July 22, 2010

That Which Life is Made Of, Dude

Living things are made of cells.

Yes, right.  It can be just one cell also. But we agree that the cell is the building block of life. But then, what are the building blocks of these building blocks? What is life actually made of?

I will tell you!

At the most basic level, we are made of atoms, just like all matter is. Living things are mainly composed of the following ingredients:

Carbon  Hydrogen  Nitrogen  Oxygen  Phosphorus  Sulfur

But we don't have these in our bodies as pure elements. You don't have bits of graphite floating in your blood stream or anything. We have these elements arranged in various combinations, making large molecules.

There are 4 main types of these molecules, and they might sound very familiar to you: proteins, carbohydrates, lipids, and nucleic acids.

Proteins are responsible for a lot of the structure in a cell and your body. When you look at yourself in the mirror, most of what you notice about yourself is protein. Your hair, your skin, your eye color. These are the workings of protein. As I've mentioned before, DNA (in all its wisdom) has instructions for making protein, which is what makes you who you are.
Proteins are used as a means of communication in the body. Cells have proteins on them that identify them as kidney cell or an immune cell or whatever else. Allergies are the body's response to an unknown protein. The body is pretty obsessive about "knowing everyone," so in this way, it's very Hollywood.

The process of forming a thought or having an emotion is run by proteins. Neurons release proteins that trigger other neurons, and so on like dominoes it goes until you have flashes in your brain that you interpret as, "I'm sad that I dropped my Oreo on the floor."

Carbohydrates are sugars, but this varies from simple sugars like regular table sugar
to big guys like cellulose, starch, and glycogen.  Carbohydrates are mostly used to store energy--which means they have a lot of calories, which in turn is why Dr. Atkins told a lot of people not to eat them.

Sugars can be drawn as a hexagon because they actually are this shape.  It's also a lot easier:

Cellulose is made of long chains of sugars, and plants use it in their cell walls for structure. We humans can't digest cellulose. We can't break any bonds and get any energy from it.  This is why celery has almost no calories. But having cellulose run through our digestive system is good for cleaning the intestines and moving things along, as they say. You may be more familiar with the common name of cellulose: fiber.

Starch and glycogen are forms of sugar for long term energy storage. Starch is the plant variety (hellooooo potatoes), and glycogen is the animal equivalent.

Lipids are fats.  Lovely, lovely, lovely fats.  The basic fat, called a triglyceride, looks like a sideways jellyfish.
(I should say jelly, not jellyfish, for they are not fish. But jellyfish is just so fun to say.)

The legs of the jelly are fatty acids--long chains of carbon and hydrogen. Because the chains are so long and there are so many bonds, lipids store a LOT of energy, which is why people try not to have too much of them in their diet. But oh, they taste so good. The long chains slipping and sliding past each other is responsible for the oily nature of fats. I'm getting hungry.

Lipids are very important to every single cell, because they make a fabulous cell membrane. To be exact, membranes are made of phospholipids, which are phosphate "heads" with 2 fatty acid tails. It's actually kind of a cute little guy.
These all line up and form a double-layered circle, and that, my friend, is a membrane.

Nucleic Acid
Nucleic acids are the information storage molecule. You have your long term storage in your DNA (deoxyribonucleic acid), and your short term storage in your RNA (ribonucleic acid).

Want to know the difference between them? They both have "ribo" in their name because of a sugar called ribose. RNA has plain ol' ribose, and DNA has a form of ribose minus one oxygen atom, so it's called de-oxy to show very clearly that it has one less oxygen. You probably didn't want to know that, but oh well, it's too late now.

July 16, 2010

DNA, Protein, and Existential Crises

I explained in an earlier post that your DNA is a manual for how to make you.

A fundamental principle about genetics is that you are born with your specific edition of the DNA manual, and you are stuck with it, whether you like it or not.  The DNA book can't be edited.  The cells that are reading the book can't revise and print a new edition.  It's a one way street.  The information goes from DNA to protein.  DNA doesn't really care if protein has a better idea of how to do things.

