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LirbaLirba 23 May 2016 14:43
in discussion Hidden / Per page discussions » Marine Tardigrade

I think the same Daniel, even I confuse the tardigrades with larvae polychaetos

by LirbaLirba, 23 May 2016 14:43

I mentioned this project to a marine ecologist, Dr. Megan Dethier who works at Friday Harbor Labs and has experience in this area. She suggested I pass on her comments, which follow:

1. Getting citizen scientists to do anything with the label of 'biodiversity' is very tricky - because the data you get will depend ENTIRELY on the training and experience of the participants. So to get 'diversity' data that you can trust, you will likely do much better coming up with a distinct species list, with photos and notes about how to distinguish them, and then try to gather presence/absence or even abundance data about those.
2. Macroalgae 'health' - health is such an unfortunately vague word! They mention color, which is a good idea. One other thing that they might look for - and I would encourage that they establish clear 'scales' for both color and this, is how intact the blades are - eg 'whole', 'frayed edges', 'reduced to stipes' - or some such words, this will depend on the species and what those familiar with them expect. One other metric that might be useful, again depending on the species, is presence/abundance of juveniles - eg are there any Durvillea in the area less than 25 cm total length? Recruitment (loss or gain of) may well be a good 'early warning' of range shifts.

Thanks for that Mickey. l'll pass on the word to the working group

by wolflikemewolflikeme, 03 Jun 2015 02:01

This project sounds great! Thank you for posting it.

For question 2, one program to look into might be ImageJ. It's a free image analyses program, originally produced by the US National Institutes of Health. I've used ImageJ for all my work with time lapse videos. It's very easy to use, can be easily extended with plugins (written in Java) or using a simple macro language, and is quite powerful. One limitation is that one has to convert video to a tif stack (it can convert Quicktime and .avi files, at least with the right plugins). That means it only works with a few hundred frames at a time due to memory limits. However, if one can deal with just a few hundred frames at a time, it can do do a huge range of things, with lots of analysis algorithms, especially given the existing plugin library. There may be plugins/macros written already to do the random dots which users can label, but it should be pretty easy to write a macro for it.

By the way, I added tags "ecology" and "oceanography" so it would show up in the "projects by field" list.

Also, it would be great to add info about the sources of those nice figures.

Best wishes.


by Mickey von DassowMickey von Dassow, 01 Jun 2015 19:44

Here are diagrams of three ideas I've had, each of which has some potential, but also some problems.


Top diagram: a cover glass is mounted on a slide at a shallow angle (thin gray bar), and media (seawater) flows from one side to the other (arrows) pulling the embryos (blue circles) with it. How far the embryos get along the cover glass should depend on a combination the flow speed, and the embryos' stiffness, size, and friction. The advantage of this setup would be that one could do large numbers at a time and it would work with swimming embryos (as long as the flow rate is greater than their swimming speed). The downside is that it would also be sensitive to variation in friction and embryo size, not just their stiffness. The size may not be much of a problem except in that it would affect the drag.

Middle: Here the embryos (blue circles) would get sucked by water flow (arrow) into a conical opening (perhaps the end of a micropipette inserted into another glass tube). As with micropipette aspiration methods for measuring mechanical properties, one could measure their deformation for a given pressure (once the embryos get stuck in the cone). It would be less dependent on friction and size (the scaling would be simple). The advantage over micropipette aspiration is that one wouldn't have to capture individual embryos: they'd flow in until they reach the part of the cone that matches their diameter. Then one could increase the suction to pull them through the hole, slow it down again, and capture the next one. The main disadvantage is that one would get only a small increase in the speed of measurement over micropipette aspiration.

Bottom: Using a fairly cheap protein (protamine sulfate) one can get swimming embryos to stick weakly to glass. If one could get enough of them stuck down, one could carefully lower a known weight (the gray bar; perhaps a thin cover glass) on top of several of them at once. This would allow one to measure the average stiffness of a large number at once. The advantage of this is that it would give a fairly direct estimate of their stiffness. Two minor disadvantages are that the embryos stick only weakly, and it would be difficult to lower the cover glass gently, and uniformly enough. A bigger disadvantage is that — in contrast to the top two methods — one would not get a very clear estimate of variability in stiffness among embryos.

by Mickey von DassowMickey von Dassow, 03 Mar 2015 23:09

What a beautiful picture. It's interesting that the pattern isn't actually regular, though I thought it was at first.

by Yasmin von DassowYasmin von Dassow, 26 Feb 2015 00:04

Thank you to Jim Strother for being the first person to join the list of people who plan to pose challenges!

