Tag Archives: Biology

The Man Behind the Curtain Turns 1

The Man Behind the Curtain turns 1 today! In the past year, this blog has had over 4800 views from people in 104 nations. This surpassed what expectations I had, and I am looking forward to another good year.

The most popular posts this year were:

Dinosaurs are not Extinct

Hot or Not

Do genes skip generations?

Testing a Claim: Ceramic Knives

The least popular posts were:

Drug-Resistant Diseases

Skipping Generations Part 2

You’re Doing it Wrong, Part 2: Post Hoc Ergo Propter Hoc

A UFO (which was my first post)

And these are my personal favorite posts:

For All Mankind

Dinosaurs are not Extinct

10% of our Brains

The Evolution of Flight

Thanks for reading! I hope 2015 will be even better. (Tomorrow I will go through and fix all of the broken images. Sorry about that.)

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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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Mutations in Movies

With the remake of Teenage Mutant Ninja Turtles coming up, I thought I’d talk about the way mutations are depicted in movies vs how they are in real life. Again, this is not to diminish anyone’s appreciation for these movies, but to understand where the science stops and the fiction begins.
Many movies, especially superhero movies, describe some sort of mutagenic event as the cause for the hero’s superhuman abilities. In the original Teenage Mutant Ninja Turtles, the four turtles and one rat were given human size and intelligence through exposure to “radioactive ooze.” It also seems to have removed two of their fingers — turtles, like humans, have five fingers rather than the three they are depicted with in the movies.

Real turtles have five fingers and five toes. Teenage mutant ninja turtles only have three. Image from collecltions.countway.harvard.edu

In the X-Men franchise, “mutants” are caused by inheriting mutant alleles. In The Incredible Hulk, one of Dr. Bruce Banner’s experiments goes wrong and he is accidentally exposed to gamma radiation. In The Fantastic Four, the astronauts are exposed to cosmic rays. In Daredevil, Matt Murdock is exposed to radioactive waste as a child.

The Incredible Hulk gained his abilities through unspecified mutations. Image from screenrant.com

In Spiderman, Peter Parker is bitten by an irradiated spider, not exposed to radiation himself. Presumably this resulted in the transfer of some of the spider’s genes into Peter Parker’s genome, making this an event of “horizontal gene transfer,” rather than a typical mutation. I plan to discuss this at some point in the future.

Now, everyone knows that exposure to radiation or toxic waste will not give anyone super powers. But what do mutations look like in real life? In short, a mutation is any time there is a change to the sequence of the DNA of an individual or cell.

An organism’s genome can be compared to a book. The book is broken down into chapters, called chromosomes, and made up of letters called “nucleotides” (A, G, T, and C). Genes can be compared to sentences, and are made up of three-letter words called “codons.” Codons are always three letters.

In English, the three-letter word “cat” refers to a group of predatory mammals with long claws. In a sentence, “I keep two cats as pets.” In the language of DNA, the three-letter word “CAT” means the amino acid “valine.” A sentence of three letter words makes up the sequence of amino acids that build a protein. The function of a protein is created by the exact sequence of amino acids that make it up, just as the meaning of a sentence in English is created by the exact sequence of words that make it up.
The DNA sentence “TACCATAAACGGGTGACT” means “Methionine, valine, phenylalanine, histidine, alanine, [stop].” The codon “ACT” is one of three “stop codons,” which act like periods in English. It means the sequence of amino acids has come to an end. Proteins are usually thousands of amino acids long.
In most written languages, minor changes in the words or punctuation can drastically change the meaning of the sentence. A change of one letter can change “I keep two cats as pets” to “I keep two bats as pets.”
Similarly, changing one letter of a genetic code can change the meaning of a sentence. Changing “TTC” to “TTA” will change phenylalanine into leucine. These two amino acids have different properties, and will result in slightly different proteins being made. This protein might work basically the same, despite the minor difference. It also might work very poorly. There is also a small chance that the different protein will work better. The first two options are overwhelmingly the most likely of the three possibilities.
A change in punctuation can change “let’s eat, grandma” to “let’s eat grandma.” The same is true in genetics. If a stop codon gets put into a gene too early, part of the protein will not be built. This may result in a complete failure of the protein to do its job. It is very easy for a mutation to cause a stop codon very early in the sequence. CAG codes for glutamine; change the C to a T and it becomes the stop codon TAG. AGA codes for arginine; change the first A to a T and it becomes the stop codon TGA.
Having one protein that is missing or incorrectly built may not seem like a big deal — after all, the human body contains tens of thousands of different proteins. But the human body is a marvelously complex machine that requires the coordination of many different pieces. Taking one piece out of the human body is like taking one piece out of a Swiss watch. There are many genetic conditions that are caused by single mutations, such as Marfan syndrome, achondroplasia and paroxysmal nocturnal hemoglobinuria.
But mutations are not always bad. Blue eyes, for example, are a relatively new trait that first originated in eastern Europe only a few thousand years ago. There is no major advantage or disadvantage to survival in people with blue eyes. Beneficial mutations are what natural selection operates on to produces complex traits over millions of years. 

