Living with Uncertainty

So in my very first blog post I talked about studying science because I wanted to discover the the Truth. This seems straightforward enough when we first learn about the scientific method in high school. You develop a hypothesis, design an experiment to test that hypothesis, and then get an answer. When you first start studying science you think that the worst thing that can happen is that you prove your hypothesis wrong. But really this is one the best things that can happen! That means that you're learning something new. One of my biggest disappointments in studying science is in realizing that no matter what field you choose the process of doing science is a lot more messy than this. There are so many opportunities for the variability of the real world combined with human error to lead to confounding or inconclusive results. Every step of the scientific process must be done with care from choosing your question and designing your experiment and most importantly interpreting your results. In some ways this is exciting, doing science takes more creativity than most people would think and for most scientists thinking about what our results mean, what questions are yet to be answered and how to design the best possible experiments to test these questions is what keeps science interesting.

Recently an article in the Atlantic Monthly magazine titled Lies, Damned Lies and Medical Science suggested that a large percentage of studies, especially when it comes medical studies involving the development of new drugs, turn out to be incomplete, misleading or flat out wrong. Similarly an article in The New Yorker magazine titled The Truth Wears Off talks about a phenomenon in which a discovery that seems highly significant at first seems less certain over time. This does not mean that science is not a useful tool for discovering the truth but it does mean that we can't take the finding of every scientific study at face value, we have to evaluate data for ourselves, and we have to keep an open mind when new data comes about that challenges our preexisting ideas. There is tremendous pressure on scientists to publish quickly and make their results sound as exciting as possible. In the pharmaceutical industry there are large financial gains or losses at stake and in academia scientists are competing for ever shrinking grant dollars and a finite supply of tenure track positions.We can't go from a blind faith in myths or magic to a blind faith in every published scientific result. Science is a slow and evolving process. Each study adds one piece to the puzzle and we have to be careful not over-interpret our results. Over time scientific findings are corroborated or rejected as other scientists repeat and build on the work that has been done before. Science does not result in a bunch of facts that can never be challenged but rather is a slow accumulation of knowledge based on rigorous interpretation of the data we have.

In my first blog post I talked about taking comfort in having an answer to my question of why the dinosaurs died out stating that most scientist believe that a meteor impact on the Yucatan peninsula caused climate changes that resulted in the dinosaurs' demise. Of course this is likely not to be the whole story. Recently researchers at the University of Alberta used a new dating method on the bone from one dinosaur to show that this particular individual was alive 700,000 years after the mass extinction event that was thought to have killed off all of the dinosaurs. Future studies will show whether this finding was a fluke and will continue to explore how different factors contributed to the demise of the dinosaurs. For me this is exciting and I continue to believe that the scientific method is the best approach for answering big questions about our universe.

Braaaiins!!!!! Part I: The gatekeepers

The brain is by far the most intriguing organ in our body. It perceives the world around us, allows us to learn new skills, forms and retrieves our memories and holds the key to our very selves. Everything that we know about the world is filtered through and depends upon the structure of our sensory receptors and the processing of that information through the communication of neurons in the brain. Understanding the brain is a daunting and intimidating task and yet the principles underlying brain function depend on the physical properties of cell membranes, ion channels and the physical connections between cells.

The whole trick of the neuron comes down to the properties of the cell membrane. The membrane is a physical  barrier between the inside and the outside of the cell; some types of molecules can pass through easily other types of molecules cannot. Ions are charged particles that cannot pass through the lipid membrane. So how do ions get in and out of the cell? Through ion channels which create actual pores in the membrane that allow different types of ions to pass through.  Ion channels act as gate keepers that open or close based on the physical surroundings. Ion channels undergo conformational changes to open or close in response to different cues some ion channels open in response to an increase in voltage while others open when they bind a particular type of molecule. All of these properties of ion channels are determined by their physical shape which is determined by the sequence of amino acids that makes up the protein, which is encoded in our DNA.

So far so good, right? Easy! We have a physical barrier between the inside and the outside of the cell and a series of transmembrane protein that act as gate keepers to either let ions in or keep them out. Coming up: how do neurons take advantage of this arrangement to create the electrical signals that serve as the communication signal throughout the brain?

Do you believe in magic?

Before studying science I viewed the world as a mysterious sometimes magical place. As child everything almost everything we encounter is incomprehensible and like every human society that has come before us we often make up our own explanations or myths to explain our experiences. Even when I first started studying science as an undergraduate, molecular processes that I couldn't see had that same magical, mysterious quality for me and I approached the molecular biology that I did in the lab a bit like alchemy. Mix this here mix that there swirl it through a tube put in a fancy machine and voila I get bands on a gel.Magic! But the deeper I've gotten into studying different disciplines of biology the more I've come to fully understand that the world is tangible, made up of physical objects with distinct physical properties that govern and constrain how biological systems behave. This is such a simple concept, but for me, really coming to grips with this fact has been profound. You would think that maybe having this feeling of the world as a magical place taken away from me would be saddening or disappointing but actually I find it to be the opposite.  Instead the world feels less scary and more amazing. Early scientists studied the natural world to better understand the nature of God and while my ideas of the divine may be a little more abstract than their's I have a similar feeling of the natural world as place whose virtues and elegance are just waiting to be discovered.

I feel less intimidated to approach scientific problems. As a kid I hated math. I found it to be completely abstract and incomprehensible and I carried this fear into college and beyond. Using math and seeing it used to model and explain real data has brought me to the realization that math isn't some abstract thing that has been pulled out of the air to torture me with but rather is a different language for describing concrete, physical principles that actually exist in the world. I only wish I had truly understood this sooner so that I would have been less intimidated to take math courses in college and could now be better equipped to wield this powerful tool. When you realize that the problems you are trying to solve, though they are breathtakingly complex, are based on processes that you are perfectly capable of understanding then suddenly you have the confidence to approach them in a rational way.