If you want to win cookies there are still several ways.

By the way, because I've been a bit slow about spreading the word about IGoR, I changed the date by challenges should start on/before to win cookies.

by Mickey von DassowMickey von Dassow, 18 Feb 2015 17:52

Over the next few days, I plan to add some diagrams of some ideas for simple devices I've had kicking around in my head for how to do this. But first I have to draw them, and I thought it might be good to let people think and use their imagination for a bit before I chime in.

by Mickey von DassowMickey von Dassow, 12 Feb 2015 21:37

This project is put up as a "challenge project", by Mickey von Dassow.

Who I am: My research focuses on the roles of mechanical processes in biological development. I am fascinated by how organisms create complex structures reliably, despite all the things that could disturb their development. I did research on the role of tissue stiffness and viscoelasticity in vertebrate morphogenesis (specifically gastrulation; e.g. [1][2]) for several years as a postdoc, before switching to sea urchins and sand dollars (which are just flat urchin) as my study organism. I am currently a guest researcher at the Duke Marine Lab, and the founder of IGoR.

Contact email: mvondass<X>gmail<->com.

Challenge duration: This challenge will be open until May. 30, 2015.

Page-specific policies: Anyone may leave comments on this challenge project's page, but please ask me before editing the page itself (email me and tell me a bit about your skills and scientific interests).

What constitutes solving this challenge: A working device or method that provides an index of mechanical properties in >15 small (100 - 200 µm diameter), soft, round objects within 10 minutes. It should be plausible that it could work for swimming organisms (e.g. urchin embryos), but does not need to have been tested with them. Basically I want something with a good enough chance of success to try with real embryos, and to compare to other, more detailed, measurement methods.

Project significance: The larger question that motivates this IGoR project is: To what extent does biomechanics control how environmental factors affect development[3]? Development of an embryo, or during the continual changes of adult tissues, involves deformations and movements of cells and tissues (i.e. morphogenesis). These deformations are driven and resisted by forces applied to, and by, the cells and tissue. Therefore, mechanical properties such as tissue stiffness, pressure, and others, are thought to be critical for normal development. The mechanical properties of cells and tissues are the result of interactions among a very large set of proteins and other molecules. It's not just the amount of one protein or another, but also the structure (e.g. how fibrous proteins are oriented and linked together, and how they are distributed)[4]. Therefore, many environmental and genetic factors might influence cell/tissue stiffness, viscoelasticity1, and force generation. Such changes could cause developmental defects (e.g. if some factor causes the cells to exert too little force to deform the embryo, the embryo may not undergo normal shape changes), or increase the risk of developmental defects.

Understanding whether and how mechanics links development to the environment should help us understand the evolution of morphogenesis (by learning about selective pressures acting on morphogenetic processes), and understand the mechanisms that cause or prevent developmental defects in natural populations. To study these larger questions, it would be very helpful to be able to screen a bunch of different conditions, possibly in combination with each other, to see which, if any, have a detectable mechanical effect. Most methods for measuring mechanics of embryos work one embryo at a time, and take at least 10 min per embryo (including setup). That may not seem like much, but — given embryo-to-embryo variability [2][5] and changes in mechanical properties with developmental stage — it limits the number of conditions one can practically test.

by Mickey von DassowMickey von Dassow, 11 Feb 2015 19:21

Based on my year of trying to get IGoR started, it's clear people won't jump in to something new just because they like an idea. However, people will try new things even if they require some effort to get started (e.g. LinkedIn, Facebook, or editing Wikipedia) if enough other people have tested the waters, and found them hospitable.

