Apr 27, 2011

Piled higher and deeper: greatest hits

Since I'm bogged down writing my thesis right now, I thought I'd share some of my favorite comics from Piled Higher and Deeper, a graduate student comic strip collection by Jorge Cham.  For those of you not familiar, it's a good intro to the culture of grad school.

Enjoy!









http://www.phdcomics.com/comics.php?f=47












http://www.phdcomics.com/comics.php?f=124










http://www.phdcomics.com/comics.php?f=125






Apr 26, 2011

Use me for general comments

Hi everyone!

Please use this post as a way to give me feedback about my blog: topics of interest you may want me to cover at some point, am I being too technical, website design, etc. (I won't publish these comments unless there's strong opinion otherwise.)

Thanks again for all your feedback!

Apr 24, 2011

Happy Easter! So how did the egg get its ellipsoid shape?

Given today is the one day of the year most people in the world appreciate the ellipsoid shape of the egg, my science pick for this week is my own research: on how the egg gets its ellipsoid shape.

Insects and birds are two animal groups that produce ellipsoid-shaped eggs, thought to be an adaptation to laying eggs on land.  But the puzzling part is that developing eggs (a.k.a. egg chambers or follicles) start out as a sphere.  So how does it become ellipsoid?  I figured this out by looking at developing eggs in the common fruitfly, Drosophila melanogaster, directly by keeping them alive for a few hours outside of mom and sticking them under a microscope and recording what happens.

Here's what I saw them do:  they spin around the long axis.  Pretty remarkable, huh?

Developing Drosophila eggs



Developing eggs spin!
(Click the link to play the movie)







So what's the point of spinning eggs?  Spinning around helps the developing egg build polarized fibrils like Collagen around its surface.  It's the oriented Collagen fibrils that helps the egg get its ellipsoid shape as it continues to grow until the eggshell is deposited.  (Collagen is the main component of our tendons and ligaments, so it's a strong molecule to deal with forces and help shape tissues.)

Interestingly, developing chicken eggs have also been reported to spin around the time its ellipsoid shape is being formed.  But because it's hard to study that process as it happens, no description at the cellular or molecular level has been made in the chicken.

Drosophila is one of the most popular animal model systems in biology because scientists can identify the genetic, cellular and molecular basis of many biological processes, and scientists have used findings from Drosophila research to discover that many processes in humans and other animals use the same genes and principles that help them grow, develop, and function.  So we hope that our work may help uncover new insights to thinking how we form organs during our own development and during the development of many animals!

For free, full access to the original paper, visit:
Global Tissue Revolutions in a Morphogenetic Movement Controlling Elongation

Hooray for the Easter egg!

Apr 23, 2011

The Basics: Right Time & Place, Necessity, Sufficiency

One of the greatest challenges for science students transitioning from the K-12 education system to the college/university setting is realizing that everything your instructor tells you is not fact. 

Why?  We grow up believing everything our elders tell us and read textbooks believing everything that it states is fact.  But there's a few problems.  Textbooks summarize a huge body of work, and while most of is it generally accepted as scientific fact, the authors are not experts in everything, and can occasionally get things wrong. We first begin to learn about cutting-edge research in a college lecture because professors like to keep up to date with the material, but because it's cutting-edge, it hasn't had years of independent validation by other scientists, so occasionally, some of it may be wrong or out-dated.  

In fact, many of you out there have probably wondered a question no one has figured out the answer to yet.  So how do we ever figure out how the world works and further our scientific knowledge base so they become fact?

This varies amongst scientific disciplines, but I will discuss how we approach questions in the biological sciences.  There are 3 basic types of experiments that help scientists become confident of their results:

1) Is it there at the right time and place? if it's not there, it can't be involved in the process
2) Is it necessary?  If it's required for the process, eliminating it should block the process
3) Is it sufficient?  If it's able to control the process, adding it to another tissue (where it normally isn't present) should allow the process to occur

Say you have a favorite gene (fave) that you hypothesize is important to form the spinal cord.  If fave is expressed in the neural cells that give rise to the spinal cord, it passes test 1).  If you remove fave from those cells and you don't form a spinal cord, it passes test 2).  If you add fave into cells that normally make skin and they become neurons of the spinal cord, then it passes test 3).  At this point, you can feel pretty confident that fave is involved in spinal cord formation.

In an ideal situation, biologists can demonstrate all these 3 types of experiments for their research project, but sometimes we can't because biology is complicated or there are other technical challenges we can't overcome.  This can affect how confident we are in the result, but by having other researchers validate our results, we can increase our confidence and eventually accept it as general scientific fact.

Hope this brief lesson is helpful!

Apr 22, 2011

Some amazing finds today!

Some of you know that I study egg shape.  Specifically, how you make an ellipsoid shaped egg.  (I will tell you how in a few days...in time for Easter!  Stay tuned.)

