science

Science basics that EVERYONE should know

Yesterday, I found myself in the same old rut; perusing Facebook when Lo! and behold, my cousin Crystal posted a video saying “1 in 4 Americans unaware that earth circles sun”. I immediately thought “NO! This can’t be … I must watch this video (and hope it’s not a virus.)” To find out, IT’S TRUE!! Don’t believe me? Watch it here.

Needless to say, today, I find myself inspired. Maybe I’m going to far in to science with my science posts? Maybe, I need to take a step back so everyone is on the same page – and, just in case you get stopped on the street for a science pop quiz, you will know the answer! Plus, trivia night, anyone?

1. All of the planets orbit (revolve around) the sun. (Feel free to watch the video again). Lighter objects always orbit heavier objects. This is why satellites and the moon orbit earth. Do you remember anything about Sir Isaac Newton? It was Newton who realized that the planets must orbit the sun in much the same way an object falls to the earth after we drop it. Basically, the sun’s gravity pulls on all of the planets, causing the planets to orbit it. It is also important to note that the bigger an object is, the larger it’s gravitational pull. It goes without saying that all of you know that the sun is the largest object in our solar system. NASA has some amazing resources for this subject. I should also mention that it takes 1 year for the earth to orbit the sun.
Sun
[Source]

2. There is a difference between a scientific hypothesis, theory and law. And those differences aren’t what the general public seems to think they are. Let’s start at the beginning. A hypothesis is an educated guess that is based on observations. You may remember making “If … then …” statements back in middle school. If not, they kind of sound like this: If I punch my little brother, then he will cry. This statement has to be testable. In our example, I could walk up to my little brother and give him a punch. Then, I will observe the aftermath. Does he cry? What’s wonderful about a hypothesis is, you could be wrong, BUT you will get a scientific answer. In our case, my brother could cry, he could do nothing, or he might yell for mom. Our observations can change our hypothesis, to make it better, so we can get better answers. To hammer home this idea, I might be able to punch my brother 10 times with him crying each time. On the 11th try, he might punch me back!  A theory summarizes a group of hypotheses made by lots of people. It’s important to re-state that these hypotheses have undergone a lot of testing and re-testing by a lot of scientists. A theory is accepted as fact as long as there is no evidence that disputes it. Once this evidence arises, the theory is not thrown out, but changed to accommodate the new observation. Basically, a theory explains why and how something happens. For example, when we talk about gravity, we use Einstein’s theory of general relativity. A law explains things, but does not describe them and it does this by generalizing a body of observations from many hypotheses that have been tested and re-tested by many scientists. A great way to distinguish a law from a theory is to see which one answers why something happens. For example, Sir Isaac Newton had a Law of Gravity. This law could predict that an object would fall, but it couldn’t tell us why it fell. For a list of 10 laws and theories everyone should at least be acquainted with, check out this article here.

3. Evolution. I was debating whether or not I should include this … as I really don’t enjoy talking about controversial things. However, everyone should at least know about it, whether you decide to believe in it or not. If you want to read more about all the intricacies of Evolution, check out Darwin’s Origin of Species (it’s even free for the Kindle App!) Many of you have heard of, and perhaps even said, the phrase “survival of the fittest!” – that’s evolution you are talking about! There are many genetic changes that can be inherited, and these small changes, over the course of time, add up to larger changes. This is why every new generation of people differs slightly from the one before it. Many of these changes have negative or neutral effects, but sometimes, there are positive ones – hence, survival of the fittest. The rate of evolution varies a lot and it depends on the organism and environment. Recently, Bill Nye (the science guy!) and Ken Ham debated evolution and creationism (see the entire debate here). When it came down to evolution and creationism, both of them said the same thing, just using different words. Ken Ham said Noah saved 7000 couples on his little arc, and because of that, we have all the ones we have today. I found the below picture to really hammer home the math. The picture’s link will take you to someone else’s perspective on the debate.
evolution
[Source]