Mutations can be caused by exposure to radiation, certain toxic substances or just random chance. This is something that the movies get right.

Mutations that are inherited will be present in every cell of a person’s body. Everyone began as a single cell. If that first cell contained a mutation, then every cell that comes from that cell will also contain that mutation. Mutations that are acquired later in life will only be present in a few cells. If a person is exposed to radiation, the radiation will cause random mutations in whatever cells it interacts with. It may only cause mutations in a couple of cells, or it may cause mutation in many cells. Each mutation is random, so the likelihood of two different cells having the same mutation is vanishingly small. It is even vanishingly smaller for the same mutation to occur in more than two cells. For every additional cell and for every additional mutation, the likelihood of the same thing set of mutations happening gets astronomically smaller. For a person to acquire superhuman abilities through exposure to radiation, two things would need to happen. First, a complex mutation would have to occur. A single mutation is very unlikely to produce the type of complex, new trait that superheroes have. Second, the same suite of mutations would either have to occur in the entire body, or at the very least in the organ system that the trait operates on.

Taken together, this things only become less likely. A collection of random mutations that builds a complex, beneficial trait AND occurs simultaneously in billions of cells? Consider the following scenario for comparison: you are transcribing notes you took by hand into a computer file. Through a series of accidental typographical errors, your economics notes turn into The Rime of the Ancient Mariner. This is analogous to a series of random mutations producing a complex, beneficial trait in a single cell. Now imagine that everyone in your economics class accidentally and independently wrote The Rime of the Ancient Mariner when trying to copy their notes. This is analogous to Bruce Banner’s exposure to gamma radiation turning him into the Incredible Hulk. Now imagine that not only did everyone in your economics class accidentally write The Rime of the Ancient Mariner, but everyone in your history class accidentally writing The Song of Hiawatha, everyone in your math class accidentally writing Where the Sidewalk Ends, and everyone in your biology class accidentally writing Beowolf. This is approximately the likelihood of Reed Richards, Susan Storm, Johnny Storm, and Ben Grimm (The Fantastic Four) all being transformed into superheroes through exposure to cosmic rays.

The Fantastic Four all got their powers through exposure to cosmic rays. Image from static.comicvine.com

The original Teenage Mutant Ninja Turtles, which came out in 1990, was one of my favorite movies growing up, and I am cautiously optimistic about the remake, which comes out on August 8. I encourage everyone to enjoy some superhero movies this summer, but don’t be fooled by bad science.

 

 

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10% Of Our Brains?

There is a new movie coming out later this month called “Lucy.” (See the trailer here.) The premise of this movie is that humans only use 10% of our brains, and Scarlett Johansson  gets superpowers by using more than 10% of hers. This idea that we only use 10% of our brains, but would be better if we used more, is a very persistent myth in our society.

