My Latest Project -- A Portable Cold Frame

First, if you are not a gardener, you may be asking "What is a cold frame?" A cold frame is something like a miniature greenhouse, typically used to start plants from seed earlier in the season than out in the open, by providing a warmer, more protected environment. If a heater were used to provide warmth, it would be called a hot frame; but a cold frame just captures the heat of the sun through a window, and a simple enclosure helps to retain the warmth.

Sometimes an old window is simply placed over a bottomless box made of boards set on edge, and seeds are planted in the earth enclosed by these boards. But I wanted a portable cold frame that could be placed over a stone walkway, and moved under the deck when not used. Other suburban gardeners, and city gardeners, with limited space, might want to set up such a cold frame on a patio or paved area, and store it elsewhere. perhaps standing on edge, when it is not used. So I'm publishing my design to share it with others -- here in this blog, and in a Picaso web album.

I decided to use deck planking for the sides, because this lumber is generally treated for weather resistance, and use to plastic for the window -- the kind made as a substitute for window glass. I wanted the cold frame big enough to comfortably hold nine seedling trays (in a 3-by-3 arrangement), the kind that you get from greenhouses or gardening stores. That closely matches a 3 by 4 foot window piece.

The bottom of the cold frame is covered with 'hardware cloth', a wire mesh with 1/2-inch spacing, to allow drainage and support for the seedling trays. But that would allow stray dirt to fall through, which is not good if used over a stone or paved walkway or a patio. So 'weed-block' fabric is lain over the hardware cloth. This kind of tough porous fabric is made for use under a bed of loose stones or paving stones to allow drainage while preventing the soil from mingling with the stones, and blocking access to the soil by any seeds that fall among the stones. For the cold frame, we get drainage without allowing soil to fall through.

All my garden areas are automatically watered, controlled by timers, either by porous 'soaker' hoses for the larger areas, or by a drip system for containers and the raised-bed herb garden. So I naturally wanted a watering system for the cold frame. But this is an optional feature; the cold frame can be built without it, and you can water it with a watering can or a hose with a spray attachment.

To make the cold frame portable, it is made of three stacked frames, each one of which is not too heavy to carry. The frames begin as identical units:

From Portable Cold Frame

One of the frames is cut on an angle, like this:

From Portable Cold Frame

Then the parts are rearranged to form this sloped shape, which becomes the top frame, with a sloping window:

From Portable Cold Frame

The bottom of the bottom frame is covered with hardware cloth, held in place with stop moulding (the kind used as a door stop on a door frame):

From Portable Cold Frame

The "weed-block" fabric is stretched over and stapled to a frame of 1/2" x 1/2" moulding, and placed inside the bottom frame:

From Portable Cold Frame

Nine seedling trays fit inside the bottom frame:

From Portable Cold Frame

The middle frame has a vertical piece fastened in each corner that protrudes one inch above and one inch below the middle frame. These verticals lock the middle frame in place to the frames above and below it, like this:

From Portable Cold Frame

(The aluminum rail in the above photo is an optional support for the watering system.)

Two ventilation holes are formed in the rear wall of the top frame by cutting notches in the facing edges of the two planks of the rear wall:

From Portable Cold Frame

A slot is cut across each notch by dropping a circular saw into the plank edge, then a piece of hardware cloth is inserted into the slot, like this:

From Portable Cold Frame

The piece of hardware cloth is captured in place, with no need for fasteners. I like minimalist designs like this.

From Portable Cold Frame

Two vertical pieces hold the two rear planks of the top frame together. These verticals protrude below the top frame, and together with the rear verticals of the middle frame, form hinges. One hinge is show here, as well as one corner of the watering system at the top of the middle frame:

From Portable Cold Frame

The edge of the plastic window is sandwiched between 'stop' moulding (below) and 'ply cap' moulding (above), which are nailed to the top edge of the top frame:

From Portable Cold Frame

The next photo is looking through the top window toward the inside of the front wall of the cold frame. Here we can see a length of 1/2" x 1/2" moulding fastened to the inside of the front edge of the top frame with two screws. Below that are two pivoting pieces of 1/2" x 1/2" moulding fastened to the inside upper front edge of the middle frame with one screw each. The pivot screws are off-center, so that pointing the short end of the shorter pivot piece upward props the top frame open with a 1-inch gap, and using the longer end of the shorter pivot makes a 2-inch gap. Similarly, using the longer pivot piece provides 3-inch and 4-inch gaps when propping open the top frame.

From Portable Cold Frame

A larger prop is used to hold open the cold frame, as shown in the next photo. This also shows the inside painted black, to increase the heat energy absorbed from the sunlight coming through the window.

From Portable Cold Frame

The above photo also shows the watering system attached to the top frame, where it is lifted up when the top frame is lifted. Earlier, I had mounted the watering system on the middle frame, where it needed to hinge separately, and needed a second prop:

From Portable Cold Frame

The watering system is built on an aluminum frame that supports nine spray heads, each centered over one of the seedling trays:

From Portable Cold Frame

The spray heads, hoses, and connectors are made by RainDrip, which calls the spray heads "misters". Here is a close-up of one of the 'misters', and a wire loop that joins two pieces of the aluminum frame:

From Portable Cold Frame

The 'mister' comes mounted on a plastic stake, which I cut short and fasten to the frame by inserting it through an X-shaped hole in the frame. Each 'mister' head emits eight radial streams of water, and can be rotated to adjust the flow, or even to turn it off.

The 'misters' are connected by quarter-inch tubing to a half-inch supply line, which connects to regular garden hose, as shown here:

From Portable Cold Frame

For more details, you can view the entire Picaso web album by clicking on the link under any of the photos above. Also, we give more details of the cold frame design (except for the watering system) next, including:

Dimensions
Shopping list
Cutting lists
Tools needed/suggested
Construction

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Dimensions of the cold frame:

Seedling trays have various designs, but are generally 10 1/2 by 13 1/2 inches, and 3 1/2 inches high. If we allow 11 by 14 inches for each tray, it will allow for some size variation and room for fingers when handling them. So a 3 by 3 configuration of trays will comfortably fit in a 33 by 42 inch space, and a 2 by 4 configuration of trays will fit in a 28 by 44 inch space; and a 33 by 44 inch space will accommodate either configuration. My design adds an extra inch to this.

