Author: paddlefish

In a discussion today I was reminded of one of my favorite experiments from college plant physiology class. We were discussing the light harvesting apparatus (LHA) of a plant cell. The molecular organization of this system relies on the primary light collecting molecule chlorophyll. Chlorophyll acts to trap light radiation and convert that into what is called an “excited electron”. This is sort of like electricity. A field of chlorophyll molecules are attached to the chloroplast internal membrane. They pass the excited electrons around until the reach some molecular machines that use that electron to create sugar. The process of making sugar is amazingly complicated, involving a proton gradient, electron carrying molecule (NADPH) and the biological “currency” of the cell, ATP. I’ll spare you the details (for now, moo hoo hah aha ahhaa!).
Anyhow, the interesting thing about chlorophyll in this case is that when it is not attached to the rest of the LHA, the excited electron doesn’t have anywhere to go. So eventually in that case, the electron will become unexcited and in so doing emit some light. However, since there is energy loss in this system, the emitted light is of a lower energy — so it is redder than the light it absorbed.
Plants look green because of the light absorbing characteristics of chlorophyll. Chlorophyll absorbs red and blue light. The water in the plant leaf is shiny and reflects the rest of the light — green.
Okay, with that background info we can go back to the interesting experiment. You can try this at home, but be very careful because acetone is flamable, and blenders can create sparks. Be sure to have fire extinguisher at the ready and also take note that I take no responsibility for death, blindness or dismemberment that results. On the other hand, I was able to do this experiment successfully with a four year old sister and my mother-in-law.
Take some spinach — or any green leafy plant, grass clippings work too. Put it in the blender with some acetone (nail polish remover works). Blend for a little while until it makes a rich green juice. Now strain out the plant matter and reserve the precious green liquid. If you look through the liquid at a bright light source, you will see the light that is not absorbed by the chlorophyll — green is not absorbed so the liquid looks green.
Now for the really cool part. Look at the liquid when it is lit by a strong light from the side. Sunlight works the best, but light from an overhead projector is okay, too. The chlorophyll absorbs the light and then emits light back out. But it emits a different color! The solution will be a deep ruby red. It is really wild to watch the color change depending on your point of view.

Well, I’ve given up (for the time being) on how to use my Macintosh to program the PIC controller. I took my lunch hour today at work to program my PIC p12F675 on the PICKit 1 Flash Starter Kit to blink its lights in a circular fashion. Since there is a lack of good info about this on the web, per my new initiative to inform the world (lol) I’m going to say exactly how I did it.
First, I installed the gnu pic utilities — of which I’m using gpasm to “assemble” my code into pic bytecode. (See below for the code.)
Next I compiled the code like this:

gpasm –dos -pp12F675 –hex-format inhx32 gp2.asm

It is necessary to add the –dos option since the upload program I use is a Windows program. Oh and by the way everything so far is Mac friendly. Now copy the resulting .hex file onto your windows box and upload it using the PICkit(tm) 1 FLASH Starter Kit application. I think I used the “Baseline Flash” instead of the “Classic” version. Control – I Imports, and Control – W writes.
Be sure you have the right kind of PIC — for my program I used a p12f675.
Voila!

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Here is the code, for those at home who wish to duplicate my experiment.

