Category Archives: Uncategorized

Could you, would you teach online?

By Dr. Roose

 

Could you, would you teach online?

Really? I just had to whine.

 

Yes, from a social distance.

It’s really university insistence.

 

I like my students in the lab,

I must generate data for them to grab.

 

It will be great, you’ll all see!

You will still learn biochemistry.

 

I can teach it here or there,

With Coronavirus everywhere.

 

I can teach near or far,

I can teach it from a car.

 

I can teach it from my house

If my dogs can be quiet as a mouse.

 

If you’ll all connect to Zoom,

I can teach from my living room.

 

Everyone plug in your machine,

We can all learn during quarantine.

 

With this virus so concerning,

We all so love online learning.

 

It will be great and you will see,

Still getting your degree.

 

Dr. Roose can teach online.

Stay calm. It will be just fine.

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

What scientists do… in summer!

This has never been more true for me than now. Academic year 2014 – 2015: It’s all over but the grading!

New Under The Sun Blog

Frozen

Let’s start the Frozen series with some summer fun for everyone. Here’s what Olaf (a snowman) thought about summer…

Have you ever wondered what scientists do in summer?

I’ve always loved the idea of summer… Really, I’m guessing you don’t have much experience with breaks, do you?

Nope, but I like to close my eyes and imagine all the potential productivity when summer does come.

There’s no classes… except that new course you wanted to develop for fall

There’s no students… except the half a dozen HHMI undergrads in the lab

No committees… except that one search that’s planning to beat the competition

PI’s will have time to work in the lab… except they don’t remember how to use the equipment.

A flask in my hand,

A burner flaming under ring-stand,

Squinting, yes, that could be a band,

So many experiments to do in summer!

The joy of preliminary data,

View original post 253 more words

2014 in review

The WordPress.com stats helper monkeys prepared a 2014 annual report for this blog.

Here’s an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 31,000 times in 2014. If it were a concert at Sydney Opera House, it would take about 11 sold-out performances for that many people to see it.

Click here to see the complete report.

Dracula (Orchids)

Dracula radiosa Credit: Eric in SF via Wikimedia

If you thought we were done talking about plant costumes, you were wrong. While the title may lead you conjure images of vampires with fangs and dark cloaks, orchids of the Dracula genus look decidedly like something else- an adorable monkey face! I admit it’s a strange nexus of nomenclature and form; nevertheless, today’s post will be appropriate for all audiences.

Dracula simia Credit: Dick Culbert from Gibsons, B.C., Canada via Wikimedia

Dracula orchids won’t be found in Transylvania. These blooms are native to the cloud forests of Ecuador, growing in rainforests at elevations of ~3000 – 6500 feet. They were given their name by botanist Carlyle Luer in 1978. The name was inspired by the dark burgundy to black petals that curve up like the stiff collar of a vampire’s cloak. The petals also taper off into sharp points reminiscent of infamous vampire fangs.

Dracula vampira Credit: Eric Hunt via Wikimedia

But back to the real costume, why would a flower need to look like a monkey? If you’ve been paying attention to the last few posts, you can probably guess that the answer has something to do with pollination. However, it’s not quite as obvious as the Orphys bee orchid connection- these flowers are not trying to entice monkeys over for pollen transfer. From what scientists have been able to decipher so far, these flowers aren’t really wearing a monkey costume so much as they are wearing a mushroom costume. Take a closer look at the floral structure posing as the monkey’s snout. These lightly colored and highly ridged structures look very similar to mushrooms found nearby on the rainforest floor. Check out this link with images for a close-up comparison.

Yes, a perfectly good autotroph in mycological masquerade. It’s not just looks either. Again, orchids dig deep into their biochemical repertoire to create a specialized perfume to go along with the visual effect. All of these smells and visual cues serve to trick small flies into coming to their flowers for pollination purposes. The flies prefer real mushrooms as a food source and place to lay their eggs, but are fooled by the Dracula orchids.

Still, this botanical mushroom costume looks an awful lot like a small monkey’s face. I don’t think scientists have completely uncovered all of Dracula’s secrets when it comes to floral form. Investigations are still underway to tease apart the factors of shape, coloration, and scent. Of course, it’s still possible that the rest of the costume isn’t exclusively for the flies. The faces may serve to deter other would-be herbivores from eating the plants. If you were an insect or another small mammal, wouldn’t you think twice before walking over for a bite if that face was staring back at you? I know I would.

Dracula cordobae Credit: Javier Martin via Wikimedia

If you’re interested in learning more about the ecology of cloud forests and the scientists that study it, check out the link below for a trailer for the Cloud Forest Project documentary film.

