.”

But the multi-billion-dollar agreement doesn’t necessarily shield Bayer from “a flood” of new litigation—some 30,000 plaintiffs who weren’t  party to the settlement. The law firms that have beaten Bayer in court three times, for example, appear poised to challenge the settlement for depriving cancer patients “of their constitutional right to a jury trial.” So the question remains: is the legal battle over glyphosate really at its end?

Vaccines are typically designed to prevent infection by specific pathogens, but this strategy isn’t nearly as effective when many diseases are spread by the same vector. Mosquitoes infect millions of people every year with malaria, dengue, chikungunya, Zika, yellow fever, West Nile and Mayaro viruses. By developing a vector-based vaccine using a protein found in mosquito saliva, researchers are working to stop the spread of any pathogen the insect may harbor, including those we’ve yet to identify.

Beta thalassemia and sickle cell disease are inherited, painful disorders without cures.  They’re caused by mutations in the genes that control  haemoglobin, the protein that carries oxygen in red blood cells, and usually treated with regular blood transfusions. But that may no longer be the case. With the help of CRISPR, scientists have edited a gene that controls the production of hemoglobin in bone marrow stem cells. These edited, healthy cells replace the defective ones the patient naturally produces.

Five people have been treated with this novel therapy so far and no longer require blood transfusions. The researchers say this is a “functional cure” for both disorders, though additional clinical research is ongoing to confirm its safety and efficacy.

Subscribe to the Science Facts and Fallacies Podcast on iTunes and Spotify.

Kevin M. Folta is a professor in the Horticultural Sciences Department at the University of Florida. Follow Professor Folta on Twitter @kevinfolta

Cameron J. English is the GLP’s senior agricultural genetics and special projects editor. BIO. Follow him on Twitter @camjenglish

parkinson

Searching for Parkinson’s game changer: No cure in sight but stem cells, other advances hold promise

A flurry of recent advances offer the promise of new avenues for treating patients with Parkinson’s disease, one of our most common and debilitating diseases. It is estimated that in excess of 10 million people around the world are currently living with Parkinson’s, with approximately 60,000 new diagnoses every year in the US alone. The healthcare costs reach tens of billions of dollars and, as of yet, no ‘cure’ has been approved for the disease. Patients are often prescribed drugs that can help control the symptoms of the disease but in reality, the majority of patients still struggle with the disease every day with medication only providing temporary relief.

Parkinson’s is a good demonstration of how widely neurodegeneration can vary depending upon the region of the brain that is affected. Diseases like Alzheimer’s affect memory regions of the brain and so the first symptoms often relate to cognitive decline. Parkinson’s, however, starts with very physical symptoms such as involuntary shaking, slow movement and stiff, inflexible muscles. In theory the core biological disease mechanism is the same as in Alzheimer’s; the loss of nerve cells. However, in Parkinson’s this happens in a region of the brain called the substantia nigra which plays a critical role in movement.

As the condition progresses, symptoms often worsen and can make carrying out daily tasks increasingly difficult. Current treatments can improve the quality of life and many people with the disease have normal life expectancies but we are still yet to see an approved therapy that leaves patients symptom free. Recent advances have, however, bolstered the research effort to find that ultimate ‘game-changing’ therapy.

canwerepairtPromising new drugs

The current strategy for patients with Parkinson’s is to treat symptoms with regular doses of drugs and provide patients with access to physiotherapy sessions to help ease muscle stiffness. Due to the current limitations with available drugs, research institutes across the globe seek to design drugs that better treat the symptoms of Parkinson’s.

The Michael J. Fox foundation is one such organization. The foundation, formed by actor and Parkinson’s patient Michael J. Fox, has invested more than $650 million into research and has recently been awarded with FDA approval of a second new therapy for the disease. In this recent breakthrough, a drug developed by Sunovion, called Kynmobi, was given the go ahead for clinical use with the research funded directly by the foundation.

The drug comes in the form of a film that can be placed under the tongue when patients start to experience a worsening of symptoms. The active ingredient, apomorphine, crosses the blood-brain-barrier and can mimic the effects of dopamine in the brain. This is critical because a loss of dopamine in Parkinson’s patients leads to the death of nerve cells and progression of the disease. The fact that Kynmobi can help counter this cell loss this is promising. Even more exciting is the fact it penetrates the blood-brain-barrier — a task which often prevents drugs from getting into the brain to help patients.

