Figs

The Fourth of July means red, white and blue to celebrate America’s birthday, but with our mild spring and ample rainfall this year it also heralds fig season in south Louisiana. If your experience with figs is limited to Fig Newtons or once upon a time you had fig preserves on toast, I am pausing for a moment of silence for your taste buds. A fresh fig picked and eaten just off the tree is something else altogether.

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Fresh figs do not keep for any significant length of time and you’ll be hard-pressed to ever find them in the grocery store. So, if you’d like to try this summer delicacy, make friends with someone that has a fig tree or grow your own (surprisingly easy for anyone in hardiness zones with winters less than 800 chill hours).The most common varieties grown in the south are the Celeste and the Brown Turkey fig (Texas ever-bearing) which produce small brown figs. The LSU AgCenter has introduced several new varieties in recent years including the LSU Purple and LSU Gold, colored according to their namesakes. I have two LSU Gold trees and as far as taste goes, I cannot sing their praises enough. They have a delicate and very sweet taste. It’s what I imagine heaven must taste like. However, in my n = 2 experience these trees get huge in a hurry. It’s great if you’re impatient for your first fig crop, but beware if your backyard space is limiting. Typically it is not necessary to prune fig trees as with other fruit trees, but you may want to rein in an LSU Gold tree in a small backyard. This is less of a problem with Celeste or Brown Turkey figs.

LSU Gold

LSU Gold

If you are new to fig tree culture, you may ask yourself, “I wonder what fig tree blossoms look and smell like? I am sure they must be equally heavenly.” Yes, that’s because the ‘fruit’ you are eating are actually a special type of inflorescence structure (read flower) with the botanical name syconium or synconium. It is basically a modified fleshy stem that encloses numerous ovaries (floral tissue). The inner pulp is the flowers.

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You should also beware that fig stems (branches and where the fruit are picked) produce a milky latex material to which some people can be sensitive. It contains the enzyme ficin that will degrade proteins. In fact, this enzyme is used commercially to differentiate blood groups for transfusion purposes. Human blood types go beyond the standard A, B, O or even Rh designations. There are numerous antigens on the surfaces of our blood cells that can affect transfusion success. The Kidd antigen type on your red blood cells and kidneys is difficult to determine in its normal state, but treatment with the enzyme ficin aids in differentiation because the partially degraded product will be more reactive while other variants are resistant to ficin degradation.

Whether or not you care about the finer points of their plant biology or use in biochemical assays, once you have your own fig tree(s), you will inevitably become overwhelmed with the glut of fruit produced in the month of July. You can pawn them off to family, friends, neighbors and acquaintances. Drying them in halves is another great option and intensifies their flavor for use in cooking later. Hardcore enthusiasts will can them as preserves. Now, I was never taught the secret of my grandmother’s fig preserves, but I have read the protocol. Even with a PhD in biochemistry and finely honed protein purification skills at the lab bench, the multi-step process of successfully preparing fig preserves gives me pause. So, who wants figs this Fourth?

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Johnna

References and Links:

https://en.wikipedia.org/wiki/Common_fig

https://www.hort.purdue.edu/newcrop/morton/fig.html

http://aggie-horticulture.tamu.edu/extension/fruit/Figs/figs.html

http://faculty.ucc.edu/biology-ombrello/pow/Fig.htm

https://edis.ifas.ufl.edu/mg214

http://www.botgard.ucla.edu/html/botanytextbooks/economicbotany/Ficus/

http://naldc.nal.usda.gov/download/15714/PDF

http://www.lsuagcenter.com/NR/rdonlyres/69df3014-f313-4784-afeb-eaac4125406e/61881/pub3018louisianafigshighres.pdf

http://hortsci.ashspublications.org/content/40/2/486.full.pdf

http://www.redcross.org/cgi-bin/pubs/16.3sm.pdf

http://pathology.ucla.edu/workfiles/Education/Transfusion%20Medicine/5B-Blood-Kidd-luPPT.75184755.pdf

Writing the Discussion/Conclusion Section

This was part of a series of writing tutorials I wrote for my students. This series is compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.

