Cheese!

This post doesn’t have much to do with any of my research or my classes. Instead I offer up a counter-argument to the idea that we should follow the diet of our ancestors.(full disclosure: I have tried the vegan diet in my quest for a healthy diet and maintaining healthy weight)

Our modern american society seems to grab onto any fad (read new research into….) that explains the why and how of obesity. Similarly with what constitutes a healthy diet. I was reading an article from the National Geographic web site http://ngm.nationalgeographic.com/2013/01/restless-genes/dobbs-text in which one paragraph discusses the lactose gene. This article is about our genetic predisposition to explore strange new worlds. This paragraph about lactose is to support the premise that culture influences genetic makeup.

The lactose gene is held up as an example of a culture-gene influences. Few individuals carried the lactose gene up until approximately 15,000 years ago. The advent of agriculture, with the supporting dairy farming, allowed individuals possessing the lactose gene a powerful advantage. These individuals were able to utilize a nutritional food source, thereby increasing their chances of survival during times of poor agricultural output and in turn increasing the likelihood of successful reproduction.  A greater percentage of survivors with the lactose gene leads to an even greater percentage of offspring carrying the gene. In other words, the cultural change of farming influenced the expression of the lactose gene.

So the fact that our ancestors did not eat dairy does not support the argument that dairy is unhealthy. Our modern genetic makeup has evolved into something different than our ancestors. Not better. Not worse. Simply different. If dairy were an unhealthy food source, the percentage of individuals carrying the lactose gene should be lower and if dairy were truly dangerous then eventually the lactose gene would disappear due to those individuals being unlikely to successfully reproduce.

This explains why I love cheese!

Another semester down

I have finished the semester.

Not as successfully as I hoped. 

What I learned:     

1. Oral exams are difficult.
2. Open book tests require a great deal of preparation.
3. Even if I think I’m too tired to edit a paper, I should still try.  

And now, back to studying for the GRE.

Update for Plant Ecophysiology project.

       What an interesting, confusing, exciting, frustratingly, long strange trip it's been. Okay, couldn't resist that one. If you read my October 25th post you know that I am working on my Plant Ecophysiology experimental design and it is not going well. I think I have a handle on it and then I discuss with the professor my new idea and realize so many things that I did not consider. I think I might be on draft number 379. Okay. Maybe draft number 4 but it seems like 379. I have begun the lab work with the new hypothesis. "The new growth leaves of plants that are producing fruit or flowers will have a greater stomatal density when compared to new growth leaves of plants that are not producing fruit or flowers." Plants in the reproductive phase of development require higher levels of energy which means the leaves must be able to bring in increased levels of carbon dioxide to facilitate increased sugar production.There is way more going on with the plant than just carbon dioxide intake and sugar production but this is a good starting point. If you want to know more check out plant respiration,potassium pump,stoma or photosynthesis for basic info. I will be comparing stomatal density of new growth leaves on the Tilia americana (Linden Tree) sampled from a tree with fruits to new growth leaves sampled from a tree without fruit. The tree with fruit was found growing in the valley along White Oak Bayou at the base of the Emerald Park Trail, whereas the tree without fruit is growing at the top of the Emerald Park trail. This is the first project that is that I have had to complete on my own. Every project up to now has been with a lab group.

        Earlier in the semester my lab group fumbled through a study design for Environmental Practicum. We are assessing current plants species and populations in a piece of farmland that is being placed into a wetland mitigation bank. Some of the many issues we ran into: How do you divide up the work? New lab partners, with different strengths and abilities. (sometimes the work spreads out perfectly as it did in my Environmental Practicum and other times all three of you are complete noobs, as in my Plant Ecophysiology)

•  What kind of sample design are we going to use?
•  Plot or transect? Why? 
• What can we expect to find? 
• How are we going to identify the plants? Down to species or stop at genus? 
• How are we going to section off the land? 
• How does that GPS work? (none of us were well versed with the Garmin) 
• Will it ever cool off? (the first three excursions to the farm the temps were above 90F)

     Some answers:

• Transects. Because they were recommended by literature we found at the EPA website. 
• Morningglory and Cocklebur! 
• Dichotomous keys from three different books, the internet, pictures and the Plant Taxonomy professor. Both species and genus. 
• Farm plot, Cadron Creek riparian area with levee, Hwy 65 border and the unique habitat in the southwest corner. 
• Give up on the GPS after we laid the baseline transect diagonally across the field. 
• And yes, it finally cooled off!

So many questions

Driving into school today, listening to NPR update the Sandy destruction I drove around a long curve and there it was. A full moon. My first thought upon seeing this particular full moon was how powerful that tiny moon is. After all, some of the destruction from Hurricane Sandy can be attributed to the high tide coinciding with the storm. My daughter lives in Brooklyn and I've been pretty anxious these past couple  of days. She is fine. She evacuated to the lake house in Pennsylvania. The storm was bad there too but they survived intact, no trees down, no power outages.