  1  ;   This file is a basic code template for assembly code generation   *
  2  ;   on the PICmicro PIC12F675. This file contains the basic code      *
  3  ;   building blocks to build upon.                                    *
  4  ;                                                                     *
  5  ;   If interrupts are not used all code presented between the ORG     *
  6  ;   0x004 directive and the label main can be removed. In addition    *
  7  ;   the variable assignments for 'w_temp' and 'status_temp' can       *
  8  ;   be removed. If the internal RC oscillator is not implemented      *
  9  ;   then the first four instructions following the label 'main' can   *
 10  ;   be removed.                                                       *
 11  ;                                                                     *
 12  ;   Refer to the MPASM User's Guide for additional information on     *
 13  ;   features of the assembler (Document DS33014).                     *
 14  ;                                                                     *
 15  ;   Refer to the respective PICmicro data sheet for additional        *
 16  ;   information on the instruction set.                               *
 17  ;                                                                     *
 18  ;**********************************************************************
 19  ;                                                                     *
 20  ;    Filename:      xxx.asm                                           *
 21  ;    Date:                                                            *
 22  ;    File Version:                                                    *
 23  ;                                                                     *
 24  ;    Author:                                                          *
 25  ;    Company:                                                         *
 26  ;                                                                     *
 27  ;                                                                     *
 28  ;**********************************************************************
 29  ;                                                                     *
 30  ;    Files required:                                                  *
 31  ;                                                                     *
 32  ;                                                                     *
 33  ;                                                                     *
 34  ;**********************************************************************
 35  ;                                                                     *
 36  ;    Notes:                                                           *
 37  ;                                                                     *
 38  ;                                                                     *
 39  ;                                                                     *
 40  ;                                                                     *
 41  ;**********************************************************************
 42
 43      list      p=12f675           ; list directive to define processor
 44      #include <p12f675.inc>        ; processor specific variable definitions
 45
 46      errorlevel  -302              ; suppress message 302 from list file
 47
 48      __CONFIG   _CP_OFF & _CPD_OFF & _BODEN_OFF & _MCLRE_OFF & _WDT_OFF & _PWRTE_ON & _INTRC_OSC_NOCLKOUT
 49
 50  ; '__CONFIG' directive is used to embed configuration word within .asm file.
 51  ; The lables following the directive are located in the respective .inc file.
 52  ; See data sheet for additional information on configuration word settings.
 53
 54
 55
 56
 57  ;***** VARIABLE DEFINITIONS
 58  w_temp        EQU     0x20        ; variable used for context saving 
 59  status_temp   EQU     0x21        ; variable used for context saving
 60  mcount        EQU     22h
 61  ncount        EQU     23h
 62  new_tris        EQU     24h
 63  new_gpio        EQU     25h
 64
 65
 66
 67
 68
 69
 70  ;**********************************************************************
 71          ORG     0x000             ; processor reset vector
 72          goto    main              ; go to beginning of program
 73
 74
 75  ; (no interrupt)        ORG     0x004             ; interrupt vector location