Disclaimer: My point here is not to rain on anyone’s parade. I love science fiction movies, and if Luc Besson’s record is any indication, this one will probably be good. (Personal note: Luc Besson wrote and directed my favorite movie.) Even though I am a scientist, I am usually willing to suspend my disbelief for whatever premise the movie asks me to accept. I am not trying to convince anyone that they shouldn’t watch this movie or that it will suck because it gets some facts wrong. The release of this movie is just a convenient opportunity to talk about an oddly persistent myth.

Now back to the show…

My first exposure to this myth was probably as a child when I read the book My Teacher Fried My Brain — the second book in the My Teacher Is An Alien series. In this book, the school bully has his brain zapped by an alien device which makes him much smarter and a much more pleasant person. I can remember speculating later that very smart people like Albert Einstein probably used more like 50% of their brains.

But none of this is true. There have been several takedowns of the 10-percent-of-our-brains myth from a neuroscience perspective by people who are more qualified than I to discuss neuroscience. I am much more qualified to discuss this from an evolutionary angle.

Evolution is incremental. Traits evolve slowly over time, with each successive version of the trait being slightly better than the last. The brains of modern humans have a volume somewhere in the area of 1200 cubic centimeters (cc). Chimpanzee brains have less than a third of this volume. We evolved from an ape that was not exactly a chimpanzee, but we can use the chimp brain size as a point of comparison. Since our evolutionary divergence from our chimpanzee-like ancestors, our brains have tripled in size. This means that, during our evolution, individuals with 450cc brains survived and reproduced better than individuals with 430cc brains, and individuals with 500cc brains survived and reproduced better than individuals with 450cc brains. Our brains eventually grew to what they are now because the modern brain allowed individuals to survive and reproduce better than individuals that had anything less than a modern brain.

Human brain (top) compared to chimpanzee brain (bottom). Image from scientificamerican.com

The modern human brain is astonishingly expensive to build and maintain from a caloric standpoint. A typical adult male at rest requires 1800 Calories per day to function. That is, a man lying motionless but awake for 24 hours will burn 1800 calories just to maintain his body. This 1800 Calories is his “metabolic budget.” The metabolic budget is just the cost of every process within the body added up. Keeping the heart beating and the lungs breathing requires some of these calories. Replacing old, worn-out cells requires some more of these calories. The average adult male brain requires 414 of those Calories, which accounts for 23% of the total resting budget. Typical adult females require fewer Calories to function (1480) than adult males. The female brain requires about the same number of Calories as the male brain (400), but accounts for a slightly larger percent of the resting metabolic budget (27%).

Malcom Holliday (1986) studied the energetic cost of the brain at different stages of life. (The data above is his.) The brain is relatively more expensive at younger ages because the brain is growing very fast and because the brain accounts for a larger portion of the body’s overall mass.

Malcom Holliday (1986) studied the energetic cost of the brain at different stages of life. (The data above is his.) The brain is relatively more expensive at younger ages because the brain is growing very fast and because the brain accounts for a larger portion of the body’s overall mass.

Evolution is not wasteful. Acquiring enough energetic resources to survive was a big problem for our ancestors. Building a smaller brain would be less expensive. If the expense of building a bigger brain was not offset by the advantage it gives, it would never have evolved in the future. If humans suddenly found ourselves in an environment where our big brains were no longer an advantage for us, our brains would subsequently evolve to be smaller. (Remember that evolution does not always make things bigger, better and more complex.)

If the brain was larger (and therefore more energetically expensive) than it needed to be, individuals with a smaller brain would be able to spend that additional energy on other important things. They could spend it acquiring resources to support more offspring. They could spend it on growing bigger muscles and repairing more damage. Or they just wouldn’t require as much energy to survive and it would be harder to starve to death. This is to say that a brain that wastes 90% of its potential could not possibly evolve. Compare this to a centipede that only used 10 of its 100 legs or a cheetah that had the anatomy and physiology to run 70 miles per hour but never ran faster than 7mph. Evolution would not produce these traits, either.