To get those first few people one either needs a lot of charisma (not happening) or clear incentives. However Jim Strother pointed about that rewards and incentives also have downsides. He said I could quote him, because he makes his point quite clearly:

"I'm glad you found the idea for IGoR useful. My only other thought would be that it may not be a good idea to offer rewards, either explicit or implied. I'm not sure how much you follow open source software projects, but this approach has been tried several times in numerous forms. The basic story line is: small project builds wonderful community, project gets bigger, project hires staff or offers rewards to help operate at larger scale, entire volunteer community gets pissed and stops contributing. When there is no reward on the table, it seems to engage a mindset of discovery and social altruism. But as soon as anyone anywhere is getting a reward, it engages a mindset of competition and cost/reward tradeoff. There are a bunch of blogs on this, the first one that came up when I googled it was The comments are the most interesting part, I didn't read any of them, the interesting part in my opinion was just that so many people thought hiring a full-time developer was something important enough to comment on. Anyway, just my two cents."

by Mickey von DassowMickey von Dassow, 03 Feb 2015 17:08

I like the idea of challenges, and I think it could work well once the site has regular traffic. Just make sure the other projects don't get overshadowed by the challenge projects. I didn't see anything substantive to change in your text above.

by Yasmin von DassowYasmin von Dassow, 03 Feb 2015 01:37

JS pointed out that framing social things in terms of what people get out of doing something can make people less likely to do it, so I've changed the language to focus less on explicitly saying how users/challengers would benefit. Also shortened it.

by Mickey von DassowMickey von Dassow, 01 Feb 2015 17:36

If people like the idea of challenge projects, I'll add links to a list of challenge projects on a separate page, and this page (and the front page) will show a featured challenge (once there are some challenges).

by Mickey von DassowMickey von Dassow, 29 Jan 2015 20:55

The new pages look great: much cleaner and easier to read. The tips are very well thought out (I still like "FAQ" better than "Tips").

The only thing I would change is to add the "IGoR will help" section back onto the front page. Maybe just above "Learn more"? I think the pages could also benefit from a little more visual interest (pictures? fonts?), but I don't have any good suggestions right now. It probably doesn't need to be a priority, though.

by Yasmin von DassowYasmin von Dassow, 19 Jan 2015 23:39

Page watching should now be fixed. Wikidot members who are logged in should now see options at the bottom right of IGoR pages to start/stop watching individual IGoR pages, categories of pages, or the whole IGoR site.

Watching can be useful: if you create or edit a page and want to know if people make changes or comments to it, you can turn on watching for that page in order to get a message about changes/comments on your Wikidot account's "activity" page. If you like, you can also adjust settings under "MyAccount" to receive emails about changes (you probably won't want to do that if you've got watching turned on for the whole site).

by Mickey von DassowMickey von Dassow, 18 Jan 2015 00:56

While working on this, I discovered some features (watching) were not working as expected. So I've changed the "tips" to reflect that, and made all editing/file management go through the tabs at the top of the page (visible in "Articles", "Projects", and "Sparks" categories).

by Mickey von DassowMickey von Dassow, 17 Jan 2015 19:44

One suggestion I received was a competition for projects to be featured on the front page. Thoughts?

by Mickey von DassowMickey von Dassow, 04 Jan 2015 18:18

That in and of itself is not specific enough to explain why this particular species has increased in abundance rather than decreased in abundance, nor why it has changed in abundance only in the last few years.

However, if there are enough long term records one could test whether this species fluctuated in abundance by similar amounts historically (maybe even over a longer term with pollen counts) and correlate its abundance changes with changes in land use, other human activities, climate, other species, etc. That could rule out some hypotheses and suggest others. Large spatial scale surveys could be useful in the same way

Re: Possible explanation.. by FredHerringFredHerring, 02 Jan 2015 02:59

After thorough investigation, I have come up with a plausible explanation for these plants. They're related to the devastation of environmental health in the US. Directly related.

Possible explanation.. by Bryttanie HouseBryttanie House, 26 Dec 2014 02:47

Thanks for your comment!

That's a very good idea. I wish I had paid attention to the wind direction, and wish I'd kept some notes on the weather at the time. I think I know the pattern you're talking about, though I'm not quite sure whether what you're describing is quite the pattern I'm thinking of.

Most materials expand with temperature, but the expansion is often very small. According to the engineering toolbox, wood expands lengthwise by just ≈3*10-4% per degree C. However — something I hadn't considered before — it says ice expands a lot more (51*10-4% per degree C). But then, if the cracks formed while the air was above freezing, the ice should have stayed at constant 0 °C (as it melted) while the tree warmed up (on the ice-free side). Then again, the cracks could have formed during a period of cooling (so the ice would shrink faster than the tree).

However, the wind-based bending that you propose might better explain the splaying at the end of the cracks.

Freezing rain and snow are pretty rare in my area, but if it happens this year, I'll try to watch those trees and keep some decent notes.

by Mickey von DassowMickey von Dassow, 19 Dec 2014 23:06
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