I have found that studying neuroscience has really driven home this point for me. In my next blog post I will use the example of the inner workings of the brain to further explain my point.  I also promise in upcoming blog posts the stop waxing lyrical about the wonders of the natural world and talk about some the frustrations and controversies of scientific research.

Jumping Spiders!

Apparently it's ugly animal week here at Bioluminate.  Here's another animal that definitely falls into the category of "so ugly it's cute."

This image is from here.  I came across this animal listening to Dr. Bruno Olhausen from UC Berkeley give at talk at the USC Integrative Theoretical Neuroscience symposium.  Dr. Olhausen research focuses on building a model of visual cortex. The cortex is the layered brain structure in mammals which gives our brain its distinct rippled look.  The primary visual cortex (V1)  processes the images we see in the world by breaking down natural images into components (for example some neurons respond best to lines in orientated in a certain directions). Higher regions of visual cortex then build these components into coherent images and interpret them. This all happens so fast that we can look at an object and say cup, or dog or cat and it seems simple, but when you think about it's actually a difficult task.  The brain must be able to recognize objects with different shapes and patterns on different backgrounds, from different angles and we can even recognize an object if it is moving through space.  Computer scientist have been attempting to build computer algorithms to allow computers to accomplish basic object recognition but this has turned out to be a surprisingly difficult task!  By building models to understand how visual objects are processed by the visual cortex Dr. Olhausen and colleagues hope to be able to apply this knowledge to practical applications.

However, as Dr. Olhausen pointed out to us, even animals with no cortex and a simple nervous system are better at recognizing objects than our best computer models. Jumping spiders are different from most spiders in that they don't build webs, instead they are visual predators.  Jumping spiders have 8 pairs of eyes 3 of which provide fuzzy peripheral vision (they literally have eyes on the back of their head) and 1 pair in the front which have good resolution and allow them to recognize mates and prey.  When a male spider is presented with a female spider or even just an image that sufficiently approximates a spider he will perform an elaborate mating dance, check out the video, it's pretty hilarious.  Even a tiny 1 day old spider is able to recognize, stalk and kill its prey.  Jumping spiders are another example of how biology has achieved elegant solutions to complex problems.

My favorite things

So here is an object that combines two of my favorite things in the world, knitting and weird sea creatures.  The pattern for this guy comes from a book called Amigurumi Knits by Hansi Singh .  The author gives instructions for knitting different organisms including bugs, vegetables and sea creatures.  It is so nerdy I really can't help but love it.

There are so many things to love about anglerfish.  1. They are sooooo ugly.  2.  They are mysterious and live in the deepest darkest depths of the ocean. 3.  Anglerfish have a lure that sticks out in front of them with a glowing ball on the end.  The end of the lure glows due to the presence of symbiotic bacteria, how the bacteria find the fish and are incorporated is unknown. Meals can be few and far between on the bottom of the ocean; the lure tricks other fish into coming closer to investigate and once they get within range and anglerfish attacks and swallows them whole!  4.  Male anglerfish are lazy!  Have you ever thought that you had a parasitic male in your life?  Well finding a mate on the bottom of the ocean is hard and finding food on the bottom of the ocean is also hard so male anglerfish have solved both these problems.  Male anglerfish are small and their sole purpose in life is to find a female, once he does he latches on to her, his blood stream fuses with hers and he loses most of his organs. Each  female can carry around multiple males.  The presence of a parasitic male on this knitted anglerfish is one of my favorite things about it.

Truth with a capital T

My first year in graduate school my fellow students a I were slogging through a research article in a required  seminar course when the professor told us “you all are not excited enough, there are only two reasons to be a scientist, either because you want to save the world or because you want to discover the TRUTH with a capital T.” It is true, the dedication and commitment to be scientist requires this kind of zeal.  I am more of the second kind of scientist; I am driven to study biology because I am intensely curious about the world around me.  When I was 4 or 5 years old I was talking to my dad about dinosaurs and why they became extinct.  “It’s a mystery” he told me, but I just couldn’t stand the fact of not knowing and that I might not ever know.  I remember asking him “do you think when I die and go to heaven that God will tell me why?”  This being a complicated theological question my dad had no answer for me.  

Now there is a general consensus that the dinosaurs died out in a massive extinction event caused by an asteroid that struck the Yucatan peninsula in Mexico.  And honestly, I do feel much better having this answer; it gives me comfort to know that plausible answers can be given to some of life’s biggest mysteries.  Of course discovering such Truths is an elusive goal that is based on the work of many scientists working together and separately (sometimes antagonistically) over long periods of time, with each experiment contributing an incremental step forward.  We are constantly revising and updating our knowledge sometime discarding old “truths” entirely and replacing them with new ones.   The debate about exactly how and why dinosaurs died out continues and it is likely that in the years to come our understanding of how this extinction event occurred will continue to evolve or be changed entirely based on new evidence.

The world around us is so amazing that it fills me with wonder and like a little kid I constantly find myself asking “why?”  My goal in starting this blog is to share with you why I think Biology is so cool and interesting, talk about the process of doing science and discuss how and whether understanding biology can help us make sense of the world and our own lives.

I welcome all comments and suggestions especially if you have a question you would like answered about biology or biologists.   Please comment here on my blog or send me an email at bioluminessa@gmail.com