How Evolution Works

Now that you know how the origin of life was a long, incremental, and random process, we can now begin to understand how evolution works. Evolution is the gradual appearance and disappearance of genes in whats referred to as a gene pool. A gene pool is the collection of all genes present in any and every individual of a single species. Lets use Darwin’s finches as our source of examples.darwin_finches.jpg

If you don’t know what Darwin’s finches are, it is a simple and observable example of how evolution acts on a species. A species of finch once exclusively inhabited the mainland and at some point migrated to several close islands off the coast. Each island had slightly different environments in terms of vegetation, animal life, and other factors. These birds, now in a completely different setting, had to “adapt” in order to survive on the island they now inhabit. The most obvious change was the birds’ beak shapes. On one island the main source of food was nuts and on another, small insects. Ill focus first on the nut eating birds. After many generations on this island the birds had developed larger, and tougher beaks in order to break through the hard shells of these nuts. What they don’t tell you in the biology books is that the birds whose beaks weren’t strong enough to break the shells starved and died. You cant pass on your genetic information to the next generation if you’re dead, so their genes were erased from the gene pool the moment they died.  With the weak beak genes gone from collective pool, only hard beak genes remain. This repeated cycle is what causes change among species.

Cell division of the replication of genetic material which is used as the blueprints to create every cell in your body. However, though rare, mistakes in this replication do happen. These mistakes are called mutations. Mutations are random. One mutation might give a mutation.pngbird an extra toe, or an addition tail feather, or even a slightly bigger beak. For one of these finches on the nut island this mutation probably saved its life. If it hadn’t had this mutation for this abnormally large beak, it may not have been able to eat just like many others. Because his mutation allowed him to live, his genes for a larger beak remain in the pool and will be passed on to his offspring and so on and so on. DNA polymerase is the mistake checker during DNA replication and misses 1 mistake every 10 billion nucleotides. Evolution is these subtle changes in DNA sequence over thousands of years. The reason this is a theory of evolution and not fact is because the process is so slow we cannot measure it in real time, but finding remains of ancestral species from the past gives us a glimpse of what was and gives us a view of the progression of evolution.

 

The Beginning

I think a lot of people learn about evolution and only have general knowledge about how it happens on the micro scale. People know that evolution is the gradual change of an organism as they respond to their ever changing environments. When learning about Darwin’s finches we are told that the birds “needed” to change their beak shape to adapt the the type of food available on each island.  Although this is true, I don’t believe it adequately communicates what actually goes on within the species’ gene pool. I think to understand this theory, you must need to go back to the beginning about the origin of life.

This experiment, the Stanley Miller experiment, demonstrates of complex molecules could have been formed in the harsh early environment of earth 3.8 billion years ago. The apparatus used is meant to simulate the same environment of earth back then. The air in the set up is methane, ammonium, and hydrogen gas which is primarily what the atmosphere back then was composed of. The download.jpgEarth was still very hot then, so the water is heated to a boil. Not only was it very hot then, it was also covered in constant lightening storms which is simulated by the electrode sparks.Now with the weather, temperature, and atmospheric contents all replicated in this system, we can see how these molecules might have behaved in that environment. Water is evaporated and mixes with the methane, ammonium, and hydrogen gas. In the next flask, an electric current is sent through the contents and this causes chemical bonds to break and reform. The reformed contents are collected and identified. Several organic compounds we see in our own bodies were detected such as amino acids. Amino acids are the building blocks of our DNA. This proves that the formation of organic molecules was possible during this time. But how does one amino acid forming out of nowhere lead to DNA and cells and life? There’s a huge gap in time most text books don’t explicitly mention. This was in no means a fast process. The world then was a very random and chaotic place. The likely hood of this amino acid forming out of a lightning strike and a few odd molecules is very VERY unlikely. Let me reiterate. These atoms and small molecules have no idea who they are going to bump into next. If an oxygen molecule happens to be next to a hydrogen molecule, a collision might form water or it might not. Again, I will use the word random to explain how these things happened. As much as we’d like to credit the beginning of life on Earth to aliens, that’s just no how it went down. So you have an earth sized pot of boiling water  seasoned with atoms from the whole periodic table. And molecules are randomly and spontaneously forming and breaking bonds. If you were to put the likelihood of an amino acid forming in this pot you might get some crazy huge number of like 1/36×10^600 or some huge number. But remember, Rome wasn’t built in a day. It took 3.8 billion years to form the first primitive cell download (1).jpgso when you literally have all the time in the world you can make these odds work in your favor.

