Big News! PLOS Ecology Community Blog Editor Jens Hegg Friday, October 02, 2015

Hello all. Sorry for the long delay in posts. I have a couple in the pipeline but I wanted to alert you to some good news on the blogging front.

I have officially been selected as one of three PLOS Ecology Community blog editors. I've already posted two posts with them on a freelance basis; 

• Fisheries Science meets Scicomm: to tweet or not to tweet. A discussion of live-tweeting ethics in the context of the recent American Fisheries Society National Meeting in Portland, OR
• What Will You Do When You Get There: A perspective on species range shifts. A review of PLOS papers dealing with species range shifts and the questions they raise for ecologists in the future.

The position will entail a couple posts a month on the PLOS Ecology blog, engagement with prominent ecology bloggers and writing collaboration with other ecologists and leaders in the field putting PLOS papers into context and creating a community for ecologists on the web. 

Wish me luck and keep your eyes open for new posts!

New Post at PLOS Ecology Field Reports Jens Hegg Monday, August 10, 2015

For those of you who are so inclined, please take a look at my first blog post on PLOS Ecology Field Reports.

What Will You Do When You Get There? Making Sense of Climate Change Induced Range Shifts

I am looking forward to more and frequent blog posts with PLOS after they asked me recently to take part in their rollout of the PLOS Ecology Field Reports Blog for ESA100 as a PLOS Ecology Community Blog Editor.

Watch for another post this month during my trip to the 145th National Meeting of the American Fisheries Society in Portland, Oregon next week!

Mai Tais for Europa Jens Hegg Friday, February 20, 2015

Yesterday my lovely wife was notified that she, along with a whole group of collaborators, will be funded by NASA! They will be to studying the recently discovered tectonic activity in the ice on Jupiters moon Europa. Getting funding is always welcome news, and doing something so cool deserved celebration…which in our house usually means a fancy mixed drink at some point.

A confluence of events sent us towards making up the original Mai Tai. First, our minds are turning toward the tropics and our upcoming honeymoon to Costa Rica. Second, we recently received awesome tiki glasses as a wedding present. Third, I've had a bottle of home made orgeat syrup sitting in my fridge for over a year and I'm always interested in finding new ways to use this amazing and perennially mis-pronounced nectar of the gods. (It's Or-zjat, not Or-Gee-ot). After being told by a friend that we should have a blog to document our drink mixing adventures I figured I had better post about these epic Mai Tai's, so here you go!

If you've never had a real Mai Tai you need to mix one up right away. It is epic! I had never had one despite how much the history of cocktails was influenced by Don the Beachcomber and Trader Vic. These drinks are all about rum, good rum, and lots of it, in different varieties. When I think of Tiki drinks I think of rum mixed with fruit juice, but most of the classics are mostly booze with some fruit thrown in for taste. The classic Mai Tai is no different.

Here is the recipe I used, which borrows a bit from the Trader Vic and Don the Beachcomber versions as well as this one from the Washington Post. These two feuded a bit over who invented this drink.

• 1oz - Pyrat blended rum (mostly Demerarra apparently)
• 1oz - Depaz Rhum Agricole
• 1oz- Cruzan light rum (it was in the bar…)
• Juice from one lime (~3/4 ounce)
• 1/2 ounce Triple Sec (no Cointreu or Orange Curaçao on hand)
• 1/2 ounce Orgeat syrup (essential for this drink, home-made is WAY better here)
• 1/2 oz Velvet Falernum (this stuff is awesome)
• 1/2 oz White grapefruit juice (I made it with and without, I like this addition a lot)
• 1/2Tbs powdered sugar (I didn't have simple syrup)

I was lazy and didn't use crushed ice. I put all the ingredients together in a blender, dropped in ice cubes and pulsed it a couple times until the ice was well cracked. DO NOT make this into a smoothy, that would be a tragedy! I garnished it with a stick of fresh pineapple and a lime wedge stuck with a fancy toothpick but a mint sprig and lime is traditional. This thing packs a serious punch and you can really taste the rum, I would avoid using cheap rum at all costs, it would ruin the smoothness of the drink. 