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The latter point of improving delivery to the brain is also the focus of another treatment under clinical trials at the moment. A study devised by collaboration between researchers in the UK and Canada involves the use of implanted ‘ports’ that allow the direct delivery of drugs to the brain.

The researchers conducted a series of trials on Parkinson’s patients with the aim of treating the disease with glial cell line-derived neurotrophic factor (GDNF), a protein that aids in the health of brain cells. Results from the study were overwhelmingly positive with the researchers observing the restoration of brain cells and a lot of excitement has been generated from the data. The lead coordinator of the study, Dr Alan Whone had the following to say about the results:

The spatial and relative magnitude of the improvement in the brain scans is beyond anything seen previously in trials of surgically delivered growth-factor treatments for Parkinson’s. This represents some of the most compelling evidence yet that we may have a means to possibly reawaken and restore the dopamine brain cells that are gradually destroyed in Parkinson’s.

At the other end of the spectrum, another new molecule is showing potential. The new drug labelled BT13 is still in early development at the University of Helsinki, Finland but early studies in mice have shown promise. What is more exciting is the fact studies like this are common and provide the next generation of drugs that we could see go through clinical trials and onward to improving the lives of patients. Drugs are, however, not the only answer to this healthcare question.

screenshot key to effective parkinson’s treatment may lie in stem cells

What about stem cells?  

Thanks to the advent of stem cells, researchers can now look beyond drugs at other avenues of therapies. Researchers in the Molecular Neurobiology Laboratory at McLean Hospital in Massachusetts are doing that with the development of a therapy based on using a patient’s own cells. The approach involves the use of induced pluripotent stem cells where cells can be taken from a patient’s skin or blood. The extracted cells can then be reprogrammed into a state of ‘stem-like pluripotency’, meaning they can be used to generate any cell type within the body. In this case the cells are reprogrammed into dopamine-producing neurons, the main cell types lost in Parkinson’s. These cells can then be transplanted back into the patient and help to regenerate what has been lost inside the patient’s brain. Dr. Kwang-Soo Kim, a leading investigator on this study had the following to say:

Because the cells come from the patient, they are readily available and can be reprogrammed in such a way that they are not rejected on implantation. This represents a milestone in ‘personalized medicine’ for Parkinson’s.

The hope is that one day, any one of these therapies could provide that game-changing breakthrough to transform the way we treat Parkinson’s — from managing it to curing it. There is a real possibility that one of the strategies outlined here could lead us to the advancement the field continues to search for. Equally promising is the fact that, should these strategies fail, we have a wealth of other options that are being explored every day.

Sam Moxon has a PhD in regenerative medicine and is currently involved in dementia research. He is a freelance writer with an interest in the development of new technologies to diagnose and treat degenerative diseases. Follow him on Twitter @DrSamMoxon

pesticides fake news

Viewpoint: Irrational pesticide fears discourage produce consumption and increase cancer risk

Moms and dads, registered dietitian nutritionists, and doctors all agree that we should eat more fruits and vegetables. The U.S. Department of Agriculture and the Centers for Disease Control and Prevention spend a lot of time, energy and money trying to convince us to increase our consumption of these healthy foods. Despite their best efforts, however, only about 1 in 10 Americans gets the daily recommended servings of fruits and vegetables.

 
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Fruits and Vegetables Can Even Prevent Cancer

The public health consequences of our poor eating habits are significant. Teresa Thorne, Executive Director of the Alliance for Food and Farming, stated in a Sound Bites podcast, “if only half of all Americans increased their fruit and vegetable intake by ONE serving a day, an estimated 20,000 cancers could be prevented every year. Both organic and conventional production methods yield safe and healthy foods that experts everywhere agree we should all eat more of each day.”

But Good News Doesn’t Get Media Airtime

The scientific consensus in favor of eating more fruits and vegetables doesn’t get much airtime on national or local news stations or on social media. Consumers are far more likely to be confronted with news stories about the dangers of pesticide residues on fruits and vegetables. Every year the Environmental Working Group (EWG) issues its infamous “Dirty Dozen” list of the fruits and vegetables with the greatest number of pesticide residues detected.