The Discussion/Conclusions section is where you synthesize the information from multiple experiments into some new insights and make connections with the wider research world. Journals differ significantly in their formats for Discussion/Conclusions and Results. Some journals combine the Results and Conclusions sections so that you can incorporate the broader significance of your results as you write them. With this style, there may also be a very short (1-2 paragraphs) section dedicated to pure ‘Discussion’ where authors can make other connections to their research field. In the absence of this as an official section, authors typically use their final paragraph to reiterate the main points of the work, what they mean for new knowledge in the field and what outstanding questions remain. Other journals will have a dedicated Discussion/Conclusions section that is separate from the Results section. In this section, you have more space to write about the significance of your results. You should include references to other related studies for comparison and contrast to your conclusions. If there are any outstanding questions left by your research or obvious future directions, you can dedicate the very end of your manuscript to writing about that.

In either format, this is the last substantive writing that your audience will read. It is important that you package your work in some coherent way (new model, refuting a hypothesis, etc) so that the reader will understand the same accomplishment. It is important to strike the proper balance when interpreting your data and incorporating it into the larger knowledgebase of your scholarly field.

A weak Discussion/Conclusion section can leave the reader wondering why they started reading the article in the first place. “So, what?” This is not the way you want others to feel about _X_ years-worth of work on your part. Remember that your first readers are reviewers to decide your manuscript’s publication-worthiness. If they can’t figure out why they read this manuscript (other than the fact that they were assigned to by the editor), then they won’t want others to read it either, at least not without major revisions). You may have a particular interpretation of your data, but if it is poorly articulated or not explicitly stated, then your readers will be left to do this on their own. When this happens, your readers will begin to ask questions like, “Why didn’t you do this experiment?” In some cases, this is a perfectly valid point and you should’ve done that experiment. In other cases, their questions and other possible conclusions are not warranted because you should have more clearly explained how your controls or previous literature argue against certain interpretations.

At the other end of the spectrum, over-reaching your data and making grand interpretations that extend beyond what you have actually shown can also get you into trouble. As fellow scholars in your field with finely-tuned BS-meters, your reviewers will call you out on egregious cases of over-interpretation. This will usually come in the form of requests for numerous, difficult and time-consuming experimentation. If you want to make bold claims, you have to prove it. If you are ready to publish, you need to rein in your writing and tone down your claims. Research always continues, so it is reasonable to stand by a decision that enough experimentation has been done to form a publishable manuscript. Just make sure that any planned future experiments or outstanding questions that you raise aren’t critical to the work at hand. If more than one reviewer disagrees with you about your arbitrary stopping point, then you really should get back to the bench and collect more data.

Ideally, the Discussion/Conclusion section should tell the story you intended when you put your figures together. By this time in the process, you’ve finally found your groove for writing and it’s important to check yourself to see if you’ve found the right balance. Re-read the first draft of your Discussion/Conclusions section with fresh eyes alongside the figures with supporting data and look for any potential weaknesses. Should you do additional experiments or include other controls? Should you clarify your claims? Should you tone them down? Is there any other relevant literature that you should cite to facilitate interpretation? In the end, you should strike the proper balance so that your work is significant and interesting within the boundaries of sound data. Your reviewers will inevitably find something they would like you to change, either with writing or experimentation, but you should do your best to avoid baiting them right out of the gate. Even if you are making a conscious effort to objectively review your Discussion/Conclusions section, as an author you are biased and too close to your own data to see some potential flaws. Have another colleague outside the author list look it over prior to submission for publication.

One final note on grammatical formatting…

For this section, you can carefully marry past and present tense. When referring to specific data or experiments (which you will do only briefly; no need to completely repeat everything from the results section), use the past tense. When describing what it means in a bigger context, these things are true, will always be true and you can use the present tense. Grammar and clear writing are essential in all sections of your manuscript, but meticulous wording is critical for this section to avoid confusion about data vs. interpretation and past vs. present work.

Johnna

Pyramid of Biochemistry Greatness

As I mentioned in my previous post, there’s at least one person in the world searching the internet with the phrase ‘everything aspiring biochemists should know.’ I feel obligated to share my pyramid for biochemist success. It’s based on Ron Swanson’s perfectly calibrated recipe for personal achievement. Click this link for context if you are not familiar with Parks and Rec.