Romancing the Open Source GIS Monster Jens Hegg Friday, February 13, 2015

Do you need to do GIS work but don't have the money for ArcGIS or the required extensions to do what you want to do? Have you heard about QGIS or GRASS and thought that they might solve your GIS woes with a free, open source solution? You might be right…or you might be very wrong. It all depends on what you hope to use them for and what your background is in programming languages.

I am a huge proponent of open source software but, before you start using a new open source package it is well worth your while to know how much time you are willing to commit. How far down the rabbit hole of coding and scripting you are prepared to go to get what you want? In some cases this isn't an issue and things work right out of the box, but it's worth it to know your limits ahead of time. This is particularly true for the open source GIS packages available out there.

I use multiple open source software packages and some are absolutely vital to what I do as a scientist. If there were one piece of software that I couldn't do without as an ecologist it would be R, the open-source statistical package that has become ubiquitous over the last few years. Open Office and specifically Libre Office have saved multiple files from Excel and Word that have been corrupted by their own office suite. I've been using Libre Office primarily for a couple months now.

Open source software promises a future where everyone can get what they need out of the software they use, rather than having features added only when it makes monetary sense for the company making it. It also provides, at least in theory, a very approachable and ever changing help system where questions can be answered by other users and problems can be reported and quickly fixed by those with the interest and skills to do it. The idea is great, and in the case of the programs I listed above it has worked out really well. But, for less developed software this isn't always the case.

I've recently been tearing my hair out trying to complete a GIS project that should have taken hours and instead has taken days. Because I'm a stubborn bastard who believes in open source (dammit!) and I didn't have an available license for ArcGIS and Arc Hydro Tools I have refused to back down, thinking that if I could only learn a bit about Python or a bit more about bash shells for Unix I could get done what I want to get done. It didn't work. What I wanted to to do is possible, but it's further down the rabbit hole than I have time or skills to go right now.

The interface of ArcMap 10.2, the industry standard GIS software

I should provide a bit of important background information. During my masters I published a paper showing that from relatively simple geologic maps, and some knowledge of the water chemistry in your study area, it is possible to predict what the strontium isotopic ratio will be anywhere along the river. This is hard to communicate over the thump of electronic music, and doesn't even go down well at refined cocktail parties. It's super interesting if you study where fish go using the isotopes in their ear bones, which is what I do as a PhD student.

Interface of ArcMap 10.2, the industry standard GIS software.

To do this work I used ArcGIS, the "industry standard" GIS platform. Personally, I dislike ArcGIS quite a bit (file names have to be less than 13 characters? This is 2015). So, for an upcoming paper on the migration patterns of giant Amazonian catfish I used a combination of QGIS and GRASS, two open source geospatial packages that inter-relate with each other and provide almost all of the functionality available in ArcGIS. Once I learned how to use them, these packages worked fine for fairly simple manipulation of maps, analysis of watersheds and geology, and creating really nice maps for publication.The vast majority of the tasks are automated and run through interactive windows like any other program. Where the problems cropped up was in trying to do anything more complicated.

Interface of QGIS 2.0. Notice the similarity to ArcMap.

QGIS in particular is a great platform that I think has tremendous promise. The interface is similar to ArcGIS but much more intuitive in my opinion. It accepts files of all kinds and is flexible about map projections. It also brings almost every other open source GIS resource into its toolbox, allowing you to use the tools available in all of them under one interface. I'm very excited about the future of QGIS, I think it will be the future. Just as R is supplanting expensive SAS licenses in academic publications I see QGIS doing the same thing to ArcGIS in the future.

Interface of GRASS 7.0 is very different, as is the functionality.

