Category Archives: funding

The Grinch Who Stole Science

The Grinch may be green, but he’s not photosynthetic.* However, here’s a grinchy science parody that fits just perfectly on this blog.

 

Every Sci down in Sci-ville liked Science a lot… But The Grinch, who lived just North of Sci-ville, Did NOT! The Grinch hated Science! The whole research season! Now, please don’t ask why. He just wouldn’t listen to reason. It could be that his head wasn’t screwed on quite right. It could be, perhaps, that his ties were too tight. But I think that the most likely reason of all may have been that his brain was two sizes too small. But, whatever the reason, his brain or his ties, he stood there on the funding committee, hating the Scis.

Staring down from his office with a sour, Grinchy glower at the warm lighted windows below in their tower. For he knew every Sci was preparing their aims, busily now supporting their claims. “And they’re gathering their data!” he snarled with a sneer. “Deadline’s tomorrow! It’s practically here!” Then he growled, with his grinch fingers nervously drumming, “I MUST find a way to keep Science from coming!” For, tomorrow, he knew… …All the Sci girls and boys would wake up bright and early. They’d rush for their grants! And then! Oh, the experiments! Oh, the experiments! Experiments! That’s one thing he hated! The Experiments! Then the Scis, young and old, would sit down to a bench. And they’d research! And they’d research! And they’d research! Research! Research! They would start on the -omics, and screens on yeast which was something the Grinch couldn’t stand in the least!

And THEN They’d do something he liked least of all! Every Sci in the tower, the tall and the small, would stand close together, with hypotheses greeting. They’d stand hand-in-hand. And the Scis would start meeting! They’d meet! And they’d meet! AND they’d meet! Meet! Meet! Meet! And the more the Grinch thought of the Sci’s Annual Meeting, The more the Grinch thought, “I must stop this whole thing! “Why for fifty-three years I’ve put up with it now! I MUST stop Science from coming! …But HOW?” Then he got an idea! An awful idea! THE GRINCH GOT A WONDERFUL, AWFUL IDEA!

“I know just what to do!” The Grinch laughed in his throat. And he made a quick Scientist lab coat. And he chuckled, and clucked, “What a great Grinchy ploy! “With this coat, I’ll look just like a PhD decoy!” “All I need is a postdoc…” The Grinch looked around. Since postdocs are cheap, one could easily be found. But they wanted benefits? No! The Grinch simply said, “If I have to pay a postdoc, I’ll make one instead!” So he called his dog Max. Then he took some red thread and he tied a big hood on top of his head. THEN He loaded some bags and some old empty sacks on a research vessel and he hitched up old Max. Then the Grinch said, “Giddyap!” And the vessel started down toward Sci-ville where the Scis lay a-snooze in their labs.

All their windows were dark. Quiet snow filled the air. All the Scis were all dreaming sweet dreams without care when he came to the first lab in the square. “This is stop number one,” The old Dr. Grinchy hissed and he climbed to the roof, empty bags in his fist. Then he slid down the fume hood, a rather tight pinch, but if phenol could do it, then so could the Grinch. He got stuck only once, for a moment or two. Then he stuck his head out of the fume hood flue where the little Sci flasks all hung in a row. “These flasks,” he grinned, “are the first things to go!” Then he slithered and slunk, with a smile most not nice, around the whole room, and he took every device! Beakers! And pipettors! Stir plates! Tris! Sequencers! Manuscripts! Timers! UV-Vis! And he stuffed them in bags. Then the Grinch, very nimbly, stuffed all the bags, one by one, up the fume hood! Then he slunk to the freezer. He took the Scis’ box! He took all the strains! He took the lab stocks! He cleaned out their chem shelf as quick as can be. Why, that Grinch even took their last can of LB!

Then he stuffed all the data up the fume hood with a rant. “And NOW!” grinned the Grinch, “I will stuff up the grant!” And the Grinch grabbed the grant, and he started to shove when he heard a small sound like donning a glove. He turned around fast, and he saw a small Sci! Little Cindy-Vi Sci, who’s qual exams were nigh. The Grinch had been caught by this little Sci daughter who’d got out of lab for a cup of DI-water. She stared at the Grinch and said, “Reviewer, why, “Why are you taking our R01 grant? WHY?” But, you know, that old Grinch was so smart and so slick He thought up a lie, and he thought it up quick! “Why, my sweet little tot,” the fake PhD lied, “There’s a fatal flaw in this aim that’ll kill the whole grant. “So I’m taking it home to triage, my dear. “I’ll fix it up there. Then I’ll bring it back here.” And his fib fooled the child. Then he patted her skull and he sent her to rethink of her hypothesis null. And when Cindy-Vi Sci went away with her thoughts, HE killed the grant until their funding was naught! Then the last thing he took was the log for their data. Then he went up the fume hood himself, the old hater.

On their walls he left nothing but hooks, and some wire. And the one speck of media he left in the lab was a crumb that was even too small for a stab. Then He did the same thing to the other Scis’ labs leaving crumbs much too small for the other Scis’ stabs! It was quarter past dawn… All the Scis, still a-bed all the Scis, still a-snooze when he packed up his vessel, packed it up with their instruments! Reagents! The tweezers! The tape! And the shakers! The centrifuges! The freezers! Three thousand feet up! Up the side of Mount Rejectit, He rode to the tiptop to eject it! “Bye-bye to the Scis!” he was grinch-ish-ly humming. “They’re finding out now that no research is coming! “They’re just waking up! I know just what they’ll try! “Their mouths will hang open a minute and sigh “Then all the Scis down in Sci-ville will all cry Why-why!”