In summary: a brain that leaves 90% of its potential untapped would not evolve. But don’t let this fact stop you from making good movies that use this as a premise. Luc Besson doesn’t tell me how to do my job, so I won’t tell him how to do his.

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A Journey Through Plant Evolution at the Lincoln Park Conservatory

I recently spent some time at the beautiful Lincoln Park Conservatory. It is very hot and humid in the greenhouse, which may not have been the most obvious choice on a day that was already 88º outside. Nevertheless, I thought it would be a good way to talk about the evolution of plants. My specialty in biology is animals, but I have always loved the story of plant evolution. Like all other major groups of life on Earth, plant life began in the water. Early plants were very reliant on water, but plants became less and less dependent on water as they evolved. In the water, life is easy. Dehydration is not a problem. Nutrients can be absorbed directly out of the water into the cells. The water will carry sperm for reproduction and disperse the offspring. Life in the water is good, but there was a lot of space to grow on land.

The Lincoln Park Conservatory is a great place to go. A cooler day is better.

The Lincoln Park Conservatory is a great place to go. A cooler day is better.

Liverworts

One of the first types of plants to live on land were the liverworts. They are very small, with leaves that lie almost flat on the ground. Liverworts have no ability to draw water up out of the ground, as later plants are able to do. As a result, they cannot grow very tall and must be damp all of the time. They cannot survive or reproduce without being wet.

Liverworts are one of the first plants to live on land.

My favorite room contains the primitive plants: ferns, moss, liverworts, and cycads.

My favorite room contains the primitive plants: ferns, moss, liverworts, and cycads.

Moss

Like liverworts, moss also cannot draw water up into their bodies. Are able to grow a little bit taller than the liverworts because they grow in dense mats that can trap water between individual plants. This allows them to grow up to about four inches tall.

Mosses do not dry out as easily as liverworts, but they do rely on water for reproduction. The male sperm must swim through the water to find a female plant.

Like an idiot, I forgot to take a picture of moss. This one form wikipedia.org will have to do.

Club Moss

Club moss are sometimes called “ground pines” because they can resemble pine trees, but they are neither pines nor moss. Modern club moss usually only grow to be a few inches tall, but during the Carboniferous period, when they were the dominant land plant, they grew as tall as modern trees.

Club moss are one of the first type of plants to have vascular tissue, which lets them draw water from the ground up into their bodies. This adaptation is of unparalleled importance for plants on land. For this reason, club moss were one of the first types of plants to be able to grow more than a couple of inches tall. Without vascular tissue, a plant more than an inch or two has no way of getting water to the upper part of the plant. Plants don’t need very much to live, but access to sufficient sunlight is one of their main requirements. When all of the plants around you are only two inches tall, a plant that can grow to be several feet tall or taller has an enormous advantage when it comes to getting sunlight. You can grow taller than your neighbors and spread out to get all the sun you want.

Club moss (not moss). Image from bio.sunyorange.edu

Coal is made of fossilized plants from the carboniferous period. The majority of coal is made up of ferns and club moss. Sometimes coal preserves the structures of the plants it was made from and we can use the coal fossils to learn about ancient plants.

A thin section of coal clearly shows the features of the stem of an ancient plant (in cross-section). Image from http://www.ucmp.berkeley.edu

Ferns

Evolutionarily speaking, ferns are slightly newer than the club moss. Like the club moss, ferns are have vascular tissue (so does everything else from here on).

Compared to most other plants, ferns grow sideways. The stem lies horizontally underground, and the fronds grow up out of the ground from it. When you see a cluster of fronds sticking up together, they are usually from the same plant.

Fern frond

Fern frond

Structures on the underside of the fronds, called “sori,” contain spores. These capsules break open, releasing the spores, and new ferns grow where the spores land.

Sori are clearly visible on the underside of fern fronds. These contain spores.

Sori are clearly visible on the underside of fern fronds. These contain spores.