GRASS is a more picky beast, like a 70's muscle car, you can feel the power under the hood but the entertainment system and seats aren't quite as snazzy as a new Ferrari. If you don't know much about map projections GRASS will teach you like an angry stepmother, with beatings behind the woodshed until you get it. For those of us who have been coddled by ArcGIS or QGIS and their "on-the-fly" projection it can be hard to make sure each new GRASS import is in the correct projection and that the import parameters are correct to make a functioning file. Then, once those files are in GRASS they disappear into a database and can't just be copied around like a .shp file, they must be exported. Figuring out the difference between a "Location" and a "Mapset" (the names for the database locations and the organization within them) is not well explained. Further, if you require overlapping polygons in one file GRASS cannot do this, it uses a different type of vector representation that doesn't allow it. This attention to map projections and reliance on a database has an upside though. Once the maps are input you can be sure that the calculations you do aren't introducing errors because of the way the layers are projected.

Both of the software packages are fairly mature, but the way they evolved has made QGIS much more intuitive and user friendly. While QGIS seems to have focussed on usability and GUI development, GRASS grew out of a command line interface in UNIX and has only recently released a somewhat polished GUI. Much of it's functionality is still accessed through scripting. You have to drag a Mapset folder onto the app to start the GUI, a double click doesn't work on my Mac. The GUI starts as a wxPython icon via a terminal window…it isn't what you expect but it work. The script languages you must use seem to depend greatly on the operating system you use and the window you pick to enter scripts. For instance, one can enter commands directly into the terminal window in bash script (who's grammar varies it seems), or you can enter GRASS scripts into the command console of the GUI using a language that seems very similar to R, or you can enter Python scripts using the Python Shell that is integrated into the GUI…or you can use the GUI interface. Making sense of the online documentation with this mess of input languages is difficult at best.

That brings us to the factor that sets good open source software apart from the rest, the online documentation and the user community. Programs like Libre Office are so mature that the documentation is very similar to MS Office and anyone can get going with it right away. The R statistical package has a steeper learning curve but the user community is huge, and growing, so there is plenty of documentation. They also have a very strict documentation requirements for packages on the CRAN repository so that it's easy to figure out what each new add-on package does and how to use it (assuming you are familiar enough with statistics to understand the concepts being used). Also, R has a single input language so every command is intelligible. That isn't the case for the open source GIS packages yet.

QGIS is making a good start, with a polished website and some good documentation. But, if you are interested in anything beyond the basic functionality it can be really difficult to figure it out. The user community seems to be pretty small, and the program relies on integrating the functions of multiple other GIS packages…most of which I was unable to make work in my installation. Because each of these other packages is built on different code bases and uses different inputs, figuring out how to make add-ons work is really confusing.

GRASS has even more problems, in my opinion. The program itself is very powerful. Unfortunately, the way the program has been developed means that the range of input languages, and even the grammar of each, depends on your operating system as well as the add-ons you use within the program. The website itself does a terrible job of introducing this coding complexity. The user community compounds the problem by doing a terrible job of specifying in their posts what script languages they are using, and on what system it is meant to operate on. In R you can pick a snippet of script and play with it until it works. In GRASS you can't be sure that the example script you find is even runnable on your machine. It's incredibly frustrating unless you have a deep understanding of multiple scripting languages and the GRASS program itself. It is not for the faint of heart and this rabbit hole is deep.

So, if you are a poor graduate student looking at the money you could save using an open source GIS package here is my advice. If you are just doing fairly basic vector editing, overlay type analysis, or basic raster analysis then install QGIS and you won't be disappointed. If you need to do quite a bit of work with rasters, watershed analysis, or other terrain based analysis then GRASS will do the job. But, remember that neither of these packages do more complex analyses easily because you will need to script anything that requires repeated analysis of different features across a map. Some of this probably isn't hard if you have a background in Python. If you don't already have that background, and sometimes even if you do, then expect to spend a lot of time learning from mistakes and trying to piece together information from cryptic message board posts. I think the future is bright for open source GIS and in a few years I expect it will be very user friendly. Until then it isn't for everyone.