Width and length: 34 by 45 inches inside, 36 by 47 inches outside.

Inside height is 2 plank-widths plus 1 inch in front, and 4 plank-widths minus 1 inch in back. Some planks are 5 1/2 inches wide; these provide a height of 12 inches in front and 21 inches in back. Allowing 3 1/2 inches for the seed trays and 1 1/2 inches for the watering system, this allows 7 inches of height for seedling growth. Some planks are 5 3/4 inches wide; these provide 1/2 inch more height in front and 1 inch more in back.

For outside height, add the thickness of the "stop" moulding and hardware cloth at the bottom, and the window frame thickness ("stop"and "ply cap" mouldings) on top. This is about an inch.

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Shopping list for the cold frame, not including the watering system:

6 8-foot lengths or 4 12-foot lengths of decking planks, weather-treated; 5 1/2 or 5 3/4 inches wide and 1 inch thick. Choose straight, unwarped pieces.

2 8-foot lengths of "ply cap" moulding
(See photo of mouldings.)

5 8-foot lengths of "stop" moulding

2 8-foot lengths of 1/2" x 1/2" (or close to this) moulding

1 3-foot by 5-foot piece of hardware cloth, with 1/2" grid

1 3-foot by 4-foot piece of plexiglass, or plastic window 'glass'

1 roll of 3-foot wide 'weed block' fabric; black is preferred

1-pound box of 2 1/2" screws

1-pound box of 1 1/2" screws

1 1/4 inch nails, about 32

thin 1 inch nails, about 8

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Cutting list for 4 12-foot lengths of decking planks:

(1) 47 + 47 + 47 inches
(2) 34 + 34 + 28 + 47 inches
(3) 34 + 34 + 47 inches
(4) 34 + 34 + 7 3/4 + 7 3/4 + 12 1/2 + 47 inches

Cutting list for 6 8-foot lengths of decking planks:

(1) 47 + 47 inches
(2) 34 + 34 + 28 inches
(3) 34 + 34 inches
(4) 34 + 34 + 7 3/4 + 7 3/4 + 12 1/2 inches
(5) 47 + 47 inches
(6) 47 + 47 inches

The 7 3/4 and 12 1/2 and 28 inch pieces are cut in half lengthwise.

Mouldings, hardware cloth, and 'weed block' fabric are cut to fit the frames.

About 2 inches is cut off one short side of the plexiglass so that the window overlaps only half of the window frame all around.

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Tools - see photos.

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Construction (Also see photos):

The six 34-inch pieces and six 47-inch pieces are used to make three frames, 34 by 45 inches inside, and 36 by 47 inches outside. Use three 2 1/2 screws at each corner, but for the top frame, mark where the front (long side) will be cut one inch from the bottom edge. Two of the screws need to be centered in this one inch so that no screws will be cut. Clamp each corner joint in position, drill three holes with a drill matching the solid core of the screw, insert the screws so that the heads sink into the wood a bit, then remove the clamps.

Bottom Frame ---

Ihe hardware cloth is probably in a 3 foot wide roll; you will need to unroll a 4 foot section of it and make it approximately flat. Use 1 1/2 inch nails for the following. Lay the hardware cloth over the bottom frame, and begin by nailing down a 36-inch edge of the hardware cloth on a short edge of the bottom frame. Use only enough nails to hold this edge in place. Then stretch it out to reach the other short edge. Cut the hardware cloth to match the length of the bottom frame (47 inches). Cut three pieces of stop moulding to match the width of the bottom frame (36 inches). Nail one of these pieces over each of the short edges of the bottom frame, anchoring the two ends of the hardware cloth. Nail the third piece of stop moulding over the center, from the center of one long side to the center of the other long side. Now cut four pieces of stop moulding to cover the exposed portions of the two long sides of the bottom frame, and nail these in place. This is the bottom of the bottom frame.

Cut four pieces of the 1/2" x 1/2" (or close to this) moulding to make a rectangular frame that will fit inside the bottom frame with a margin of 1/8" all around. Fasten these pieces with two thin 1-inch nails at each corner. Cut a rectangle of 'weed block' fabric that is about 36 by 47 inches. Stretch this fabric over the frame of moulding and staple it to the outer edge of the moulding. Place this inside the bottom frame with the stretched fabric on the hardware cloth and below the frame of moulding.

Middle Frame ---

You should have four small pieces of planking 7 3/4 inches long, with a width one-half the width of a plank. These 'verticals' will be fastened to the long sides of the middle frame, at the inside corners, protruding one inch above and one inch below the frame. (See photos.) Use three 1 1/2 screws for each vertical. Clamp each vertical in position, drill three holes with a drill matching the solid core of the screw, insert the screws so that the heads sink into the wood a bit, then remove the clamp. With a coarse file, taper the outside edges of the protruding parts of each vertical to make it easier to fit the frames together.

Try stacking the frames. If the fit is too tight, try turning one of the frames around, or turning the middle frame up-side-down. If a better fit is found this way, mark the frames to indicate which sides should be aligned. If the fit is still too tight, use the coarse file to remove some wood from the outside edges of some verticals.

While the top frame is stacked on the middle frame, mark on the bottom rear plank of the top frame the location of the inner edges of the rear verticals of the middle frame. This will help to locate the verticals of the top frame.

Top Frame ---

For the top frame, mark where the front (long side) will be cut one inch from the bottom edge. On each side (short side), mark a straight angled line from the center of the top edge to one inch above the bottom of the front corner. First cut each short side on these lines. Then adjust the tilt of the saw blade to match this angle, and cut the long front side lengthwise one inch from the bottom edge.

Ventilation holes

Cut notches for the ventilation holes in the edges of the rear planks of the top frame that will be facing each other. Each notch is 4 inches wide and 1 inch deep. Mark each edge 10 and 14 inches from each rear inside corner, adjust the saw for 1 inch depth, and cut across each mark. Before cutting out the notches, mark the center of the edge across each notch, at least 1 inch past the notch on either side. Then adjust the (circular) saw depth to 2 1/8 inches, and cut a slit in the center of the edge by dropping the saw blade down on the center line. With a general-purpose saw blade, the cut should be wide enough for the hardware cloth to fit. (For a handheld circular saw, you need to lean the front edge of the saw guide on the plank edge, line it up, turn on the saw, and slowly tilt the saw down to a level position.) The center of the saw blade should land over the center of the notch; but to be sure, slide the saw a little to either side of the estimated center position.