“That’s a noise,” grinned the Grinch, “That I simply must hear!” So he paused. And the Grinch put a hand to his ear. And he did hear a kick-starter rising over the snow. It started in low. Then it started to grow… But the sound wasn’t sad! Why, this sound sounded rational! It couldn’t be so! But it WAS full of hope! No dope! He stared down at Sci-ville! The Grinch popped his eyes! Then he shook! What he saw was a shocking surprise! Every Sci down in Sci-ville, the tall and the small, was researching! Without any grants at all! He HADN’T stopped Science from coming! IT CAME! Somehow or other, it came just the same! And the Grinch, with his grinch-feet ice-cold in the snow, stood puzzling and puzzling: “How could it be so? It came without R01s! It came without panels! “It came without fellowships or reviews through normal channels!” And he puzzled three hours, `till his puzzler went can’t. Then the Grinch thought of something he hadn’t before! “Maybe Science,” he thought, “doesn’t come from a grant.”

Maybe Science…perhaps…means a little bit more!” And what happened then…? Well…in Sci-ville they say that the Grinch’s small brain grew three sizes that day! And the minute his brain didn’t feel quite so tight, He whizzed with his load through the bright morning light and he brought back the equipment! And the laserjet toner! And he… …HE HIMSELF…! The Grinch became a top donor!

 

Johnna

*I just wanted to clearly state that since I know at least one person stumbled upon my blog with the search term “Is the Grinch Photosynthetic?”

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Superhero PhD: Nike!

We last left Superhero PhD and her labmates in a state of noncompliance with the system that is supposed to support them. Fortunately, their misdeeds did not attract the attention of accountants higher up in the matrix. Even the recently purchased equipment from e-bay works just fine. These small triumphs make the days in the lab pass easier, which was good since several more days passed beyond the funding agency’s deadline for divulging the fate of tenured PI’s latest grant renewal. Finally, the e-mail from the Program Manager arrives… victory! The grant is renewed for another three years. Tenured PI must send a flurry of additional e-mails as slight adjustments to budgets must be made, but these are a welcome burden given the possible alternatives.

Superhero PhD takes a break from benchwork to battle with the peers who reviewed her latest manuscript submission. She has spent the last months painstakingly repeating experiments to satisfy their demands for MOAR DATA! Now is the time to revise, remake figures and resubmit. Tenured PI submits a more appropriately censored version of the responses to reviewers’ comments to the editor than the first draft provided by Superhero PhD. It’s probably for the best. It will be another few weeks before the next battle with reviewers over this manuscript.

Back to the routine of research Superhero PhD focuses on projects that have been on the sidelines. A new mutant is giving unexpected results, but our heroine knows better than to get too excited. DNA samples are submitted for sequencing analysis to check for possible errors in the intended sequence. It seems like an easy task, but the new on-line system for submitting the samples and payment information requires more steps and approvals than acts of congress to approve federal budgets. Tenured PI even gets automated and unrecognizable e-mails from the system requesting approvals. Finally, the analysis is complete and Superhero PhD receives the results. “Nooooooo!” she cries, shaking her fist at the screen. The construct has a point mutation in addition to the complex construct she has pieced together. The mutant is unusable because it runs afoul of a central tenet of scientific experimentation- only change one variable at a time. These results sentence Superhero PhD to weeks of molecular biology work to remake a clean version of the mutant. In all truthfulness, Superhero PhD already had a stint of molecular biology ahead of her with other constructs and mutants to be made for her new project. For biochemists, molecular biology is a necessary evil.

Despite the occasional sequencing error, Superhero PhD also has molecular biology superpowers as well. She sets out to spend her days tediously pipetting PCR reactions, restriction enzyme digests and running agarose gels. To visualize these gels, she must rely on departmental common equipment whose other users can be less than meticulous. Today, she finds something even more unusual. An unexpected power outage overnight has forced the computer to restart, a computer still running WindowsXP that probably hasn’t restarted in three years. Sigh. Login required. The password is not written anywhere in the area of the computer. Superhero PhD summons her powers of clairvoyance to divine the password, and she is correct.* She captures the image of her gel on the screen. Print. But something again is wrong. “Damn, the printer is out of the special thermal paper. Chances of other users reporting it to the Departmental Coordinator in charge of ordering the replacement- zero.” But Superhero PhD is prepared for such instances; she keeps a secret stash in her lab for just these occasions. “Incomplete lab notebook, I think not.” she chuckles. “However, I will have to step up my notes describing the proper procedures for acquiring more paper from passive-aggressive to full-on aggressive.” Superhero PhD muses.

Another consequence of molecular biology work is defrosting the frost-free freezer. For those of you wondering why a sophisticated modern research lab would have a frost-free freezer, it is because the precious enzymes used for these projects must not endure the temperature cycles of a typical modern freezer. They must remain cold at all times and fluctuations too warm will diminish their activity. Superhero PhD’s lab has still-active molecular biology enzymes whose purchases pre-date the births of many undergrads working there. However, after about a year of opening and closing the door of a frost-free freezer, the ice build-up inside necessitates the removal of all contents and a manual defrost. Superhero PhD uses her skills of organization to temporarily store all of the contents of the full size frost-free freezer, taking special note to remember where each item must be returned. It would be nice to say that Superhero PhD then uses her laser vision to melt the excess ice on all of the shelves and coils, but alas, that is one superpower she lacks. Instead, she and Graduate Student use a hair dryer** and spatula to melt and hack away at the ice for about an hour.