4. The sky is blue because of scattering. It’s not blue because it’s a reflection of the ocean waters (like what I believed when I was in elementary school). Let’s think about this. We have a sun, that we orbit around (see #1 above), and in order for that sun’s rays to reach earth, the rays have to penetrate the earth’s atmosphere. This atmosphere includes things like gas and particles that cause the sunlight to bounce (or scatter) off of them in many directions, and this sunlight is actually a lot of different colours. Have you ever seen a light flashing on a prism or maybe Pink Floyd’s Dark side of the moon album cover? All of the colours in sunlight have different wavelengths, with blue being very short. So, blue light can make it’s way through the “filter” (i.e. atmosphere) easier than colours with larger wavelengths, and, as a result, the blue light is scattered very widely. This is why the sky is blue when the sun is at the highest point in the sky, in relation to where you are standing. So, how do we explain the beauty of sunsets and sunrises? At these points, the sun is not above where you are standing, it’s much farther away. The sunlight has to cross a great distance to reach you, and this distance allows the blue colour to, essentially, fade away, allowing us to see the reds and oranges and yellows of the light!
prism
[Source]

I think we will stick with these four things for now. If you are curious about anything, feel free to post your questions in the comments section below. Remember, we aren’t debating anything here (there are other blogs and forums for that).

The first ever plague

Time to talk about one of my favourite things: Infectious diseases. Seriously, I got in to science because I fell in love with the movie Outbreak! I know you would probably have never guessed, considering I’ve been studying neurodegenerative diseases for the past 8 years (Sheesh, am I really that old?), but I do really love them. Well … infectious diseases, serial killers, and mother nature. What can I say? I’m obsessed with destruction.

A new article was just published in The Lancet Infectious Diseases journal (you can sign up for a free account and gain access to all of their articles here) called “Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis.” This article is so recent, that it’s not actually in print yet, but you can find it in the “Online first” section. There is also a Comment made on this same article (kind of like a short ~1 page synopsis) that you can read too.

Lancet
[Source]

Anyway – on to the amazing things found in this article!

To begin, it is important to mention that there have been at least three human plagues: The Justinian Plague (6-8th century), Black Death (14-17th century) and the Third plague (19-20th century). I guess we ran out of cool names for plagues – but because they found that it came from the Yunnan Province of China, they could have called it the Yunnan Plague. Anyway, if you want to know more about plagues in general, visit the CDC and read away! This current journal article is going to focus on the Justinian Plague because of a few reasons: it’s not clear where it originated, the link between the first plague and the other two is not clear, it’s not clear whether or not the second two plagues evolved from the first one (did the plague get stronger or weaker over time?), and it’s not clear whether or not all of the plagues were just the same disease but continuously mutated (like our flu viruses) or brand new versions.

These researchers came upon a medieval burial site that contained many bodies (indicative of people dying from an outbreak) and when they radiocarbon dated the goods in the burial site, they found they dated back 1500 years – during the Justinian Plague! The coolest part is this: the researchers pulled some teeth and they still had blood in them and they were subjected to DNA sequencing! How amazing is that? Teeth, bones AND DNA surviving 1500 years?!

They found that the first pandemic was spread by fleas that bit some rats and, like the other plagues, they originated in China! They actually followed the Silk Road Trade Route!

Silk_Road
[Source]

Another finding? The first pandemic is a unique strain passed from rodents in to humans. It is not like the other Plague strains!

Internet Quizzes, Wizards, and Science (oh my)

It seems that these last few weeks have been all about the Zimbio quizzes. Everyone I know has done at least one. So, I thought, heck! I’ll do all of them. It was mostly for research purposes (of course) because they all focus on the minutia. How are you most like a certain character, who may not be overly complex. But, we as individuals, are the exact opposite. Shrek says it best:

Shrek: [peels an onion] NO! Layers. Onions have layers. Ogres have layers. Onions have layers. You get it? We both have layers.
[walks off]
Donkey: Oh, you both have LAYERS. Oh. You know, not everybody like onions. What about cake? Everybody loves cake!

We have so many layers and I don’t think just one quiz could even peel the first layer off that onion. This is why I did multiple quizzes. I wanted to see, in the end, how well they could analyze my character by asking questions like ‘out of these movies, which is your favourite?’ or ‘are you good or evil?’. In the name of Science, this was almost an unbiased test, as I don’t watch many of these shows and I haven’t read some of these books. So, I took the following quizzes (Which character am I in the Hunger games, Harry Potter, Star Wars, Mean Girls, Grey’s Anatomy, The Simpsons, Pretty Little Liars, Anchorman, and Game of Thrones, Which creature am I in The Hobbitt, and Which Disney princess am I) and got the below results.

