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.

On Coffee and Science Education: sometimes a millimeter makes all the difference Jens Hegg Thursday, December 04, 2014

I'll tell you the moral to this story right off the bat. Sometimes a millimeter is the difference between something great and something terrible. Sometimes it pays to look at the details, understand why things work the way they do, and work through a problem logically. Sometimes it's fun to geek out on something, roll your pants into high waters, put in your pocket protector and act like an engineer. It might even save you twenty bucks. Sometimes I wonder if our country's lack of interest in science is partly due to our willingness to unthinkingly replace rather than understand and repair.

I recently bought a new coffee maker at World Market, a Pezzetti italian style moka pot. I did it because I thought the espresso machine I was given last year had kicked the bucket. It turns out that it's working fine again after apparently deciding to go on a short sabbatical for no reason I can determine. I was excited for the new moka pot because I just love the thick, almost syrupy coffee filled with deep caramel flavors that these little pots make. People confuse them with espresso makers but they really excel at the bottom end of coffee taste. Moka coffee usually lacks most of the high, bright, citrus notes in espresso. Both are good but they are very different animals. But I digress...

I filled the new pot with coffee and water and put it on the stove anticipating a stout cup of coffee. It boiled…and boiled…and boiled some more with steam coming out the top tube before it started spitting a tiny bit of extremely thick black coffee out of the collection spout. Then, after a few tablespoons it just quit and started making sputtering, spitting noises and smelling like the worst church-basement-percolated-through-a-two-hour-sermon brew you can imagine. That two tablespoons could have been mistaken for motor oil mixed with paint stripper. In a word it was undrinkable. I tried again a few days later and the result was the same.

I'm wasn't very familiar with these things, but the idea is pretty simple. Build up vapor pressure in the base, which forces the hot water up a siphon tube, through the grounds and into a collection chamber at the top. It's like a cross between a percolator and a pressure cooker. Take a look at this awesome video for a bit of geeky imagery of this in action filmed with neutron imaging. This isn't a complicated machine, so what was the problem?



I couldn't immediately see a problem when I took it apart. The seal and all the filters were fine. I ended up putting it away but I kept thinking, "this is too simple for it not to work when all the parts look right." My mind kept churning on it off-and-on before I realized what had to be happening. If no water was going up the tube then somehow it was losing the vapor pressure in the bottom chamber, since that is the force that sends the water upward. But how was that happening if I couldn't see or feel a leak on the outside?

Top rim is a millimeter or so higher than the filter basket

Then I remembered that steam had been coming out the top for quite awhile before any coffee came out. So, steam was somehow getting out around the filters inside. I went to look at the seal again and happened to notice that the top rim of the bottom half of the pot was slightly higher than the filter that fits inside it and holds the coffee. It was only a millimeter or a bit more, but perhaps that distance was too much for the rubber seal to bridge, letting steam out around the edge of the coffee basket. Hmm…

grinding down the rim on a water cooled lapping wheel

Over the next week I dropped into a couple of stores to take a look at their moka pots. Sure enough, all of them had rims on the bottom chamber that were the exact same height as the filter basket. It was time to experiment. I loaded up the coffee pot with water and grounds, then tightened it as hard as I could to, hopefully, create a better seal. It didn't really work, but I did get about twice as much motor oil/paint stripper solution out of the pot this time around so i figured a better seal must be helping.

Luckily, I had an easy way to fix the problem. I took the pot to my lab and ground the rim down with the sandpaper on a lapping wheel. You could do this easily enough with sandpaper mounted to a board, but a lapping wheel takes less time and the water jet helps keep things cool. You can see from the picture that the rim matches the height of the filter basket now after just a minute or two of grinding.

Rim even with filter basket after grinding

Then came the moment of truth. I loaded the filter basket with freshly ground Indonesia Gajah Aceh from Stumptown, filled the bottom chamber with water, and put it on the stove. This coffee is already just full of deep, intense, earthy flavors…my mouth was watering imagining how rich this coffee would be. I hoped I wasn't going to be disappointed yet again.

