Friday, May 23, 2014

coast horned lizard ~ 05/23/14 ~ Pinnacles

Apparently, this cool lizard is now supposed to be called Blainville's horned lizard?  Sigh.  I can't keep up with all the name changes, scientific or common.  Eh, that's not the point of this post, anyways, even though I have seen a few impressively large horned lizards during my many recent activities.

Paul has suggested I try iNaturalist as a way to document and share what I find during my weekly Pinnacles visits.  I haven't decided yet, because I have questions about macro photo quality and GPS capability in a smart phone where there's no cell service.  Click here to see Paul's photo of this same horned lizard using his iPhone 5 (don't know which letter c or s), and then click on my photo above to enlarge.  What do you think about the photo quality comparisons?  I think Paul's appears very tan colored and a little flat, even though my depth of field is shallow.  I'll mainly be taking photos of little butterflies about the size of the lizard's head anyways, but coloring is important.  And, I'm still unsure how to resolve the pseudo-GPS in phones issue.  I heard there are GPS units that bluetooth to the phone, but what a pain and more crap to carry.  Does anyone have any suggestions to obtain accurate GPS linked to a phone-generated photo?  Are there actual GPS phones, not the fake ones reliant on cell service?

Oh, have I mentioned I don't currently have a smart phone?  I've had my flip phone since 2006, which I think is the responsible thing to be aware of in this day and age of disposable everything, including electronics.  I had my last computer for 10 years before I upgraded to iMac.  I really don't need the latest and greatest toy, but it may be time to update.  Plus, we've been needing to switch carriers for some time since many of my calls get dropped at home on the Peninsula where ocean meets spotty cell coverage.  We never had a land line.  There was a bit of a city hall brouhaha over additional cell towers being installed.  On one side were the monarch butterfly lovers who didn't want the overwintering butterflies or themselves to be radiated (is that the term?), and on the other side was the city needing to offer basic public services, like cell phone coverage for emergencies.  The towers went in, cleverly disguised as chimneys.  Are we all being microwaved now?

ps 05/30/14 -  One of the take-aways I got from the Citizen Science Session of the Ocean Science Trust Conference last month was that citizen science could and should be able to provide data rigorous enough for scientific review (Thanks, Lisa Emanuelson!).  So, when a few days later CalAcademy announced their acquisition of iNat, I paid attention.

Ken-ichi Ueda, co-founder of iNaturalist, has been kind enough to reply to my numerous criticisms (hopefully, constructive!) and questions as I figure out the best recording method(s) for my project, which in an unexpected way could also help shape its initial purpose.  With Ken-ichi's permission, here's what he said, "Ok, let's talk tech. For iNat, my recommendation is to get the latest iPhone. Our iOS app is quite a bit better than our Android app, and the iPhone's GPS and camera are great. Here's are some particulars:

As you pointed out in your post, the iPhone isn't quite as good as a conventional camera, but it's still pretty good. It doesn't give you much DoF control, but it can be quite sharp, particularly for stable subjects that are close.

Any device with a real GPS chip should get coordinates *anywhere* it has a clear view of the sky, since it works by communicating with satellites, not ground-based towers. Reception may vary depending on weather, topography, or the particular configuration of satellites in line-of-sight from your position. Devices like the iPhone can improve both the speed of coordinate acquisition and the accuracy of those coordinates by using cell tower and wifi signals, but they aren't required. Almost every cell phone has a real GPS chip on board, including every iPhone and most Android phones. Note that the majority of tablets do NOT have onboard GPS. This includes the iPad.

In my experience the iPhone's GPS functionality is very accurate. If you get a chance to look over someone's shoulder, you'll see that the iNat works by continually acquiring coordinates until it gets the precision below 5m."

To keep this from becoming free advertising for phones and plans, I'm skipping some of what Ken-ichi recommends.  Then, he goes on to say, "Regarding iNat recording devices, keep in mind you don't need a phone to use iNat! You can upload images directly. My usual practice is to use my phone for most observations, but to also carry around my SLR and a handheld GPS in my pack. The GPS is always recording a track, which I use to add geotags to my SLR photos later (I use for this, but there are many other such applications, including Lightroom). The SLR is much faster and sharper, so for things like butterflies, that's usually what I'm going to use. Getting identifiable lep shots with a phone takes more time and patience than you can probably spend if you're doing a research project. Most high-end point-and-shoots would probably be as good or even better (in terms of flexibility) than my SLR setup."

Then, I asked questions about iNat itself.

I haven't found where it explains the different color map markers (red, blue, green?).
"Colors relate to the "iconic taxon" of the thing observed: blue for most animals, orange for insects / spiders / molluscs, green for plants, purple for slime molds, brown for chromists, pink for fungi. It isn't really explained anywhere. There are a lot of things on the site we just assume people will figure out for themselves."

I also don't understand how the "Redo search in map area" works, because it comes up with new and different points depending on the zoom level on the map.
"It redoes the search using the bounding box of the current map. It loads different observations because some of the observations in your previous search will be outside the bounding box."