If you inherit a typo in your DNA manual, there it stays.  (Although, the goal of "gene therapy" is to replace the pages with typos.  But that will have to be another post, sorry.)
The flow of information from DNA to protein is sometimes called the "central dogma" of biology.  I don't refer to it as such, but teachers and textbooks seem to have taken a real liking to the term.  The central dogma in part explains why traits acquired during one's life won't be passed to the next generation.  Again, the DNA book can't be edited by experience.  

So I was merrily going through life with this absolute rule in my head: DNA to protein.  Never the other way around.

But as my high school biology teacher used to say, "always and never are never true in biology."  

DNA can be changed.  

mind... blown....

Not the sequence exactly, but portions of DNA can be turned "on" and "off."  From what I've read, this only happens during fetal development.  The uterine environment can alter the baby's DNA.  Not by editing carefully, fixing a typo here, adding a paragraph here.  No.  It's more like ripping pages out.

I didn't realize how much comfort I found in the absolute rule that DNA-to-proteins provided me until I discovered this exception.  I felt like someone took my blankie away.  But I have learned my lesson: never get too attached to rules when it comes to biology.  There's always some cheeky exception.  While I was a little shaken by the news, I was comforted by the simple fact that this is just really cool.  There is a system built in that could in theory prepare a fetus for the world it will be entering.  There are several assumptions at work in that statement, but the idea is tantalizing. 

Most unfortunately, I've only heard of detrimental in utero DNA-switching effects.

When a pregnant woman smokes cigarettes, she can actually alter her baby's edition of DNA to give the baby asthma.  If the fetus is a female, and therefore has her eggs, the next generation, already stored within her, that DNA can be affected as well.  So if a woman pregnant with a girl smokes enough cigarettes, her grandchild will have asthma too.  The gravity of this news weighed on me.

My god, we can ruin two generations at once?!  We're not supposed to be able to change anything about DNA, and you're telling me I can alter my grandchildren? Zaaaa!!

If the feedback was going to help the new addition to the world, it would go the other way around.  If a woman was smoking, it should send messages to the baby that "Hey, the air out here is really bad.  You better be able to deal with this.  Make yourself some super lungs." But then women would have incentive to smoke while pregnant, so I guess the universe works after all.

Survival of the Sickest: The Surprising Connections Between Disease and Longevity (P.S.)I have also heard that if a pregnant woman is eating nutritionally poor food, the baby will be underweight, even if the mother is overeating.  In Survival of the Sickest, Sharon Moelem theorizes that this could be adaptive in the sense that it's telling the baby, "Hey, there's no good food out here, so don't show up hungry," hence, tiny babies.

This is relatively new information, so the exact mechanism isn't fully understood, nor is the full list of signals that can turn genes "on" or "off."

While I gave two negative examples here, that doesn't mean this only works to that effect.  As we learn more, this phenomenon could explain how huge evolutionary steps could be taken in relatively few generations.

The fact is we often learn how things work by observing what happens when they don't work.  The road to understanding human biology is paved with disease, injuries, and genetic disorders.  I mean, our understanding of neuroscience for the longest time was based on observations of people with head injuries.  You take what you can get, and that often means learning about the bad stuff first.

Anyway, this discipline that studies how DNA can be turned "on" and "off" is called epigenetics.  Isn't it just awesome? I know, right? (That was for you, Sharin.)

July 14, 2010

Photosynthesis is Pretty Awesome

I'm going to revisit this topic.  One of my first posts was about photosynthesis, but back then, my blog posts were 2 unfortunate things: wayyyyy too long and not nearly illustrated enough.  So here we go.

Plants do this thing called photosynthesis, which translates to "using light to make stuff."  We all know that plants use light from the sun, but what are they doing with that energy?  What are they making, and what are they making it out of?

This is a seed.

It is tiny.

How on earth does this seed turn into this tree?

Where did all this "stuff" that makes this tree come from?  What are the building blocks?

If you ask what trees are made of, most people will say water and soil.  Let's examine this.