KatnissEverdeen_HG Dumbledore_HarryPotter Tiana_DisneyPrincess Mulan_DisneyPrincess Obi_WanKenobi_StarWars CadyHeron_MeanGirls CristinaYang_Greys Lisa_Simpsons Caleb_PrettyLittleLiars Drogo_GOTWizard_Tolkien Veronic_Anchorman

Where to begin?

You’ll notice, there are two Disney Princesses up there. That’s because, I took that quiz twice. I forgot to save the result image, and when I took it again, I got a different Princess. Rather than say one was an outlier, I included both because there was some truth in both.

Some of the common themes amongst all of these characters (according to the descriptions given, because, again, the only movies/books I Have seen/read are The Hunger Games, Harry Potter, Mulan, and Mean Girls. — my wife watches Grey’s Anatomy, so I’ve seen some episodes of that show, but not enough to say I could swing the quiz towards one character) are traits I highly value in myself, which is pretty neat.

Those traits are: honest (sometimes to a fault), ambitious, intelligent, and hard working. Even my introvert-ness came out in these quizzes, along with my ability to dream big and do whatever it takes to achieve those dreams (which can make it hard for me to fit in). I am selfless and giving and caring.

What’s pretty neat is, if I didn’t take all of these quizzes – and only took, say the Big Bang Theory one, I would have given up on these stupid things. Tiaras? Really? I can fit in, I’m not that awkward … So she and I don’t seem to make a huge connection (if you can call it that). But, when we combine her results with the rest of these characters, then the puzzle makes more sense.

Kind of like in science – the more data points you collect and the more technical and experimental replicates you perform, the closer your data approaches the true mean!

I know who I am, but now, you can see a glimpse of that for yourself.

Nice to meet you! I seem to be an awesome jaundiced wizard who can hold her/his own in the wild and I will always follow my heart and it should keep me out of trouble. But, when trouble comes, I can hold my own.

Expectations of growing up

There are a few questions in life, which I feel, are always relevant. Some of these questions are never even re-phrased as we get older. My favourite?

“What do you want to be when you grow-up?”

When I was younger (much, much younger), I wanted to be a teacher. After all, it was the first “big” word I could spell and it was who I was surrounded by all the time. Not to mention, I loved (I mean LOVED) school. Seriously, it was a treat to do homework every night.

My cousin Matt and I were inseparable when we were younger. My family would often tell him he was going to be a doctor one day, and I would be his nurse. I thought this sounded like the best plan. I would be able to help my cousin make everyone feel better, plus, I would be able to see him all the time. It really was win-win for me. That is, until I started questioning why I couldn’t be the doctor and why he couldn’t be my nurse. Or, why we both couldn’t be doctors?!

But then, I went on to middle school and started to have science classes. Not the generic science classes, but chemistry and biology. I then wanted to be a scientist. I had no idea at that time that there were types of scientists. All I knew was I loved my science classes, despite struggling with them the most. In Michigan, we had to take these achievement tests from California (CAT) until Michigan eventually made their own (MAT). Anyway, I would always score the lowest in the science and english categories, and I would always score the highest in math. This has never changed during the course of my life. The ACT, the SAT, and the GRE all followed these trends. I actually think it’s because of my amazing math skills that I even got in to graduate school in the first place.

Back to my story.

When I was 16, I was nearing the age of getting my first job. I was super excited! I could earn some money to buy myself some new school clothes, or save it up for something more grand one day. It was very important to earn our own money growing up, especially because I lived in a single-parent household with 2 other sisters. All 3 of us hated asking our mom for any money, and we would often go without the things we wanted because we had everything we needed. When I was 16, and I could get a job, I was all for it. But what to do? I knew I didn’t want to work with food. I was awful with people, and I didn’t want to carry heavy trays to tables (let’s face it, I’m pretty clumsy, and this would have been disastrous). So, I began where most people did – I looked in the newspaper to see if there were any funeral homes in the area that could use a receptionist. I figured – I wouldn’t really have to deal with angry people yelling at me, and how perfect of a job would that be?! At this point in my life, I wanted to be a Mortician. Alas, a funeral home wasn’t my first job. I ended up as a game master for a local lazer tag joint. It was the best first job ever! But, it really had nothing to do with what I wanted to be for the rest of my life. That one was getting trickier and trickier to answer.

What did I want to be when I grew up?