Mark the bottom of each notch one inch from the plank edge. Here are two methods of cutting the bottom of each notch:

(1) With a 1/4 inch drill, make holes along the bottom of the notch, including the corners. The holes should be tangent to the line marking the bottom edge of the notch. Use a chisel to break away most of the wood from the notch area, then finish with a rough, then smoother, file.

(2) With a 1/4 inch drill, make holes only at the corners. With a saber saw, cut the bottom edge of the notch from one hole to the other.

Cut two 3 by 5 inch rectangles of hardware cloth, and cut away the four half-inch corners of each piece, as shown in the photos. Make sure that each piece is as flat as possible.

By now, the slit that was cut across each notch is filled with sawdust. Use one of the hardware cloth pieces to scrape out the sawdust. Now insert a hardware cloth piece in each slit of the larger piece of the top frame. The center of the hardware cloth piece should align with the edge of the plank. Now stack the smaller piece of the top frame on top so that its slits fit over the top half of the hardware cloth pieces.

Verticals

While the top frame was stacked on the middle frame, you marked on the bottom rear plank of the top frame the location of the inner edges of the rear verticals of the middle frame. This will now be used to locate the verticals of the top frame. Make a vertical line at each mark, that is, parallel to the corner of the top frame.

You should have two pieces of planking 12 1/2 inches long, with a width one-half the width of a plank. These are the verticals for the top frame. Place each piece alongside one of the vertical lines that you made, on the side of the line away from the corner. The top of each vertical piece should be 1/2 inch below the top rear edge of the top frame, and the bottom should protrude below the top frame. Clamp in place, then fasten each vertical piece with six 1 1/2 inch screws, three screws into each rear plank, and alternating the positions of the screws toward the left and right sides of the vertical. (Drill holes for the screws as before.)

Each side of the top layer of the top frame is a triangular piece that extends from a rear corner toward the center of one side. Line up each of these pieces with the plank below it, and drill a hole for a 2 1/2 inch screw 4 inches back from the pointed end down through the pointed piece into the plank edge below it. Then, holding the pieces in alignment, fasten with a 2 1/2 inch screw in the predrilled hole, sinking the head of the screw into the wood a little.

Window

Cut pieces of 'stop' moulding to go on the top sloping edge of the top frame. To make mitered corners, cut these to overlap at the corners, and hold in place, overlapped at the corners, with two temporary nails on each piece, about 10 inches away from the corners, and only partly hammered down. With a hacksaw or other fine-toothed saw, cut across each corner on an angle from the outside corner to the inside corner through both overlapping pieces. Remove the cut-off scrap, and the moulding will lie flat with mitered edges at each corner. Remove the temporary nails, and re-nail with 1 1/4 inch nails with about 10-inch spacing all around.

Lay the window plastic sheet on the top frame and position so that two or three edges of the plastic overlap half the width of the border of 'stop' moulding. Mark the remaining one or two edges of the plastic where it should be cut so that all edges of the plastic will overlap half the border of moulding. using a grease pencil or crayon and a straight-edge. Then cut the plastic as marked, with a hacksaw blade.

Cut pieces of 'ply cap' moulding to go on the top edge of the top frame. The thicker edges of the 'ply cap' moulding go toward the outside, the stepped side down and the curved side up. Make mitered corners as for the 'stop' moulding, but don't nail permanently.

Put the plastic window on the top frame, overlapping half the width of the frame of 'stop' moulding all around. Then put the 'ply cap' moulding pieces in place so that the thin inner edges lie on top of the window and the thick outer edges lie on the 'stop' moulding and trap the plastic window in place. Nail with small nails, piercing the 'ply cap' moulding at the step edge where it meets the window edge.

Props ---

Here we describe devices for propping open the cold frame, either a little bit for ventilation, or high enough to reach in and work with the contents.

Cut three lengths of the 1/2" by 1/2" moulding, 6, 10, and 13 inches long. The 1 1/2 inch screws can be used with these, but 1 1/4 inches would be better. Fasten the 12 inch piece centered on the inside of the front wall of the top frame, with two screws, 2 inches from each end of the piece. Drill a hole (for a screw) in the 6-inch piece 2 1/2 inches from one end. Drill a hole in the 10-inch piece 4 1/2 inches from one end. On the inside of the front wall of the middle frame, make two holes 1 1/2 inches down from the top edge and 4 inches from the center to the left and right, that is, 8 inches apart.

Screw the 6 and 10-inch pieces to the middle frame using these holes. With these pieces each fastened with one screw each, they can pivot on the screws. When not used, these pieces are horizontal with the longest arms pointing toward the corners of the frame. But one of the four ends of these pieces can be turned upward to prop open the top frame. Depending on which of the four ends is chosen, the top frame will be propped open 1, 2, 3, or 4 inches for varying amounts of ventilation.

Take one of the 28-inch pieces that are half the width of a plank, and cut a notch in each end. Cut each notch by making two cuts into the end 3/4 inch from each edge, and 3/4 inch deep. Draw a line for the bottom of the notch, from the bottom of one cut to the other. Cut out the bottom of the notch by either of the methods described for the notches use for the rear ventilation holes.

This prop is used to hold the cold frame wide open, for working inside. The notches keep it from slipping off the edges of the top and middle frames. When not used, it can be stored inside the bottom frame alongside the front wall, or alongside a side wall if you prefer that.

If you like, you can fasten a handle to the front edge of the top frame.

Comparing Technologies

I heard that Wolfram Alpha was finally available, and I wanted to try it out. Wolfram Alpha is designed to be more than a search engine -- it's an answer engine. A search engine tries to find Web documents that contain information you want. But Wolfram Alpha will try to calculate an answer for you from data that it can access.

For example, if you want to know the "weight of the earth in pounds", it figures that (1) by "weight" you really meant mass, (2) the earth mass is available in a table of data about the planets of the solar system (although in metric units), (3) a table of conversion factors is available, and (4) a formula for converting units is available. Moreover, it has the 'smarts' to know that this is the data needed to get the answer, and it knows how to find and combine the details to get the answer.