Well, in searching for some hard-to-find references for my thesis, I was very excited to see on Wikipedia's media depository (Wikimedia Commons) that there is this classic late 19th/early 20th century illustration of eggs from a variety of organisms!  It's an amazing find for me to see someone who captured the beauty and variety of the very process I am interested in appreciating so long ago!




from Nouveau Larousse Illustré [1897-1904], vol. 6 p. 473.
(click on link above for key)






Shortly thereafter, visiting the good ol' Bioscience library to borrow a book so I can scan/print a book chapter, I end up in the embryology section of the library.  Hans Spemann (1st Nobel Prize winner in embryology (1935) for discovering 'organizer' tissues - parts of the embryo that can tell other parts what to become), C.H. Waddington (one of the most influential thinkers of biology in the pre-molecular era of the mid-20th century); what great finds!  My lab looked a little surprised that I had brought back nine books!

(Gasp! Bbb...books?!  Yup, I know.  You might think modern scientists just read papers from the internet using PubMed to keep up with the latest cutting edge papers.  Most do.  Some of those scientists think that papers pre-1985 are not worth reading, but there's a lot of really interesting descriptions, observations, insights and even conundrums that can get glossed over.  We even have the potential to figure these conundrums out with the advent of the molecular and genomic era of the 1980s to now.  So become a fan of the classic scientific literature; I am!)

Apr 20, 2011

Current Status of the NIH Budget

National Institutes of Health (NIH) - Policy Update released by the Genetics Society of America today:

"The US Congress finally passed a budget resolution on Friday, April 15, at the eleventh hour before the government came grinding to a halt.  The resolution, which funds the government until September 30, 2011, the end of the 2011 fiscal year, resulted in flat-funding for NIH for the rest of the fiscal year, although two areas sustained $260 million in cuts – a $210 million cut for all of the Institutes/Centers and the Office of the Director at NIH and a $50 million cut for Buildings and Facilities. NSF sustained a $53 million cut in two accounts:  $43 million cut for Research and Related Activities (funding level is $5.56 million) and $10 million cut for Education and Human Resources (funding level is $862.7 million). For more information, read the Appropriations Committee Press Release and follow the links there."


The large majority of our research funding support comes from the federal government - specifically the NIH - through grants of various kinds, most notably by R01 grants supporting principle investigators (PIs; code for college/university faculty).  While the NIH fared off better than most govermental agencies, these cuts still affect current researchers who joined at a time when the NIH was growing.  The cuts the NIH faces means that labs with solid research plans that have been supported in past years may not get their grants renewed or new faculty may have trouble getting their first grant application approved, making it even more competitive to get funding support in an already competitive arena.  

What does the news mean for grad students and postdocs?  Some senior lab members may be forced out of their labs due to the funding crunch by their PIs...before they have secured a job in academics, industry or elsewhere.  And we don't get paid very much to begin with, so it places a major financial strain on us because we don't get unemployment benefits (us grad students don't have typical job positions with W2 forms) to help float us until we can find our next (semi-)permanent position.  These are scary times to be in academics!

Last post for tonight; back to thesis writing. =)

The current crisis in academic science

It's been on the minds of many senior Ph.D.s and postdoctoral fellows in my department.  When it becomes newsworthy for one of the top science journals (Science, Nature, and Cell) to report, you know it's a crisis.  Please visit the link to read more:

Day 1: Balancing this blog and my need to finish my thesis

Hello readers!

I am very excited to start my blog.  I will begin by sharing with you what I'm up to right now.

I am graduating one month from today and I must write and file my dissertation within 3 weeks in order to obtain my Ph.D.  Yikes!  (I am behind on my writing.)  Fortunately, it's an exciting time because I get to reflect on how my research area has changed from the time I started my Ph.D. project (4 years back) to now, and because I get to speculate where it's headed based on my own research I've done that adds to our growing body of knowledge. Or even change the way scientists think about a given phenomenon!  I am also trying to decide what I will do next after I graduate - an academic postdoc position but in whose lab I have not decided.  So I apologize that my first few posts may be sparse as I develop this website and work on my dissertation and figure out what's next in the coming weeks.

Welcome!

I came back from the Society for Developmental Biology (SDB) West Coast meeting in Honolulu, HI, inspired by P. Z. Myers to start my own website and blog, as a public service mission to communicate the excitement of science to you, the general public.  
I've started this blog because I believe I have a social responsibility as a professional scientist to communicate science openly to the people.  I will blog about what I think are important topics in the biological and biomedical sciences and explore the value, current issues, and realistic expectations of what we gain from doing research on that topic.  In addition, I'll explore how science is done, share with you why I think the research I'm working on is of interest and worth funding by taxpayers, give you a taste of what my daily activities entail, and share the latest cutting edge research published in science journals.  All in layman's terms, so you can follow too.  
I hope through my posts you will come to appreciate the value of academic science and learn about a world which may seem 'foreign' to you.  And also to learn something neat along the way.  Enjoy!