Tag Archives: Bacteria

What Does It Mean To Be Supernatural?

Image from clipartpanda.com

Halloween is coming up, and popular culture is being filled its annual dose of references to the supernatural (including the recent season premier of the show Supernatural, which is probably not a coincidence). Ghosts, monsters, black magic, vampires, witches, and others all fall under this umbrella of “the supernatural.”

But what does it mean to be supernatural?

My dictionary defines “supernatural” as “(of a manifestation or event) attributed to some force beyond scientific understanding or the laws of nature.”

Being beyond scientific understanding is actually very mundane. Most of the way the brain works is beyond our current scientific understanding, but no serious researcher is throwing up his or her arms and declaring it supernatural. The relationship between mass and energy was beyond scientific understanding until Albert Einstein figured it out. The origin of mitochondria and chloroplasts were beyond scientific understanding until Lynn Margulis figured it out. Every issue of every scientific journal is filled with things that were beyond the understanding of science just a year or so prior. This is not what people mean when they say that something is supernatural. They mean the second thing — beyond the laws of nature. The word supernatural literally means “above nature,” or, more figuratively, outside or separate from nature.

But what is nature and what are its laws?

Consulting my dictionary once again, “nature” is defined as “the phenomena of the physical world collectively, including plants, animals, the landscape, and other features and products of the earth, as opposed to humans or human creations.” And once again, my dictionary fails to provide a completely cogent or useful definition. If humans and our creations are not natural, does that mean that the computer I’m writing on is supernatural? Again, no one would reasonably make this claim. The first part of this definition, “the phenomena of the physical world collectively,” is actually pretty good as it is. Nature, or the physical world, is made up of two things: matter and energy, which Einstein showed us are the same thing. Nature is everything that exists. It is all of the animals, plants, fungi, bacteria and all of the rest of life. It is all of the rocks and minerals and water and air. Even humans, which are animals, are part of nature. Everything beyond our planet is part of the natural world, as well. All of the undiscovered types and forms of matter and energy are part of nature. Every answer to an empirical question is part of nature, and it is the job of scientists to discover nature as it exists.

Are ghosts real? This is an empirical question because the answer is not subject to ideology or personal preference. It’s not possible for ghosts to be real for me but not real for someone else, any more than  the statement “the earth’s atmosphere is 78% nitrogen” can be real for me but not real for someone else. Correct answers to empirical questions are correct whether you like it or not. Likewise, either ghosts are real or they are not. If they are real, they are part of nature, and are therefore natural phenomenon. It may come as a surprise to people that, if ghosts are real, it will be scientists who discover them. This is true of everything else that is commonly labeled as “supernatural.” If everything that exists is part of nature, then what does that mean? If something is truly supernatural, it doesn’t exist.

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Drug-Resistant Diseases

Drug-resistant pathogens are in the news more and more these days. The World Health Organization recently released a report about the declining effectiveness of antibiotics. Many believe that the age of antibiotics is coming to an end. This is very troubling, given that antibiotics are unquestionably one of the greatest advancements in the fight against disease.

Infectious diseases are caused by a variety of organisms: viruses (HIV, chicken pox, dengue fever, ebola, influenza, rotavirus), bacteria (tuberculosis, meningitis, gonorrhea, tetanus, whooping cough), worms (schistosomiasis, ascariasis, whipworm, pinworm, elephantiasis, river blindness), protists (malaria, sleeping sickness, giardia, leishmaniasis, chagas disease, cryptosporidium), and fungi (athlete’s foot, thrush, valley fever, aspergillosis).

Organisms that cause disease (such as those listed above) are not fundamentally different from the organisms that do not cause disease. Parasites are subject to evolution by natural selection just like anything else.

A toxin may broadly be defined as a chemical that negatively affects the physiology of an organism when the two come in contact. Drugs that we use to fight parasitic infections within a person’s body are toxins. Ideally, the toxicity of the drug is much greater to the parasite than it is to the host.