Elsewhere in the departmental common equipment room, Research Technician is battling with the ultracentrifuge, an expensive and formidable foe. “The imbalance error light is on, but there is no imbalance. I cannot get it to start.” he says. Superhero PhD gives him a hard, disbelieving look. “No, really. It’s balanced.” he retorts. Instances of imbalanced ultracentrifuges are the stuff of scientific research legends. The instruments turn rotors at such high speeds that failures in components or user error like imbalanced samples can turn these metal rotors into dangerous projectiles that penetrate walls and kill unsuspecting graduate students down the hall. “Did you turn it off and turn it back on?” she asks. “Yes, the error is still there.” Research Technician says exasperated. Superhero PhD then uses her superpower of pressing seemingly random buttons on the control panel (SET, IMBALACE, CLEAR, ENTER) and the imbalance error is cleared. The instrument will now be able to start the run. “What buttons did you push? I’ve been pushing buttons too!” he says even more exasperated. Superhero PhD’s fingers fly too fast in that mode, “I’m not sure.” is all she can answer. She shrugs, “But wait until I leave the room to start the run.” She’s not completely convinced there may be an imbalance. For the record, there wasn’t.

There are other problems in the lab. She senses trouble immediately because Research Technician and Undergraduate Researcher bombard her with their pleas as soon as she opens the door. “Something is wrong with the cooler! The blotter won’t work! What do we do?” they cry.*** These things only happen when Tenured PI and Lab Manager are out of the lab for the day. Superhero PhD assesses the situation. Indeed, the deli cooler is a mess. It seems to have cycled much cooler than normal at some point overnight causing the coils to ice up. This caused the case to stop trying to keep the temperature low and the ice build-up was currently dripping all over the contents inside. “What a mess.” she thinks. However, experiments must be salvaged. “Remove the blotter from the cooler. We need to get it to work or borrow a replacement.” she decides. The blotter screen wasn’t giving a reading of the output voltage, but the electrodes appeared to be responsive to the controlling knob. Superhero PhD estimates the correct setting based on her perception of the rate of bubbling along the wires (and the transient flashing of a reading on the LED screen). “Take it to the cold room, and run it for two hours. Turn off the cooler. Take everything out of it. Turn it back on in the morning and monitor the temperature.” she orders. The blots are saved. The blotter screen miraculously starts working during the run. The cooler works normally after the reset. Another crisis averted.

Later that week, Tenured PI receives an e-mail from the editor regarding Superhero PhD’s latest manuscript. The verdict is favorable. Finally, acceptance! We can put that research behind us. He comes to share the news with Superhero PhD. He says only one word, “Victory!” She is having her lunch at the moment, so she only gives him a puzzled look. “What are you talking about?” she asks. He responds, “When the Greek messenger Pheidippides ran from Marathon to Athens to announce the victory over the Persians, he exclaims ‘Victory!’ Well, ‘Nike!’, in the Greek language. Your paper was accepted, so I said ‘Victory.’” Superhero PhD smiles to herself at the triumph, then says, “But in the legend, Pheidippides falls over dead after that exclamation.” Tenured PI answers, “Yes, that’s how I feel!” Superhero PhD agrees. So she announces, “Me too. I’ll be taking that Biochemistry Instructor teaching position in the Department.” At that moment, Tenured PI fell over dead.

NOT REALLY, but his heart probably stopped for a few beats to mourn the death of Superhero PhD’s research career.****

What will happen to the research projects that were on Superhero PhD’s to-do list? Will Tenured PI find a replacement SuperPostDoc to work on the recently renewed federal grant? Does Superhero PhD have instructional super powers? Stay tuned next time for the answers to these questions in the continued adventures of Superhero PhD: The Instructor Chronicles.

 

Johnna

*It’s the same as the login ID BTW.

**Yes, our lab has a deluxe model hair-dryer with a very powerful temperature and speed output. If your lab doesn’t have one for this purpose, you should get one, but good luck justifying the purchase with accounting.

***If you read the footnotes of my last post carefully enough, you know how critical the blotter instrument is for our research.

****He really should have written his reference letter more carefully.

Superhero PhD vs. The System

Uncertainty and The Unknown are constant adversaries of Superhero PhD. Careful application of the scientific method keeps them at bay. It is a battle that never ends. However, other enemies can come from within the Ivory Tower- well-intentioned policies band together to create formidable bureaucracies that mire progress. At times, Dr. PhD, her crew and common sense run afoul of the system. This is one of those stories.

A good deed…

Graduate Assistant needed some spinach to prepare samples for her experiments, but her lack of transportation prevents her from going to the MegaLowMart to get what she needs in sync with her experimental schedule. Fortunately, Superhero PhD can easily stop by there at any time in her PhDMobile. The wall-o-produce at the MegaLowMart has what she is looking for- bagged spinach, not that baby stuff but mature leaves full of PSII. Mission accomplished. Dr. PhD thinks to herself, “What else was on the lab shopping list?” Ah yes, batteries. Tenured PI had used up the lab’s supply when changing out the batteries in the portable light meter last week. The battery kiosk is next to the checkout, and batteries are added to Dr. PhD’s cart. She pays with her institution-issued credit card aka TheCard, making sure to alert the cashier to the purchase’s tax-exempt status and keep the receipt to file the appropriate accounting paperwork. All this productivity and efficiency before 8 a.m. One would hardly think a rule had been broken.