Now, what problem would I use to try out this new answer engine? Well, I recall reading that DNA is an incredibly dense data storage and retrieval system, but I didn't have any number for the data density in, say, bytes per pound. So, I tried to get the number from Wolfram Alpha. But "DNA in pounds" was not precise enough. How much DNA? Just one 'base pair' (one unit of the chain), or an entire chromosome? And if a chromosome, which kind? (because they have different lengths)

DNA is a chain of information units called nucleotides. The chain is shaped like a twisted ladder, with each rung a pair of nucleotides that encodes two bits of information. There are four kinds of the nucleotides, so I began by asking for the mass of each kind, using their chemical names:

adenine mass in pounds: 4.9468*10^-25 lb
guanine mass in pounds: 5.53252*10^-25 lb
thymine mass in pounds: 4.51683*10^-25 lb
cytosine mass in pounds: 4.06729*10^-25 lb

I also needed the mass of the 'backbone' unit, for the 'sides' of the ladder:

deoxyribose mass in pounds: 4.45458*10^-25 lb

Then, assuming that the four nucleotide types are used equally, I could now compute the data density of DNA:

1.084547*10²⁴ bytes per pound
(That's about a one followed by 24 zeros.)

Now, what man-made data storage and retrieval system could I compare this to? I have an 8 GB thumb drive that weighs a quarter of an ounce, which may not be the most dense, but it's denser than a DVD or a hard drive. I calculated it's data density to be:

5.5*10¹¹ bytes per pound

That means that DNA is about two trillion times more dense than the thumb drive. That is, the data capacity of a quarter of an ounce of DNA is equal to about two trillion 8 GB thumb drives! Engineers would love to be able to design a data storage and retrieval system with the density of DNA, but they don't know how.

Yet there are atheistic scientists that believe that mindless evolution accidentally created DNA millions of years ago. I have two reactions to this evolutionary belief:

First, as an engineer, I feel insulted that people actually think that a random process can out-do what none of my engineering colleagues can accomplish.

Second, it is clear to me that I don't have enough faith to be an atheist.

A Disingenuous Argument

In Steve Mirsky's article An Immodest Proposal in the Opinion section of the June 2009 Scientific American (p. 37), Mirsky quotes from Jonathan Wells' article Darwin's Straw God Argument on the Discovery Institute web site (http://www.discovery.org/a/8101) without the courtesy of naming the article and with the discourtesy of insulting the name of the web site. The quote:

Darwinism depends on the splitting of one species into two, which then diverge and split and diverge and split, over and over again, to produce the branching-tree pattern required by Darwin’s theory. And this sort of speciation has never been observed.

Then, apparently pretending to be ignorant of the fact that most creationists, and Wells in particular, make a distinction between macroevolution and microevolution, Mirsky goes on to waste an entire page of ink to propose that the breeding of dogs is proof that the sort of speciation that created all of the species has indeed been observed.

The first part of Wells' paragraph from which Mirsky quotes reads:

The best way to find “evolution’s smoking gun” would be to observe speciation in action. There actually are some confirmed cases of observed speciation in plants -- all of them due to an increase in the number of chromosomes, or “polyploidy.” But observed cases of speciation by polyploidy are limited to flowering plants, and polyploidy does not produce the major changes required for Darwinian evolution.

Later in Wells' article, he writes:

So although Darwinists believe that all species have descended from a common ancestor through variation and selection, they cannot point to a single observed instance in which even one species has originated in this way. Evolution's smoking gun is still missing, and Dobzhansky’s working assumption that macroevolution equals microevolution remains nothing more than an assumption.

So it is obvious that Wells makes a distinction between macroevolution and microevolution. For the sake of readers not familiar with these terms, I will briefly explain: Microevolution refers to the small genetic changes as observed within the various 'kinds' of life. Macroevolution assumes that larger genetic changes or an accumulation of small genetic changes has produced all the species from a common ancestor. Microevolution postulates many genetic trees, and macroevolution postulates one tree. In both cases, the details of the tree branching are only estimates, and for microevolution the division of 'kinds' is also estimated.

Microevolution, creationists admit, has been observed. (So has the continual breaking of world records. But does that even suggest, let alone prove, that one day athletes will jump across the Hudson River from Nyack to Tarrytown?)

So Mirsky's disingenuous proposal does not disprove Wells' statement. His line of argument needs an observation that breeding of dogs has produced cats or lizards or anything other than more dogs.

Bird Rescue

It began as I was cutting down this spruce tree, which had gotten way too big. I was cutting off the branches, a preliminary to cutting the trunk. As I cut a branch above my head, and the branch began to sag, I heard a fluttering sound, then saw a small bird flutter to the ground and then noticed a nest dangling from the branch, barely attached.


Each branch is a horizontal fan of dense needles, which makes a nice shelf for a nest, but I was unable to see the nest from below. In the photo, you can see the partially cut branch dangling. I climbed down my ladder, and there was a fledgling bird huddled motionlessly on the ground, well camoflaged amidst the debris that typically collects under an evergreen tree. Somehow, my first guess was that it was a mourning dove, which was confirmed later.

When I invited my wife Donna out to see the young bird, she noticed another one nearby. I was relieved that I hadn't stepped on it, and carefully verified that there wasn't a third one. I left a message with a local bird rehabilitator in case professional help was needed, then proceded according to professional advice that I remembered reading.

Both fledglings were remaining motionless, and there was no immediate danger, such as cats, so I fetched a small, shallow, wire basket and two pieces of soft wire, and climbed up the ladder again. I fastened the basket on a nearby limb, and put the nest in the basket. I also cleared out a few twigs above it so that they wouldn't scratch the young birds when I returned them to the nest.

I had to chase each bird a little, because they could flutter and run on the ground a little. But I formed a cage around it with my hands, then gently closed in, folding the wings gently back to the normal resting position, at which point the bird would calm down, Knowing the nest would be on my left, and I would need one hand on the tree for my own safety, I held the bird in my left hand from above before climbing the ladder.