Cycads

Cycads look superficially like palms, pineapples or yuccas, but is not closely related to any of them. They were one of the dominant types of plants during the mesozoic era — the age of the dinosaurs.

Cycads were among the first plants to use pollen in reproduction. Pollen is produced by the male structures on plants, and is responsible for carrying sperm to the ovule in the female structures on other plants. Unlike the earlier plants, which require water for the sperm to swim through, pollen is carried by the wind. This is great for plants that live away from water and want to be able to reproduce with individuals that are far away. The problem is that it is fairly inefficient. Plants whose pollen is carried by the wind need to produce vast quantities of the stuff in order for some of it to get to other plants. I grew up in New Hampshire, where there a lot of white pine trees (which are not cycads, but also reproduce with wind-borne pollen). I got up many a morning to find my car completely covered in yellow pollen. All of that pollen that didn’t end up on the right part of the female plants is wasted energy.

Cycads were also among the first plants to have seeds, instead of spores like the older plants. Spores are fine, but they cannot travel over long distances or lie dormant for a more opportune time to sprout. A seed contains the plant embryo as well as nutrients to keep it alive for months or years. If a spore happens to land on the back of a bird on its way to the other side of the country, the embryo inside may not survive the trip because its mother didn’t pack it lunch. An embryo inside a seed will survive the same journey because it is surrounded in an oil-rich substance called “endosperm.” When we eat nuts, it is the endosperm that we are after.

Cycads can superficially resemble pineapples, yuccas or palms, but they are not part of the same group.

Cycads can superficially resemble pineapples, yuccas or palms, but they are not part of the same group.

Flowering Plants

Flowering plants became the dominant plants of the world during the late mesozoic, and today account for the majority of plant species.There are over a quarter million living species of flowering plants, compared to only about 12,000 species of fern, and fewer than 10,000 species of liverwort.

The flowering plants have two evolutionary advancements that allowed them to be so successful: flowers and fruit. These allow plants to solve two big problems in the area of reproduction.

Flowers represent an exchange of goods and services between plants and animals. Big, colorful, aromatic flowers are nature’s equivalent of an “eat here” sign. Flowers produce sugar-rich nectar that animals like ants, butterflies, birds, and bats like to eat. While these “pollinators” are eating the nectar, they get covered in pollen. When they go to the next flower, they drop some pollen off and pick up some more. This results in animals carrying pollen directly from one plant to the next, with very little waste. Remember all that energy that earlier plants wasted trying to pollinate my car? Flowers allow plants to use their energy more effectively. The energy this saves over relying on wind pollination is part of why flowering plants are so successful evolutionarily.

Flowers attract certain animals, which carry pollen between flowers, helping the plants reproduce.

Flowers attract certain animals, which carry pollen between flowers, helping the plants reproduce.

Spreading seeds is another problem for plants. If seeds just fall off the parent plant and onto the ground, some will roll away or get kicked away. The others will sprout right next to their parent and compete for the same nutrients and light. This will reduce the success of both the parent and the offspring. Some (but not all) flowering plants produce fruit to solve this problem.

Fruit is a sugar-rich substance that is easy to get eat, which surrounds the seed, which contains an oil-rich substance that is protected by a hard shell. In human terms, the plant “wants” you to eat the fruit, but does not “want” you to eat the seed. If you eat the seed, you are eating the tree’s offspring. If you (or another animal) eat the fruit, there is a good chance that you will swallow the seeds by accident. The hard shell protects it from being broken in your mouth or digested in your stomach. After eating the fruit, you (or whatever animal) will walk or fly away and eventually deposit the seeds far away in a nutrient-rich pile of fertilizer.

Flowering plants are better at life on land than any other plants. They can draw water and nutrients out of the soil through their roots and vascular tissue, and they are very good at reproducing and spreading their offspring without the aid of water. This is why they are beating all of the other plants.

Cladogram showing the evolutionary relationships of the plant groups and major evolutionary advancements.

Cladogram showing the evolutionary relationships of the plant groups and major evolutionary advancements.

