Tuesday, March 28, 2017

Found Objects: Phenology Calendars




Wednesday, March 22, 2017

My Search for the Best Writing Implements.

During the early 80s, as I returned to the University, my future was to some extent determined: I would need great writing instruments, and likely something that would work in the field.

For over 3 years, this was an everyday experiment, while taking lecture notes.  I also started recording lectures, and going over notes later.  The recording was a discouraging prospect, as I took sparse notes in a large notebook, and filled them in while reviewing the recordings.  It discouraged me that I needed to spend so much time reviewing each lecture, and since I took as many as 22 quarter credits per term, there were a lot of notes.

The upshot of the recording project was that I learned how poorly I understood the message of the lecturer.  Whatever the cause, I would completely miss the intended meaning.  For example, many lecturers would say terms like "on the other hand" or "however" in a low tone, almost whispered.  So the counterexamples being given would be misinterpreted by me as the core message!

I may have lost an opportunity, however: had I NOT recorded the lectures, perhaps I would have forced myself to become a better note taker.  I have been keeping notebooks ever since those years, and perhaps become a better listener and recorder, but I will never know whether my experiment impeded my acquisition of better note taking skills.   I will note that paid note-takers whose notes I also purchased did not have this problem:  their notes were typed up and available for pick up, by the next day.

My intentional  search for the best writing instrument was most fruitful.  One criteria was unbendable: I must be able to take notes that will be permanent and not damaged by water or weather.  So I needed to find a notebook as well.

A small number of writing instruments still stick in my mind, after these 30 some odd years.  But one habit I developed was especially useful over the years: carrying a compact, durable pen/pencil case in my pocket.  (Later on, my habit of using a belt pouch--- a"thunderbag" as they are called in Chuuk---served both as an extension of and  a convenient carrier for both the pencil box and the notebook.  After I had started using fountain pens, the pen case became central to a ritual of writing: unwrapping the pen from a small cotton rag, filling the pen (or sometimes changing cartridges), resupplying leads for the mechanical pencil.
And, for the record, Mead Composition Books can br cut to a smaller size that fits in the pouch, by a printer, for a dollar or two, using a guillotine cutter. 


Lead pencils are at the top of the list of water proof implements. They have been referred to as Billion Bit word processors (billion bits of wood!)

I came to love a certain mechanical pencil: a Staedtler drafting pencil that used fine leads, that advanced the lead automatically, or by shaking.  It worked quite well.  Keeping it in the case prolonged it's life.  I also experimented with 2mm lead holders. (I am currently using a Pentel Graph Gear mechanical pencil; it is comfortable, but does not use the automatic advance).  It is relatively affordable.

JetPens is a goto site for information about pens, notebooks (and the great Wise Walker bags).  In their "Guide to Mechanical Pencils" are listed several types:
  1. Push Button (top or side)
  2. Shaker
  3. Twist
  4. ! Bend or Body Knock.  ???
  5. Automatic
  6. Unmentioned: auto lead rotation
Even JetPens.com has only one Automatic pencil: a Pilot, at about 50.00.  This is completely out of reach to me.  Numerous shaker pencils are listed at prices from about 6.00.  None of them has the look of a technical pen.  Lead rotating pens are interesting.

Wirecutter's choice is the Uni-Ball Kuru Toga

Drawing pencils are much nicer to write with.  I use B9 soft pencils to apply graphite to the nut slots of my guitar, because the softer grades have the lowest clay content.  For everyday use, Dixon Ticonderoga have never been matched.  

Ball Point Pens

A field anthropologist had recommended regular ball point pens, as sufficiently waterproof.  I never experimented with them.  He referred to cheap bic pens.  This option would bear research, but in truth, I don't like writing with them, and for some purposes---taking notes in a laboratory---I would not use them. 

JetPens.com has the Pentel EnerGel pens.  I like writing with Gel pens, but I do not trust them for longevity.