It worked! No steam came from the tube in the center of the collection pot, instead a steady stream of coffee issued forth with no sputtering or spitting until the pot was full and the water chamber was empty. The coffee was awesome…and is fueling this late night blogging session as we speak; thick, rich and chock full of bitter chocolate, carmel and straight up dirt.

Sometimes it pays to work through a problem like an engineer, understanding how things work and the principles behind it. I think too often now days we would rather buy something new than fix what we have and that is a shame. My grandfather used to spend lots of time tinkering and fixing things, and creative repair is a daily occurrence for my father the wheat farmer. Watching them taught me that if you understand how something works you can usually fix it or improve it. That is the essence of engineering and science.

Perhaps we Americans have so few kids interested in science because we aren't teaching them how rewarding it is to observe, troubleshoot, and creatively repair things in our lives. You can't learn that skill if you throw things away every time they don't work. Which reminds me…maybe I should figure out why that espresso machine decided to quit turning on for two weeks and then fixed itself for no reason. I'll keep thinking on that one while I try desperately to finish my PhD. Until then, my advice is to avoid moka pots from World Market unless you want to repeat what I just did.

The moment of truth. A perfect brew with no sputtering!

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.

Do they have otoliths? Jens Hegg Saturday, March 21, 2009

Luckily Dogbert hasn't tried microchemical tracking using their ear bones!!

Tropical Insanity Jens Hegg Friday, January 30, 2009

These new “secondary” forests are emerging in Latin America, Asia and other tropical regions at such a fast pace that the trend has set off a serious debate about whether saving primeval rain forest — an iconic environmental cause — may be less urgent than once thought. By one estimate, for every acre of rain forest cut down each year, more than 50 acres of new forest are growing in the tropics on land that was once farmed, logged or ravaged by natural disaster.

This article from the New York times really gets me. The gist is that due to economic conditions in the tropical countries many people are moving to the city and abandoning arable land. This land is then growing back into forest and acting as a carbon sink. Apparently, according to the article, there is a "debate" among scientists as to whether or not we should decrease our efforts to save tropical forests since these new second growth forests may be sucking up enough carbon to make up for the lost primary forest.

This is wrong on many levels, maddeningly wrong. First, I doubt that there is any serious debate on this topic. However, the news must make a story so they find some wingnut and twist his story into a debate. This happens way too often and is die in large part to the lack of qualified science editors in news organizations.

For a primer and some great pictures of the difference between primary and secondary tropical forest visit this site.

Second, there is a clear distinction, even in temperate forests, between primary (old growth) forest and secondary forest. Yes, it is true that secondary forests are carbon sinks, they may even suck up carbon at a faster rate than old growth due to their higher growth rate. However, the forest is very different. It only has one canopy, there is a marked decrease in species richness (marked being often greater than 50% fewer species of all animals, plants and birds), it is also more susceptible to fire (a previously virtually unknown problem in the wet tropics until we started cutting down the forest at the clip we have become used to). Also, it is not guaranteed to proceed into primary forest, and even when it does develop taller trees and multistory canopy it is much less diverse. Worse, some forests have a very delicate balance that, if disturbed, would likely never return. This includes things such as Varzea forest in the Amazon in which the annual flooding has induced fish, bird, insect, tree and mammal species to develop complex interrelationships. These forests will never come back the way they were if they are destroyed.

Third, who says that economic conditions won't change. Up until recently it was easy to get a job, now with the economic downturn that may change drastically. For poor peasants in the third world it is better to be a subsistence farmer than a poor, homeless bum in a city. People will begin to recultivate these areas. Large farms will probably do well. Commodity prices could easily spike again as they did last winter in the midst of the current recession. Also, commodities are fairly stable and concrete compared to other investments. I'd rather have an acre of fertile tropical soil than a $100,000 mortgage derivative investment at this point. To divert money from saving primary forest in the hope that abandoned land will stay as forest is a pipedream.