Pyramid

Here is a link to the PDF with a little better resolution. Now, go achieve your dreams. I would say good luck, but as Ron says, “Luck is a concept created by the weak to explain their failures.”

Johnna

2nd Blog-iversary

New Under the Sun Blog is 2 years old! Because WordPress keeps such detailed statistics, here’s the annual numbers rundown. Here is the link to the first year’s numbers. 

Followers: 928

Still not exactly sure how this gets counted, but I’m definitely up from last year (668) and still completely amazed that many people outside of my immediate family chose to follow a blog about photosynthesis, plants and biochemistry.

Total page views: 35679

This number is waaay higher than last year. Thanks Google and social media. My all-time most-viewed posts and pages are still my basics of the photosynthetic reactions. Lots of students seem to be still confused about this topic and many variations of ‘photosynthesis-related’ Google searches send clicks my way. I hope my pages were helpful.

I have a new winner for the all-time highest single day post: Two Tales of a Manuscript at 304 views that day (Big thanks to the Plant Cell Facebook page for posting a link!). It faded pretty quickly, but still a good long read about the process of science that struggling scientists and even non-scientists will appreciate.

Also, internet users search for ‘cotton’ a lot and end up clicking on my post from last Labor Day. It’s on pace to even out hit my post on the world’s tallest tree (Hyperion), which continues to be my most popular non-photosynthetic post.

I also like to troll the stats on the least common and crazier search terms that earn me a click. This year’s favorite ‘everything aspiring biochemists should know.’ This search term alone gives me hope for the future and I hope that the clicker found something useful on my site. In addition to the Rules of Biochemistry and the Molecular Biology Code, I do have plans for Dr. Roose’s Pyramid of Biochemist Greatness coming soon ala the Ron Swanson Pyramid of Greatness (coming soon).

Now for the bad news as to why the sequel isn’t as good as the original- only 55 posts this year (about once a week)Sigh. In my first year, I was able to churn out 165! My only excuse is I had to keep my new day job. So, on this free site, you get what you pay for. This summer has been less than productive on the blog front as well. It is hard to write clever, informative posts now that Jr. PhD has hit the stage where he is constantly asking questions. Tonight’s topic- Why did the Giant Sloth go extinct? (We went to the library today and got an encyclopedia on dinosaurs and prehistoric animals.) I’m a plant person and I don’t have a short answer that he will accept.

I was able to finish out some series this year. Check out the Frozen Parody series for a new twist on plant science topics and the Holiday Plants series for the botanical companions to your holiday traditions (also available in almanac-form downloadable PDF for free!). Still working on finishing some others and I’ve definitely have no shortage of post topics- just time to write about them. Please be patient.

Here’s to another year of science blogging!

Johnna

Writing the Results Section

//This is part of a series of tutorials I wrote for my students. Toward the end of the semester as deadlines were looming, they became more specific for the assignment in my course. So it’s taken me a while to modify them. Since part of this series got picked up over at the Addgene.org blog, I feel like I should really finish up this series. This series is compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.//

The results section is the main course of your manuscript. This is where you lay out all of your data in carefully arranged figures to build the case for your conclusions. Since you have already decided what data get to leave the pages of your lab notebook and have rendered them as informative figures, the majority of the work of your results section is finished.

General

The results section is written in the past tense because you are describing experiments performed and observations made previously. “The ADH purification procedure gave a 6-fold purification with a 20% yield.” In some contexts, your results will yield new truths about ADH, which will always be true. It would be appropriate to use the present tense in these contexts, but be careful how you do this. It is generally easier to restrict results to the past tense and save the new insights for the discussion section where they can be mentioned in the present tense. The reason for this is purely grammatical because it takes some practice to successfully blend tenses within sections/paragraphs without it turning into a hot mess.