Then, how do you select the marker that sits just below another one when on max zoom?
"I guess you don't, but you can see them all in the list on the right. You can also zoom in much farther with the satellite tiles."

Is it possible to select by week number to see everything found at a particular location in that week of any year?
"You can't look up observation by week, but you can do it by month. If you go to and click the "Search" button you'll see a bunch of filters, one of which is a month filter. If you set that and leave year and day blank, you'll see all the observations added in that month, regardless of year."

... He did say he privatizes his locations, does not carry a GPS unit, guesses based on a google app, so maybe that was the result of being "obscured" as well.  It doesn't seem like that should qualify for "research grade".
"... his observations for that day is due to the fact that he obscures the coordinates, which means each observation is displayed at a randomly chosen location somewhere within 10km of the true coordinates. iNat's "research" quality grade doesn't consider how precise the coordinates are, just that you've added them. The name "research" was probably a poor choice since it seems to get people's ire up, but it just means observations of that grade are probably more accurate / complete than others. Then again, the definition of "research" is pretty flexible. For some studies, precision of 50k might be adequate."

Finally, in the spirit of encouragement to become better, I had the audacity to question Ken-ichi's algorithms.  It's a bit meta, and I've noticed not everyone appreciates the different perspective.  In fact, he seemed very receptive to it.  I agreed with him that the freedom to make errors is educational, which is why this hobby blog has been so liberating for me over the past 5 years.  By being okay to make mistakes, being honest in the not knowing, asking those questions, and accepting of others' help, I have learned so much.  Here's Ken-ichi's reply to my algorithms charge:
"I would argue that our crowdsourcing approach generates data that is close to the accuracy of professionally collected data, with the added benefit that it usually comes with media evidence for independent verification. It is generally not as comprehensive as professionally collected data (most casual naturalists aren't going to identify every carabid under a log in the way that a working coleopterist would), but if you look at the inaccuracies present in supposedly professional collections at museums or in GBIF, you will find most of the same geographic biases (no collections far from roads or trails), identification mistakes, and taxonomic confusion... except it's really hard to see this errors because either there's no associated media evidence or you have look at a specimen. An actually quantitative comparison between professional and crowdsourced data collections like this would be a pretty cool outcome of being at CAS. We shall see."

This is all very helpful information for me.  Thanks, Ken-ichi!

The future of natural history documentation is at our feet, a path extending into the digital age through the eyes and hands of millions of curious participants.  I know that sounds corny, but it's true.  This is exciting stuff!  It's too bad it currently selects for the well-to-do with expensive phone requirements, GPS devices, and fancy cameras.  The reality of the situation is nature is available to pretty much everyone... and it's free, if we just put down our electronic devices.


Jeannette said...

Interesting tech questions...I have my flip phone pre you know i won't be any help.

I will have to show Mark the horned toad, they were a common encounter in the part of his childhood spent in the Mojave and he remembers them fondly.

Imperfect and Tense said...

Hmmm, first thing, don't confuse ionising radiation (from nuclear bombs or power stations) with non-ionising radiation (from cell phone base stations or microwave ovens). With the latter, it's all about the heating effect, which it is possible to calculate for any given level of transmitted power, distance from antenna, size of thing being heated (e.g. us or Monarch butterflies) and length of exposure. Time was when cell phone frequencies were such that the average human head would be a preferential absorber of the energy. Hey, like the world needs a few more hot heads :o(

Jennifer said...

What a prehistoric looking creature!

I'm also archaic - have had my phone since 2006 - everyone in my family is trying to get me to change it.

John W. Wall said...

I don't even know how old my flip phone is, and I think I got it refurbished in the first place. :)

What I didn't like about the iPhone image was its small size. You couldn't click on a version that was very big. I have not submitted to iNaturalist, in part because I'd already submitted a bunch of images to Calphotos before iNat came along.

I'm also waiting for the trendy "bioblitz" phenomenon of using non-scientists to make recordings of species, to produce something that's actually interesting. What is all this for? Who is using it, and for what purpose?

It seems like something I would be excited about, but I'm not.

Katie (Nature ID) said...

Looks like we're all in the "old phone" group, except maybe radiation aware, Graeme. Good golly!

What do you mean "time was", Graeme? Do we all have hot heads now?

John, I've been unsure what to make of the BioBlitz phenomena, too. From what I can tell, it's a lot of networking for the industry folks, and a cool PR event for the public. One of the biggest problems I see are the unexplainable holes in the data sets. I'm not sure there are stats that could cover that, unless the sheer volume allows you to stand as far back as Pluto. I'm hoping to design my project so that it's focused and crunchable.

Imperfect and Tense said...

LOL! I'm guilty as charged, Katie. I ditched my 'old' phone (one of our girls' cast-offs) back in 2012. In the UK, the networks have moved some of their traffic up to the 1800MHz band and above, so less at the old 900MHz. If I recall correctly, when the mobile phone and base station are having trouble talking to each other, the phone can ramp up power output to 5 Watts. I wouldn't want to be using that clamped to my ear for any length of time. For the record, I consider you to have a very cool head :o)

Katie (Nature ID) said...

Very interesting. Thanks, Graeme.