PiPC9: Leonard Nimoy.

Leonard Nimoy passed away yesterday. And that hit me hard. I grew up really relating to Spock, his iconic character. Logic could solve problems. Science could solve problems and allow us to explore the universe and everything within it. It was a big influence on me growing up. He seems to be an introvert too, all the more reason to relate to him.

His final plant-biology including Tweet was:

A life is like a garden. Perfect moments can be had, but not preserved, except in memory. LLAP

— Leonard Nimoy (@TheRealNimoy) February 23, 2015

Something I hadn’t thought about with plants is just how much they do reflect passage of time, moments that are fleeting, and just how the world moves on even after a bloom senesces. There are perfect moments, or meditative ones when we pause and really notice our surroundings, the plants, smells, sights, sounds, the people we’re with.

I’m writing this with a cat on my lap. I am aware of soreness in my body that’s been bothering me lately. I’ve spent my night writing for my other blog. I feel like I have let Spock down. I haven’t been rigorously applying logic to all my decisions in life. I have tried to pursue science as best I can. I’ve failed the Starfleet motto to. I haven’t boldly gone as yet. to me that implies taking decisions and seeing where they lead. I am getting better at this, but still.

Leonard Nimoy’s passing is making me reflect. How can I build more perfect moments into my life? Even if they’re fleeting, they were there. Nimoy always struck me as a thoughtful and contemplative person, even though I don’t know much about his personal life. I will miss him.




Short post 6.

You know the drill by now. 5 minutes, keyboard down at 5 minutes.

I was exhausted today. But that shouldn’t have stopped me from getting going.

Yes, I had a long week, and another long one ahead. I do need a rest. And I have committed to trying to take one day away from work each week.

I did get my laundry done. And I purged a bunch of clothes I don’t wear/need/use anymore.

Of course, my day-to-day isn’t all that interesting. I’m trying to figure out if I’m spending my time productively, mindfully, etc. To that end, I set a calendar even for myself each week where in the notes for the event I asked a series of questions about what I have done that week that matters to me. This week, it’s all about careers, etc. What have I done to figure out what is next for me. And where. And just what it is that’s important to me.

I mentioned last time that I think I want to buy a domain, start a science blog and just see how it goes, because I’m curious about what that process is like. I want to learn to do it better. I was brainstorming names today that I hope aren’t already registered; though I don’t think I came up with anything really great. I also am not fully sure what the project is all about, but the initial thing is just to write about plant science in myriad forms and perhaps see if I can find interesting connections in disparate work.


PiPC7: I am Groot.

This is a series on the blog where I write about plants that feature heavily in the plots of popular culture. Spoiler alerts apply to these, even though some of the series writes about things that are quite old. However, for this one, about “Gaurdians of The Galaxy”, spoilers definitely apply.

Note: I talk about the science behind trees in this post. I am not a tree biologist or physiologist. I’m taking my knowledge of how plants work and writing about it in a hopefully fun way.

In “Guardians of The Galaxy” over the weekend. One of the Guardians is Groot, a walking tree that is sort of intelligent but doesn’t speak English very well (or whatever it is they’re supposed to be speaking in the galaxy). It’s a fun movie overall, when the opening titles have an old school Walkman with Peter Quill dancing to Redbone’s ‘Come and Get your Love’, I had an inkling I was in for a pretty fun time.

I was particularly interested in seeing this when I heard that one of the Guardians is a walking tree. One that can branch and grow almost at will, extending his legs to grow taller, sprouting twigs, releasing luminescent pollen to light up a room, and even protecting his friends in a wooden cocoon. He has a face, but hasn’t mastered speaking as all he says in various intonations is ‘I am Groot’ (this is exactly how R2D2 is used in “Star Wars”, Chewbacca too come to think of it); other characters speak to him and the audience imagines what the beeps actually say). Groot can also flower at will, as when he produces a flower, a nice small, blue one for a little girl (which could be weird too….flowers are the reproductive organs of the plant after all).

Groot is far from the first walking tree in popular culture. There are the Ents from the ‘Lord of The Rings’ trilogy. They are interesting; like real trees, they live on time scales greater than those of humans and so take their time, having an extended meeting before deciding to go destroy Isengard. The Ents are also tree-farmers; maintainers of a forest that they can move around and have the trees follow them. It’s like all trees are Ents, and can transform and move about when roused.

There’s also a walking tree in the first series of the rebooted ‘Doctor Who’. The Doctor and Rose visit the year 5 Billion to witness the destruction of the Earth by an expanding sun and luminaries gather to witness the event, including a tree-woman from Cheem. She moves like a person, not really wooden at all. And in something relatively creepy to me, she gives away cuttings of her grandfather as greeting gifts for everyone. Would those cuttings grow into intelligent beings too? Or just be plants? And no human would do something like that…give a cutting of a relative as a gift. It’s one example of just how different and alien plants are.