Pesticide Residue Stories Scare Buyers Away from Fruits And Vegetables

According to the EWG, 70 percent of the produce sold in the U.S. has pesticide residues, including organically produced fruits and vegetables. In 2019, strawberries topped the EWG list for the fourth year in a row. The report states that strawberries are the fresh produce most likely to remain contaminated with pesticide residues, even after being washed, with the dirtiest one containing 23 separate pesticides residues.

A number like that is high enough to frighten anybody, and it’s no wonder that such stories make consumers leery of buying fruits and vegetables. Nobody wants to expose themselves or especially their children to toxic chemicals, and pesticides would certainly seem to fall into this category. Many pesticides can cause cancer and are highly regulated by the Environmental Protection Agency. It seems to make sense to reduce exposure as much as possible. And tragically, this can result in consumers buying less of the very foods that they most need to become healthier.

But Our Fruits And Vegetables Are Safe To Eat

We need to bear in mind that just because something can cause cancer does not mean that it does cause cancer. As the Swiss physician and philosopher Paracelsus so aptly put it 500 years ago, “The dose makes the poison.” Even water is toxic if we drink too much. Several people actually die each year from its toxic effects—but does that make it a good idea to avoid water? Certainly not! Paracelsus was right: the amount of a material involved makes a tremendous difference in whether it is harmful—or highly beneficial—to human life.

 

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We are much safer than the EWG Dirty Dozen food pesticide residue list might lead us to believe at first glance. A 2015 analysis of dietary exposure to pesticides in the International Journal of Food Contamination concluded that pesticides in the diet continue to be at levels far below those of health concern. The paper’s author, Dr. Carl Winter, Department of Food Science and Technology, University of California, Davis, stated: “Consumers should be encouraged to eat fruits, vegetables and grains and should not fear the low levels of pesticide residues found in such foods.”

Notwithstanding good research proving that our food is safe, reports like that from EWG and marketing campaigns by some food producers continue to influence public perceptions about the safety of conventional food compared to food labeled natural or organic. Hundreds of articles are written and news stories presented each year on the purported dangers of pesticides in our food. Consumers are paying attention. But they are afraid rather than informed.

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Pesticide Fear Hurts Low-Income Shoppers the Most

Yancui Huang, at the Center for Nutrition Research at the Illinois Institute of Technology, wondered how these types of communications might be impacting fruit and vegetable consumption in populations that cannot purchase organic produce, because of lack of accessibility, budget constraints, or other barriers. Huang and his co-authors conducted a study to see if campaigns like the Dirty Dozen could be discouraging low-income shoppers from purchasing fruits and vegetables.

What he found was that low-income individuals were indeed less likely to purchase any fruits and vegetables after receiving information about the 12 fresh fruits and vegetables with the highest pesticide levels. This is particularly concerning, because, as Huang wrote, “Low-income individuals constitute a financially vulnerable group of people with challenges to meet many daily household needs, including consuming a healthy diet.” Stories about the Dirty Dozen and pesticides can be confusing and demotivate shoppers to purchase safe and nutritious fruits and vegetables.

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These findings are consistent with the challenges we discuss in the article on decision fatigue (“How tired brains make bad food choices.”) The simple message that “we should eat more fruits and vegetables” becomes more complicated with the news that some produce contains pesticides, which may, or may not, be a risk to health. Rather than do further research to discover that the pesticide residues on food are perfectly safe, wealthy shoppers simply choose organic produce to reduce their exposure.

However, most shoppers are price-sensitive and can’t easily opt for higher priced products. When confronted with the need to balance the benefits and risks of conventional versus organic produce for their families, it is often easier to choose neither, and not purchase fruits and vegetables at all. This is a terrible irony, because it means that these consumers are being harmed by information that is supposedly meant to help them.

Pesticide Fear Is Ill-Founded and Harmful to Public Health

There is nothing inherently wrong with sharing information with the public about the presence of pesticide residues in food. Consumers are constantly asking for greater transparency about the food they eat. However, it is also critical to provide consumers with context for such information. We have the safest food supply in the history of the world. Consumers should not be afraid of the food they eat. Instead they should feel confident that whatever fruits and vegetables they purchase will be safe and nutritious and contribute to the well-being of their family.

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Jack Bobo is a food futurist. Jack has delivered more than 400 presentations in 50 countries around the world. He was named by Scientific American one of the 100 most influential people in biotechnology. Jack can be found on Twitter @Jack_A_Bobo

This article was originally published at Futurity and has been republished here with permission. Follow Futurity on Twitter @futurityfood

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