Your figures and tables frame your story

The order of your figures is usually not the chronological order in which you did the experiments. Care should be taken in arranging your figures in an order that will best support your conclusions. The first figures typically describe the experimental system and its verification (creation and validation of a mutant, isolation of a protein, demonstration of a new analytical method etc). Subsequent figures show the application of the experimental system to a relevant question to generate new knowledge. These can be used to build evidence for a particular model of how you think something works or to eliminate possible explanations. Either way, the order of your figures should take the reader through a logical sequence that will culminate in your conclusions.

Tell the story

Once you have laid the groundwork with your properly assembled figure sequence, the text of your results section should guide the read reader through each figure and how your data lead you to new knowledge of your research topic. If your writing takes strange circuits or you have difficulty in transitioning between sections, you may want to re-think the order of your figures. It typically means there is some conflict between the data in your figures and the way you want to write about it. Speaking of sections, it is often useful to break up the text of your results into useful sections with headings that describe the analysis or main conclusion from the results.

While your figures should be clearly understandable with legends to describe what the reader is looking at, the text in your results section should give the context for that data and highlight the key findings. When you refer to your data, refer to them by their figure (and panel) or table number. Since you have multiple gels and graphs, you cannot just refer to them generically by experiment type without designating a specific figure without causing confusion. Also, it is more succinct to say ‘Figure 5A’ vs. ‘the graph of absorbance/activity vs. elution volume.’ In the context of the assembled manuscript, the figures and their legends will be pages and pages ahead of the results section. So, you must direct the reader to the proper place. In the final version of the manuscript that actually gets published, the figures will be re-sized and type-set into journal pages where they are closer to their results text, but never assume that your reader will be able to pick out the proper panel of a figure on their own.

Methods context and purpose

To set up the descriptions of your figures and what they possibly mean, it is important to give some context for the experiment. Describe the purpose for the experiment. The data in your figures should accomplish this purpose and you must describe how so in the text of your results section. Remember also that the details of the methods used will likely be pages and pages previous, so it’s perfectly acceptable to reiterate some method highlights for context, especially if they are important for interpreting the data in your figures. You should be able to read your results paragraphs and have a good understanding of what is being done without having to flip back to the methods section.

Discussion within the results section

How much discussion you include in your ‘results’ section will vary depending on the journal for which you are submitting your manuscript. Some journals have a separate discussion section where you are allowed a designated space to expound upon the meaning of your results in a larger context, outstanding questions, links to previous studies etc. In this case, keep your results section focused on the data at hand. Don’t dwell too much on implications or what the results may mean unless those conclusions transition into your next figure. If there is no separate discussion section, then write your conclusions where appropriate, but overall your writing should still stay grounded in your data. Too much elaboration is a symptom of over-interpreting your results and reaching beyond what the data actually means. Stick to the facts and qualify the conclusions where appropriate. It’s always a good idea to connect your work to other studies, but too much may again be stretching your data more than is necessary. Too many conclusions or integrating your work into a complex model at the end also risks a call for additional experimentation by the reviewers that get the first look at your manuscript. If your data along with previously published work doesn’t support every aspect of your conclusions, they maybe you should do some more work in the lab. If that suggestion just made you throw up in your mouth a little, then maybe you should be more conservative in the interpretation of your results.

Johnna

Superphotosynthesizer: Cat Island Baldcypress

Today May 18, 2015 is ‘Fascination of Plants Day,’ an initiative organized by the European Plant Science Organisation with other events organized by the American Society of Plant Biology. On this blog, there’s no shortage of reasons why plants are fascinating, but to most they are still just the scenery. Take some time today to consider all that these primary producers do for you. Here are just a few things plants do for us- food, forestry products, paper, pharmaceuticals, energy, and beauty.

Of course, I am partial to the oxygen that they provide for us. In that spirit, today’s post will feature another superphotosynthesizer: the Cat Island Baldcypress located on the Cat Island National Wildlife Refuge in West Feliciana Parish, LA. This tree is the national champion of its species and also noted as the largest tree of any species east of the Sierra Nevada range.