So could Groot actually work, as an organism? Trees on Earth, as are all plants have a decentralized body plan. As Groot demonstrates repeatedly, he can branch, and grow in many directions at once at the rate of a super-weed or at least within human second-to-second time scales. So it’s a little hard to imagine a plant developing centralized senses (i.e. a head, like we have) although plants do have sophisticated sensors of their environments, including for light; as that, more than anything is essential for plants to know (Go look at my friend Johnna’s blog for a primer on Photosynthesis; a lot of the other light receptors plants have are designed to optimize the position of plants for photosynthesis).

Plants DO move. Bunchberry plants have a hair trigger pollen launcher; whenever they’re hit, or touched, the trigger gets tripped and pollen gets flung out of the flower. It’s a really fast biological response. Cucumbers and other viny plants grow in a circular motion until the vine finds something to cling onto, and then it coils around it, all plants ‘nutate’ or rotate in a circadian rhythm as they grow and of course, thigns like sunflowers famously track the light during the day, changing flower and leaf direction. Flowers can also close and open at various times. And of course, roots grow down into the soil. Venus flytraps can also close fairly quickly when triggered by prey.

Trees can be flexible and strong, though lignin; the complex molecule that gives wood it’s toughness, is not the most flexible substance ever. And Groot does have a certain stiffness about his movements.

The amazing thing about Groot is that he walks and runs and keeps up which implies the flexing of ‘muscles’, even though plants don’t really have those. They can expand and contract cells by changing water pressure inside of their cells, so perhaps some kind of hydraulic muscle system could evolve. The other thing I thought about with the fast growth responses Groot displays are just how many hormones must be coursing through his plant vascular (circulatory) system to promote and inhibit growth of plant cells that really cause directional changes in growing plant organs. Particularly the hormone auxin, which is involved in places.

It’s also not clear that Groot photosynthesizes; he doesn’t have a lot of leaves. However, plants also have mitochondria, celluar energy factories and it’s possible he’s evolved to metabolize more by respiration alone; although then there’s an issue because a large part of plant life is that they take carbon dioxide from the atmosphere and turn it into sugars that fuel the growth and provide the ‘stuff’ that the plant is made of (plants build themselves from the air! And I imagine Groot can eat things and is root system is his gut, absorbing water and other nutrients all plants need). So when Groot is extending himself quickly, just how much carbon is he burning through? Plants can store carbon in the form of starch, but they use those reserves during the night or seasons when photosytnthesis can’t occur (like the winter time). As far as I know, the activity of photosynthesis at night is quite low (e.g. star/moonlight are too faint to really significantly drive the process significantly, but I’m sure some is going on).

Groot sacrifices himself at the end and is smashed into a lot of pieces, but Rocket takes a cutting of him and the end credits show Groot slowly growing back. This is in fact, possible for plants to do. It’s possible to regenerate a whole plant from a single cell, so long as there’s a living cell there, the whole plant can re-grow. The new Groot will have the same genetics as the previous Groot, though it’s unclear whether he’d remember his past life. There is some evidence that plants can ‘remember’ things, even cross generationally largely via epigenetic mechanisms (chemical changes to how DNA is structured/packaged that don’t actually change the DNA sequence itself)…but it’s not a brain as such; and I’m having trouble figuring our just what a centralized plant brain would look like. It may not be impossible. It just means I haven’t thought enough about it. Groot isn’t the brightest bulb, it seems, so perhaps he has some sort of rudimentary brain that hasn’t mastered everything about the world for non-cellulose structured life.

Another funny thing about trees is that most of their biomass is in fact not living. Tree rings represent annual growth cycles, but those previous layers end being a structure for the living tree tissue to grow around (trees tend to get thicker as they get older). Groot can seemingly thicken and re-thin almost at will.

Groot is a fun character, and one that I hope gets people thinking more about plants and just how they work down here on Earth.




[Editor’s note: Things have been quiet around here. I’ve been busy living life, writing in other places and work has gotten hectic. Hope to be back to regular posting soon! ]

pre-Plant Biology 2014 (#PlantBiology14) post.

As I prepare to head to a conference with my newer mindset (as in not as depressed, experimenting with life more), I’m thinking about conferences, what they are for, who they are for, and what it is I’m trying to get out of attending this one (#PlantBiology14).

Even though I’ve been going to a conference or two every year for my whole scientific career, I’ve almost always felt out of place, not like I belong (hello impostorism!). And like I haven’t really been present enough to take advantage of what is on offer there.

I largely thought that conferences were for PIs (‘real’ scientists; those could certainly be grad students and postdocs) to get together to swap stories of funding, writing, ideas for new or old collaborations, grants, and things like that. PIs always seemed to be writing furiously at their computers between sessions, presumably writing grants? Furiously emailing? Perhaps updating their talk? Getting the latest dispatch from their labs? Analyzing ALL the data? It did seem largely specific to PIs to my eye; not as many postdocs or grad students doing that. I guess that’s why PIs earn the big bucks. Paid to always be (look?) busy and exhausted constantly? I’m sure any PI reading this will laugh at just how wildly inaccurate my projection of what it is they’re up to is; even though I’m a postdoc, I don’t get that great a sense of what actually goes on in a PIs mind.