Then I removed all my equipment, knowing that my project would be on hold until these fledglings learned to fly and no longer needed the nest. I had a pile a spruce branches about 60 feer away, where I could keep an eye on the nest while cutting the branches small enough to fill leaf bags. There were some small leafless trees that gave me some cover, but also partly blocked my view of the nest site. Nevertheless, I soon heard the sound that mourning doves make when they fly upward.

Later, I sat waiting at a distance from a different angle where I could see better. From there, I saw two adult mourning doves come to the nest, and one flew away. Now I knew that the parents had found them. The next day, sometimes I would see an adult on the nest when I checked, and sometimes not. Here's a few photos of the nest, taken with a zoom lens. In the last photo, there may be two adult heads. (The fledglings keep their heads tucked in, with no neck showing.)





Once, when the adults were away, I got out the step-ladder again to get a close-up photo of the fledglings, and to verify that both were in the nest. It didn't show the nest contents as clearly as I hoped (next photo).



The step-ladder was standing on its own near the tree, so next I folded it and leaned it against the tree for a closer look. But as I held the camera for this close-up, one fledgling jumped out of the nest and fluttered to the ground, achieving a little more horizontal component of his flight this time. Also, he was a little harder to chase down, so he was noticeably stronger and more ready for real flight.

Just after I caught him, my daughter Susan arrived home, so I asked her to take a photo of the young bird before I returned him to the nest. Note the tucked-in head position and the flight feathers.



Just after I got him back into the nest, I spotted three hawks soaring together overhead. I got him out of sight just in time, I thought. Later, it occurred to me that hawks don't normally hunt in groups. A young hawk or two must have been out on a training exercise.

The Genetic Code - how to read the DNA record

(NOTE: The end of this article has been revised and expanded from the original.)

DNA is the kind of molecule that stores genetic information in every living cell. It describes how our bodies are made, and to a degree, how they operate. The translation of DNA, a sequence of nucleotides, to a sequence of amino acids (protein units) is a complex but fascinating process. Here's a simplified account of the essentials:

A selected portion of the DNA is copied in complementary form, making a messenger RNA (mRNA) chain molecule. There are four kinds of nucleotide in the DNA, abbreviated G, T, A, and C; and four kinds in the RNA, called C, A, U, and G. When copying from DNA to RNA, the correspondence is:

G -> C
T -> A
A -> U
C -> G

So, for example the DNA sequence

GTACCATG..

when copied to RNA, makes the RNA sequence

CAUGGUAC..

A sequence of three nucleotides, such as GCC, is called a codon. Each codon sequence encodes for one of 20 amino acids, or else is a stop codon. The genetic code is a scheme that translates the 64 (4 x 4 x 4) types of codon to the 20 amino acids and the stop signal. The codon for the amino acid Methionine also functions as a start signal. There are three codons that mean 'stop', and there are one to six codons representing each amino acid. Here's the complete genetic code:

[START], Methionine <-- AUG
Alanine <-------- GCU, GCC, GCA, GCG
Leucine <-------- UUA, UUG, CUU, CUC, CUA, CUG
Arginine <------- CGU, CGC, CGA, CGG, AGA, AGG
Lysine <--------- AAA, AAG
Asparagine <----- AAU, AAC
Aspartic acid <-- GAU, GAC
Phenylalanine <-- UUU, UUC
Cysteine <------- UGU, UGC
Proline <-------- CCU, CCC, CCA, CCG
Glutamine <------ CAA, CAG
Serine <--------- UCU, UCC, UCA, UCG, AGU, AGC
Glutamic acid <-- GAA, GAG
Threonine <------ ACU, ACC, ACA, ACG
Glycine <-------- GGU, GGC, GGA, GGG
Tryptophan <----- UGG
Histidine <------ CAU, CAC
Tyrosine <------- UAU, UAC
Isoleucine <----- AUU, AUC, AUA
Valine <--------- GUU, GUC, GUA, GUG
[STOP] <--------- UAG, UGA, UAA

The key elements of translation are small transfer RNA (tRNA) molecules. Each kind of tRNA molecule has a region called the anticodon that can recognize and attach to a particular codon of a messenger RNA (mRNA) molecule. The tRNA molecule has another region called the "3' terminal" that attaches to a particular amino acid. This attachment is aided by molecules called aminoacyl-tRNA synthetases, of which there is generally one kind for each kind of amino acid. There are even helper molecules that provide a proofreading function to detect and correct any translation errors.

Each kind of tRNA molecule associates one kind (sometimes a few kinds) of codon with a particular amino acid, so there are one or more kinds of tRNA for each row of the above genetic code table. For example, there is a kind of tRNA with a region that attaches to Tryptophan (with the help of a specific kind of aminoacyl-tRNA synthetase), and with another region that recognizes and attaches to any part of mRNA with a UGC codon.

So if the RNA sequence is

AUGUUCUUAUACUCCUAG

we can divide it into codons as

AUG UUC UUA UAC UCC UAG

Five tRNA molecules will attach to the first five codons, and five amino acids will attach to the tRNA molecules, something like this (with abbreviated names for the amino acids):



No tRNA molecule will attach to the last codon, because it is a stop codon, and the translation will stop.

The amino acids connect into a chain in this sequence, like this, which detach from the tRNA molecules:

Met-Phe-Leu-Tyr-Ser

Each tRNA molecule detaches from the mRNA and from the chain of amino acids, to be 'loaded' with another amino acid and used again. The detached chain of amino acids, a protein, folds into a three-dimensional shape to function as a protein. (This folding is another complex process, often needing the aid of specialized helper molecules.)

These are the basics of the translation, but it is actually more complex than this, because other molecular machinery is needed to make everything happen in the right sequence. The 'work bench' of the mRNA reading machinery is a collection of tiny particles called ribosomes that look like tiny dots in the center of a living cell (but huge compared to the tRNA molecules). There are also other tools such as initiation factors, releasing factors, and various enzymes that control the process.

Each ribosome has a small and large unit that link together on either side of the mRNA ribbon, forming a bead that can slide along the mRNA, reading it. Many ribosomes typically read one mRNA strand at one time, producing proteins. Each ribosome has three sites on one side of the hole through the 'bead' that hold tRNA molecules in position to attach to, and detach from, the mRNA as it passes through the hole. The ribosome 'workbench' has other sites to hold the various other 'tools' in position to operate on the various stages of the process.