Doesn’t go unpunished

The spinach is turned into samples for useful experiments in the lab by a grateful Graduate Assistant. The stash of batteries is full so the next time one of the small electronics in the laboratory dies, it can immediately be resurrected without inconveniencing any experiments. The original receipt, signed and labeled with the appropriate account number to be charged, is turned in to the accountant. Lab life goes on… Until… Superhero gets an e-mail from Departmental Accountant asking for clarification. Every transaction is audited to prevent fraudulent purchases and he needs to know what “the salad spinners and batteries” were used for. Superhero PhD, “Huh?” Oh, yes. The abbreviation on the receipt was ‘salad spin’ for salad spinach not spinner and it was turned into PSII. Batteries are used to power small electronics in the lab. (No, there isn’t a non-snarky way to describe what we use batteries for in the lab, especially not on a Friday afternoon.) Later, another e-mail; this one is a warning from Departmental Business Manager. Her superpower is generally keeping the system from negatively interfering with laboratory science. Sometimes even she can’t keep the system from impeding research. Departmental Business Manager informs Dr. PhD that batteries are available at a cheaper price with next day delivery from WorkplaceSupplySupreme via the Online Institutional Ordering System. “That’s great! Anything to keep me away from MegaLowMart.” thinks Dr. PhD. Well, there’s more to it than that explains Departmental Business Manager. Our institution is contractually obligated to buy them from WorkplaceSupplySupreme, and elders in the main institution accounting office may deny the transaction and send Dr. PhD a ‘Noncompliance’ form. Sigh. In the meantime, Dr. PhD will wear a scarlet ‘N’ on her lab coat and be prepared to personally pay for the illegal transaction. This will teach our hero to think of WorkplaceSupplySupreme the next time random consumables are needed for the lab.

Additional noncompliance and other rebellions

Apparently, Superhero PhD is the bad apple spoiling the whole bunch because the other individuals in the lab have also been fiscally rebellious. Research Technician bought spinach at a produce stand that did not provide a receipt with detailed item descriptions, such that there is no way for accountants to tell if he really purchased $6.00 worth of spinach for the lab or a few bananas for his own consumption. Laboratory Manager had to replace the lab’s blender, which is used to grind the spinach for PSII preparations. Scientific supply companies will sell versions of this appliance with features the lab doesn’t need for exorbitant fees, but a decent kitchen supply outlet will sell the basic model for less than half the price. Lab Manager had to spend a lot of time responding to e-mail correspondence from institution accountants as to why she purchased a food blender on her TheCard and federal grant funds. Sometimes there are unexpected difficulties when your model organism is also a common food. Tenured PI also decided to join in the fun of noncompliance by ordering a piece of lab equipment from e-bay using his TheCard. If it were new, it would cost $5000.00, but by shopping victoriously it was only $100.00. Tenured PI has not technically gotten a noncompliance notice, but his transaction makes too much financial good sense to be legitimate, and notification is likely to be imminent.

Schrodinger’s grant*

All of this fiscal (ir)responsibility is amplified by the fact that Tenured PI has not received notice on the funding status of his federal grant renewal submission. For months now, it has been in the pipeline being checked, reviewed, discussed and ranked. Federal Agency Officers can give no information on the status of submissions. Since they have significant power over amounts of funds and release dates, Tenured PI knows not to press the issue. The only response, “No new information will be provided until 2 weeks from this date.” Tenured PI’s grant exists only as Schrodinger’s grant. It is the superposition of both the funded and non-funded states. There is no way to really know at this time which state it really is, and thus it can exist as both states simultaneously. Ultimately, the e-mail from Federal Agency Officer is the black box that entangles both states. When this e-mail arrives in Tenured PI’s mailbox, he can click on it to collapse the superposition of dual states and make the observation to know for sure whether the grant is truly funded or not funded. Until then, the lab waits, conjuring ideas for alternative funding strategies and sources for lab consumables.

Slow River Honky Tonk Extravaganza

Our hero’s lab isn’t the only place feeling the squeeze of governmental budgets. It’s a state-wide problem, and Dr. PhD’s institution has discovered how profitable it is to rent out our MegaStadium for a weekend’s-worth of country music. No one knows for sure how the money is split, but with seating for just under 100,000 it can’t be a bad racket. Of course, an event of this size has logistical implications and repercussions for Superhero PhD and other institutional employees. Weeks in advance the police department sends out e-mails describing the parking situation. Even though Superhero PhD pays for a parking permit, the spaces will be sold or made available to concert goers. The specifics are unclear, but what would normally be restricted-access will be publicly available starting at 1pm. The concert doesn’t start until 530pm, but our state accounts for a requisite four-hour window for the public consumption of alcoholic beverages prior to large events such as this. Vehicular navigation on campus will be such a cluster&@#% that commercial delivery services will not run their normal routes. Outgoing packages will just have to wait until Tuesday. Superhero PhD arrives to a campus that appears business-as-usual in the morning and is not asked for additional payment for parking. However, by 330pm there is a steady influx of buzzed women in tank tops and cowboy boots- all Reba’s biggest fans, no doubt. Their escorts all have crisp new cowboy hats. Superhero PhD wraps up her experiments earlier than usual and the roads appear to be moving reasonably well. Just like that she disappears from the Ivory Tower and begins her escape from campus. Half of the intersection is blocked where she normally makes her left turn, but a car in the oncoming lane is disabled. There are no pedestrians to yield to for the left turn. Dr. PhD thinks, “Here’s your one chance PhDMobile, don’t let me down!” Fancy that, the rest of the commute to the PhD lair is smooth sailing.

Stay tuned for the continuing adventures of Superhero PhD and the rest of the lab. Will they all be relegated to noncompliance and have their purchasing privileges revoked? Will Tenured PI’s grant get renewed so there will even be money to spend? The answers to these burning questions will be in the next episode.