1. Water just happens to be correct. Plants use water in photosynthesis and they store large amounts of it in each cell to make them sturdy. You can see evidence of this if you have cut flowers out of water for too long. They get droopy and depressed as the water in each cell evaporates, but as soon as you put it in a vase of fresh water, it draws that water into all the cells, and it perks up.

It sure looks happy for a severed flower head. It'd be really cool if this worked with human body parts too.

2. Soil. Okay, yes, plants usually need soil, but that doesn't contribute to its mass--the "stuff" that makes a tree so big. Don't believe me? Well, when you plant a seed in a pot, and the seed grows into some lovely plant, isn't the soil still there? The soil isn't contributing to the size of the plant. No, sir. It's just there for support.

So if it's not soil, what are plants made of? Where are they getting all the "stuff"? We get our "stuff" from the food we eat, but plants don't eat anything. That's what makes them plants. (Okay, yes there are carnivorous plants, but I'll talk about that in another post.)

I won't keep you in suspense any longer. Plants make their stuff from CO2, carbon dioxide, from the air.  This is the carbon source for the billions of cells that make up the plant's body. (We get our carbon by eating plants and other animals.)

This is the equation for photosynthesis.  It probably looks somewhat familiar, but hopefully it makes a little more sense now.

The problem is that even if someone memorizes the equation for photosynthesis, they still think that plants are made of soil.  The idea that AIR could create a massive, sturdy tree is totally counterintuitive.    Most people think that air is nothing--just emptiness. But tell that to someone whose house is blown away by a tornado.  You know what caused the damage?  AIR.  Air has mass.  Air has stuff.  I swear.  I'm gonna make some billboards with PSAs for this:

So yes, this is a little strange.  Plants are literally pulling building blocks out of thin air.  They're just clever like that.

July 09, 2010

Evolution Doesn't Have to Ruin Your Birthday Party

Sorry, this isn't going to be a silly, doodle-filled post. I need to vent.

I've been thinking a lot about evolution vs. religion lately, or rather, how the "vs." need not be there. But I know that I'm in the minority with that sentiment.

I keep seeing it everywhere...

On my drive home last night, the car in front of me had one of those "truth" fish eating the "Darwin" fish. Ugh. I won't mention that the basis for this bumper decoration is a Darwinian concept of survival... but oh, wait. I just did. Also on the vehicular front, a friend of mine saw a van with this on it's back windows:

Why can so much of this debate be seen on the butts of people's cars? I feel very strongly about this, but I'm not about to decrease the resale value of my Toyota over it.

This is one of those ongoing debates where the line has been drawn and everyone has picked a side. And not unlike Coke vs. Pepsi, this debate hinges on people's gut reactions more than actual information. I argue that the majority of people on both sides know very little about evolution or Biblical scripture.

Last week, NPR posted a link to a story about evolution on Facebook. The article was about an ancient fish that all land vertebrates descended from, including us. The comment thread (which I'm sorry to have read--ha! that rhymes) disturbed me. Many people simply said something along the lines of "I'm not no fish." Confusion and double negatives.Yay. But people started chastising NPR for even posting a story that would alienate creationists. Evolutionists chimed in, and the blood bath began.  Back and forth.  Science and religion cannot be reconciled.  Read the Bible. Everyone is going to hell. On and on and on. And these are NPR listeners, who supposedly are some of the more educated people in our country. Here come the suicidal thoughts.

I so desperately want to moderate this debate and show how easily all these views can be reconciled, but the Catch-22 is that the people that I most want to reach would never read anything I might write. And I weep...

I keep taking for granted that the vast majority of people understand evolution and don't feel that it conflicts with their entire world view. I know there are fundamentalists that take the Bible completely literally and adhere to that Bible-based calculation that the world is 6,000 years old. But I thought those were just a few people. I just recently read Unscientific America, and their scariest statistic was that 46% of Americans believe this "young earth" concept. To which I say, "bahsldjfadlsfj, what?!"