There are many naturally occurring toxins in the environment. Ethanol, along with many other alcohols, is a very powerful toxin to most living things. It is because of this toxicity that we use various alcohols to sterilize various surfaces (including our hands, in the case of hand sanitizers) and sometimes instruments.

Humans have a fairly high resistance to ethanol, but not to other alcohols. Most people can drink the equivalent of a couple of ounces of pure ethanol and be fine. The same quantity of methanol or propanol (which are chemically very similar to ethanol) would lead to pretty severe physiological consequences, including death. The ability of humans to metabolize ethanol is attributed to our evolutionary history of eating fruit. Fruit contains a lot of sugar, which is a good source of energy. Ancient people who ate fruit whenever it was available had more energy available in their bodies for building muscles, repairing damage, reproduction, hunting, and whatever else they needed to do. If fruit sits on the tree (or the ground) too long, yeast lands on it and starts eating the sugar for itself. When yeast eats sugar, ethanol is produced as a waste product. If a person eats that fruit, they will also be eating some ethanol. A person who is able to withstand a lot of ethanol is able to eat a lot of fruit and gain the energetic benefits of doing so. Over time, the average human became more and more able to cope with consuming toxic ethanol. Modern humans can safely consume quantities of ethanol that would be fatal to many other organisms.

Methanol, ethanol and propanol are all very similar molecules. Ethanol is the only one we can consume.

Methanol, ethanol and propanol are all very similar molecules. Ethanol is the only one we can consume.

So what does any of this have to do with diseases? Just as humans evolved to cope with the toxicity of ethanol, pathogens can evolve to deal with the toxicity of the drugs we use to fight them.

The most toxic substance to an organism is going to be one that is “evolutionarily novel” — that is, the substance is one that the species has not encountered over its evolutionary history. Why? Because a species that frequently encounters a particular toxin will evolve physiological mechanisms to resist the negative effects of the toxin. For example, if you want to poison a human with an alcohol, you’d use methanol, not ethanol, because ethanol is more evolutionarily familiar to us.

When we use the same drug to fight the same pathogen over many years, the drug becomes evolutionarily familiar to the pathogen, and the pathogen can evolve to cope with it. For decades, physicians used the same antibiotics to treat bacterial infections, including those caused by Staphylococcus aureus. After they used the antibiotic methicillin for a long enough time, the methicillin became a normal part of the bacteria’s environment and the bacteria evolved to cope with it, eventually becoming Methicillin-Resistant Staphylococcus aureus, or MRSA.

The rate of evolution for any given species is inversely-related to the generation time of the species — species with long generation times evolve very slowly, and species with short generation times evolve very quickly.

Organisms with a shorter generation time evolve faster

Organisms with a shorter generation time evolve faster

This is because evolution is a process that happens in between generations. If new generations occur more closely together, more evolution can happen in a shorter time. The human generation is about 20-30 years. A generation for bacteria can be as short as 20 minutes — that’s 72 generations per day, over 26,000 per year, and over a half million within the span of a single human generation. For perspective, a half million human generations is about 10 million years. 10 million years ago, gorillas, chimpanzees and humans had not yet evolved into separate species. What does this mean for antibiotic resistance? It means that bacteria can evolve very quickly to be immune to a given antibiotic.

This is obviously bad news for us. Not all pathogens evolve as quickly as bacteria, but they are all pretty fast. Recent history is full of examples of drugs that worked well until the disease evolved immunity towards it.

Malaria, tuberculosis, HIV, Staphylococcus aureus, Escherichia coli, gonorrhea and many others all have strains that have evolved immunity or resistance to the drugs we use to treat or cure them. We are going to need a new way of fighting these diseases.