 76  ; (no interrupt)        movwf   w_temp            ; save off current W register contents
 77  ; (no interrupt)        movf    STATUS,w          ; move status register into W register
 78  ; (no interrupt)        movwf   status_temp       ; save off contents of STATUS register
 79  ; (no interrupt)
 80  ; (no interrupt)
 81  ; (no interrupt); isr code can go here or be located as a call subroutine elsewhere
 82  ; (no interrupt)
 83  ; (no interrupt)
 84  ; (no interrupt)        movf    status_temp,w     ; retrieve copy of STATUS register
 85  ; (no interrupt)        movwf   STATUS            ; restore pre-isr STATUS register contents
 86  ; (no interrupt)        swapf   w_temp,f
 87  ; (no interrupt)        swapf   w_temp,w          ; restore pre-isr W register contents
 88  ; (no interrupt)        retfie                    ; return from interrupt
 89
 90
 91  ; these first 4 instructions are not required if the internal oscillator is not used
 92  main
 93          call    0x3FF             ; retrieve factory calibration value
 94          bsf     STATUS,RP0        ; set file register bank to 1 
 95          movwf   OSCCAL            ; update register with factory cal value 
 96          bcf     STATUS,RP0        ; set file register bank to 0
 97
 98
 99  ; remaining code goes here
100
101          bcf     STATUS,RP0  ;Bank 0
102          clrf    GPIO        ;Init GPIO
103          movlw   07h         ;Set GP<2:0> to
104          movwf   CMCON       ;digital IO
105          bsf     STATUS,RP0  ;Bank 1
106          clrf    ANSEL       ;Digital I/O
107          movlw   08h         ;Set GP<3:2> as inputs
108          movwf   TRISIO      ;and set GP<5:4,1:0>
109                              ;as outputs
110          bcf     STATUS,RP0  ;Bank 0
111
112  go
113          ; D0
114          bsf     STATUS,RP0  ;Bank 1
115          movlw   b'11001111'
116          movwf   TRISIO      ;and set GP<5:4,1:0>
117          bcf     STATUS,RP0  ;Bank 0
118          movlw   b'00010000'
119          movwf   GPIO
120          call    delay
121          ; D0
122          bsf     STATUS,RP0  ;Bank 1
123          movlw   b'11001111'
124          movwf   TRISIO      ;and set GP<5:4,1:0>
125          bcf     STATUS,RP0  ;Bank 0
126          movlw   b'00100000'
127          movwf   GPIO
128          call    delay
129          ; D0
130          bsf     STATUS,RP0  ;Bank 1
131          movlw   b'11101011'
132          movwf   TRISIO      ;and set GP<5:4,1:0>
133          bcf     STATUS,RP0  ;Bank 0
134          movlw   b'00010000'
135          movwf   GPIO
136          call    delay
137          ; D0
138          bsf     STATUS,RP0  ;Bank 1
139          movlw   b'11101011'
140          movwf   TRISIO      ;and set GP<5:4,1:0>
141          bcf     STATUS,RP0  ;Bank 0
142          movlw   b'00000100'
143          movwf   GPIO
144          call    delay
145          ; D7
146          bsf     STATUS,RP0  ;Bank 1
147          movlw   b'11111001'
148          movwf   TRISIO      ;and set GP<5:4,1:0>
149          bcf     STATUS,RP0  ;Bank 0
150          movlw   b'00000010'
151          movwf   GPIO
152          call    delay
153          ; D6
154          bsf     STATUS,RP0  ;Bank 1
155          movlw   b'11111001'
156          movwf   TRISIO      ;and set GP<5:4,1:0>
157          bcf     STATUS,RP0  ;Bank 0
158          movlw   b'00000100'
159          movwf   GPIO
160          call    delay
161          ; D5
162          bsf     STATUS,RP0  ;Bank 1
163          movlw   b'11011011'
164          movwf   TRISIO      ;and set GP<5:4,1:0>
165          bcf     STATUS,RP0  ;Bank 0
166          movlw   b'00000100'
167          movwf   GPIO
168          call    delay
169          ; D0
170          bsf     STATUS,RP0  ;Bank 1
171          movlw   b'11011011'
172          movwf   TRISIO      ;and set GP<5:4,1:0>
173          bcf     STATUS,RP0  ;Bank 0
174          movlw   b'00100000'
175          movwf   GPIO
176          call    delay
177         goto go
178
179
180  ;delay loop
181  delay   movlw   0x4f
182          movwf   mcount
183  loadn   movlw   0xff
184          movwf   ncount
185  repeat  decfsz  ncount,f
186          goto    repeat
187          decfsz  mcount,f
188          goto    loadn
189          return
190
191  ; initialize eeprom locations
192
193          ORG 0x2100
194          DE  0x00, 0x01, 0x02, 0x03
195
196
197          END                       ; directive 'end of program'
198
199