I went through high school knowing I was going to go to school to be a scientist. I ended up at Michigan Technological University in the upper peninsula of Michigan studying Molecular Biology. Just 1 measly year in to this degree and I knew it wasn’t exactly for me. It was heavy on the biology, as the degree was offered through the Biology Department, and biology seemed very much like the english and art classes to me. What I mean is, biology was more qualitative and I was more quantitative in nature. I decided to switch to Chemistry. I am so glad I did. My grades were improving, and I liked the classes I was in. Then, I graduated with my degree and …. now what? I guess I should find a scientist job somewhere.

Oh boy, did you know there are many types of scientists? I sure didn’t. So, again, I had to figure out what I wanted to be. I went on to my first job at a prominent institution working as a biochemist in population genetics studying Parkinson’s disease. It was pretty cool, but that lab wasn’t a great fit for me. I also had to move from Michigan to Florida, far away from any familial support system. I got a second job to help pay some bills at a local movie theatre, where I met (and still talk to) some amazing people. After this job, I went to another prominent institution and I worked as a Chemist in R&D helping to develop new contact lenses (you probably have tried them out, if you wear contacts). I loved learning and using all of the instrumentation (which was available in huge quantities, so I barely had any waiting time – it’s like a dream for any scientist!) but it really felt like an assembly line. I would go in to work every day, log in my hours, work as fast as I could, then go home. When I was at home, I never thought about this job. Although I made great money in this Industrial job, I craved the research I did at my first real job outside of university. So, I went back, hesitantly. I knew the work environment could be catty and I hated the drama. So, I made a sacrifice. I took a lesser pay for doing something that seemed important to me. I went back, this time working as a Biochemist and Biophysicist on Alzheimer’s disease. Time when on, and I began hearing that pesky voice in my mind asking that same pesky question. This job is great and all, but what do you want to be when you grow up?

I decided to go on and get a Ph.D. in Biochemistry, with a heavily biophysics influenced project. Would it surprise you that I kept with the neurodegenerative disorders too? I am 4.5 years in to this degree, and I hope I only have 1.5 years (at most) left. It would be wonderful if my pain and suffering could be ended much sooner though (I’m not going to lie)! With this degree, my world is going to open up. The jobs won’t be flowing in like I always imagined due to this economy, but I could be anything my little heart could desire. … but what does that even mean anymore? 

Alas, I arrive at the same crossroads I have been at my entire life.

Have you read Hamlet by William Shakespeare? Basically, Prince Hamlet wants revenge on his uncle for killing his father. Prince Hamlet ends up exacting this revenge, taking the throne he was born to have, and marrying his father’s widow (i.e. his mother). It’s a crazy story that just gets more and more crazy, especially as Hamlet becomes more enraged and more grief-stricken … and, if you weren’t picking up what I was putting down, Hamlet goes mad. This tragedy explores a lot of different themes along the way; of course there is incest, the corruption of morality, revenge, and even treachery. Hamlet is by far, one of Shakespeare’s greatest works, and it has a lot of wonderful quotes. The one you may be most familiar with is

“To be, or not to be, that is the question—
Whether ’tis Nobler in the mind to suffer
The Slings and Arrows of outrageous Fortune,
Or to take Arms against a Sea of troubles,
And by opposing end them? To die, to sleep—
No more; and by a sleep, to say we end
The Heart-ache, and the thousand Natural shocks
That Flesh is heir to?”
-opening phrase to the soliloquy in the Act III Scene I of Hamlet (modern version)

Bare with me as I take this entire passage (which I have significantly shortened) out of context and apply it to my non-incest, non-treacherous, non-morally corrupted, and non-revengeful life that is slightly mad.

What do I want to be as I grow up? Should I suffer doing research that I don’t necessarily like and doesn’t feel important to me, while making a lot of money? Or should I go into the scientific abyss, doing something I really enjoy, that constantly engages me, while making a meager wage? Either way, we all die in the end, and with that death is the death of all our worldly troubles.  …. This brings me to current day. I have done these two things, I have chosen the meager wage and my happiness. I hope this trend keeps happening, because I would love to be able to sleep at night.

So, my friends, I ask you – what do you want to be when you grow up?

Discovery of a new cell death mechanism: Ferroptosis (fair-oh-toe-sis)

I have decided that I want a section of this blog to be about science, not just my frustrations with it. I will summarize some awesome papers (awesome to me) one at a time in as simple of a way as I can. I won’t be able to dismiss all the science jargon, but I will do my best. This topic is very dear to my heart because it is what granted me candidacy (where I went from a graduate student to a Ph.D. Candidate …. super cool title). Here, I present to you, a new cell death – but before we go in to that, I explain cell death first. I wrote this research summary for the undergraduates here at University of Nebraska-Lincoln, and I wanted to share it with all of you (assuming you don’t fall asleep). If you ever want a science-y topic to be discussed, hit me up in the comments below or send me an e-mail!