Poster sessions were the worst. I sometimes would wonder exactly what I was doing there, taking up space, that someone else could actually use to do something actually productive and contribute to the world. I’m strongly introverted. I was (& still can be) shy and anxious. My history of being depressed doesn’t help either; a combination of not wanting to spread my depressed thoughts to anyone else and feeling completely unworthy of existence. I tended to not think highly of myself– still don’t very often though I’ve gotten better at acknowledging that I too, can do decent work sometimes.

Other people do great things (I now count myself amongst the doers, creators and builders of the world; one reason I started blogging– of course that means I am always striving to do more than I have done); I will continue to try and find the good in what others are doing and help them improve their work if I can or help them learn a new thing about the world or point them to a place they may not have been aware of.

Of course, I can discount connecting people to ideas these days because we all have a fire hose worth of information coming at us constantly now and the key skill is to be a good filter for all that information– the conference environment can be overwhelming. Maybe the best I can do is try to ask good questions when people are talking about what they are doing, even though I imagine most things I would ask are probably naïve (but maybe those are valuable too).

That said, it’s hard to be a connector of people to ideas if you aren’t actively interacting with people; especially at a conference where interacting and building community is the main reason for the event (Introversion does not mean aversion to people, FYI). A place where grad students and postdocs can land jobs (or at least start that conversation) and maybe get out of their own narrow confines for awhile. Outside that one conference at the end of my Ph.D. where I found my postdoc position and on that same trip met a girl who I dated for 8 months, conferences have mostly been drab affairs where I become a zombie, not really actively engaged and kind of put off by the crowds of people at booths and feeling largely isolated and not just because of exhaustion; because I couldn’t push beyond my largely mental barriers.

I’m trying to re-frame the conference in my mind. More as a place where good things can happen to anyone (me included). Where you can meet new people and find your ‘scene’ as entertainers like to call it; your group of people you come up with, learn from and bounce ideas off the wall, get feedback, etc. (this happens in science too; clusters of scientists that grow and succeed together in their independent careers; I’m sure these are fascinating Venn diagrams). Where it’s not perfect, but in the chaos, interesting ideas come out, new people are well met. I started Tweeting a few years ago and last year, tweeted up a storm which was a lot of fun for me and I plan to do it again this year. There’s now a more formal social media framework for the conference: the iConnect with Plant Biology team. We’ll be extending the meeting beyond the meeting with The Internet coverage from attendees and interacting online with anyone who’s interested. I met people last year because of Twitter.

I posted a fill in the blank elevator pitch based on the opening of Star Trek the other day. I think it’s not a bad mantra to take into a conference either:

Screen Shot 2014-07-08 at 12.00.56 PM The full text, if you don’t know is (no worries if you’ve never seen this before):

“Space, The final frontier. These are the voyages of the Starship Enterprise. Its ongoing mission: to explore strange new worlds, to seek out new life and new civilizations, to boldly go where no one has gone before.”*

Conferences are a place to expand your mind, push your comfort zone, grow some new brain connections with new ideas, systems, scientists and thoughts and importantly, to build the community of like-minded people; plant scientists in this case. While my research contribution is small, I fully intend to connect people, find new places and avenues I haven’t really looked into before and to cover my experiences on Twitter. Of course, I’ll catch up with old friends too. One good thing about going to the same conference for years in a row is just this; you see the people from your ‘science scene’ again and again and catch up (and perhaps incorporate new people into that scene– if you see someone standing alone, invite them into your conversation or just say hello; sure, it may go nowhere, but you don’t find out by ignoring people; cultivate curiosity).

There’s a notion that I even joked about above, that PIs with their heads in their computers kind of takes them out of the conference. I don’t fully subscribe to that; I think that tools like Twitter and other digital media (even just note taking) really are game changers for conferences and scientific ideas to spread beyond the confines of the actual attendees. And even for attendees, digital coverage can help them have a richer conference experience, as one person cannot attend all things.

Mindfulness is kind of a buzzword these days with some good reason. I am going to try and not be blindly mindful, but really actually notice what’s there in front of me and then tweet and photograph (within the rules) the entire thing to help others have an enhanced experience. I am also going to try and manage a blog post or two during the conference, as Twitter is great for some things, but not for longer form thinking like this.

Conferences are for germinating ideas, a starting point for new growth, for interacting with the forest, and pollinating ideas. They’re a leaping off point to new places.

Here’s to a good Plant Biology 2014 (#PlantBiology14) and may we all boldly go where no one has gone before (just know my boldness more likely will show up on Twitter rather than in person).





*Yes, I forgot the ‘strange new worlds’ clause in my version with blanks. I’m a horrible nerd, more impostorism.