 

Johnna

References and Links:

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

http://en.wikipedia.org/wiki/Dracula_%28orchid%29

http://www.odditycentral.com/pics/the-amazing-orchid-that-looks-like-a-monkeys-face.html

http://www.botanicalgarden.ubc.ca/potd/2008/10/dracula_simia.php

http://whyevolutionistrue.wordpress.com/2012/05/28/orchid-mimics-simian/

http://orchids.wikia.com/wiki/Category:Dracula_species_images

http://orchids.wikia.com/wiki/Dracula_dalstroemii

https://www.google.com/search?q=dracula+simia+ecology&tbm=isch&tbo=u&source=univ&sa=X&ei=hEsxVPTHHteiyAT8mICYAw&ved=0CB0QsAQ&biw=1708&bih=821&dpr=0.8#tbm=isch&q=dracula+simia&imgdii=_

http://imgur.com/gallery/eTcGZ

http://www.flmnh.ufl.edu/ecuadororchids/Dracula_eng.htm

https://scholarsbank.uoregon.edu/xmlui/handle/1794/18404

http://namyco.org/images/publications/Dracula_orchids_Dentinger.pdf

http://www.tc.umn.edu/~dent0015/Dracula/Dracula.html

http://cascade.uoregon.edu/fall2010/natural-sciences/natures-masters-of-disguise/

http://uonews.uoregon.edu/archive/news-release/2012/10/cloud-forest-project-premier-uo-features-research-bitty-roys-lab

Transition

Today is the first day in my new role as Biochemistry Instructor for my department. It’s a change I’m very excited about. I’ve inherited a great lab course along with some experienced TAs. Of course I’ll be teaching my students the rules of biochemistry. However, the lab course also incorporates a great deal of molecular biology as well. Stay tuned on the blog for the rules of molecular biology. As for this blog, I’ll keep posting as much as time allows. There may be some topic deviations, but I plan on keeping the primary subject matter the same. After all, somebody has to speak for the trees.

 

Johnna

What’s not new under the sun? This blog!

Today marks the 1 year anniversary of this blog. That’s right, it has been one year today since I clicked the publish button on my first post (UNLESS: What is your truffela seed?). It’s hard to remember how much anxiety I had over releasing my writing onto the internet to an audience of maybe three people. What a difference a year makes! Thanks to all of the stats that WordPress collects, here’s the year-in-review rundown with links to what you may have missed*…

The blog has 668 followers, which I find pretty amazing for a photosynthesis and plant science blog. This means that 668 people took the time to click the follow button or submitted their e-mail address to automatically receive my posts. This doesn’t really even count my lazy friends and family on Facebook or Twitter followers that catch my links via shameless self-promotion on social media.

Altogether, the blog has had 18,605 views with almost 1.5 page views per visitor. I’d like to think that means that most people that have stumbled upon a post have dared to click another. My all-time best for a single day’s worth of page views was Postdoc Appreciation at 275 views, but I can’t take too much credit because it is mostly just a collection of highly entertaining PhD Comics. However, the all-time most-viewed posts over the last year were somewhat surprising to me:

  1. Photosynthetic Light/Dark Reactions
  2. The Home Page
  3. Photosynthesis: Not Just for Plants

Well, not that surprising considering that most of the search terms that landed visitors to my site included terms like “photosynthesis light and dark reactions or photosynthesis not plants.” I hope that the visitors using these search terms were students seeking clarification or a different presentation of something they saw in one of their classes or life-long learners trying to refresh their memories of a fundamental metabolic process. I hope they found what they were looking for, but they sure didn’t feel strongly enough one way or the other to comment positively or negatively below the posts/pages they found. Though not common, the winners for my favorite search terms leading to blog post clicks were “can pandas do kung fu” and “photosynthesis is crazy.” If you’re new to the blog today, that should really give you a feel for my range as a science blogger.

Beyond these basics, size matters when it comes to blog post popularity. The next most popular post after photosynthesis basics and whatever happens to be on my home page- Super Photosynthesizer Hyperion (The World’s Tallest Tree).

Some posts that were among the least popular but definitely deserve a click: SLIPS, Cyanobacteria shed, Mass out of thin air and Adamantium (for plants!). Not to mention this holiday favorite: The Scientific Night Before Christmas. Don’t miss them again this time around. Some other of my personal favorites that I thought would be more popular: Why bother being a scientist?, Science, Pandas and Kung Fu, The Rules of Biochemistry and Behind the Music: Plants. Click and read, remember I will know if you don’t.

In addition to writing for this blog, I’ve also written posts elsewhere. Check out this piece from the ASM Blog Small Things Considered on a mysterious microbial marriage that borders on scandalous. I’ve written a personal postdoc perspective for The Postdoc Way. I’ve also written posts for and hosted the plant science blog carnival Berry Go Round.