Fountain Pens

India Ink was the ink of choice for taking waterproof notes.  Other waterproof inks were investigated, and I tried using a variety of inks with fountain pens.  I used  cartridges betimes; but a fillable pen made it possible to at least experiment with waterproof drawing inks, including India Ink, a carbon based ink.

I tried a variety of commodity fountain pens from office supply companies, and the University store.  One or two Parker Pens had fairly good qualities when used with India Ink.  They all clogged, but since I had incorporated a cloth in the pen case as a wrapper/cushion, I could use it also as a wiping cloth to dislodge caked ink from the nib.  This was constantly necessary, making it somewhat inconvenient for every day carry.

In August   1984, I matriculated to the University of Guam Marine Laboratory, where I worked for two and a half years.  During the summer I had been in Truk (the name then, it took on its new name in 1986, I believe).  This was the first test of my note taking system.  I had settled on black and white marbled composition books: they are sewn bound, and some of them are made with decent, if not great paper, and they are easily available and cheap.  India Ink was the standard, but I had not found the ideal pen.

After moving to Guam I discovered a pen that was, if not cheap, at least somewhat affordable at 30.00, and readily available on the island in Duty Free Shops: a low end Mont Blanc pen, a neat little pen with a cylindrical, slim barrel, usable with either cartridges or a really nice refillable insert.  From the beginning, this pen was the very best I have ever used.

What was so great about it?  It accommodated India Ink  almost without a hitch.  I could take notes for an entire 1 or 1.5 hour lecture without much fuss or bother.  It wrote cleanly, having a fine tip.  Even better, they lasted a very long time.  And they were easy to clean.  No pen has ever matched it, though since discovering it, I never tried any other.  Not only that, using standard laboratory labeling tape, they worked awesomely for making labels on reagent bottles  or on samples.  I could write labels on on rag paper to be kept in jars with preservatives or fixatives, though I have not had access to any of those samples for a long time, so I don't know whether these labels were stable in the long term.  Pencil is still probably the best for this.  (I also used pencil to write directly on specimens of Millepora spp, and mark the colonies in the field).

My need for a Fountain Pen has been somewhat mitigated since I am not living in the islands and taking field notes.  Fountain pens are rare in the garden variety office supply, and JetPens has several interesting types of low cost fountain pens.  In the Philippine Islands, I found fountain pens in National Book Store, that were quite cheap.  I still have one around, so maybe I will start it up again.

As an aside, on Saipan, one could buy fountain pen ink, but not a fountain pen, in National Bookstore!

Regrettably, Mont Blanc pens' prices have inflated dramatically to something like 200.00 for a "SlimLine" model, that may be similar to the ones I used in the 80s.  This is far too expensive.  Perhaps I can seek crowd funding...   Or perhaps, starting from one of the guides on JetPens.com I can find a more affordable option. 

Monday, March 20, 2017

I really WANT to believe nothing could go wrong

Using Hippos to control Water Hyacinth in the Delta.  A stroke of genius.  Maybe.  One of the problems with the oversimplification of problems, a al Donald Trump, is factors that are ignored, brushed aside, misunderstood, or unanticipated.  The use of exotic species to control other invasive species doesn't normally go well.  Cases in point are the Mongoose in Hawaii, Cane Toads on Pacific islands to control Monitor Lizards, Gambusia (mosquito fish) to control mosquitoes.

Yet, here is an ingenious plan to use gigantic mowing machine herbivores to control Water Hyacinth.  One hopes it will work.


If anything, these are technological fixes for technological disasters.

Here's where I invoke my theory of the burden of engineering: the impossibility of design of perfect systems by the Human Brain.  It's not that the human brain is deficient, but we evolved to SOLVE problems, not to anticipate them.  Take the history of science and technology: scientific knowledge has grown incrementally, each step depending on the previous one.  So, for example, as the tale goes, Newton and Leibnitz concieved of Calculus co-temporally.  Without the Shoulders of Giants upon which to stand, would this next step have been possible?