It is located at the end of an easy walking trail (0.75 mile round-trip), but it only accessible for part of the year. Access to portions of the Cat Island NWR is prevented by levels of the Mississippi River since at least a couple of low bridges must be traversed to get you from the main road to the trailhead. If the river stage at Baton Rouge is greater than 20 feet, which is usually between February and June, there is no vehicle access to the trail. I was able to make a trip there in early February just before the river restricted access. It’s not quite clear whether the base of the tree itself is submerged at any point during the spring flooding because there is a really nice decking just before the tree at the end of the trail. As of today, the river stage at Baton Rouge is 27.8 feet, so it may still be another month before access is regained.

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The tree is impressive. At 96 feet it is taller than all the other trees around, but it’s certainly not the tallest tree east of the Sierra Nevada. However, its girth is undeniably impressive. It has the characteristic buttressed-base of all baldcypress trees, which measures 17 feet in diameter and 56 feet in circumference.  It has knees as tall as me. Well, for those of you who know me in real life maybe that’s not so impressive, but for a random root outgrowth that is still significant.

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This brings me to one of the real secrets of the swamp- cypress knees. These strange growths at the base of cypress trees have been puzzling botanists and plant biologists for centuries since Francois Andre Michaux wrote in 1819, “No cause can be assigned for their existence.” Many people have had theories as to how they contribute to cypress biology- increased aeration capability for growing in inundated swamps, methane (swamp gas) emission conduits, vegetative reproduction, mechanical support, nutrient acquisition, and carbohydrate storage. None of these hypotheses have really held up to analysis and the biological function* of these root outgrowths are still fascinating plant biologists today.

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This is just one local fascinating plant example. Check out the links below for more information about Fascination of Plants Day or follow #FOPD on social media.

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Johnna

*These expendable appendages are painted and carved for folk art projects. They are also fairly proficient at disemboweling lawnmowers of homeowners with cypress trees in their yards and capsizing careless motorboat operators in the swamps. Perhaps this is a plant defense mechanism ahead of its time.

References and Links:

http://www.plantday.org/

http://fascinationofplantsday.org/home.htm

http://blog.aspb.org/fascination-of-plants-day/about-fascination-of-plants-day/

http://blog.aspb.org/fascination-of-plants-day/

http://www.fws.gov/refuges/profiles/index.cfm?id=43697

http://www.fws.gov/refuge/Cat_Island/visit/plan_your_visit.html

http://www.monumentaltrees.com/en/trees/baldcypress/deep_south/

http://www.na.fs.fed.us/pubs/silvics_manual/Volume_1/taxodium/distichum.htm

http://en.wikipedia.org/wiki/Cypress_knee

http://www.venerabletrees.org/good-knees-said-baldcypress/

http://arnoldia.arboretum.harvard.edu/pdf/articles/2000-60-4-cypress-knees-an-enduring-enigma.pdf

Becoming Real

I’ve been in my new teaching position for an academic year now. It has been quite the transition from my research position as a postdoc. Because of the designed transient nature of research training as a graduate student and a postdoc, I’ve often joked about not being ‘Real’ for quite some time. The elusive career path of many PhDs seems to be filled with the same question as the Velveteen Rabbit in the tale by Margery Williams.

“What is REAL?” asked the Rabbit one day.

There has been much discussion about what this means for a career in science these days. It used to only mean one thing- a tenure-track position at a research university. However, more often that path is less traveled, only the fantasy of whispered voices among labs of senior members who were fortunate (?) enough to be raptured away to the ranks of assistant professors. The majority of us are still working out what it means to be real in terms of career and still live with ourselves as human beings. I am still on that path, but the way seems to be clearing.

THERE was once a velveteen rabbit, and in the beginning he was really splendid.

I love research and working with my hands in the lab. I’m very good technically at performing biochemical experiments. I like developing new experiments to answer questions stemming from previous results. I even like meticulously assembling publications from my results; there are not many details I miss in the instructions for authors. I can graciously respond to reviewers’ comments. While I do fewer of these things today, all of these things are still true for me. Despite years of tedious experimental drudgery and the inevitable walls you encounter during research, I still say that I enjoy it, but the systematic practice of research wears down even the tenacious. Eventually, you realize you are not new and splendid any more, but you are not yet real.

“Real isn’t how you are made,” said the Skin Horse. “It’s a thing that happens to you. When a child loves you for a long, long time, not just to play with, but REALLY loves you, then you become Real.”