All of this writing has amounted to 168 posts or about one every other day. I’ve started a few blog post series: Holiday Plants, Superhero PhD, A new social contract between science and society, GMO Food, Journal Club. Writing this year-in-review has made me painfully aware of how much I’ve let some of these lapse. Sorry! I will continue them eventually (or your money back).

Even though this domain name isn’t shiny and new anymore, the sun isn’t setting on this blog. It will continue to be your source of new science related to plants and photosynthesis. So, check out the links for what you may have missed this past year and make sure to give the blog a follow so you don’t miss another post.

 

Johnna

*I tried to warn you that I knew what you were clicking, but you just don’t listen.

Blackberries: Jewels of Spring

101016Southern springtime brings many botanical treasures, which are usually proudly displayed in orderly fashion in well-kept garden beds. However, the jewels I cherish most are found along overgrown fence lines and creeping into unkempt pastures. I’m talking about wild blackberries or dewberries or whatever you would like to call species of the Rubus genus. In early spring, X’s can be marked on treasure maps when a profusion of white flowers bloom almost synchronously on two-year old canes. After this display, the plants blend into the background greenery nearly lost and relegated to the shadows of honeysuckle and other trees that finally decide to leaf out. Persistent foragers are rewarded several weeks later when ripening berries can be seen in flashes of red, purple and ultimately black.

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Like all precious treasures, blackberries are heavily guarded by barbed brambles. Personally, I’m as at home in a briar patch as Br’er Rabbit and won’t let the snags and sticks of the berry canes keep me from my delicious prize. I’ll endure encounters with bugs of all kinds- mosquitos, fire ants, chiggers, ticks, spiders, and stinging caterpillars. Larger animals will elicit a stronger startle response from me- the flutter of birds, the scurry of rabbits or field mice, the scamper of feral cats and even once the bustle of an extremely near-sighted armadillo. There is only one thing that will cause my stomach to pucker and lead me to call it a day on blackberries- the slither of a snake. This time of year in Louisiana, a snake encounter is a statistical certainty during blackberry picking. Even if I don’t see them, I accept that they are there. I will even go so far as to acknowledge their right to exist in my berry patches.* I would just never like to confront them. So, I tromp heavily in boots and use a cane knife to shake the briars a bit before plunging into them up to my elbows. When I do happen upon the fearsome reptiles, the encounters are never lethal despite my cane knife, but I do lose the nerve for berry-picking for the day.

Blackberry bucket

Blackberry bucket Credit: Johnna Roose

Dewberry canes

Dewberry canes Credit: Johnna Roose

The internet tells me that there are some cultivated varieties without thorns at all that can be grown orderly-like vineyard-style, but it is difficult for this southern girl to reason why you would take the effort to tend such plants when wild varieties produce such deliciousness for free with no aid from a gardener. Nevertheless, several links at the end of this post provide details on blackberry cultivation if you are not a wild-blackberry purist like me. For many wild varieties, some have prominent prickles on the stems and spines on the leaves, while others have additional sharp hairs along their stems. This brings us to an issue of nomenclature dear to some people’s hearts. (No, I’m not talking about thorns vs. prickles vs. spines. I’ve covered that previously.) I’m talking about blackberries vs. dewberries. While blackberries may be an umbrella term for this type of fruit, I’ve noticed that southerners prefer to make the distinction when dewberries are what you are really talking about. I am an equal opportunity berry picker and eater, but here are the highlights when it comes to dewberries. Dewberries, Rubus trivialis**, are slightly larger than most wild blackberries and ripen a few weeks earlier. Their canes are red and contain hairy bristles in addition to prickles, while blackberry canes are green and lack the extra layer of hairy bristles. Blackberry plants have a more upright form, while the dewberry canes bend and creep along the ground with tips that root easily to conquer more ground.

Blackberry, an aggregate fruit of drupelets. Credit: Johnna Roose

Blackberry, an aggregate fruit of drupelets.
Credit: Johnna Roose

While we’re on the subject of nomenclature, there’s something more fundamental we need to talk about. //looks over both shoulders and whispers// They aren’t really berries, botanically speaking. Yes, it’s true. This is another instance when common or culinary usage of a term differs from the strict scientific definition. In the world of plant science, a simple berry is a fruit containing the seeds and pulp from a single ovary. So, things like blueberries and cranberries are examples of fruit both commonly and scientifically referred to as berries. Other believable berries include grapes and currants. You may not believe me, but based on the botanical definition avocados, tomatoes and watermelons are also berries. Incidentally, strawberries are not berries either, but that is a subject for another post. Blackberries, dewberries and raspberries are aggregate fruit, in which each tiny round fleshy piece (a drupelet) is derived from a separate ovary in the flower but bound together in the form we commonly refer to as a berry. Don’t worry, I’ll still call them blackberries because blackaggregatefruit just doesn’t have the same ring to it.