This is to say nothing of the need for species diversity. If this is ignored completely in favor of simply looking at this from a carbon balance perspective we've lost the battle. We are currently causing one of the greatest extinctions in the histroy of the world. Like it or not we are tied into the food web, the fewer species there are the less stable that web becomes. Similarly, we lose the opportunity to sustainably exploit these resources in ways we have yet to discover. The argument is tired and old but there may indeed be great medicinal value in some of the species in tropical forests. And this is all glossed over by our moral imperative to keep our world safe for our children.

I would like to know the full story on this. I doubt that there is truly a large debate in the scientific community, although I would say there is certainly a good amount of righteous indignation toward this Joe Wright guy. His position is completely untenable and lacking any long-term thinking. If we were to take him seriously we would lose one of the greatest treasures and greatest resources this world has to offer. If this story did indeed paint Joe Wright and the controversy in the proper light he is a stooge to be ignored, not a serious force in tropical science or conservation.

Slowing Down for the Dog Days of Summer Jens Hegg Sunday, July 27, 2008

Hello to all the regular readers as well as the new folks visiting from Tangled Bank this week. Things will likely be slow for a while here but it is for a good purpose, trust me.

I am moving this week to start graduate school in aquatic ecology at University of Idaho. I will be working with Dr. Brian Kennedy in the Water Resources Program on a Masters project in salmon otolith microchemistry and life history analysis.

The non-technical way of putting this is that I will be plucking out the ear bones of salmon and analyzing them much like you would the rings of a tree. Strontium isotopes are different for every river and stream due to changes in underlying geology. These isotopes are deposited in the "tree rings" of the fishes ear bones. With this knowledge in mind you can decipher where a fish has been along its migration route over it's entire lifespan. Further analysis of the ear bone can give you the fish's age, allowing you to know with amazing accuracy the date that a fish was in a particular river or stream.

This information is vital to understanding the dynamics of a species' migration and how this is effected by dams, fishing, global warming, genetics, and any number of other factors. I hope to expand the research in salmon as well as expand the technique to other migratory species about which we know very little.

With the start of school I am considering turning this blog into more of a science/"trials and tribulations of a grad" student blog. We will see in what direction I head, but I think no matter where it goes it will be quite a ride. Hang on!

Wish me luck! Moving across the country with a three year old is not an easy task. I will keep you updated on my progress as time allows.

Cool Fake Fish...And a Penguin Kayak Jens Hegg Thursday, May 15, 2008

Credit: Jindong Liu, University of Essex

This fish from the University of Essex is the worlds most advanced, fully autonomous, robotic fish. It swims, dives, and avoids obstacles on it's own and has some pretty amazing specs for speed, acceleration, and turning ability. For this and other demonstrations it has actually been speed limited to conserve battery power.

For those interested in how this came to be, take a look at this large but VERY informative video of the design process behind RoboCarp.

This fish is not the only robotic fish out there. Robotic-fish.net keeps a listing of a large number of them here. These include a robotic coelacanth and manta ray. The forum Ornithopter Zone has numerous home made RC fish as well if you search the forum.

I think these things are totally cool. First, the engineering behind them is impressive, and second, the mechanics have real potential to improve the efficiency of any water based vehicle. An example of this crossover from animal biomechanics to engineering is the Hobie Mirage kayak that uses two fin like sweeps to generate pedal power. The drive system is apparently uses a similar design as a penguin wing.
The video demonstrates the effeciency and power of the Mirage fairly well. If you want, take a look at this video that shows a Mirage beating one world champion paddler and holding it's own against two world champion paddlers.

(Sorry for the promotional nature of the vids, it's all I could find. I promise I'm not shilling for boat manufacturers on this site, it's been years since I paddled a kayak and I have never pedaled one)