 

Johnna

*I can’t take credit for this bit. It was all Tenured PI’s idea.

Also, for the record, better judgement and common sense has prevailed regarding noncompliance. While time was wasted by all in terms of e-mail correspondence, no lab members were held personally liable for the purchases described here.

Behind the Music: Plants

I’ve spent a lot of time on this blog writing about the importance of plants. They are the energetic foundation of our biosphere. We use them for food, fiber, fuel and building materials. This is why it is so important to understand how they work to further extract useful work and energy out of them. Today’s post explores an area that plants have not been adequately exploited, and I have no idea why we haven’t jumped on this sooner. I’m talking of course about music production.

Before you can even utter LOLWut!?!, allow me to introduce Data Garden. They are a group dedicated to creating new electronic art and have successfully completed a Kickstarter campaign to fund MIDI Sprout. It’s a cool idea with an even cooler logo (also true for Data Garden generally). MIDI Sprout is a device that allows users to create biofeedback art from plants. Huh? You attach the electrodes to the leaves of your houseplant and it records the changes in electrical signals emitted by the plant into an output readable by synthesizers and computers. So, basically it allows you to turn your plant’s existence into music. They’ve already had an exhibit at the Philadelphia Museum of Art and the recording is available for purchase on their website.

So many thoughts on this…

This may blow your mind, but so many of us plant scientists, photosynthesis researchers specifically, have been communicating with our plants using light and fluorescence to determine how healthy or sick they are. We haven’t been listening to them. Maybe I can finally get a Science or Nature paper if my methods include synthesized acoustics as an assay for plant fitness. Those journals just fall all over themselves when it comes to new methods. The evil scientist in me wants to hook up my lab plants to the MIDI Sprout electrodes and run all of my usual experiments and treatments- red light excitation, treatment with the herbicide DCMU, plant hormones, methyl viologen, DBMIB, or high or low CO2 conditions. I would also require an instrument with submersible electrodes so I can record my algal and cyanobacteria cultures as well. Why should plants be the only photosynthetic organisms to hit the top 100?

The MIDI Sprout is advertised as an instrument to listen to your houseplants, but I don’t think my singular Cristmas cactus will cut it. I’m sure it’s just because you need a pluggable power source, but a portable version can probably be developed with enough solid state storage capacity to cache recorded responses until you can get back to the studio and remix everything. Then you can listen to gardens, natural environments, GMO cornfields or whatever you want. Move over Sound Garden, here comes Garden Sound. Interestingly, there are already quite a few musical recordings close to the genre if you search iTunes for ‘photosynthesis.’ They Might Be Giants has a catchy song about photosynthesis on their ‘Here Comes Science’ album. There’s also a group called Carbon Based Life Forms experimenting in the new age genre with plant-related themes. There’s even a group called ‘Plants’ on the new age label Strange Attractors in the same spirit. However, these are all humans as far as I can tell- autotroph imposters or interpreters- and not actual plants.

Plant-based music could introduce entire new genres and bands. What could they be called? Well ‘photosynthesizers’ is a little obvious and hack and I use it for something else. Phonosynthesis is already taken (recommend the album BTW). I’m copyrighting the term ‘autotrophony’ today as this new music genre. I’m sure it will stick if I hashtag it up on the interwebz. Regardless just think of the possibilities… Chard in G minor, Cacti concerto, Solanum sonata, tulip tunes, floral phonics. Autotrophic American Idol. Move over Beyoncé, here comes Botanée. Producers could create the perfect plant boy band equivalent with different potted species with no chance of a break-up. Can’t storm off stage if you’re immobile! If you hated Monsanto as an agribusiness empire, just wait until they break into the music industry. They will surely negotiate for royalties on music made by plants their seeds produced.

I’m thinking we could kick this movement into the mainstream. Some of the plant-synthesized music has some potential. It just needs some help from our species, since we will be the ones purchasing it. Collaborations with existing artists are what we need. Just think- there could be actual black-eyed peas on The Black Eyed Peas album. Remixes are where it’s at, so I just need the Skrillex Ilex, Avicii Vitis or David Guetta Betula remix. I’m thinking clap tracks ala LMFAO and vocals by Pitbull and Ke$ha. There’s gotta be a hit in there somewhere. I really just need to be a one-hit wonder to fund my photosynthesis research for the rest of my career, but short of that I could probably just DJ weddings, parties and bar mitzvahs on the weekends to independently sustain my lab outside of federal funding dollars.

Dr. Z Scheme PhD Sigh, there were no female DJ clip art images.

Dr. Z Scheme PhD
Sigh, there were no female DJ clip art images.

Of course, there are other artistic experimental ventures I could do with this system. I could try something totally meta. Remember that Talk to a Plant museum exhibit aimed at influencing plant growth with sound? What if you played music to plants while you were recording them for their music? Would it sound similar to the music in the room? Would those recordings be different than the music plants make in silence? Yeah. Mind. Blown.

Why does it have to be just an auditory experience? Why can’t you record the music of your food plants then eat them while listening to their music. I’m also trademarking the ‘Salad Soundtrack Bistro.’ If you live in a state like Colorado, recordings could be made of certain plants used for other recreational purposes and they could be sold as a packaged altered experience. Note, it’s just a good business plan to put my Music Munchie Bodega next door.