Bikini Atoll: a concrete dome is constructed to contain the genie, after it was released from the bottle.  Years later, who anticipated that Sea Level Rise would render this solution moot?   Like the possibility of space travel without an incident, or the engineering of a perfect, unsinkable ship, biological systems would seem equally to impossible to engineer perfectly.  We can anticipate many potential consequences, but can we foresee every one? 

Pacific Islands are microcosms of, say continents, or of larger islands.  Just as it is impossible to turn back the clock, I would argue that, should any single example of   intervention in previous invasions appear to be successful, then who can say there are no overlooked or unknown consequences?

One hopes that Hippos will be able to clear the waterways of weeds.  What could go wrong?

Monday, February 27, 2017

Macro explorations: Studies of an unknown Cypress

"The best camera is the one you have in your pocket."  Who said that?

I want to document some work I have been doing with a shrub/small tree outside our apartment,.  Over recent months, I have been photographing the development of flowers, and taken thousands of photos.  Only a few are worthy of saving, but part of the project---and part of what I have been doing with the phone in general---is to document seasonal events.   I haven't gotten that far with this plant.

I used several methods.  Some were obviously not macro shots.  One or two may have been taken using a low cost clip-on macro lens (that turns out not to be very effect overall), and several using a Moment Macro lens.  I were taken on an iPhone7 plus.  Microscope shots were taken through a vintage Olympus Stereomicroscope; it obviously needs cleaning.

My limited googling has led to the understanding that related Cypresses flower and reproduce in Winter.  The mechanics are apparently complicated. 



Remnants of a (cone?)  I thinkit's complicated.

February 24, 25, 2017

Notice the drop of liquid.  It was NOT raining.  On the lower flower.


Bug (pollinator?)

On plant

MIcroscope shot
Microscope shot

Sunday, February 12, 2017

i3 training wheels: help on a scratchpad

[I have had a looksee at Manjaro i3 edition, and it's way beyond this.  It has a built in help screen for i3.  With the plethora of keybindings and tweaks to i3, this help file is a bit over much.  Maybe I'll still need a quick cheat sheet.  Notice, though, important keybindings are displayed as a conky]

i3 is a fast and simple tiling window manager for GNU/Linux that really does work.  I have a penchant for trying new window managers.  Each of them has it's pitfalls, the pitfalls where I just say, No More!  That might happen sooner, or later, with i3.  For now, it's an interesting new interface, and it's incredibly lightweight ... and fast! 

I'm going simple for now, grabbing keybindings and tweaks from several online sources.  The key bindings are not altogether intuitive.  They are not many, at least the ordinary ones.  I need some training wheels.

I generated a simple PDF with a table of sorts of keybindings.  It doesn't matter whether it's a PDF: it just needs to be a viewable file.  Now start the viewing app, and send it to a scratchpad.

Scratchpads in i3 are really useful, especially for this application.  Since i3 is not yet overburdened with all kinds of tutorials and forums and mailing lists---that I have seen---one isn't overwhelmed with advice.  Some useful documentation will be helpful at some point.  (I have been using mostly Ubuntu in this experiment.  Arch Linux has a relatively large number of packages, so a full exploration of those resources might lead to some things I would find useful.

I have found that some of the tweaks online do not work for me.  Probably I just don't understand them.  In particular, marking, tagging, and some other interesting ideas are not yet clear to me.

My Training Wheels

I used these keybindings for the scratchpad.  If I understand correctly, this is just any application in a window that can be buried and remains invisible until it is called up.  In which case, for my training wheels, the window becomes tantamount to a Pop-Up.

