Posted: February 23, 2011 in attitude, education, philosophy

College is a difficult time, a transitional time. This applies to ALL students, regardless of background or experience, age or philosophy. Whether you are fresh out of high school and learning to exist on your own, laid off and creating new opportunities, or just plain tired of the same old thing and forging a new path – the one consistency is change.

The most important thing you can do is: COME TO CLASS. Be there. It doesn’t matter what demons you escaped, it doesn’t matter what happens outside those (crappy) wooden doors – inside our classroom you are nothing but yourself, and you are everything to me. I have never met a failure. I have yet to encounter a single student who could not do it. I have only met students who were too afraid to try. I know what this looks like because I was once that student. My reasons were probably different than yours, and yet the same. I got over it, and so will you.

Consider the amount of time you spend beating yourself up. Feeling regret, shame, embarrassment, or anxiety. I challenge you to now take HALF of that time, be it an hour or ten, and commit to volunteer that number of hours each week. Perhaps you may choose to study instead. Either way, you probably gained a significant amount of freedom during that five-second thought experiment.

Let’s do another experiment, only this one more than just thoughts (this coordinates with the new assignment I’ve posted for you in CampusCruiser…). I want you to really evaluate your daily schedule. Make to-do lists, and actually cross things off. Reward yourself for doing so. Set a consistent and reasonable daily wake-up time, study time, and bed time. Moreover, set a DAILY WORRY TIME. No joke. Maybe set two.

What am I talking about? Well, we all have issues. I remember looking that those “perfect” people when I was in high school and college and wondering, “How the heck can they be so confident, so happy? What is the secret?” And I spent years (and probably knocked years off my life) trying to figure it out. You know what I know now? Those people have problems, too. They’re just better at faking it than me. So what.

Okay. So here’s what I do. This, by the way, is hard. It’s nearly impossible at first, especially for those of us with OCD and perfectionism… I have a ten minutes scheduled at 9:00am and again at 2:00pm in which I’m allowed to worry. So if any anxieties or concerns or paranoias leap out at me during any other time, I make a note of them. Then I say, “I will worry about this at 9 or 2.” I then go about my day productively, and at my next regularly scheduled worry time, I wear myself out with concern. However, when the ten minutes are up, I MUST go back to being a productive, normal, happy self.

As ridiculous as this sounds, IT WORKS. For reals. Try it. In addition to working on its own, it often makes me laugh out loud at myself. By the way, whoever first noted that “laughter is the best medicine” was clearly a genius, for laughter absolutely is the very best anecdote to all ailments. I would hate to pay a doctor who didn’t laugh, or have a lover who couldn’t laugh. Life would be so lame.

Stop taking yourself so seriously; for goodness sakes, stop taking ME so seriously. We’re all in this together. You are so capable, so get yourself into class and study at least nine hours per week and then show me what you’re made of. That first exam was really, really hard. But by and large, you aced it. You deserved those great grades, and I cannot wait to see what you have in store for me in the future. Let yourself be proud.

¡Arriba! ¡Abajo! ¡Al centro! ¡Pa’dentro!

Neat Tricks

Posted: February 13, 2011 in helpful hints, just for fun

For those of you less-than-confident in with your light microscope skills, check out this virtual scope! Virtual Microscopy

Now, some of you were asking about using an electron microscope…and here’s a virtual one to play with! Virtual Electron Microscopy

Need some help studying? Look inside a cell or take a virtual cell tour!

Want a little visual for how diffusion and osmosis apply to membrane transport? Build yourself a phospholipid bilayer and check out what happens!

Wondering how cells communicate? Use this awesome tool: Dropping Signals

Make it a game (and beat people)!!! Here are just a few of the fun online games designed to help make biology fun:

This guy has compiled an amazing list of even more virtual activities!

One Gene = One Protein

Posted: February 12, 2011 in biochemistry, genetics

Once upon a time, every organism was a single cell. Whether the product of binary fission, mitosis, or sexual fertilization, all of life’s secrets are held in a microscopic unit with an average (eukaryotic) diameter of 0.00001 meters.