Clearly, I have tons of creative ideas for future plant exploitation for the sake of the arts and making money. I’m very curious as to the general availability of the MIDI Sprout on the horizon. If any readers have connections in the music industry, tell them to contact me. Otherwise, I guess I will have to figure out how to start my own youtube channel to get noticed. My music mogul persona is Dr. Z-scheme PhD on my P680 Fluorescent label.* Let’s do this.

 

Johnna

*My plant science nerd friends reading this will get it.

References and Links:

http://www.theguardian.com/technology/2014/may/08/cosmic-soundscapes-plants-midi-sprouts

http://www.dazeddigital.com/artsandculture/article/19191/1/midi-sprout-uses-houseplants-to-play-synth-electronic-music

https://www.kickstarter.com/projects/datagarden/midi-sprout-biodata-sonification-device

http://datagarden.org/7940/midisprout/

http://www.youtube.com/watch?v=WN833bCXXJk

http://datagarden.org/about/

The Science of the Shamrock

Happy St. Patrick’s Day! Everyone else may be drinking at the pub and kissing everyone else that claims to be Irish today, but let’s talk about the foliage behind the festivities. The patron saint of Ireland used the typical shape of the shamrock as an illustration of the Holy Trinity. The Latin name of the white clover genus, Trifolium, literally means three leaves.

Spot the four-leaf clover Credit: Kristie Phillips

Spot the four-leaf clover
Credit: Kristie Phillips

More four-leaf clovers Credit: Kristie Phillips

More four-leaf clovers
Credit: Kristie Phillips

As symbolic as the common foliage form may be, we all know that the four-leaf clover is a symbol of good luck. This is because the four-leaf variety is quite rare (about 1/10,000). I am not a lucky person and have never personally found a four-leaf clover. All of the pictures of 4+-leaf clovers in today’s post are from my friend Kristie Phillips* whose special superpower is finding rare clovers with more than three leaves. Check out this link for more science-based tips on finding your own four-leaf clover. If you are just interested in the statistics behind finding a four-leaf clover check out these posts. Even rarer are clovers with more than 4 leaves. The world record for most leaves on a shamrock is 56!

Five-leaf clovers Credit: Kristie Phillips

Five-leaf clovers
Credit: Kristie Phillips

You may be wondering what the underlying reason is for these deviations from the typical three-leaf form. You are not alone. Other plant scientists have had the same question. They have been working on determining the genetic basis of leaf number and other valuable ornamental traits in clover. This has been slow going because clover is an allotetraploid, which is a hybrid that has four times the number of chromosomes of 1n gamete cells. With these complex genetics, clover prefers to outcross giving a wide range of phenotypic forms. Surely, there is a genetic component to the multiple leaf form of clover- some rare recessive gene that is infrequently unmasked to give four-leaf clovers. Scientists were able to map this trait along with a few other desirable ornamental traits. This was a real breakthrough for breeders that are seeking to enhance the frequency of these traits in clover used as ornamental bedding plants. Note, that genetics isn’t the entire answer because environmental conditions also contributed to the frequency of the four-leaf foliage variety. Will the four-leaf clover be any less lucky once its frequency is increased to 1/100 or 1/10? I’m not sure, but maybe I’ll finally be able to find one.

Even more than six-leafed clover Credit: Kristie Phillips I told you she had a superpower!

Even more than six-leafed clover
Credit: Kristie Phillips
I told you she had a superpower!

However, an exact gene controlling this trait has not yet been identified, but scientists may not be that far away from tracking it down. The genome for red clover was published earlier this year and I’m sure it won’t be long before breeders and scientists will correlate the markers used by breeders to the assembled sequences within the genome. The molecular mechanism for four-leaf clovers is still a mystery for now, but understanding how this works will provide new insights into plant development. Breeders have long sought after ways of controlling patterns in complex leaves for ornamental plants and the secrets of the shamrock may prove useful toward attaining this goal.

These types of scientific discoveries make for good blog fodder on days like today, and maybe I’ve tricked some of you into learning some plant science**. However, some of you out there may be wondering if your tax dollars were really spent determining what makes clovers have four leaves. Before you get all grumpy cat on scientific research spending, let’s talk about how important clover really is. Even if you could care less about ornamentals (and the market value of our nation’s garden centers would disagree with you), clover still has a lot to offer from a functional standpoint. We may not regularly eat shamrock salads, but clover is an important forage crop for animals we like to eat. According to the USDA, it’s “the most important pasture legume.” It’s nutritious and delicious herbivores like to eat it. As a nitrogen-fixing crop, it adds this essential nutrient back into the soil using gaseous nitrogen from the atmosphere making it useful as a cover crop in pastures and crop fields. Therefore, any traits that can be added as markers on a genetic map of this important crop are useful for breeding strategies in general. That kind of luck isn’t just frivolous, it’s practical.

Johnna

*All photos were used with permission. Copyright Kristie Phillips, all rights reserved.