The origin of life is defined as the moment when a simple single strand of amino acids, RNA, met with this bubble made out of these balloon looking molecules that act as a barrier. If this meeting didn’t happen there may not have been life on Earth. This was the formation of the first protocell, a strand of RNA enclosed in a sphere of fatty acids. This may not seem to exciting but the strand of RNA being protected from the chaotic world outside that membrane is what allowed evolution to occur. Ill finally explain how evolution works next.

 

 

Mimi, Mama, and Mega

Once again, I was looking through RadioLab and I found a very interesting show about giant viruses. The average size of a bacteriophage is about 6.5 nm long. Spherical viruses average around 100 nm. The average for these newly discovered giant viruses called are about 400 nm in diameter. These huge viruses enter a bacteria and float inside the cell. Instead of just injecting its DNA and going through that normal viral lytic cycle, it lives there in a commensalistic relationship. Inside the cell, the virus is called a virus factory. The virus takes in materials floating around the cell and reassembles them into components to build more giant viruses. Get this-the holes where the materials go in and out are called stargates. Awesome right? And turns out there are even bigger viruses other than the 400 nm mimivirus. In order from smallest to biggest: mimi, mama, mega, and then pandora, measuring over 1000nm.pandoravirus

The theory of the origin of these huge viruses are that they might have been living cells and switched sides for some reason. At some point a microbe finds itself inside another cell and is able to thrive there. It basically had protection from the environment, and food delivered to it. From there evolution got rid of there energy forming processes, for they are no longer necessary.

This discovery is very eye-opening because it shows how not only can life on Earth evolve to become more complex, but can also evolve to become more simple. In the case of the giant viruses, they started out as full sized microbes and over time shrunk due to evolutionary pressures. In human evolutionary history we were once able to produce our own vitamin C but lost that ability some point in history. This was allowed to happen without hurting the human population because vitamin C has always been plentiful in our diets. Like I said in my last blog post, cell division is not always perfect. There had to have been a mutation in a cell where their vitamin C producing mechanism was damaged. However, since humans were still able to receive vitamin C from fruits, this mutation was able to remain in the gene pool and passed on to future generations. This sparked an interesting question. If humans have lost functions before, couldn’t we lose more in the future? What if a mutation arises where we are born without a toe. Prosthetic and custom shoes and whatever else can make life with one less toe normal. Therefore, this gene for 9 toes will remain in the gene pool and spread and eventually humans as a species could have only 9 toes instead of 10.

In the brilliant shoe, West World, Dr. Ford, when referring to the human race in the distant future says, “this is as good as we get.” With every disease cured, every disability fixed, there is no evolutionary pressure being put or our species. No genes leave the gene pool and that’s including the bad genes. I guess this is a problem we’ll confront later when we are washing our hands with bleach because that .001% of bacteria that your favorite antibacterial soap didn’t kill have grown in numbers.

 

How do Viruses Reproduce?

A virus is an infective agent that typically consists of a nucleic acid molecule in a protein coat and is able to multiply only within the living cells of a host.

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The genetic material is held in the capsid or head of the virus. The head is made up of proteins arranged in an icosahedron pattern. Under the head is the sheath. The sheath is a long chain of proteins arranged into a tube like structure that leads from the capsid to the base plate of the virus. The pins around the base plate are long coils of proteins that are wide at one end and become slimmer forming a “spike.” The tail fibers are also long protein chains that help attach to the host cell. Once the tail fibers have attached to the membrane of the host cell, the spikes begin to drill an opening. The genetic material moves down the sheath tube into the host cell. The genetic material is integrated into the host DNA’s and later the cell will build the viruses babies for it.

Once in the cell, a protein called retroviral integrase protein cuts and pastes the viral DNA into sequence with the host DNA. The infected host can go into two cycles: the lytic cycle and the lysogenic cycle.

18_07lamdalyticlysocycle

The lytic cycle is the virus’ life cycle. A virus finds a host cell, injects its material and the cell creates several new viruses. Once the new phages have been made, they exit the cell and leave behind large holes that kill the cell. The other cycle is the lysogenic cycle where the viral DNA stay transcribed in the host’s DNA and the host goes through meiosis, spreading the viral DNA into future generations. Occasionally, some of these new infected cells will undergo the lytic cycle. Because it is the cell doing all the work for the virus, the cell’s mistakes do effect the offspring. The reason viruses have been evolving over time is due the the fact that cells occasionally make mistakes during replication and if one of those mistakes happens to be on the viral DNA it will be present in all new viruses produced.

Our bodies can defend themselves from viruses however its no easy task. When you are infected with the flu, you could be sick in bed for 3-5 days. During this time the viruses are reeking havoc on your cells killing many in the process. Our bodies can defend because our specialized white blood cells produce these little protein sticks called antibodies which basically work as a tire clamp that grabs onto the virus and stops it in its tracks. Although this can stop many of the viruses we encounter it can take time, or not be able to stop them at all. A well known viral disease that our bodies cannot fight is the AIDS virus. This virus only attacks specific cells, white blood cells. For most patients, its not the AIDS virus that kills them, but instead other common, usually harmless viruses such as the common cold.The AIDS virus kills a large amount of the bodies white blood cells effectively destroying the body’s defense system. Without white blood cells the body cannot produce antibodies to fight off a disease.

http://www.virology.ws/2012/03/22/a-spike-for-piercing-the-cell-membrane/

http://eol.org/info/458

https://www.ncbi.nlm.nih.gov/pubmed/16291214

Are Viruses Alive?

A virus is a nasty little parasite-like molecule that uses living cells to replicate itself. Viruses affect all living organisms- plants, animals, even bacteria and archaea. There are about 5000 different viruses and are thought to be the most abundant biological entity. If you’re into scifi then you can basically call these guys nanobots. They don’t die. They cant reproduce. They are little killing machines is what they are. rick and morty.png

Though they aren’t quite as vicious as they are shown in Rick and Morty, however, if the show was to stay accurate, and if they were to show it, Dr. Xenon’s death in this scene would’ve been something out of an Alien movie.

What makes something alive? Being born? viruses are “born” when they erupt out of a living cell, killing it. Reproducing? Viruses do that too, they just need a little help from a third party but this doesn’t rule them out. Most plants depend on pollinators to move the pollen to the egg. How about free thought? Its debatable to say that us, the most mentally developed organisms on earth, have free thought. To some, life is just a series of complex pathways and mechanisms. You can argue the definition of life all day but scientists define viruses as a gray area between living and nonliving or “at the edge of life.” Another reason they cannot be ruled out as living organisms and be called complex molecules is because viruses are also subjected to evolutionary pressures. Although it is the living cell doing the replicating for the virus, therefore the one causing any mutations. Regardless, the scientific community has agreed upon the gray area answer.

Regardless of being alive or not, viruses are by far the most persistent, most successful organisms on Earth. Every organism that has ever existed has had some type of run in with viruses. Viral DNA is always being integrated into our own DNA. The DNA can stay hidden in our cells for long periods before the cell finally starts to build the viruses itself ultimately causing its own death. I keep referring to this horrible end of the host cell- I will go into more detail about how this process goes about in the next blog post. But for now, imagine a flash mob. If you were to arrange one, the first thing you would need to do would be to get others to flash with you, right? Viruses can do the same thing. With the dormant DNA in a living cell, the host will reproduce normally, passing on the viruses DNA to its children. Then at some point in the future all these new infected cells “flash” and produce more viruses. Some diseases such as herpes can stay dormant for years. Now if you were able to follow that flash mob analogy then you can see how this could be a problem. However our bodies are pretty good at defending itself. Ill explain next…

 

http://serc.carleton.edu/microbelife/yellowstone/viruslive.html

http://eol.org/info/458

 

 

What are Allergies?

Allergies are hypersensitive immune responses to substances that either enter or come in contact with the body, such as pet dander, pollen or bee venom. This basically means that the immune system is doing its job too well and attacking harmless substances like pollen or pet dander. Or in some cases over reacting to them like bee venom and peanut allergies.

When an allergen comes in contact with a white blood cell, the cell begins to release certain chemicals that alert your body to take certain procedures. For me, when pollen enters my nose can comes in contact with my nasal walls, special cells called mast cells attempt to neutralize the “threat” by releasing histamine. Histamine is a compound that acts as a neurotransmitter that regulates physiological functions. In my case, histamine tells my nose to produce more mucus to flush out the allergen, hence the runny nose and sneezing. When an allergen comes in contact with your skin, redness and swelling is also common. That’s because histamine causes blood vessels to contract around the affected area, trapping the allergens making them unable to circulate through the body. This causes swelling as well as congestion. While the intruders are trapped within the inflamed area, phagocytes engulf the allergens, digesting them.

Image result for inflammatory response diagram

In more extreme cases, this harmless but annoying response can become deadly. Anaphylaxis is an allergic reaction where the immune system over reacts to the allergen and can have life threatening symptoms. Food allergies, for example, can cause inflammation in the tongue and throat making it impossible for air to enter the lungs. Other reactions can cause the muscles around the air ways to contract also preventing breathing. An anaphylactic shock can be remedied by an immediate injection of epinephrine or an epipen. epinephrine is another neurotransmitter that inhibits a lot of the symptoms that arise during an anaphylactic shock. The neurotransmitter increases blood pressure reducing swelling. It also increases heart activity temporarily preventing heart failure during a shock.

The number of allergy effected individuals is increasing. Allergies effect around 30% of adults and 40% of children. Americans spend over $17.5 Billion on health costs for allergies. There are no cure for allergies- and only 3 treatments: avoidance of the allergen(-_-), medication, and immunotherapy. None of these treatments are guaranteed. All still have risks. There are other ways to treat allergies. For example in my last post I talked about how helminthic therapy could possibly get rid of allergies, and a few others. My last visit to the SFSU health center about my allergies, the doctor suggested i try a 3 day long water fast where i consume nothing but water for a full 72 hours which is said to “restart” your immune system possibly getting rid of my allergies. Sounds like torture but maybe one day(but I think I’d rather have worms in my gut than not eat for 3 days).

I am considering changing my future plans from studying infection disease to studying allergies. Maybe be a part of some sort of cure and possibly get in on that action to get rid of my own allergies hehehe.

 

Helminthic Therapy

So if you’re anything like me, you know what a struggle having allergies is! Avoiding going outside in fear of pollen crawling up your nose! Not being able to hold that cute kitten because the dander may cause an outbreak. And not to mention the hundreds of dollars spent on allergy medication every year! If there were a way to get rid of them for good wouldn’t you jump on that??

 

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Many kinds of Allergy Medication

OK OK. I don’t wanna get y’all all excited by telling you there is some miracle cure. However, ya boy did hear of something…

Being a microbiology major, it can be assumed that i am a huge nerd. Which would be true. Being as such, I am very drawn to nerdy, science-y things. Who has heard of RadioLab? If you haven’t, you should definitely look it up. Its a very nerdy and very interesting NPR podcast that discusses all sorts of science related topics like neuroscience, ecology, psychology, and lots more. And one day as i was scrolling through to find an interesting title I found one called Parasites. Being a microbio guy of course this had me hooked so i gave it a listen and it happened to be about allergies… But why was it called parasites?

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RadioLab Logo

Who knows what helminth means? A helminth is a parasitic worm. With that new information let me tell you what was spoken of on this episode of RadioLab. So a guy by the name of Jasper Laurence really really bad allergies. Nothing life threatening or anything like that but he had them. And like all of us he had to deal with it with frequent doctor visits and allergy meds and asthma inhalers and whatever else. And he came across this interesting statistic that said people who have had hookworm infections were 50% less likely to have asthma. Taking this information as hope for relief he tries to get some hookworms for himself.

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Cameroon has a high hookworm infection rate

Unable to find them from anywhere he travels all the way to Cameroon in Africa to find his own. He goes to a village along the coast. Finds their lavatory area. Takes off his shoes and takes a nice stroll. And one day a few weeks later at the beginning of allergy season he walks out his house expecting to get his usual swelled itchy eyes and needing to use his inhaler and start sneezing and all that… but he didn’t. He was free of his allergies.

 

Helminthic Therapy is intentionally infecting oneself with parasitic worms, specifically hookworms. These worms can inhibit autoimmune responses preventing the body’s immune system from responding to all the allergens in the environment. Would you try this method to getting rid of your allergies?

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