What the components of any given cell are, whether it contains organelles, and which, and a number of other variables are dynamic between creatures and over time. The one thing all cells have, however, that defines them as living organisms, is heritable information – nucleic acids – and the machinery required to process those directions – ribosomes.

When our DNA directs growth and development, and provides the defining characteristics of our selves, what really is happening? How can a four-letter sequence of sugar-phosphate-nitrogenous bases create a living being? And then, in the case of multicellular organisms, build it up to a coordinated, functioning whole?

Excepting our red blood cells, all our somatic (body) cells contain our entire genome. The only difference between cells in different parts of your body is WHICH genes are turned on, to what degree (level) each is expressed, and when. In addition, the genes you turn on and off even within distinct body regions are dynamic over time – coordinating the correct set of genes is essential for proper development, proportional body growth, to maintain homeostasis in an ever-changing environment, and to regulate life cycles.

What does it mean to say that a gene is expressed? Less than 2% of our entire genome actually consists of “genes” – these are the stretches of nucleic acid “words” that encode instructions for the creation of a specific protein. Proteins themselves are composed of amino acids – your DNA is read as three-letter words; each triplet of bases, termed a codon, specifies one particular amino acid equivalent. If you had a random collection of objects from which to choose, you might say “hat” – and could then also select the literal item itself. You could then perhaps say “bat,” and so on. Your DNA gene would be the complete list of three-letter codon words like “hat”  and “bat,” and the piece of the protein it referred to (individual amino acids) would be the objects we named a hat and bat and etcetera. A gene, then, is a stretch of DNA that refers to an actual object; genes are said to be expressed when that gene is read as directions and the object, a protein, is assembled within your cells. When all these components have been properly created and distributed, you might have a full game of baseball, or a functional organism.

To protect that most precious of all molecules, DNA, your cells enclose it in a membrane-bound nucleus. When a particular gene needs to be expressed, that specific DNA region is copied into an RNA transcript. This RNA copy of the DNA gene is then exported from the nucleus to the cytoplasm, where expression is completed. The process of creating an RNA copy of a single gene from the DNA template is called transcription; just as the general definition of the term would imply, this process involves making a same-language copy of the DNA words. The alphabet looks nearly the same (the letters are G, C, A, and U – where U is substituted for the T of DNA); you can think of RNA as a different dialect, or accent, of the language of DNA.

The RNA transcript of a demanded gene is now greatly shorter, and therefore easier to work with, than the original full DNA genome. This sequence may be further processed before the act of translation occurs in the cytoplasm. During translation, the RNA triplet codons of nucleic acids are exchanged for the associated amino acid in a growing peptide chain. In other words, just as with the general definition of “translation,” one language is changed into another – but while retaining the original meaning. As the polypeptide grows, it is folded and processed and eventually emerges as a functional protein. At this point, your original DNA gene has been expressed.

All of your characteristics are the result of protein creation during gene expression. Your eye color is the accumulation of proteins that reflect certain wavelengths of light back to the eyes of others (if you have green eyes, or brown eyes, or hazel eyes, it’s because the protein pigmentation in your eyes does NOT absorb that particular color and shade, reflecting it for others to see). Likewise for your hair color and skin color, and all color! All of these phenotypic traits are coded for by not one, but a complex combination of genes. Not only do individual genes and proteins make you who you are, but the interactions between multiple genes and proteins also contributes to your unique self.

“There is grandeur in this view of life, with its several powers, having been originally breathed by The Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”

(Last paragraph from Darwin’s The Origin of Species)

Incidentally, ladies and gentlemen, today, 12 February is International Darwin Day.

Photo 51

Posted: February 12, 2011 in biochemistry, genetics

How does DNA work? How can something so seemingly arbitrary – something composed of four bases each containing simply a sugar, a phosphate group, and a nitrogen-containing compound – determine our appearance, instincts, thoughts, behaviors, and very existence?