**All part of my larger plan for world domination.

References and Links:

https://getd.libs.uga.edu/pdfs/tashiro_rebecca_m_200905_ms/tashiro_rebecca_m_200905_ms.pdf

https://www.crops.org/publications/cs/abstracts/50/4/1260

http://www.guinnessworldrecords.com/records-1/most-leaves-on-a-clover/

http://blog.minitab.com/blog/real-world-quality-improvement/the-odds-of-finding-a-four-leaf-clover

http://blog.minitab.com/blog/adventures-in-statistics/the-odds-of-finding-a-four-leaf-clover-revisited-how-do-some-people-find-so-many

http://www.noble.org/news/news-releases/2010/10-030/

http://onlineathens.com/stories/071210/uga_674945701.shtml

http://www.sciencedaily.com/releases/2010/06/100624141000.htm

http://www.newscientist.com/article/dn19112-plant-nurseries-in-clover-after-finding-fourleaf-gene.html#.UyIkIIXFm_t

http://www.scientificamerican.com/video/how-science-can-help-you-find-four-leaf-clover-video/?utm_source=twitterfeed&utm_medium=twitter

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

http://en.wikipedia.org/wiki/Four-leaf_clover

http://plants.usda.gov/factsheet/pdf/fs_trre3.pdf

The continued adventures of Dr. PhD

Today, in the continued adventures of Superhero Dr. PhD

From high in her ivory tower, Dr. PhD senses something ominous and dreadful. Something is hanging in the foggy fall air. Death.* No it’s Deadlines! Just after coming down from post-summer meeting euphoria and getting into the routine of the new semester, there they are. Deadlines looming every other week.

The most obvious of deadlines this time of year in academia (and beyond) are job application deadlines. Fortunately, Dr. PhD has a few finely honed superpowers essential for this process. She can update her CV and research plan in a flash. She can tailor cover letters for any position. She provides her references with meticulously curated lists of requirements and submission dates for letters, and then relentlessly hounds them until all letters have been e-mailed away. Each week more applications are due. Her fingers fly across the keyboard to finalize submissions to online systems. PDFs of application materials are compiled in a snap. Her entire professional persona is neatly and persuasively bundled in tidy electronic packages and clicked away into the oblivion of the internet. Goodbye, hope to hear from you soon.

Speaking of hearing back- the reviews are in on Dr. PhD’s latest manuscript. While not completely dead, more experiments are needed to bring it to life in the reviewers’ eyes. The clock is ticking on the resubmission timeline. With Dr. PhD’s prescient super-sense for this kind of response, precious samples are already waiting in the freezer. More antisera will have to be ordered, but alas, one critical antiserum is not commercially available. Superhero PhD will have to send out a signal to the international community for help. (OK, really it’s just an e-mail to the only other person that has used this antiserum in a publication a number of years ago.)

While Dr. PhD spends her days experimenting to revive her manuscript, her labmates have their own deadlines. She’s only seen glimpses of Undergrad Minion since midterms- his time in the lab waning in the face of other deadlines in his last semester of classes. Dr. PhD-β is leaving the country at the end of the year and is a flurry of activity to finish up critical projects. Graduate Assistant has a handful of key presentations to give this semester to fulfill her degree requirements. However, she is still cultivating her superpower of putting together Powerpoint presentations. Dr. PhD, Dr. PhD-β, Tenured PI and Research Associate painstakingly pore over her slides offering mountains of editorial corrections until every typo, inconsistent capitalization and un-credited figure are refined by fire into pure presentation gold.**

This deadline season has also been hectic for Tenured PI as well. There’s a grant submission deadline looming on the horizon, and the lab only speaks of it in hushed whispers. Before we can worry about any new money, Tenured PI must give his own presentation for our current funding overlords. It is not a meeting one can miss. Slides are put together. Additional data is analyzed. More slides are put together. The margin is slim on this timeline and Research Associate doesn’t get to use her scrutinizing superpower on all of them. Nevertheless, Tenured PI gives an entertaining performance with captivating data and a joke about a dual colored laser pointer that only biophysicists will get. It went over well and let’s just say that’s one deadline he killed- in a good way.

Of course, the absence of Tenured PI on a weekday in the semester means that Superhero PhD must come to the rescue as a substitute teacher. Slides are quickly transferred to Dr. PhD. She looks through them. Ugh. Tenured PI always sticks me with lectures that involve some kind of ∆G calculation. It takes all of her superpowers to create a stimulating lecture on the Na/K Pump and Bacteriorhodopsin.*** The students are hung over from their recent exam (No, I did not have those results.), but they are especially attentive during the explanations of enzyme mechanisms (Yes, you have to be able to explain those from memory.). Of course, not all deadlines are met perfectly. The lecture went well, but 36 hrs later Dr. PhD thinks of an awesome active learning exercise to do for the Bacteriorhodopsin mechanism. Next time Biochemistry I, next time.

View from inside a gorge, Turkey Run State Par...

View from inside a gorge, Turkey Run State Park, Indiana, 6-2005 (Photo credit: Wikipedia)

The final deadline of the season is our annual regional meeting on photosynthesis- The Midwest**** Photosynthesis Conference at Turkey Run State Park Indiana. Yes, it is as exciting as it sounds and an annual culinary experience that will test any scientist’s digestive superpowers. This means more lab presentations must be churned out. Travel accommodations and associated departmental forms must be filled out. Accounting paperwork is another one of Dr. PhD’s superpowers. Yes, Graduate Assistant you will need to fill out this form if you have never used that card for travel before or it will be denied. Don’t listen to what the other coordinators tell you! But also this year, Tenured PI is Co-Chair of coordinating this meeting. Abstracts must be catalogued. Registrations must be done. A program must be scheduled. A program booklet must be assembled, printed and shipped to the meeting location. Deadlines, deadlines, deadlines. Don’t worry, we made all of them. The program looks to be interesting, so stay tuned for upcoming posts with breaking photosynthesis research from the meeting.

But what will become of the other deadlines? What about all those applications? Will the reviewers appreciate the additional experiments and give life to Dr. PhD’s manuscript? Will the lab get additional funding? Stay tuned for the continuing saga of Superhero PhD.

Johnna

*No, that’s just the unfortunate feral kitten that met an untimely end under the hood of the PhD mobile. Alas, feline detection is not one of Dr. PhD’s superpowers. Bang on your hoods on cold mornings for God’s sake people!