How different would this storm have been if the moon was in a different phase? I haven't had any course work into tides and tidal forces beyond the basics in freshman level sciences classes. I'm sure someone out there has done modeling to show the answer to my question but would I even understand the papers that explain computer and mathematical models on that level? Probably not. Fascinating to say the least. I envy people who get math on that level.

How are the ecosystems going to be affected by this storm? So many studies to be done up and down the eastern seaboard. Maybe some of the internships I am applying to this summer will be studying this storm's effects upon the Chesapeake Bay ecosystem. I do hope that I'll get to participate in the research.

Salt water moving into areas where it hasn't been before. The tidal force pulling up sea grass beds, oyster beds, and just plain scouring the dunes and coastal areas of all vegetation. How long will it take for the areas to recover? One season, two seasons, never? Are the wild pony populations of the outer banks islands suffering? Does commercial fishing improve or suffer immediately after a storm of this magnitude? Are there species of plants that can hang on in such a storm? What attributes lead to a plant surviving this storm? In areas that are swept bare what will the re-population look like? What are the pioneer plants for the sea shore? So many questions and soon I will be one of the scientists looking for answers.

The application process

          I'm beginning the application process to summer internships. REU (research experience for undergraduates) and never realized how hard it is to present the best side of myself in less than 250 words. But I'm getting there and have a great mentor at my university helping me with it all.

What is a proper gift to give your mentor to show them how much they have helped you?

What is a good resource for how to write up a resume?

A little bit everyday. An hour a few days a week. And soon the project is finished. Whether it is a research project or the application to a internship these small increments make it seem smaller.

Now I need to go put in my 30 minutes of time on my water resources paper.

            I'm in the process of practice. Practice, practice, practice. I'm practicing writing. This blog. I re-read my previous entries and believe me, I need the practice.Of course you probably already realize this. Every type of writing increased my communication skills and communication is a skill every scientist needs. So here goes nothing. Err, something. Oh what ever.

I found a great website of science videos. Go check it out. Now.
http://www.youtube.com/watch?v=Vh2MWgfPiPU

          Oh good. You are back. More thoughts on my Plant Ecophysiology project. I'm considering looking into the physiology of semi-deciduous plants, the kind that grow new leaves in the autumn because...I don't know why. So I've got a question. Why do some plants experience new growth when all the others around them are losing their leaves? Is there an evolutionary advantage to this new growth? To the research then.
More on this tomorrow.

Thanks for reading.

developing a research project

               In plant ecophysiology we are to develop and carry out an independant research prioject. I developed and wrote up what I thought was a fairly good proposal and my professor approved it. Then came the presentation to the class in order too get feed back prior to starting the project. I failed. Flat on my face failure. I know that I need practice on how to present ideas when standing in front of the class and that I am new to all of this but still... I was horrible, looked unprepared (because I was unprepared), and fumbled through my outline. The professor gave a few ideas, my classmates said nothing.
             One of the grad students gave his project proposal. Polished, concise, clear, with measurable parameters. I want to be at that level. I must have had a defeated look on my face because my professor asked why I looked mad. I said that I was  disappointed in my ability. The grad student was awsome, pointing out that learning how to do research is a learning process. A. Learning. Process. As I am writing this it comes to my mind that some people may think the professor was mean to me or rude. I want to assure my readers that I did not feel singled out, or belittled in anyway. He reminded the whole class that it was why we set aside a class period to discuss eachothers projects. We all have to help eachother get better at research.
             I do enjoy these upper level classes that mix grad and undergrad students. This type of class gives examples of the knowledge and skill level that I want to attain. Fall break started today and I'm starting over, using the things that I learned during the class proposal review I'm off to develop a new project. Wish me luck.

Sunday morning readings....musings

             I love to sift through my google reader feed and my Zite content on Sunday mornings. In days gone by (oh the loss of good newspapers) I would spend the morning with the NYT sunday edition and the local Arkansas papers along with a big pot of coffee. Sprawled out across the living room rug. Never really knew what to expect. What interesting tidbit would jump out at me at this time? Is there a topic I did not even knew existed? With Zite and google reader not so much. Zite's algorithms are too small in the categories it provides. I have used this web app for about a year and now the majority of articles presented for my amusement are science (primarily biology) related. The Google reader is a little better as it doesn't predict anything, just gives me exactly what I ask for. Alas, no surprises. I still miss my Sunday morning papers (they just aren't up to par) and every once in  while I will purchase said papers and settle in on a sunday morning to read. It's just not the same as the content is now 50% of what it was a decade ago.  That said, today's surprises.

             A website called book porn. Just pictures (think pintrest) of book shelves. Amazing pictures of book shelves. There was even a book shelf made of books strategically stacked to create the book shelf without any other structural component.

            A website (i think it is a tumblr account but i don't understand tumblr) titled "Things I Learned as a Field Biologist. I read post after post and laughed. I have one professor this term who refers to students as 'Biologists' After reading this author's small stories I now realize...I am a field biologist! I am a field biologist? WOW That is so cool.

