It’s been a mixed week, which has caused me to reflect on two beautiful posts – and put them here so that I don’t lose them.
First, the evolution of dealing with a paper being rejected through your career.
And, naturally, the evolution of having your paper accepted throughout your career.
You all know me. I’m a sucker for an awesome marine ecology music video. So it gives me great pleasure to present this product from the always amazing and ambitious ZEN (Zostera Experimental Network).
Another excellent piece describing the intricacies of a complex field of scientific inquiry from Saturday Morning Breakfast Cereal, as always.
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Ah, parasitology. So glad that a certain someone makes sure it gets its day in the sun over at SMBC. And that the two of them have an awesome podcast.
I….I…I… Oh yes. Oh….Yes.
Want to capture the essence of the crazy things that go down in the course of marine science? Steven Colbert is there! *YEAH!*
Yes, folks, this really is what it’s like.
It’s always good to see some rockin’ Science Music videos coming from my alma mater. The use of crabs here? Genius. Also great to see the Big Man Himself making a special guest appearance.
Enjoy!
OK, folk on the Twitters – if you’re not following @DATACURATORHULK, I take no responsibility for what may happen to you. And if you’re not curating your data properly, or making sure that it is open?…hide.
Best. New. Twitter Account. Ever.
I’ve been pretty stoked about the This is What a Scientist Looks Like project on tumblr. So much so that I felt compelled to submit an (old) photo of me doing field work. I mean, when one things science, they often think labcoats and microscopes. When one thinks ecology, they often think hiking in a forest or working out on a sunny grassland. (note: these are impressions I’ve gotten to people when I say these words – not what I think myself, natch.)
So, why not throw in something of what a marine ecologist at work looks like. So here’s my shot:
Yeah, I admit, it’s kind of a marine ecology beefcake shot, and definitely falls into the ¿Quien es el mas macho? school of marine ecology, but I kinda love it (and thanks to Kristin Hultgren for taking it on our wacky marine ecology roadtrip).
But I was not prepared for what was to happen next. Namely, a good friend of mine getting hold of it and showing the picture for what it really is – me making my James Bond escape after blowing up the Evil Villan’s lair.
This is totally going to be the photo on the door of my lab one day.
I am part of an incredibly exciting project – the #SciFund Challenge. #SciFund is an attempt to have scientists link their work to the general public through crowdfunding. As I’m one of the organizers, I thought I should have some skin in the game. But what skin?
Well, people are pitching some incredibly sexy projects – tracking puffin migrations, coral reefs conservation, snake-squirrel interactions (WITH ROBOSQUIRRELS!), mathematical modeling of movements like Occupy Wall Street, and many many more. It’s some super sexy science stuff.
So what is my project going to address? Measurement error.
WOOOOOOOOO MEASUREMENT ERROR!
But wait, before you roll your eyes at me, this is REALLY IMPORTANT. Seriously!
It can change everything we know about a system!
I’m working with a 30 year data set from the Channel Islands National Park. 30 years of divers going out and counting everything in those forests to see what’s there. They’ve witnessed some amazing change – El Niños, changes in fishing pressure, changes in fishing pressure, changes in urbanization on the coast, and more. It’s perhaps the best long-term large-scale full community subtidal data set in existence (and if there are better, um, send ‘em my way because I want to work with them!)
But 30 years – that’s a lot of different divers working on this data set under a ton of different environmental conditions. Doing basic sampling on SCUBA is arduous, and given the sometimes crazy environmental conditions, there is probably some small amount of variation in the data due to processes other than biology. To demonstrate this to a general non-statistical audience, I created the following video. Enjoy watching me in my science film debut…oh dear.
OK, my little scientific audience. You might look at this and think, meh, 30 years of data, won’t any measurement error due to those kinds of conditions or differences in the crew going out to do these counts just average out? With so much data, it shouldn’t be important! Jarrett just wanted an excuse to make a silly science video!
And that’s where you may well be wrong (well, about the data part, anyway). I’ve been working with this data for a long time, and one of my foci has been to try and tease out the signals of community processes, like the relative importance of predation and grazing versus nutrients and habitat provision. Your basic top-down bottom-up kind of thing. While early models showed, yep, they’re both important, and here’s how and why, some rather strident reviewer comments came back and forced me to rethink the models, adding in a great deal more complexity even to the simplest one.
And this is where measurement error became important. Measurement error can obscure the signal of important processes in complex models. A process may be there, may be important in your data, but if you’re not properly controlling for measurement error it can hide real biological patterns.
For example, below is a slice of one model done with two different analyses. I’m looking at whether there are any relationships between predators, grazers, and kelp. On the left hand side, we have the results from the fit model without using calibration data to quantify measurement error. While it appears that there is a negative relationship between grazers and kelp, there is no detectable relationship between predators and grazers (hence the dashed line – it ain’t different from 0).
This is because there is so much extra variation in records of grazer abundances due to measurement error that we cannot see the predator -> grazer relationship.
Now let’s consider the model on the right. Here, I’ve assumed that 10% of the variation in the data is due to measurement error (i.e., an R2 of 0.9 between observed and actual grazer abundances). So, I have “calibration” data. This error rate is made up, just to show the consequences of folding the error in to our analysis.
Just folding in this very small amount of measurement error, we get a change in the results of the model. We can now see a negative relationship between predators and grazers.
I need this calibration data to ensure that the results I’m seeing in my analyses of this incredible 30 year kelp forest data set are real, and not due to spurious measurement error. So I’m hoping wonderful folk like you (or people you know – seriously, forward http://scifund.rockethub.com around to everyone you know! RIGHT NOW!) will see the video, read the project description, and pitch in to help support kelp forest research.