Oh, were you wondering how I got the nice formatting for the code? I used VIM like this
:runtime! syntax/2html.vim. Do :help 2html in VIM for more info.

I’ve discovered an entirely new realm of geekiness in PIC microcontrollers. These inexpensive ( ~$2.00 ) computers can be programmed to control lights, motors or whatever and can also be controlled through switches or knobs. My mind is exploding with possibilities with what you can make with these. For example, the good old simon says toy, where lights flash in a random sequence which you have to remember, and then you press buttons in the same sequence back. Or a christmas decoration which twinkles. Or lights that zip in a pattern on a billboard sign. Or a robot that drives itself around towards a light source.
Help! I need some ideas of what my first project should be.
I’ve also noticed, as my friend Stacie the librarian preaches, that the internet is indeed a lousy place to find information. Thus as a public service to the world at large, I would like to publicly answer a question that took me about a half hour to figure out. With hope, Google will index this question and answer the future generations of geeks will be spared the pain.

Question: Where do you get GCC 3.1 for Mac OS X (Darwin) version 10.3 or higher?
Answer: It is in a package called gcc3.1.pkg on the XCode 1.5 disk image. You can download XCode from Apple if you set up a free Developer Connection user account.

Well, next I’m trying to use Fink to install libusb so I can build usb_pickit and hopefully get it to work with the PICKit 1 Onboard firmware version is 2.0.2. Apparently the Mac OS tools for the PICKit stopped working when Microchip updated the firmware — doh!

Becka got me into this week’s drawing. This week the word was Fiesta and this is what I drew:

(click for full size)

I drew this picture a few days ago. Can you think of a caption for the picture?

If you haven’t read the first entry in about pitch black mountain dew’s blue foam…
Well, after much eager anticipation, my analysis about why the bubbles on the weird pitch black mountain dew turn blue is complete. At the end of my previous post, I had a couple of ideas for some experiments to help clarify this issue. I’ve now finished my experiments and am happy to report that I think the mystery is solved!
I was able to collect a sample of the blue foam. This was difficult at first, because it doesn’t turn blue until it’s almost entirely gone. However, I discovered that if I shook the bottle up with the cap closed, and then carefully released some air, the soda would foam up inside the bottle. After a few moments, the foam in the bottle turned blue. Then I released some more air by opening the lid a small amount and collected some of the foam that ran out.
I blotted nine drops of the liquid from the blue foam and nine drops of regular soda onto a paper towel and let it dry for several days. Then I scanned the towel into Photoshop and drew rectangles around each drop and looked at the red and blue values for each

The picture doesn’t really do it justice, the difference is far more startling that that looks. But who am I to trust the human eye to discern differences? This table presents the raw data for the red and blue channels’ average pixel value as well as the ratio of the two, the averages of those six data sets and the p value from the Student’s T Test on the ratios.

	regular red	regular blue	foam red	foam blue	regular ratio	foam ratio
	247	213	232	219	1.15962441	1.05936073
	248	209	229	224	1.18660287	1.02232143
	246	218	231	219	1.12844037	1.05479452
	240	210	229	222	1.14285714	1.03153153
	248	220	227	220	1.12727273	1.03181818
	241	209	228	221	1.15311005	1.03167421
	247	217	225	228	1.13824885	0.98684211
	240	220	232	221	1.09090909	1.04977376
	242	221	225	222	1.09502262	1.01351351
average	244.333333	215.222222	228.666667	221.7777778	1.13578757	1.03129222
std. Dev	3.5	4.99444135	2.6925824	2.818589088	0.03022589	0.02251282
p					3.6661E-05

The T Test comes to the same conclusion as my eye — the colors are different!
The results of a second experiment were negative. When I mixed dish detergent with the soda and whipped it up using my nifty milk frother, the resulting foam bubbles did not turn blue. This suggests that my hypothesis advanced in the first posting about blue dye having the ability to diffuse into bubbles is not correct.
So what does this mean? The conclusion I have come to has to do with a technique known as column chromatography. Column chromatography passes a mixture through a tube that is packed with a material that has an affinity for some of the molecules in the mixture. This will slow the molecules down a little, so as water is washed through the tube the molecules come out the other end at different times. Typically a person will collect a few drops of water into a series of tubes (these are called “fractions”). Then you test each fraction to see what is in it. Using a variety of different columns you can actually purify things pretty well.
Anyhow, I had noticed that the foam only turns blue after the bubbles on top had been bursting for a while. This causes those bubbles near the top to turn back into liquid and flow through the foam underneath. The foam bubbles underneath act like a column, to which the blue dye apparently has a higher affinity than the red dye.
Sorry, I can’t write now – West Wing is starting!

You may know that I work for a software company that is highly respected for its digital imaging products. As a result, I’ve been trying to learn more about photography. For example,

Near Snail Lake, MN
As it turns out, there is a lot of science in photography. It is much more than I can discuss in a single entry — there is the chemistry of film, optics, exposure, not to mention the artistic concepts such as composition, mood, etc… Besides, I’m not much of an expert yet so I’m not really qualified to discuss most of that (yet!).
So let’s start out by considering the worlds simplest camera, the Pinhole camera. Once we understand that camera and its limitations, we can move on to understand why people use other kinds of cameras most of the time.
A pinhole camera is quite simple. It consists of a box with a large piece of photographic paper mounted at one end, and a very tiny hole that can be covered up at the other end.