Fear in the Field: Now is the time for the fisheries field to act. Jens Hegg Monday, September 22, 2014

A mixed group of fisheries field workers - Gary Peeples/USFWS

"If not me, who? If not now, when?" - Emma Watson, UN General Assembly, 2014 

As a male graduate student I rarely have to think about gender issues, at least not in terms of their affect on me directly. Still, I have a fiancé who is a professor in geology, a sister who spends plenty of time abroad for her work, and numerous women in my lab and department. It doesn't take long to hear stories about how gender affects your experience as a scientist, how comments about appearance or femininity undermine confidence, or how double standards often surround the expectations of female scientists.

I have seen this, and dealt with the fallout of these gender issues fairly frequently. Still, it appears that there is a large segment of male scientists who don't get it. The same problems seem to persist year after year and I rarely if ever hear anything about it from those in authority. When I do it's invariably vague and comes without any concrete action. With Emma Watson's excellent and moving speech before the UN last Saturday there has been a groundswell of media coverage surrounding her statement that gender equality is everyone's problem to solve, most positive and some proving her point.

Those of us in field-based sciences face some very specific gender related issues to solve; problems that have been put in stark relief by another recent event, a paper released in July in PloS One showing that field research can be a forbidding and abusing experience for trainees. The abstract of this recent paper in PloS One by Clancy et al. should be shocking to scientists of all genders:

"...harassment and assault were commonly experienced by respondents during trainee career stages. Women trainees were the primary targets; their perpetrators were predominantly senior to them professionally within the research team. Male trainees were more often targeted by their peers at the research site. Few respondents were aware of mechanisms to report incidents; most who did report were unsatisfied with the outcome." - Clancy et al., 2014

Most of us who work in fish ecology, or natural resources in general, are here because we fell in love with working outdoors, in the field. We all have memories of great times with new friends at field sites during college courses, summer internships, or technician positions. These are often the formative experiences in our pursuit of this as a career. But this graphic from the paper indicates that more than half of the women, and a good share of the men, I've been in the field with haven't had such a great experience.

To me this is shocking and disturbing, especially knowing that fisheries is dominated by white males and already has a problem with diversity. A quick search of the American Fisheries Society monthly magazine "Fisheries" shows that there are a few articles related to women in fisheries, but the most recent are spotlights of the prominent females in the field and discussion of more philosophical approaches to including female perspective in fisheries writ large.

There hasn't been a pointed discussion of the inherent problems that field-based fisheries research creates for women. I haven't, for example, heard a peep out of my own department about this. This could easily be because it hasn't been visible, but with the Clancy paper including almost 50% of it's respondents in biological and other related sciences this can't be ignored. I feel like it requires a concerted response, and not just another online sexual harassment training. It cuts directly to the core of the culture of field work in a way that needs to be addressed by the field at large as well as university departments and government agencies.

Most undergraduate programs require some sort of internship or field experience to graduate. At University of Idaho an internship is required and many students take part in summer field experiences with faculty researchers and government agencies to fulfill this requirement. This means that UofI is requiring students to take part in field experience that, if this paper can be generalized, is exposing women undergraduates to harmful interactions. Further, these experiences are often outside of the control of the University; students might never spend enough time with their employer to fully understand how to report inappropriate behavior and yet reporting through the University might not result in any help. Even if mechanisms are in place at the University they may be hundreds or thousands of miles distant, effectively useless as Christie Aschwanden makes clear in her essay in the New York Times. 

"Reflecting back, I’m struck by how ill equipped I was to deal with this kind of situation, especially at 19. My university undoubtedly had a harassment policy, but such resources were thousands of miles away. I was alone in a foreign country and had never received any training on my rights and resources in the field."

Remember, not only did the paper show that harassment and assault happens, it showed that the ability to report it is often not even there for victims and when it is the results are poor. It's time for departments, agencies and individual labs to step up, take charge.