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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.

Have a topic you want me to cover? Let me know in the comments or on twitter @CGEppig


Skipping Generations, Part 2

A few weeks ago, I wrote about traits skipping generations. Be sure to read that entry to get caught up. Genes that are located on the X-chromosome sometimes, but not always, lead to traits skipping generations. But this is not the only way traits can skip generations. Skipping generations can also occur with genes that are not located on the sex chromosomes. The rules of inheritance are such that, given the right combination of alleles in parents, traits can sometimes skip a generation.

When sexual reproduction occurs, the offspring gets a random combination of alleles from their parents. Each parent has two copies of each gene, and one of those copies from each parent is given to each offspring. There are four possible alleles to choose from — two from each parent — and each offspring gets one at random from each parent. This is exactly the same way it works for the sex chromosomes.

Here is one way a recessive trait can skip a generation:

In genetics, it is the convention for dominant alleles to be expressed with a capital letter, and recessive alleles with a lower-case letter.

The parents in our first generation are Sam and Jess. Sam has two copies of the dominant allele (“AA”) — which causes him to express the dominant trait — and Jess has two copies of the recessive allele (“aa”) — which causes her to express the recessive trait. It doesn’t matter what the trait is. It could be attached vs free earlobes, widow’s peak, knuckle hair, or any other trait that follows the basic rules of inheritance. (There are traits that follow slightly different rules, but I’m not going to talk about them right now.)

sam and jess

When they have children, every child will get an “A” from Sam and an “a” from Jess, because Sam has only “A’s” to give, and Jess has only “a’s” to give. All of the children will express the dominant trait, although they all carry (but do not express) the recessive allele. Unlike with x-linked traits, the expression of these traits is not related to sex.

Ann grows up and marries Luke, who is also “Aa.”

ann and luke

There are four possibilities for the children:

(1) They can inherit Ann’s “A “and Luke’s “A” (“AA”).

(2) They can inherit Ann’s “A” and Luke’s “a” (“Aa”).

(3) They can Inherit Ann’s “a” and Luke’s “A” (“aA”).

(4) They can inherit Ann’s “a” and Luke’s “a” (“aa”).

Options (2) and (3) result in the same combination of alleles — “Aa” — even though the source of the alleles are from different parents. That is, it doesn’t matter whether the “A” comes from the father or the mother. It will always be dominant over the “a.”

In the three generations of this family, the recessive trait is only expressed in one individual in generation 1 (Jess), and in one person in generation 3 (Tim). Nobody in generation 2 expressed the recessive trait, even though people in generation 2 carried the recessive allele.

As I said before, these types of traits only sometimes skip generations, but do not always skip generations. By changing the genetics of the example above only slightly, the scenario will play out very differently. If Sam is “Aa” instead of “AA,” half of his children with Jess will be “aa” and the other half will be “Aa.” The recessive trait will be expressed in the second generation and there will be no skipping of generations.

Sometimes generation skipping can happen with dominant traits, too, although by a slightly different mechanism. Recessive alleles can be carried by individuals who do not express the trait, making it easy for the recessive traits to be silent. The only way for a dominant trait to skip generations is if the dominant allele is not passed on in a family, and it is then added in a subsequent generation.

For example, Jim (Aa) and Jill (aa) have children. There is a 50% chance that any child they have will inherit an “a” from both parents. If they have two children, there is a 25% chance that both of them will be “aa.”

jim and jill

Their daughter, Liz, grows up and marries Bill, who is also “aa.” Since neither of them has any “A” alleles, all of their children will be “aa.”

liz and bill

Their son, Rob, grows up and marries Kim, who is “AA.” All of their children will be “Aa.”

rob and kim

Between the first and second generations, the “A” allele was removed from the family lineage. It was not until Kim that the allele was introduced back into the gene pool. The dominant trait skipped generation 2 entirely. Again, this is not because of something to do with the trait itself — the various allele combinations of everyone interacted in certain ways to make the trait skip a generation.

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