A Pinhole Camera
We all know that light moves in a straight line. By using a tiny pinhole, each point on the film only sees a tiny piece of the outside world. I’ve drawn to small grey lines showing how the light from the tree passes through the pinhole to a corresponding point on the film. One incidental result of this is that the image is upside down on the film.
If you make the box longer, the image will get bigger. If you don’t believe me, draw a new pinhole to the right, and trace from the back of the box to see how much of the tree you’ll see on the film. You should see less of the tree — so the image is “zoomed in”. This is one fundamental concept of photography : The longer your focal length, the more zoomed in you are. In fact, when photographers talk about lenses, the talk about the focal length. For a standard camera, a typical lens might have a focal length of 30mm. My friend Jessie’s favorite lens is a 50mm, which is a little bit more zoomed in. A “fish eye” lens might be 15mm. A telephoto lens is in the range of 75 to 300 (or more) mm. 300mm is about a foot, which starts to be a pretty awkward length of lens hang off the front of your camera.
This raises an interesting side question : Why do you need zoom, can’t you just move closer to the subject? For some things that is true, a similar effect can be achieved by moving the camera closer to the subject. But in some cases, the use of zoom provides an important tool in how an image is composed. Consider a scene with a tree and the moon on the corner of the block. You are the photographer, and you stand in the intersection using different focal lengths on your pinhole camera. For this example, I’ll assume that you adjust the position of the camera so that the tree is the same size in each picture.

The same moon and tree picture taken with a very short focal length, medium focal length and long focal length
What you notice is a striking difference in composition. With the very short focal length (e.g. “zoomed all the way out” according to our “focal length / zoom” rule) distant objects (such as the moon) appear very far away. Also, things at the perifery of your vision are more prominent in the picture, such as the street extending away to your right and left. With a very long focal length (e.g. “zoomed all the way in”), distant objects appear larger relative to close objects. Also, objects in the perfery are absent as being “zoomed in” restricts your field of view.
There is a corollary to the “focal length / zoom” rule. As the focal length gets longer, less light makes it to the film. Imagine that the tree is covered with ten christmas lights. If the whole tree is in frame, then ten christmas tree lights worth of light is making it to the film. If you zoom in to show only light, then one tenth as much light is making it to the film. Just because that light looks bigger doesn’t mean that it gets any brighter.
This brings us to the final issue I wanted to talk about: exposure. Exposure means how much light makes it to the film. Exposing film is a chemical reaction, and a specific amount of light is required to make the reaction work. Too much light will make the picture look washed out, or “over exposed”. Too little light will make the picture dark, or “under exposed”. A pinhole camera has four ways to adjust exposure. You can use a shorter focal length to get more light, but at the cost making distant objects look tiny (as discussed above). You can expose the film for a longer length of time (it is not uncommon for pinhole cameras to have exposures lasting minutes or even hours). Long exposures make it hard to take pictures of anything that moves, however. (Early cameras were really little better than pinhole cameras, and took several minutes to expose. This is why pictures from that time are so serious — it is not possible to hold a smile for several minutes without moving, so people held a relaxed pose that they could stay in for several minutes.) You can put a filter in front of the pinhole to reduce the amount of light getting in. You can also alter the chemistry of the film (this is called the ISO of the film) to change how reactive it is to light.
The long exposure time of a pinhole camera is the primary reason that people invented lenses. I’ll save a discussion of lenses for another entry, however.

Jesse and I stopped by Lake Johanna on our way to work this morning. The fog was visually stunning:

Fog forms over bodies of water when the atmospheric temperature drops below the water temperature. The vapor pressure of the warm water is greater than the vapor pressure of water vapor in the air. Thus there is a movement of water into the air, which immediately condenses as it mixes and gets cold. Sun “burns off” fog by raising the temperature of the air. As the air temperature increases it’s vapor pressure also increases — which means that it can hold more water.