I know from my experiences that fieldwork tends to have a loose, relaxed vibe. It's a time when we can get out of the office and into the field, away from the strict expectations of office work. There is usually plenty of time for socializing after a long day of work. Depending on the work there might be alcohol around a campfire or at a local watering hole. It feels more like a camping trip than a job sometimes. But, as the superiors of (often younger) students we need to realize that it's not ok to adopt the, "what happens in the hunting camp stays in hunting camp," mentality. Lets face it, that mentality isn't healthy even in most hunting camps we shouldn't expect it to be healthy on the job. This is a job, and for the undergraduates and graduate students this is a necessary route to a career. We need to understand and respect the power dynamics at play in the field. We also need to explicitly clarify how to report problems and then make sure that reports are followed up and those who break the rules get punished.

A recent article entitled "Science's Sexual Assault Problem," by A. Hope Jaheren in the New York Times both sums up the problem well:

"I listen to my colleagues talk endlessly about recruiting more women into STEM (science, technology, engineering and mathematics) disciplines, and postulate what the barriers might be. Sexual assault is a pernicious and formidable barrier to women in science, partly because we have consistently gifted to it our silence. I have given it 18 years of my silence and I will not give it one day more."

It also provides a sobering reminder of what it means if we don't act and fix these problems and instead decide to sweep it under the rug. 

"In August, Lego began selling a set called “Research Institute” that features three female scientist minifigures: a paleontologist, an astronomer and a chemist. I am well qualified in two of those fields, and I am here to say that playing with a different set of dolls will not adequately prepare your daughters for a career in science. You must teach them, rather, to manage their dreams. They need to know that daring to act upon their dreams of science can be both a beautiful and a dangerous thing."

I, for one, don't like the idea that anyone should have to manage their dreams. The very idea disgusts me. I hope the rest of my peers feel the same way and are willing to speak up and pro-actively do something about it. 

This article shows that just because there haven't been any reported incidents of harassment or assault reported to supervisors doesn't mean it isn't happening. We can't wait until something happens, because it is already happening, we just don't have the tools or culture in place that lets the news get out. We need to act decisively, vocally and openly to make sure that everyone can enjoy their field experiences. Nobody should ever have to balance a future career against the despicable actions of their superiors in the field. I think Christie Aschwanden gives us something to aspire to.

"It will take chief executives, department heads, laboratory directors, professors, publishers and editors in chief to take a stand and say: Not on my watch. I don’t care if you’re my friend or my favorite colleague; we don’t treat women like that."

As Emma Watson made clear, gender equality affects all of us and all of us must stand up and make it right. There is already a nascent conversation in fisheries and natural resources surrounding the need for more female perspective in our data and in our field, and there is a much broader conversation across the sciences as a whole. Clancy et al. make it clear that it is high time to ensure we aren't driving away that positive perspective through willful blindness of what happens in the field.

“How can we affect change in the world when only half of it is invited or feel welcome to participate in the conversation?” - Emma Watson, Emma Watson, UN General Assembly, 2014

Clancy et al. are showing, in cold, hard data, that we may indeed be driving away a very large percentage of entry level women in field-based sciences like our own. Other professional societies have led the way, and I would like to see my fields do the same. The Southeastern Archeology Conference has done a self study which shows much the same results as Clancy et al. and is drafting clear field policies for members to follow. The American Geophysical Union and American Anthropological Association have issued strict policies. Closer to my own field, the Ecological Society of America will host a panel discussion at the upcoming meeting in Baltimore.

Meanwhile Fisheries, the monthly publication for the fisheries field, has mentioned gender discrimination only a handful of times over the last decade and has neglected to respond to this study at its meetings or within its covers. Its time for all of us to stand up and make clear that we won't stand for any mistreatment of women and trainees, in any form, in fisheries sciences.



Here is the entirety of Emma Watsons speech, introducing the He for She Campaign for gender equality.