## scratchpad
To make the currently focused window a scratchpad:
       bindsym $mod+Shift+minus move scratchpad

To show the first scratchpad window: 
               bindsym $Mod+minus scratchpad show

The window is shrunk when invoked as a scratchpad, and it can be converted from floating mode to fullscreen mode with $mod+f.  I have my setup tweaked so that if I repeat this command.  I warn, though, that toggling the window back and forth between floating and tiling mode and back to floating mode again will erase the previous custom sizing, and the window will no  longer be a scratchpad.  

I also found it useful to use the resize commands on the scratchpad to adjust the size for comfortable viewing over an open window on the workspace.   I didn't see an explicit example or instruction for using the resize commands with a scratchpad.  They do work.  In resize mode ($mod+r) puts us into the mode):

            downarrow:   lengthen the window from the bottom
            uparrow    :   shorten the window from the bottom.
            rightarrow:    widen the window from the right.
            leftarrow  :    narrow the window

In normal mode

            $mod+Shift+<arrow>  :  Move the floating window around


Thursday, December 15, 2016

Low Tide at Crab Cove: Splash Zone

Exposed Branching Bryozoan
I walked along the edge of Crab Cove last night during a substantial minus tide.  When I arriived, about 5:30 PM, it was dark.  In a narrow band along the landward edge of the concrete walkway the water pools, among rocks of various sizes.  along the seaward edge is trapped a very narrow and shallow line of water; along one part I find a branched bryozoan, exposed but we  t enough to possibly be alive.  I am searching for hydroids.  None will reveal themselves this evening.

Looking back toward the visitors center
Along this narrow band, I was experimenting with the camera.  I have a selfie stick that I hope to use for photo transects along the mudflat, but in this darkness I am reluctant to try it.  The selfie stick is capricious, depending on the camera app I employ and the settings, so it requires further experimentation before trying this in the field, on the mud.  I am wearing my mud boots, but tonight I will not walk out onto the mud; the only other time I did so in these boots, it was also dark, and I got stuck in the mud for a brief time.  Neither am I experimenting with the macro attachment lens. 

Along the edge is a railing.  It is possible to kneel with one knee on the lower rail.  Many amphipods and isopods are scudding about, and insects are around.  I take some random shots, found a few insects.   A large limpet had emerged from a small crevice, where some conspecifics were still ensconced. 

Some denizens of the splash zone

An invasive Bryozoan (arrived in the 40's)

A Bryozoan appearing to be Cryptosula pallasia

 In the field (photo at night)

In the bowl

In the microscope

The shape of the Aperture appears to conform with Cryptosura pallasia. 

Camoflaged, a Scale Worm. 

 A Scale worm

This might exhibit light flashes.  Something to check.

An unidentified insect

An unidentified insect, and some other critters.

Monday, December 12, 2016

Macro Photography with an iPhone 7+: Moment Lens

I have found the iPhone 6 and 7 to be amazing tools for photography.  Even though their low resolution (12MP)  presents an insurmountable wall, as far as optical enlargement, the cameras themselves seem almost magically better than those of other zmart phone cameras I have used.  The Photos image management tool is, for me, leaps and bounds better than those I remember from past phones, giving almost instantaneous access to large numbers of photos (if only it allowed instant deletion also!).  I loved the ability to deploy the Note 5 camera almost instantly; but the iPhone 6 immediately took my photography to a new level.  This is what happened to me many years ago, when I traded in a Nikkormat and several lenses for a used Leicaflex, and a low power telephoto: my photographs were instantly much, much better.

Macro Photography has a strong pull on me.  Give me a camera, and the first thing I do is check how close I can focus.  Well, I was fooled by the iPhone 7+, when I tried it at the Apple Store.  I took a shot of my finger, and was amazed how close I could get and how sharp was the photo.  I'm not sure I understand what was the difference, but later, using my own phone. I found that it was extremely difficult to get a photo of the same sharpness and magnification.  The problem was, I think, that the two cameras work together in mysterious ways, driven by the algorithms in the firmware.  Some of the algotrthms---as well as the functionality of the photo management infrastructure---seem to concentrate on the lowest common denominator of snap shots that an average consumer would take.  Face identification, pets, landscapes, kids.  Not that these are not important, but these cameras can do much more.  The iPhone7 and 7+ cameras can save photos in raw format; but the canonic camera app does not allow this feature to be exploited: I am learning to use other "cameras" to utilize this feature, as well as to access the functions of the physical camera with a more hands-on approach.   I'd be extremely pleased to be able to do my photography algorithmically.  Various cameras take better advantage than others of certain features.  Camera+ has a macro mode.  Several cameras can directly bypass the algorithms that select which of the iPhone 7+ cameras is being used for a specific shot.