If we’re going to use a 30 year data set to understand kelp forests and environmental change, we want to do it right, so, let’s figure out how much variation in the data is real, and how much is mere measurement error. It’s not hard, and the benefits to marine research are huge.
Whew, it’s been a bit since I posted here. Rest assured, little sea squirts, there are some interesting new things in the works. Some things that are science-y (in which I try and use this blog as a sounding board/ lab notebook) and some things not so much.
In the not so much category, a ton of my time has lately been going to the organizing of the #SciFund challenge – a large initiative to try and crowdfunding for science! If you haven’t been following it, check out our initial manifesto here.
I’m pretty stoked about the whole thing – it’s a real way of connecting science to the public via a funding mechanism. And with us launching on November 1st, it’s been an absolute pleasure to watch the creative and innovative videos that participating scientists have been putting together to solicit funds.
Videos, you say? Am I doing one?
Why yes! So to give you a hint of what’s to come, here’s a brief preview of my #SciFund video. I think you’ll all agree, it’s vintage me, attempting to sell one of the more arcane (to the public) pieces of my research in a way that might just connect. We shall see.
More to come in a week…
So, I’m-a-gettin’ hitched in, what, just less that 6 weeks to a singularly lovely lady. As I determine the proper haute couture for the nuptials, I’ve begun to have fun with one piece in particular. Cuffilnks.
I mean, if you’re going to go Tux (and I do so love a good tuxedo), cufflinks are a must. But what kind of cufflinks should a gentleman marine biologist wear? Why, sea-creature themed, of course. I began my search looking for ascidian themed cufflinks and studs. Sadly, no jeweler, even on etsy, has yet decided to imortalize the beauty of a Ciona intestinalis or the distinctive star-shaped patter of Botryllus schlosseri for one to wear on their French cuffs. So I began to search further afield. I’ll give away the ending right here, I’m going with these urchin cufflinks by Ashley Childs actually cast from urchin tests, but, I thought you all might be interested to see some of the lovely, beautiful pieces I found along the way.
Nothing says style and elegance like a piece of urchin test adorning your wrist.
Phylum Echinodermata, Class Echinoidea
While the ones I’m going with are cast from tests, it is not for lack of trying to find cufflinks made from actual tests. I’ve long coveted these made from small urchin tests found washed ashore. Sadly, they are only available in pink, green, and brown, and won’t match anything else color-wise at the wedding. (What, I used to be in theater, so design is very important.)
So, cast or inspired it is. I really liked these urchin-styled cufflinks by David Yurman, but, sadly, silver, which clashes with the purple & gold thing we’re going for. Also, these slightly more abstract urchin ‘links were awesome, but, likewise, silver. (See also this great ring by the same artist).
So, gold (or, rather, plated). I thought these were elegant and lovely, but Tiffany and waaay too pricey for me. Similarly, these were great, and had a maching studset, but, a little plain. So, if I was going to go urchin, I was going to go with the cast piece.
Phylum Echinodermata, Various Classes
That said, I was not quite ready to give up on echinoderms. On a bit of whimsy I tried searching for some Sea Cucumber ones. No dice. Sand dollars turned up a few interesting natural or cast ones. I’ve never studied sand dollars, though, so…I continued looking. What about Pycnopodia? No dice for the multi-armed beast. However, I did turn up some cool Pisaster-like ones as well as a few more abstract. There were even a few made from beach drift (I hope) (and that person’s store is full of similar neat stuff), but nothing really caught me like the urchin test cufflinks.
Phylum Mollusca, Class Gastropoda
What about getting out of Echinoderms all together, and going with mollusks? Surely, there must be many gastropod-inspired cufflinks out there. And there are! Many are just ho-hum plain seashells, though. Some, though, are exquisite, such as these conch shells, which really could do for any whelk biologist. Or these silver lovelies by Danielle Meshorer which reminded me of nothing so much as our Californian Lithopoma. There were also some great ones made from actual shells.
I'd say these were second place. They're pretty fabulous. And pointy, so, useful to stab unruly wedding guests.
Phylum Mollusca, Class Cephalopoda
Now, like a good nerdy marine ecologist with slightly steampunkish leanings, the question begs: why not cephalopods. Indeed, I just finished reading Kraken, and do annually celebrate Cephalopodmas. A search for squid cufflinks can turn up a lot, but many of them are cameos or kinda kitchy. Instead, what really impressed me in cephalopods was Octopus cufflinks. This particular version with a hole in the head popped up all over the place, and is really rather stylish. Or you can find this set with a matching tie pin. Or even get into something a little more abstract. I liked them, but, eh. As I’ve never studied cephalopods, I felt like I should be true to my roots.
What gothy Cthonic octopodes these are!
Phylum Arthropoda, Class Malacostraca
I have, however, spend a lot of time with crabs and lobsters. Crabs also made a lot of sense as I am a boy Baltimore bred. The crab cufflinks out there are all very classy, if I do say so. I think my favorites just featured claws. Some where very cool and artsy. Other’s more steampunky. But nothing that really grabbed me. Similarly while there were some wonderful silver and gold lobsters out there (and some quite pricey!), nothing really said, yes, I am what you want on your wrist when you say “I do.”
I like to pinch.
Fin
So, really, it came down to urchins. I mean, nothing says commitment like the commitment of a ravening spiky beast gnawing through an entire kelp forest. That takes desire, work, perseverance, and a lot of love…of kelp. An apt metaphor, no? Well, at least my future wife will get a chuckle out of that one. I hope. And given the elegance, whimsy, and biological accuracy of the urchin test cufflinks, I think it’s where I’m going to go. But for the rest o’ ye, enjoy what I’ve listed here, and if you’ve found anything that you feel is truly amazing, please, post it! Also, I’m still looking for studs…