After all, when it comes to food plants, being scientifically accurate takes a backseat to culinary use. ‘Berry cobbler’ just triggers a Pavlovian salivation response that ‘Aggregate fruit cobbler’ doesn’t. I know this isn’t really a food blog, but I feel strongly about wild blackberries, and it’s my blog and I can do what I want. Blackberries should be eaten out of hand using sunshine and dew as the only condiments. If there are any surplus berries, then you should bake them into a cobbler, tart or pie. There are many pastry recipes with berry ingredients, and I’m sure many are delicious. However, I am a minimalist. I rely on the berry cobbler recipe from the ‘Quick-N-Easy’ section of the 1981 Istrouma Baptist Church cookbook. Ingredients: 1 stick of salted butter, 1 cup of flour, 1 cup of sugar, 1 cup of milk and 2 cups of berries. Melt butter in baking dish. Mix other ingredients (except berries) together in bowl and pour over melted butter in baking dish. Pour berries over entire mixture and bake at 400 F until golden brown. It’s not fancy, but the simple gooey batter is the perfect medium for the tart flavorful berries. If you’ve really gotten more berries than you can handle in a single dessert preparation, then cook them for juice to make into jelly. Check out this resource from the LSU AgCenter for more information and recipes.

 

Blackberry cobbler and vanilla ice cream Credit: Johnna Roose

Blackberry cobbler and vanilla ice cream
Credit: Johnna Roose

The good thing about this treasure is that there is plenty to go around for all determined prospectors. Grab your boots and bucket. It’s berry pickin’ time (or soon will be for those of you just a bit further north).

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Johnna

*My brother would disagree with me. He is convinced that all snakes are copper-headed rattle moccasins. It’s either kill or be killed, and he will put down a layer of cover fire from his handy sidearm at the first sound of scales.

**trivialis, as in trivial. Really, botanical nomenclature, really? I find it hard to believe that anyone that has tasted dewberries would have called them trivial in terms of flavor. They probably should have been named Rubus heavenlyflavorexplosiononmypalate.

References and links:

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

http://aggie-horticulture.tamu.edu/fruit-nut/files/2010/10/blackberries.pdf

http://aggie-horticulture.tamu.edu/syllabi/608/Lists/second%20ed/Rubustrivialis.pdf

http://www.eattheweeds.com/have-dewberry-will-travel/

http://blog.al.com/living-press-register/2010/05/a_blackberry_guide_dewberries.html

http://thepapershell.com/blackberries-or-dewberries/

http://plants.usda.gov/java/ClassificationServlet?source=profile&symbol=RUBUS&display=31

http://www.wildflower.org/plants/result.php?id_plant=RUTR

http://www.texasbeyondhistory.net/coast/nature/images/blackberry.html

http://www.lsuagcenter.com/NR/rdonlyres/5DD47469-DA9F-4398-AD57-85FDB3E9327E/27320/pub1553blackberriesFINAL.pdf

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

http://www.lsuagcenter.com/NR/rdonlyres/3859EFB2-776D-4071-AC6D-0F2B12A76646/2173/pub2483berry2.pdf

So, this link provides an unbelievably detailed 15-step protocol (15!) for blackberry picking.

http://www.wikihow.com/Pick-Dewberries

Here’s my version:

  1. Put on boots.
  2. Grab cane knife and bucket with handle.
  3. Tromp to back pasture and walk along fence line.
  4. After unripe red berries catch your eye, look for fully ripe blackberries nearby. For every ripe blackberry in the sun, there’s five more hiding under the shade of the leaves.
  5. Be careful not to step on ant piles, field mice, or snakes.
  6. Curse birds and small mammals that scurry out of the berry patch as you approach.
  7. Pick ripe blackberries and eat one for every five you toss in your bucket.
  8. Use yoga breathing techniques, balance and poses to reach ripe berries deeper in the patch.
  9. Curse the perfectly ripe succulent berries that fall from your grip into the dark depths of the ground below the briar patch.
  10. Curse the thorns, prickles and spines of the brambles as they get caught in your clothing, hair and flesh.
  11. Enjoy the morning sunshine until you remember you didn’t put any sunscreen on your neck.
  12. Curse because you forgot to put on insect repellent.
  13. See two inches of what must be a six-foot-long venomous snake. Shriek curses and defy gravity to escape blackberry patch.
  14. Upon entering a human dwelling, pick the ticks off of yourself. (Ironically, this step is unnecessary for any canine companions that have been adequately treated with flea and tick preventatives.)
  15. Cook and eat blackberry cobbler, served with vanilla ice cream.