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Why We Eat Spicy Food

Imagine you are some kind of small mammal, like a rodent. You are minding your own business when you notice a snake sneaking up on you. What do you do? Run? Hide? Fight back? These are all are fine choices. Now imagine that you are some kind of plant. Lacking any ability to detect the presence of animals trying to eat you, you are completely unaware of the cow sneaking up on you. And even if you were aware, what could you do about it? With no ability to locomote, you cannot run, hide or fight back. Now, some plants can hide by being inconspicuous or by blending into their surroundings, but this is not the norm. Some plants can fight back with thorns or spines or hairs, but not all plants do this, either. The third option is to produce chemicals that lower the digestibility of the plant, make the plant taste bad, or are harmful to animals. These three strategies (hiding, fighting and chemical warfare) are all very cool, but it is the third option that I will be talking about today.

Those plants couldn’t run away from the water buffalo. Image from wikimedia.org

Plants actually produce chemical defenses for two reasons: The first is to prevent being eaten by herbivores, and the second is to prevent infection. Plants do not have an immune system in the same way that animals do, so these chemicals are very important in repelling pathogens.
But what does all of this have to do with us? Plants suffer from the same type of parasites that we do — viruses, bacteria, worms, fungi, and protozoa. Before the advent of the pharmaceutical industry, people had to rely on plants for medicine. The compounds that plants produce to keep themselves safe from infection can be harnessed by humans for the same purposes.
Which brings me to the point of this: spices.
Cultures across the world vary in how much spice they use in their food, particularly with meat. Consider the types of cuisine that are the spiciest — e.g. Mexican, Thai and Indian. It’s no coincidence that these countries are in the tropics. Research has shown that spices are used most in areas of the world where there is the highest burden of infectious disease: both in numbers and intensity.

The birds-eye pepper is high in capsaicin, which has antimicrobial properties. Image from wikimedia.org

The most common spices in the world — such as garlic, thyme and cloves — have been shown to be powerful antimicrobial agents. Adding these to food can prevent food spoilage and food-borne illnesses. (Please don’t rely on this as your only method of keeping your food safe.) Infectious disease is a big problem for people in the world today, and has been a big problem throughout human evolution. Food-born illnesses that are a problem for people today include typhoid fever, hepatitis B, Salmonella, Escherichia coli, Listeria, cholera, and Norovirus. Cooking with spices will not eliminate these diseases, but they can reduce the likelihood that you will catch them. Spices don’t just taste good — they can save your life.

Here’s simple experiment you can do at home to test the antimicrobial effects of spices:

I’ve made a simple bread recipe and separated the dough into two equal portions. Store-bought dough will usually contain preservatives (which prevent the growth of bacteria and mold), so you’ll have to make your own if you want this to work.

I’ve kneaded in 1.5 teaspoons of red chile powder to one half of the dough and the same amount of flour to the other, just so both conditions are as similar as I can make them. I used chile powder because I like to cook with it, but you could do this with any spice or herb you wanted:

The dough has been made, and the spice measured out.


The spice and extra flour has been kneaded into the dough.

I pressed them into flat, round loaves, baked them and sliced each one in half:


The bread has been baked and is ready to grow mold.

I put all four pieces into a big ziplock bag with a a couple of pieces of moldy cornbread. Mold would grow fine on its own, but seeding it with some already-mature mold helps things move along more quickly. I put a few drops of water in the bag, too, so it stays moist:


The bread will stay in the bag for the remainder of the experiment. The fresh bread has been seeded with a piece of moldy old cornbread.

After about a week, the plain bread is covered in mold. The spiced bread has a little bit of mold on it, but is mostly mold-free:

At the end of the experiment, the spiced bread is almost entirely free of mold.

At the end of the experiment, the spiced bread is almost entirely free of mold.

The plain bread is covered in mold.

At the end of the experiment, the plain bread is covered in mold.

The chile powder didn’t completely prevent mold growth, but there is certainly a lot less mold on the spiced bread than on the plain bread. Depending on where you are in the world, even a little bit less spoilage could mean the difference between life and death. Try this out on your own and let me know how it worked out.


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