The Skin Horse has some good advice for PhDs. It isn’t how we are made. There isn’t a single formula that we should all be following. This is terribly disappointing for someone like me that so enjoys checking items off of to-do lists. If only I could accomplish all these tasks and then I would be real. However, it doesn’t just happen to you either. You have to be an active participant. At some point, you must make a decision and take some risks. Real involves risk. For me, it was leaving a research career for something my training had only minimally prepared me for- teaching.

“Does it hurt?” asked the Rabbit.

“Sometimes,” said the Skin Horse, for he was always truthful. “When you are Real you don’t mind being hurt.”

Risk means you could get hurt. Of course, I run a tight ship around the lab (even more so in the teaching lab) so there was little chance of actual physical pain in my transition to teaching. Nevertheless, there was a steep learning curve for figuring out time management in a teaching position. The feedback from my students has been rewarding so that weakens the memories of late-night grading sessions and last-minute-laboratory-troubleshooting.

“Does it happen all at once, like being wound up,” he asked, “or bit by bit?”

“It doesn’t happen all at once,” said the Skin Horse. “You become.”

“It takes a long time. That’s why it doesn’t happen often to people who break easily, or have sharp edges, or who have to be carefully kept. Generally, by the time you are Real, most of your hair has been loved off, and your eyes drop out and you get loose in the joints and very shabby. But these things don’t matter at all, because once you are Real you can’t be ugly, except to people who don’t understand.”

I’ve only been in my current position for an academic year now. The jury is still out on real, but I am becoming. No matter the career choice (teaching, tenure-track, private, start-up, other altac) if you have a PhD, you are not someone that must be carefully kept. If you are happy in the career choice that has made you real, then you can never be ugly, ‘except to people who don’t understand.’

And so time went on, and the little Rabbit was very happy–so happy that he never noticed how his beautiful velveteen fur was getting shabbier and shabbier, and his tail becoming unsewn, and all the pink rubbed off his nose where the Boy had kissed him.

I have been surprisingly happy in my instructor position, but I am quite certain the teaching has given me a new wrinkle or two. I furrow my eyebrows together much more in my new position puzzling over the interpretations of instructions by my students than I ever did interpreting the results of new research. I also have an eye-twitch at the thought of grading some assignments. Thankfully, my blonde hair has resisted any grays up to this point, but I may not be able to stave them off for many more semesters. I really haven’t noticed these changes too much, and I’m sure I will lose a few more whiskers along the way.

“He doesn’t smell right!” he exclaimed. “He isn’t a rabbit at all! He isn’t real!”

“I am Real!” said the little Rabbit. “I am Real! The Boy said so!” And he nearly began to cry.

The students call me ‘Dr. Roose’ and even sometimes ‘Professor.’ Remembering to answer to these titles was the strangest part of the transition into my new role. In my head, imposter syndrome raised doubts. “A real instructor would have already made that presentation. A real teacher would have worded that question more clearly. A real professor would have graded those exams by now.” I just took it day by day, but sometimes I still felt like the rabbit yelling into the wind. “I am real! I have a laser pointer and a remote slide-changer. I wrote a syllabus! I use Moodle!” I’m sure I’m not the only PhD on a career path with delusions of insufficiency. The truth is, we are simultaneously none of us real and all of us real. You just get up every day and become as best you can and that’s real enough for today.

“Wasn’t I Real before?” asked the little Rabbit.

“You were Real to the Boy,” the Fairy said, “because he loved you. Now you shall be Real to every one.”

No, my tears this year did not conjure a nursery magic fairy to restore my wrinkles. Teaching has not suddenly become easy and perfect. As much as I thought I was real getting through two semesters, I have more improvements that I would like to try for the future. Given the budget climate for higher education in my state, I (like the Velveteen Rabbit) am just glad to have escaped being burned with the garbage pile. However, the Department did make me real to everyone in one way- my very own legitimate name plate for my office door. Becoming real indeed.

Door

He was a Real Rabbit at last, at home with the other rabbits.

Links

http://digital.library.upenn.edu/women/williams/rabbit/rabbit.html