***

There are many types of cell death mechanisms. The one you are probably most familiar with is apoptosis (a-poe-toe-sis), or programmed cell death. In trying to understand apoptosis, more cell death mechanisms were discovered because certain things were just not consistent with apoptosis. Take necrosis, another type of cell death, as an example. In apoptosis, the cells shrink because components of the nucleus (DNA and proteins called chromatin) were condensing. Once everything gets so small, it starts packaging itself into smaller bodies, and breaks away from the original cell. Eventually, all of these dead bodies are taken in by other types of cells and completely destroyed. In necrosis, the cells get larger because the membrane is breaking which allows some of the extracellular fluid to get inside of the cell. This starts happening to all of the compartments within the cell, and eventually all of the contents, including enzymes and proteases, spill in to the extracellular environment. The released enzymes and proteases then chew away at the cell until it is destroyed. The differences between these 2 types of cell death can be seen in the figure.

Cellular differences between 2 major cell death pathways

Cellular differences between 2 major cell death pathways

In May 2012, a group recently started characterizing a new form of cell death, which they decided to call Ferroptosis [1] , mainly because it involves iron (Ferro) and they see death (so they just stuck with the ‘ptosis’). They came across this unique cell death pathway when they were trying to use a drug called Erastin to selectively kill certain types of mutants (RAS family of small GTPases) that cause cancer in 20-30% of all cancer patients. First, they took their cancer cells and incubated them with erastin, and in just 6 hours they noticed a lot of their cells were dead. They then decided to incubate the cancer cells with an iron inhibitor (called deferroxamine, or DFO), and they didn’t see any death at all. Next, they wondered what would happen if they put BOTH the erastin and the DFO on the cells. There was no death! This means that the death caused by erastin depended on iron being present! This is the very first time any cell death mechanism has required iron! Using these same scenarios, they measured the toxic products generated via the mitochondrial electron transport chain, called reactive oxygen species (ROS). This group did some measurements with a flow cytometer and found out that erastin also caused a lot of ROS to build up and the ROS were also dependent on the iron.

In science, just because you have a neat discovery doesn’t mean you neglect some controls. So, this group had to prove ferroptosis was in fact different from apoptosis and other types of cell death. So, they used a different type of cells and chemically induced the different types of cell death. After enough time had gone by, they took those cells and looked at them under a power microscope. They noticed the mitochondria were smalled in ferroptosis but any of the other cell deaths. So far, so good! They did a lot of complicated tests with many cell death inhibitors, and cell death inducers, to really hammer home the idea that ferroptosis was indeed unique.

Now, we have ferroptosis, which isn’t like any other type of cell death, and it requires iron and ROS. This group decided to figure out what makes ferroptosis genetically distinct. To do this, they used 8 different cell lines, and lowered the mRNA levels (with something called short hairpin RNA, or shRNA) for 6 genes they recently found in a screen. They found some iron proteins, and proteins important for translation, to be important in ferroptosis!

Because ferroptosis is new, this group had to find a way to restore growth so they could look at this death mechanism inside of a mouse, and they did this by finding an inhibitor of ferroptosis. They are a witty group and decided to call it Ferrostatin-1. When they were trying to figure out how ferrostatin-1 inhibited cell death, they realized that lipid (fat) generated ROS were crucial for this death mechanism.

Overall, this group found a new form of cell death, which they decided to name Ferroptosis. Ferroptosis requires iron-dependent production of ROS, NADPH-dependent oxidases (proteins that can transfer electrons across a membrane to an oxygen thereby generating superoxide, a type of ROS), and lipid peroxidation (oxygen takes away an electron from the lipids, thereby creating more ROS). With the use of a power microscope, it could be seen that the mitochondria were much smaller in cells that died from ferroptosis. Therefore, ferroptosis is a truly unique way for cells to die!

REFERENCES

1.                   Dixon, S.J., et al., Ferroptosis: an iron-dependent form of nonapoptotic cell death. Cell, 2012. 149(5): p. 1060-72.
IMAGE:      http://www2.uah.es/daviddiaz/Apoptosis/caracteristicas.htm