Where does the genetic code come from? It is not the result of chemistry or any laws of physics. It is determined by the set of tRNA molecule types, and aminoacyl-tRNA synthetase types, which are constructed according to DNA information, which encodes not only the building materials and the building plans, but also the building tools and the building methods. In other words, the genetic code is just information that has always been there since life began.

The number of possible genetic codes is a huge number, 85 digits long:

1,510,109,515,792,918,244,116,781,339,315,785,081,841,294, 607,960,614,956,302,330,123,544,242,628,820,336,640,000

and all of these many codes would work equally well. But all of life uses just one genetic code, about 280 bits of information, the one that scientists Watson and Crick discovered in 1953, but was there since creation. The theory of evolution has no explanation for how the genetic code began, because it can't explain how information can arise from no information. Nor can it explain why there is only one genetic code (out of such a huge number of equally workable codes), even though there is extreme variation of everything else. The mechanism of the present genetic code is very complex; and evolutionary theory supposes that it randomly evolved from a simpler, smaller code. But because there are so many equally viable genetic codes, random evolution should have produced species with many different codes. The evolutionary explanation is far more unlikely than dumping a bucketful of dice on the floor and expecting them to all land with the same number up.

The creationist explanation is that the universal genetic code is like a signature of the creator, who chose a uniform code for all of the designs of life. A short story will illustrate the principle:

During the Cold War, Russia was suspected of stealing American technology. Proof came when some Russian war equipment given to a third country was captured and examined. It contained an integrated circuit that was identical to an American design. It is theoretically possible that the Russians had the same design concept, leading to a similar design. But digital circuits have thousands of component parts connected by thousands of wires. There trillions of ways to position the parts on the chip and trillions of ways to route the connecting wires that work equally well. It would be impossible for the Russians to independantly produce the same positions and routings even if the logical design were identical. But examination showed the details were identical, even details left over from correcting wiring errors. In effect, there was an American 'signature' in the copied design.

Life is more than chemistry

In my retirement, I have been studying organic chemistry and how life works. Since I spent 43 years before I retired designing computers and related hardware and software for communicating information, it is natural for me to think of computer hardware and software as analogies to illustrate the general principles of how life works. In the following, I'll explain some of the essentials of life from this point of view, while trying to keep it simple.

Living things are made of more than chemical components, just as a computer is more than hardware. A computer is 'dead' if it doesn't have software -- the information that tells it how to function. Likewise, living things of all kinds -- even bacteria -- need internally stored information to function. So life is made of chemistry and information, just as a computer is made of hardware and software.

Life's information is stored mostly in DNA, and some information in similar structures. There is a mechanism for reading the DNA, interpreting the information to construct proteins and even to control the process. Even the proteins of the reading and controlling mechanisms are constructed from the DNA information. This is like having a CD with all the data needed to construct a computer, including the CD reader, and including the information for making the construction tools and how to use these tools.

In multicellular life, such as animals, the DNA information is actually stored in EACH cell. Imagine a computer where all the information for making and using the computer is stored in each small component (integrated circuit) of the computer!

There is also a mechanism for copying the DNA information onto new DNA media. This is used to make duplicate cells. Again, the DNA includes information for making and controlling the copying mechanism. This is like having a CD copier that can make duplicate CDs.

For all the various forms of sexual reproduction, a more robust copying process is used, one that can merge information from two configurations of the design. This allows a species to adapt to its current environment. The closest that modern computer designs come to this kind of functionality is the kind of redundant design used for computers used in satellite and military applications. These computers are made with many spare components and switches arranged so that if one component fails, a replacement component can be switched in.

But life lacks one function that computers have. CD readers would not be useful unless we have CD writers for putting information on the CDs -- else there would be no information for the CD readers to read. But nowhere in any life-form is there any mechanism for writing (recording) information in the DNA!

In fact, it is not possible by any chemistry to create the information in the DNA, as this would violate information theory. Likewise, it is not possible to design any hardware to create information on CDs. It is possible to design hardware to generate bit patterns (I've done a lot of that), but there is no more information in the patterns than the small amount of information used to make the hardware.

So modern scientists observe that life is full of information, but have no scientific way to explain how the information got there. To understand this conundrum better, imagine the following scenario:

Suppose that a global atomic war destroys most of society, and the survivors struggle to rebuild modern civilization. Apparently all the computers are destroyed, and no one can be found that knows how to design or build a computer 'from scratch'. Then someone discovers a computer manufacturing plant. It has computer-controlled robotic machines that operate and control the entire manufacturing process, turning sand (raw silicon) and various metals and plastics into complete, working computers, and even more robotic manufacturing machines if selected. There are even generators for making the necessary electricity from simple fuel.

The happy discoverers study this autonomous manufacturing plant carefully. They find that all the software is stored on CDs, and there are lots of CD readers and copiers and the facilities for making more CD readers and copiers. But there are no CD writers, nor data for how to make them, not even on paper. The existing software has the flexibility of making different kinds and configurations of computers, but since there are no longer any computer designers alive, there is no hope of making newer computer designs.

As I said, modern scientists have observed that life is full of information, but have no scientific way to explain how the information got there. Now Darwin didn't understand this problem, because he didn't understand anything about how the cell works, let alone that DNA existed. (Cellular life is still not completely understood.) Since Darwin, as the theory of evolution itself evolved, the problem (actually, very many problems) of how to get from non-life to life gradually became more apparent. I have discussed the chemical impossibilities of making life from non-life in other blogs, but here we discuss only the information source problem.

The atheists and humanists saw in Darwin's theory the potential for ruling out God as the source of all things scientific. As more knowledge and understanding of DNA was gained, a mechanism for each species to genetically adapt to changing enviroment became better understood. This mechanism, now known as micro-evolution, has been shown to use selection of existing DNA or loss of genetic information, but never creation of new genetic information. But it is not the same as macro-evolution.

Micro-evolution is a science, but macro-evolution is a theory -- that one species can change into another. The one is like learning how to train an athlete so that he can break world records. The other is like assuming that since records are continually broken, athletes will eventually be able to leap across oceans, given enough time. (You CAN go continually higher even though there is a limit: Stand 16 inches below a ceiling, then move twice as close repeatedly: 8 inches, then 4, 2, 1, 1/2, 1/4, 1/8 ...)