          The intelligent octopus https://vimeo.com/44791802

        The Washington Post has an article with the headline "In Hawaii, fisheries service relaxes bycatch limits on endangered sea turtles"  stating that swordfishermen can catch 26 leatherback and 34 loggerhead turtles before suspending fishing. Appalling, right? If you read the entire article you find that, according to Michael Tosatto (regional administrator for the fisheries service) no turtles were killed this year. All were released alive. If this is true and the bycatch is not resulting in death of turtles and the fishermen are reporting truthfully, then is there a problem here? What a great research opportunity. If a scientist could partner with the swordfish fishermen and geo-tag the turtles caught on the swordfish hooks a wealth of information could be obtained without having to create and implement a large, expensive study. Maybe someone is already doing this, it just doesn't make the news.

The Ozark Hellbender

  Wow, two posts in one week. I can't help it. I'm really having a great time this semester. I've given my first talk (just a couple of minutes on a news item of the day), written my first lab report (plant ecophysiology), already working on my second lab report (also plant eco). That may sound a little crazy that we've done two lab reports but the first report was a short lab study of plasticity in leaf morphology and the second lab is a refresher on plant growth graphing of sigmoid curves and the math that goes with it.

    Friday we'll be visiting the site of our wetland remediation (Practicum)  for the first time which is awesome.
      
  The other major project is in Anthropology of the Ozarks and I have developed the topic for my research project. The current incarnation of my project is a literature review of the research involved in the attempt to save the Ozark Hellbender (Cryptobranchus alleganiensis bishopi) which was put on the endangered species list in 2011. I say current incarnation because tomorrow in class we present the outline to small groups and get feedback, input ect. After tomorrow's class the outline may change. 

Photo courtesy of the Sierra Club copied from Google Images

As always,
thanks for reading

A new semester has started

      It is the second week in the new semester and I am excited about the work I will be doing this semester. I am part of a team conducting the initial assessment of a piece of property that a local family is putting into a wetlands mitigation bank. I'll be working primarily in the plant population assessment and will also assist the other students working on vertebrate assessment. The first look at the property will take place on Friday and I'll have an update then.
       I have an independent research project my Plant Ecophysiology class that is yet to be determined. Papers to write in Religion and Pop Culture, Cultural Anthropolgy, and Water Resources. I also will be conducting an independent research project in Cultural Anthropology--the Ozarks.

Nature Retaliates

I was reading a blog post http://scienceline.org/2012/04/manhattan-the-next-atlantis/ (in case you want to check it out) and the statement was made; "we are not safe from the retaliation of which nature has already demonstrated itself capable." and I got to thinking. Retaliation? Retaliation! Hmmmm. I really don't think that Nature is going to retaliate against anything or anybody. I don't think Nature notices us. That isn't to say that humans have no effect on nature but this entity that is referred to as Nature is an abstract concept we use to make sense of the world. Using a word like 'retaliate' causes negative emotional responses from readers serving only in creating a frenzy in which people want to fight, against something, anything, each other. We can focus on an issue and discuss solutions without fear mongering. The truth is emotional enough.

The Gulf Oil Spill 2 Years later

       My ichthyology professor, last week, asked us to read articles concerning the newly discovered effects of the BP Oil Spill  over the weekend. Being the over eager student that I am I dove into the subject matter. However I was quickly sidetracked by other articles, studying for finals and cooking for the week ahead. So today I open up my google reader and return to the subject. I happened upon an article discussing the differing approaches taken by McNutt (USGS) and Lubchenco (NOAA) in the weeks and months during attempts at mitigation.http://www.eenews.net/public/Greenwire/2012/04/20/1
The issue that struck me, and I have read this in other places, was the idea that it is a necessity for peer review of the research before findings could be provided to the government or to the public. The article provides the following quote: "We rightfully got a lot of grief from the academic community," McNutt said during a recent interview. "But we had no option to get it peer-reviewed! If there was an action to get it quickly turned around and reviewed, we would've loved to have taken it."
       I stopped reading at this point and realized that 23 years as a police officer made me rebel from this attitude. Just make a decision, take action! A visceral reaction on my part but still, I can't help it. I've been a student now for a couple of years and understand the importance of peer review but not for something this drastic. The BP oil spill required action not peer review. I'm not going to monday-morning-quarterback any of the actions taken by specific people but we as a scientific community should assess honestly what was done, what wasn't done that should have been, and what to do next time.  This is something that we do in police work after every crisis situation. There will be a next time. Drilling continues. The scientific community should be working on a game plan for what to do, how to jump over peer review in situations such as a massive oil spill, and allow the experts to make decisions on the fly. 

Master's degree

Update to finding a research adviser.
So last week my Ichthyology professor gave me some advice. Don't choose the grad school, choose the graduate adviser. Wow. And this professor already has someone in mind that would fit my personality and career goals. So my next step is to stay close to this professor.

New info.
I found a great app for flash cards. I'm using it for Ichthyology and am finding it to be intuitive and easy to navigate. It's called "flashcards" and its designed for the ipad. The price is $2.99 which is not bad since a stack of 3 X 5 cards will cost about that. This app allows typed or hand written and has a print option.

Biology club committee for organizing fund raisers. Am I taking on too much? Naw.