**She did an awesome job on her talk and will again soon.

***That one is basically primitive photosynthesis, so it’s fine.

One gradient to rule them all…

Here’s something new about the proton motive force in photosynthesis.

If you think about bioenergetics at all, and I realize that many of you probably don’t do this, you may remember that the universal underlying mechanism for creating biochemical energy involves a chemical gradient across a biological membrane system. The ultimate goal is to make ATP, the fundamental energy currency of living systems. Photosynthesis and Cellular Respiration are often presented as opposing processes, but their function is the same- to make ATP. These processes just use different energy sources to accomplish this feat (photosynthesis-light; cellular respiration-glucose). The chemical gradient used by biological systems is a proton gradient. So, energy sources (light or glucose) are used to pump protons across a biological membrane. The proton imbalance across this barrier results in potential energy that can be used for biochemical purposes because energetics favors the flow of these protons back down the gradient to the side of the membrane with fewer protons. The enzyme ATP synthase takes advantage of this proton potential, allowing protons to flow back over the membrane, but coupling that energy to form ATP.

made for chemiosmosis article from Chemiosmosi...

made for chemiosmosis article from Chemiosmosis1.svg (Photo credit: Wikipedia)

This coupling of a proton gradient to generate biochemical energy is called the chemiosmotic theory. This mechanism has been well-established for decades and the Nobel Prize for its conception and proof has long since been awarded. You wouldn’t think that anything related to something as basic as the proton motive force and chemiosmosis would be fodder for a glam* journal like Science, but you’d be wrong. It turns out scientists are still finding new components of this established theory.

In the October 4th issue of Science, Carraretto and colleagues report on a potassium channel that is essential for balancing the components of the proton motive force and fine-tuning photosynthesis in response to environmental conditions.** The proton motive force has two components: the chemical pH gradient (∆pH) and the electrochemical gradient (∆Ψ) from the ionic imbalance. The ∆pH component plays a major role in facilitating mechanisms of light energy dissipation to shunt energy away from photosynthesis when the system is functioning at maximal capacity. The physical relationship as to how the two components are regulated remains unclear, but something must be controlling them since the photosynthetic machinery is particularly sensitive at optimizing the competing processes of photochemical efficiency and photoprotection. Carraretto and co-authors report on AtTPK3, a potassium channel in the thylakoid membrane that controls the magnitude of the ∆Ψ component. It does this by counterbalancing ions across the thylakoid membrane. As H+ ions are translocated to the thlykaoid lumen, AtTPK3 moves K+ ions into the stroma to maintain overall charge neutrality. Without this protein, plants cannot optimally partition the components of the proton motive force and have problems with optimizing photosynthesis under changing environmental conditions.

TPK3 moves potassium ions out of the lumen and into the stroma as protons are pumped into the lumen

TPK3 moves potassium ions out of the lumen and into the stroma as protons are pumped into the lumen

While the chemiosmosis theory is accepted dogma among today’s scientists, when the theory was first postulated by Peter Mitchell in his 1961 Nature paper***, it was controversial. Mitchell had to be tenacious and careful in his arguments for the chemiosmotic theory and against substrate-level phosphorylation (an opposing theory at the time with its own loud and credible proponents). It is also worth noting that the scientific career path of Peter Mitchell is an interesting read. I recommend checking out the links below. He successfully worked his way through a traditional academic career track, but not long after publishing his initial paper on the chemiosmotic theory, health problems necessitated a change in research venue. He left his research for two years while he renovated Glynn House as a personal residence and laboratory. He, along with his research colleague Jennifer Moyle, founded Glynn Research Ltd, an independent research laboratory funded by personal holdings from Peter and his brother. He continued at Glynn for the remainder of his research career.

With respect to the personal careers of scientists, maybe there isn’t anything new under the sun. The same struggles of work-life balance, advocacy for controversial research conclusions, and alternative funding strategies have been played out before. Maybe we ‘early career’ scientists are being too conservative and selling ourselves short. Maybe the structure of the science community would be vastly different if more of us said “yes” to the mad ideas we have as did Peter Mitchell and Jennifer Moyle. From Passionate Minds: The Inner World of Scientists:

“But when I got ill and had to leave, I went down to live in a cottage next door to Glynn, and started to think, well, what am I going to do now, because I can’t be idle. So the possibility arose that one might found an independent institute. As it was most unlikely that you could do all that on your own, I wrote to Dr. Moyle, and said ‘I have a mad idea. Would you be prepared to give up science for two years and work with me to restore Glynn House, and then try and establish an independent charitable foundation?’ Of course, she should have written back and said ‘No’, but she didn’t. She wrote back and said ‘Yes’.”

Johnna

*glam journal: Cell, Nature or Science, the upper echelon of the scientific publishing community, if your work can attract the attention of these guys, you’ve got a golden ticket for your career path.

** Sorry, as with all glam journals, it’s behind a paywall.

***Yes, it is fifty years old, but still behind a paywall.

References:

http://www1.umn.edu/ships/db/mitchell.pdf

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

http://en.wikipedia.org/wiki/Peter_D._Mitchell

http://www.life.illinois.edu/crofts/bioph354/mitchell.html

http://www.biologyjunction.com/chemiosmotic_theory.htm

http://www.brimr.org/Reprints/PeterMitchell.pdf

http://www.amazon.com/Wandering-Gardens-Mind-Mitchell-Making/dp/0195142667

http://www.nature.com/nature/journal/v191/n4784/pdf/191144a0.pdf