But the problem of the origin of genetic information is a more obvious problem -- so much so that many scientists with little or no religious inclinations have turned to the investigation of "intelligent design" as a way to solve this problem without admitting to the existence of God. Some see "intelligent design" as evidence of a supernatural intelligence (God), but others look for the information source as coming from alien life - from another planet somewhere. But these people haven''t solved the problem -- they have only moved it to another planet. They 'solve' the problem of how life origninated on earth by creating another problem: How did life originate on Planet X?

The problem is that people don't want to believe in a Creator-God, because it is clear that He may rightly define the rules and demand something of us. It is our nature to want to be free and unrestrained. But God will not leave us alone. He reveals Himself by the marvels of His creation. (Would those discoverers of that self-replicating computer-controlled machinery ever think for a moment that it was not designed by intelligent minds?) And furthermore, He has given us His Word, the Bible. Unlike all histories of human origin, that boast of human achievements while glossing over the failures, this one includes all the failures, and more. This Word not only records the past, but includes predictions of the future that have been observed to be accurate. I could go on with more examples, but the point is that God's 'fingerprints' are on His Word as well as His creation. So, as the Bible says, we are "without excuse" for ignoring God:

... what may be known about God is plain to them, because God has made it plain to them. For since the creation of the world God's invisible qualities -- his eternal power and divine nature --have been clearly seen, being understood from what has been made, so that men are without excuse. (Romans 1:19-20, from New International Version)

Restraining Evil

I was studying 2 Thessalonians 2:1-9 lately. In the New Kings James Version, it reads:

Now, brethren, concerning the coming of our Lord Jesus Christ and our gathering together to Him, we ask you, 2 not to be soon shaken in mind or troubled, either by spirit or by word or by letter, as if from us, as though the day of Christ had come. 3 Let no one deceive you by any means; for that Day will not come unless the falling away comes first, and the man of sin is revealed, the son of perdition, 4 who opposes and exalts himself above all that is called God or that is worshiped, so that he sits as God in the temple of God, showing himself that he is God.

5 Do you not remember that when I was still with you I told you these things? 6 And now you know what is restraining, that he may be revealed in his own time. 7 For the mystery of lawlessness is already at work; only He who now restrains will do so until He is taken out of the way. 8 And then the lawless one will be revealed, whom the Lord will consume with the breath of His mouth and destroy with the brightness of His coming. 9 The coming of the lawless one is according to the working of Satan, with all power, signs, and lying wonders.

Using Greek resources as a guide, I constructed the following rough translation of 2 Thess. 2:6-9, mostly following the word order of the original Greek, and including various inferences of the Greek words:

6 And now you know [perceive, understand] what holds [holds back, holds accountable] that he may be revealed in [this] his time [due season, opportunity].

7 For the mystery [as of a secret society] already works [is effective, is evident] of [that] iniquity [lawlessness], only he who holds [holds back, holds accountable] [will do so] now [henceforth] out of the way [midst, among them] is done [he is taken].

8 And then [at that time] shall be revealed that wicked [lawless] one whom the Lord Jesus will kill with the Spirit of his mouth and [alse, even] shall destroy [do away with, bring to nothing] with the brightness [appearing] of his coming [presence].

9 [Even him] who is [the one] coming after [the manner of] the working [operation] of Satan with all [manner or means of] power [miracle-working, mighty wonderful work] and signs [tokens of the supernatural, miracles] and lying [false] wonders.

Biblical scholars identify the "man of sin" and the "lawless one" as the Antichrist, and identify "He who now restrains" as the Holy Spirit. Since the subject of the passage is "the coming of our Lord Jesus Christ", the "taken out of the way" of verse 7 is a reference to the "rapture" described in 1 Thess. 4:13:18. The explanation is that the Holy Spirit is in all believers, so that when the believers are taken way by Christ, the Holy Spirit thus is also taken away.

The Holy Spirit was given to the apostles by Jesus (John 20:22) and first given to other believers at Pentacost (Acts 2) and ever since. The epistle of Paul to the Romans makea clear that only true believers have the Spirit, because in Romans 8:9, last part of the verse, it says "Now if anyone does not have the Spirit of Christ, he is not His." (NKJV), and in Romans 8:16 it explains "The Spirit Himself bears witness with our spirit that we are children of God." (NKJV) The fact that the Holy Spirit confirms salvation is also taught in 2 Corinthians 1:22 ".. [God] who also has sealed us and given us the Spirit in our hearts as a guarantee." (NKJV)

My observation is that since the Holy Spirit restrains (or holds back, or holds accountable) the working of lawlessness and the appearing of the lawless one, He does this restraining through the believers that He indwells. When I think about this, I envision the Christians as a bunch of people pushing back on a wall that is about to collapse, threatening to cause an entire building to collapse. At the rapture, Christ snatches them away, and the building collapses. Perhaps this is how the US will fall as a world power and cease to have a role in Tribulation prophecy.

The lesson here is that we believers should be diligent to restrain, or at least hold accountable, all forms of iniquity where we can exercise any impact. In particular, in this election season, we should be voting against any charismatic, lawless deceiver who could be the lawless ONE.

Doing Science in History Class

First I learned that lightning is seen before the thunder is heard because light travels much faster than sound. But I was really fascinated when I learned that the distance between the lightning and the observer could be measured by the time between the lightning and the thunder -- five seconds correspond to about a mile. I was fascinated because I figured that by making such measurements and plotting them on a graph, one could track the movement of an approaching thunderstorm, and could estimate the time of its arrival. The graph would look something like this:

The vertical scale would measure the lightning-to-thunder delay in seconds (inferring distance), and the horizontal scale would record the time of each measurement. As the storm approaches, the distance would decrease, so the graph would show a downward trend. If all the lightning came from the exact center of the storm, and the storm came toward me with constant speed, the graph would show a straight line. But, of course, the lightning strikes would be scattered throughout the storm cell, so the plotted measurements would also be scattered. However, by estimating a straight line through the center of the plotted points, the path of the center of the storm could be estimated.

I wanted to try this idea the next time that I heard the thunder of an approaching storm. To be prepared to record measurements immediately, I prepared a blank chart and kept it inside one of my textbooks so that I would be prepared whether at school or at home.

The opportunity came when I was in History class. The sky outside was darkening, and soon I began to hear thunder in the distance. I pulled out my chart, and started counting the seconds between lightning and thunder while trying to listen to the teacher -- or at least try to look like I was listening. But now and then I would glance toward the clock and my head would dip as I recorded another measurement.

As the storm approached, the measurements became more frequent, and I became more absorbed in my science project. At some point, I suddenly realized that the history teacher had stopped talking, and when I looked toward the front of the classroom, the teacher was not there.

Then I heard the teacher's voice right behind me, asking "what are you doing?" As I turned to look over my shoulder, I saw that she was looking over my shoulder with a puzzled look, trying to figure out what my chart was all about.

It was too late to hide my chart. I might as well explain what I was doing, I thought, especially since she seemed a bit curious. I hoped that I might get by with just a warning. As I explained my chart, the teacher asked me to speak up so all of the class could hear. I ended by pleading that I really didn't plan to do this during history class, but since that was when the storm came, I didn't have any other choice.

To my surprise, the teacher told me to continue my experiment! Furthermore, she said that when I had enough data to predict when the rain would start, to raise my hand and announce my prediction, announcing this to the rest of the class.

With a sense of relief, I returned to my counting and recording in earnest, no longer worried about hiding my activity. At some point, I had enough points plotted to be able to hold a transparent straight-edge over the graph and estimate a best-fit straight line. The point where this line intersected the bottom edge of the graph (representing zero distance) indicated the arrival time of the storm.

I raised my hand, and the teacher interrupted her lecture. "Two minutes after the hour" I declared, hoping that I wouldn't be embarrassed by a big error. I continued with more data recording, hoping to confirm this estimate as I completed the experiment.

When the rain started, it didn't creep up gradually with an uncertain start time. It suddenly crashed against the tall windows along the entire left side of the classroom, as though some giant had thrown a huge bucketful of water against the windows. Everyone was startled and first looked to the left at the rain suddenly pouring down the windows, than all heads turned in unison to the right, toward the clock. It was two minutes after the hour! exactly! and cheering erupted spontaneously. I was surprised by the accuracy of the prediction, but felt completely exonerated.

I did the same experiment later, at other opportunities, and learned that there was generally a difference between the arrival of the average center of the lightning and the arrival of the leading edge of the rain. Also, if the storm passes by one side of the observer, the graph would tend to be curved rather than follow a straight line. As I looked back at my first experiment, I realized that I was lucky that a number of errors happened to cancel, resulting in an unusually accurate prediction.

Fluorescence -- Getting Pumped Up

At the close of the Sunday message, I was praying (as I often do) that the message would bless and empower all those that heard it. As I prayed, the Holy Spirit (our prayer Assistant) gave me an analogy that I want to pass on.

I prayed that the power of the message would "fluoresce" in the hearts of the listeners, confident that God would understand what I meant by this.

When a material fluoresces, light falling on the material absorbs the energy of the light, and shortly afterward the energy is released as light of another frequency. The process actually involves individual particles: A photon of light strikes an atom or molecule and "pumps" (yes, that's the technical term) it to a higher energy level. Shortly afterward, the atom or molecule "relaxes" back to a lower energy level, releasing the energy difference in the form of another photon with a different frequency (different color of light). Some energy is typically left behind as heat.

(In a fluorescent light bulb, ultraviolet light generated by the electrified gas in the tube pumps up atoms in the chemicals coating the inside of the tube, which then pass on most of the energy as visible light. The remaining energy becomes heat.)

When a message from God's Word, the Bible, is absorbed by an individual Christian listener, the power of the message "pumps" him up. When the Christian applies the message in his life, the power of the message is released into the situation where the message is applied. The application in this situation may not be recognizably of the same form as the original message (not the same 'color'), but the power is nonetheless passed on. And some good of the message is left behind in the Christian's heart (as 'warmth', at least).

Thinking about it further, I think there is a difference between the physics of fluorescence and the application of the Word. Fluorescence is limited by the law of Conservation of Energy (total energy is never increased nor diminished). But when the Holy Spirit helps us to apply His Word, it works like the loaves and fishes -- blessing is multiplied as it is dispersed.

My Summer Projects

I have taken pictures while doing a series of projects over the last two months, and put them into an album on PicasaWeb, with captions. The link below goes to this album.

After we had new siding put on the house, it became apparent that the fiberglass wall on the west side of the house looked bad by comparison. But we liked the fact that the fiberglass, which is translucent, lets light into the shop/storage area, which has no windows. So we decided to hide the fiberglass wall with a trellis, and hide the air conditioner as well.

We had a string of potted herbs and flowers along that wall, and I had been thinking of making a raised bed for planting herbs. Over the last two years, I have been developing soil from compost for this raised bed, in another area. So we decided to put a raised bed for herbs and flowers below and in front of the trellis. We could also plant clematis in the bed to climb on the trellis.

The raised bed would require that the walkway of stones (small stones and round stepping stones) would need to be moved further away from the house. Over the years, debris falling on the stones has turned into soil, making it difficult to stop weeds from growing. So we might as well sift out the soil and wash the stones while moving them. Around the corner (south), the dirty stone problem was even worse, due to a bird feeder at the back of the house. So the stone cleaning operation would include that area, also. The soil from the stones could also be used for the raised bed.

We also have had a problem with grass along-side the stones growing in among the stones, causing the stone/grass boundary to migrate. So we would also add plastic edging (mostly underground wall) at the stone/grass boundary to prevent the migration.

When making a list of the required lumber for the raised bed and the frame to support the trellis, I realized that I would need to rent a truck to transport the lumber. I also wanted to build two shelf units to better organize the shop/storage area, so I added the lumber for the shelves to the list to save an extra truck rental.

So the trellis idea led to the raised bed, which led to stone cleaning; and the trellis and raised bed led to getting started on the storage shelves. I made detailed measurements and plans for all these projects, but absolutely no schedule. But once I got started, I wanted to keep going as much as possible.

Yes, I'm retired. But retirement isn't doing nothing. It's having no schedule.

Summer Projects Photo Album