Evidence for change over time, which is really all evolution is, is everywhere. Just look at people. If you're a creationist you believe we are all related as descendants of Adam and Eve, and if you are an evolutionist, you also believe we are all related. So we all agree on this. Phew. Now then, the different peoples we have--different races and cultures--have come about because as we have spread across the earth, there have been isolated populations that slowly changed based on chance and what benefited them in their surroundings. Our languages changed in the same way. If you put people in one place long enough and they don't come into contact with other cultures, their language will slowly change into something related but different. Such as Spanish and French. I don't mean the Spanish and French never came into contact with each other, by the way, just that there was enough isolation for these two romance languages to diverge.

People offended by this post so far: evolutionists, creationists, Spaniards, Frenchmen.

So for a creationist who believes that God created people with Adam and Eve, can't they see that this change that brought about all these different races of people may have also happened with other life forms? Doesn't that make a whole hell of a lot of sense?

Also, the creation story isn't all that unlike evolutionary theory, ignoring the concept of Biblical "days."  God created...
1.  Heaven, Earth, Light.
2.  Water, Land.
3.  Plants.
4.  Stars.
5.  Marine Life. Birds.
6.  Terrestrial Life.   Humans.

With the exception of stars on day 4--which seems like a day 1 sort of activity--this order of events is essentially the same as evolutionary theory.  That is, if you don't think about bacteria, archaea, protists, and fungi (poor little fellas, being left out of the creation story).  Since most of those are microscopic, it makes sense that people didn't talk about them before the invention of the microscope.

When I taught high school biology, my students made a diagram of the geological time scale from the pre-cambrian era through present day. 1 inch of poster was equivalent to 2 million years. It showed life in the oceans, and then fish, amphibians, reptiles, dinosaurs(!), land plants, birds, mammals, and then humans. I hung all the posters in order on the back wall in the room. As they looked at their class project, I opened up the evolution debate. I asked them what the big debate was about. A student said, "People say it conflicts with the Bible." I asked him what the Bible says about this.  We went over the order of the creation story, and as they observed their illustrated geological time scale, I asked them, "Isn't this pretty much the same thing?" They all looked surprised. A few nodded, a few said, "Yeah...wow."  It made sense to them. Evolution wasn't scary or weird or crazy. It was the idea that things have changed slowly over time. It made sense to all my 14-year-olds, many of whom were religious. Why doesn't it make sense to adults?

Lastly, I think evolutionists need to stop attacking religion in general. While everyone is free to their opinion about religion, it's not relevant to the evolution debate. We need to emphasize that there is common ground: being religious need not mean that one can't also understand evolution.

Let's strive for the separation of scientific understanding and personal beliefs in the name of coexistence. Teaching evolution doesn't have to destroy anyone's religion. That only emphasizes the direct conflict between them, which implies that religion and science are comparable equals. They are two completely different disciplines. No one has to annihilate one to serve the other.

So stop fighting, or so help me, I will turn this car around!

(Note: I apologize for focusing solely on the Judeo-Christian religious "conflict" here.  It's the debate I'm most familiar with.  I'd be interested to know how all religions look at this.)

July 07, 2010

Who You Callin' a Vaccine?

Vaccines allow your immune system to familiarize themselves with potential invaders.  This is helpful, because viruses are tricky.  They sneak around your body and often have the chance to make you sick before your body can figure it out.  Figure it out, body!

Viruses are like wedding crashers.  When you're dealing with a lot of people coming and going, it's really easy to let someone in who wasn't invited.  But, if you know the uninvited person, such as the bride's crazy ex-boyfriend, you'll know right away to bust him.  That's what vaccines do.  No, they don't bust ex-boyfriends.  I mean they get the immune system acquainted with future intruders.  It's like circulating a picture of the potential wedding crasher so everyone can recognize him.

I wonder if my analogies are getting stale.  Back to reality for a moment: vaccines are weakened or dead viruses that you inject into the body.
They can't make you sick because the viruses are damaged, but the chemical signals on them can still give your immune systems the low-down so they can recognize them in the future.

The Y-shaped guy, who looks perhaps too much like a piece of toast, is an antibody.  They are indeed Y-shaped.  You heard it here first.  And yes, viruses do mutate (symbolized above as wearing a disguise) and can sneak past the body's immune system and make you sick before everyone realizes it's the same guy with glasses on.  Why do we fall for this?