So, fooled at first, I still am discovering its capabilities.   will mention that the wide angle lens brings much better results to dim light photography.  Perhaps to available light macro?

In this post, I am focusing on macro photography with the Moment Macro lens.

A review, of sorts

[The following comes from  a letter to Moment.]

   I am still climbing the learning curve.  During the time since I took delivery
   on my the iPhone 7+, I have tried out several camera apps.  I spend more time
   on Macro than anything else, so my experiences are biased in that way.

   Each cam has its own feature set, so I think that over time I will find myself
     using each cam for it's strengths.  None has all the advantage in any way.

   - burst mode is extremely useful to me.  I do alot of handheld macro (eg
     flowers, insects, etc.)  Taking a burst serves well: often, one of even 100
     photos in a burst is sharper or has a more salutary plane of focus or angle
     on the subject. 
   - The "Photos" app is remarkably facile for sorting through a burst or a bunch
     of photos quickly.  Rapid deletion without need for feedback is found on at
     least one camera;  I Would like to have that abillity from different cameras.
   - It would be be terrific if deletions or selections from bursts were
     reversible in some kind of trash bin for a while.
   - I don't quite understand whether the iOS photos app actually permanently
     deletes, when a selection is made from a burst.  For me, it would be best if
     these changes were indeed permanent.  I don't like sorting through my photos
     more than once.
   - The brush works well to clean the lens, so far.
   - I didn't realize that the diffuser on the macro lens is removeable.  I have
     been pleased with the results using the diffuser, which enables me to use the
     iPhone7+ flash with pretty good effect.  Not perfect.  I am thinking, how
     could a shiny metal reflector be used to effect on the other side of the
     diffuser bowl.  This would approximate the Lieberkuhn attachment for
     microscopes of 150 and more years ago.
   - Finding that I can use the lens without the diffuser: what a boon!  And how
     well designed is the hood!  It fits either way.  (Although I am disappointed
     that I must use an implement if my fingernails are cut short, to dig the hood
     out if it is pushed down into the diffuser too far.  Nice detail.
   - Camera+ app has a macro mode that is useful.  I haven't learned enough how to
     use it yet.
   - The photos I take are much better.
   - Night time macro walking out in the garden, the flash works great with this
     lens and diffuser.
   - I'm a little freaked out about the bracket, that at some point I might tweak
     the lens hard enough to bend the bracket.  The bracket sticks out far enough
     to make it possible to bank it or scrape it, putting the phone down.
   - My Silk iphone7+ case (see Wirecutter) works very well with the lens
     bracket.  Love this case.
   - I need to get access to raw.  This brings up the point that the Moment Camera
     is simple and nice, but except for recording the lens specs in the exif info
     it doesnt seem more useful than other cameras, esp the native camera.  BTW,
     access into complete exif info would be a boon from the camera app when
     reviewing pix.  Even better would be to record tags or comments in the exif
     of a photo.
   - So far I am very pleased with the quality and design of this lens.  KUDOS!

Some Photos

Looking at these, I want to do more.  Darn!  It's been raining quite a bit.  Time to hit a botanical garden, and check the possibility of using this as an "aquarium microscope" (through the glass). 

African Violet, using diffuser and flash, zoomed
Christmas Cactus
Bouganvilla FLower
Spider in apartment on paper towel