What do you do again? Jens Hegg Wednesday, July 16, 2014

I quit blogging before I filmed this video. If you've ever wondered what I do in my research this is the video for you. With some fun music and pretty pictures it explains what I do and why. 

Skiing with Berlyn Jens Hegg Sunday, February 15, 2009

My lab group went to Silver Mountain last week to go skiing. What a blast. My advisor brought his kids so we had a gaggle of youngsters plying the slopes for the first time. Berlyn is a natural. Here is a video taken in the first 15 minutes of skiing, followed by a video from later on in the day. Sorry for the poor quality of my phone cam.





about 5 minutes after the first video was taken some skiers saw berlyn in mid run and gave him a thumbs up. Berlyn had the presence of mind to look at them and give a thumbs up while hurtling at toddler speed down the hill. The effort unbalanced him and he nearly wrecked but pulled it out into a sweeping spin that left him gliding the last 25 feet or so in a reverse snowplow. I know that I was not that coordinated when I was his age.

For more pictures of the mountain, and riding the worlds longest gondola to get there, check out my photobucket page here.

Back from Whence Ye Came Jens Hegg Thursday, October 23, 2008

Salmon are pretty incredible creatures. I stopped by Spalding Park near Lapwai, Idaho (officially known as Nez Perce National Historic Park and containing an excellent museum of Nez Perce art and historical pieces reclaimed with the help of Walt Disney's wife, a native of Spalding, ID) to see the spawning Coho salmon this past week. I've never seen salmon spawning so it was an exciting moment. Watching them makes you realize that life is circular. Ashes to ashes and all that, but not in a depressing way at all.

The picture above is a spawned out female that I found while peering off the bank at a female preparing her redd. She had already begun the next cycle, the nutrients she carried from the ocean helping to keep her spawning stream healthy and productive for the next generation.

Salmon prepare a redd, or nest, in the gravel of the stream bed into which they lay their eggs which are subsequently fertilized by the male and covered. Each species does it differently. Coho are adapted to more silty areas and their redd making entails sweeping away the silt with their tails, while other species may mound the gravel more or less and choose particular sized gravel and silt levels to suit their evolutionary taste. The picture to the right show a female coho preparing her redd by laying on her side and flapping her tail to clear the silt from the gravel. The next picture shows what the redd looks like from above. The oblong patch of lighter colored gravel on the right side of the picture next to the bank is her redd. Bonus points if you can find the salmon in the picture. She saw me on the bridge and moved off her redd into the darker and more camouflaging area of the stream.

Coho were declared extinct in the Snake River and only recently have been reintroduced by the Nez Perce tribe. Lapwai creek runs into the Clearwater river at the park which is located on the Nez Perce reservation. The Park is named after Henry Spalding, a missionary from the 1800's who's grave marker is shown to the right.The park encompasses the mission site as well as the historic cemetery.

While I was there I had a bit of an epiphany about life and death. I'm not sure if the salmon were the spur to my thinking or
not.

A member of one of my classes, which centers around cross disciplinary issues of salmon recovery on Lapwai creek, is a Nez Perce Tribal member. While visiting the park earlier he mentioned that a close friend had died and that he would be buried in Spalding cemetery. I watched the grave being dug and saw it again when I returned to see the salmon.

I noticed that rather than dig the grave with a backhoe friends and family came out, peeled back the sod, and dug the grave by hand.
Regardless of your personal convictions I think most people are horrified when they learn how we bury our dead. I can say that when I die I hope I am not filled with immutable fluids and placed in an impermeable casket within a concrete box (to keep the grave from sinking as I decompose), and placed in a hole dug by some anonymous and surly city employee who will likely throw his cigarette butt in the hole when he's done.

I can only hope that I surround myself with friends and family that would see the social value in coming together to dig my grave the way it aught to be dug, by hand. I can only dream that I would be laid down in a simple pine box or shroud so that, like the salmon, I can go back from whence I came.