Humans have 46 chromosomes, or 23 paired sets (one each from ma and from pa!). Altogether, the human genome has roughly 3 billion base pairs – in other words, the genetic information directing our lives is a “book” containing 3 billion “letters.” If you were to stretch it all out end-to-end, you would discover yourself to be carrying about 6 feet of DNA per cell, or 2 billion miles of genetic information total. Wow! The alphabet itself contains only four letters; most of the words are the same for each of us (think: if they weren’t, you might have limbs or organs in different places than the guy next to you!), but the difference between any two humans can reach up to 0.1% (this may seem like a small number, but it is still about 3 million letters). Most of the differences, called single nucleotide polymorphisms, are singular and located in isolated spots rather than in full “words” or long stretches.

Journey Into DNA

Humans have an estimated 20,000-25,000 genes. These “words” – the part of your DNA that is coded into protein – make up only about 1.5% of your total genome! What does the rest do? Well, that question is a work still in progress: http://www.genome.gov/

How do we know what DNA looks like? How do we explore our genes at the molecular level? In biochemistry, form and function go together like peanut butter and bananas (trust me, it’s good). Most of our knowledge comes from analyzing data garnered during elegantly designed, indirect experiments. Today, we often use highly sophisticated computer programs to discern the secrets of our genes, but originally we relied heavily on X-ray diffraction.

From this image, taken by Rosalind Franklin in 1952, did modern genomics emerge:

The Anatomy of Photo 51

Flowers wilt. Chocolates melt. Roaches are forever.

That’s why I just named one of the Bronx Zoo’s Madagascar hissing cockroaches in my Valentine’s honor. Like my special someone, my roach is resilient and resourceful, and always around.

Vote for your classmates!

Posted: February 11, 2011 in current events

Hey everyone – Take this opportunity to click on the 1406/7 tab and hit the link to vote for one of your colleagues in a scholarship contest she’s entered!!!! (Or just click here: http://www.brickfish.com/Pages/PhotosAlbums/PhotoView.aspx?qsi=55189338) In addition, when you enter your own contests, please post your link here as well so we can support you too 🙂


Posted: February 10, 2011 in chemistry

So the concept of tonicity refers to a comparison between two solutions. It is not a type of chemical reaction, nor does it make sense all on its own.

When you are looking at two different substances, you may compare them if you want to know various properties, such as which way diffusion will occur between them. If they are separated by a semi-permeable membrane, the diffusion which takes place will potentially be only that of water – termed osmosis. So in biology, when we ask about tonicity we may really be asking about osmotic pressure (see handout from this week’s lab; it can also be found in our Campus Cruiser lecture page “Shared Files” under “Handouts” as “Crossing the Membrane” – online in color it may be more help than printed in black and white).

What did I just say??

Let’s boil it down (pun intended…): Wikipedia says this about tonicity. Once again, I officially denounce Wikipedia!! Whew, now that that’s out of the way, I totally suggest you read the Wikipedia entry for tonicity 🙂 I also suggest you supplement this brief tidbit of knowledge with the information provided here.

Additionally, this website cracks me up. I mean, really. I am a fairly extreme nerd, but a website with this name? I feel better about myself already. And you will not only laugh but also learn from it. Whoa!

At this point I encourage you to revisit (or just look up) the concept of dynamic equilibrium. I think you may find a good ideological fit here.

When we say that something is hypertonic to something else, it means that particular substance has a higher concentration of dissolved solute particles than the object of comparison. On the other hand, when we say that something is hypotonic to something else, it means that substance has a relatively lower concentration of dissolved molecules within the solvent. When two substances are isotonic, the solutions have equal (relative) concentrations of solute and solvent.

None of these terms imply a chemical reaction has taken place, as diffusion and osmosis occur in absence of energy release or gain. It is merely a balancing act – fulfillment of the laws of thermodynamics, which take place in absence, and without regard to, living systems.

Here are some useful videos: