Tuesday, October 14, 2008

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)

Monday, October 06, 2008

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.

Friday, August 22, 2008

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.

Wednesday, August 13, 2008

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.

Monday, August 04, 2008

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

Saturday, May 24, 2008

The Day I Saw a UFO

A scientist was once asked if he believed in UFOs, and he replied like this: "Of course; any flying object that is unidentified is a UFO."

I remember when, many years ago, I saw a UFO. I was spading the garden, and taking a break, I thrust my shovel into the soft earth and looked around. I was near the pear tree, where hung the wren's nest box, so I looked to my left to look for the wren that I'd noticed coming and going earlier. I watched her enter the nest box with an insect that she'd found, then after feeding her brood, fly off again.

I looked forward again, and there was the UFO, hovering in the air in front of me, close enough to touch if I only dared to do so. I'd heard of UFOs darting about in the sky, but this one hovered motionlessly just two feet in front of me.

It looked like a wooden ball about an inch and a half in diameter. I suppose some would have looked for little doors or windows for the tiny aliens. Still others might have looked for the face of Mary; but I just stood there pondering the laws of physics.
(unretouched photo of reconstructed scene)

I remember seeing tent caterpillars hanging from invisible threads, but they swayed in the breeze. I guessed that a wooden ball that size would be too heavy for one of those threads; but nonetheless, I looked up. No, the pear tree was too far away, and there wasn't even a cloud to hang the ball from.

I would have to experiment a bit to figure this out. I passed my hand over the ball, then under it, then on its left and right, as though slicing a box of air around it. So far, the wooden UFO hovered undisturbed. There remained just two sides of the 'box of air' to be checked: in front and behind the wooden UFO.

As I sliced the air behind the UFO, it was quickly obvious what the 'flying object' was, and immediately it lost its 'UFO' status. The wooden ball was the tip of the handle of my shovel that I had thrust into the soft earth in front of me, and had forgotten. The round end of the handle was two feet away, but the blade of the shovel was about seven feet away and thus out-of-focus. The handle of an old-fashioned shovel has a slight bulb-like swelling of its tip, so that the shaft cannot be seen behind the tip even when the shaft is not exactly pointed toward the observer's eye.

To get the above photo, I reconstructed the scene by thrusting an old shovel into a strip of spaded ground between our lawn (on the left) and the neighbor's fence (on the right). If I were more adept with advanced camera settings, I might have made the background more out-of-focus, to simulate what the eye sees. But instead, I found an angle where the shovel blade is hidden behind the much-closer tip of the handle.

What if I were not so cool and patient in my reaction, but instead had panicked and ran away without investigating? Then the object might have remained a UFO forever. But it is also possible that an explanation of the observation as the tip of the shovel might be discovered later. Lacking the experiments that I did which confirmed that it was the shovel-tip, this explanation would be essentially theoretical, although it probably is the only plausible explanation.

Some people believe that observations of UFOs prove something, but that is not logical. Until you have an identification or an explanation, nothing can be proved. You simply have a question with insufficient data to get an answer.

Friday, February 22, 2008

Can Chemical Evolution Work?

In a previous blog, Why the Search for Extra-Terrestrial Intelligence (SETI)? , I discussed how the SETI project has been dramatically unsuccessful in finding signs of extraterrestrial intelligence, thus unsuccessful in finding evidence supporting the premise that life can arise spontaneously from non-life. I pointed out that there are other, more convincing, scientific avenues for examining this issue, and that such one avenue is biology, which I might discuss another time. This is that time.

Miller’s Experiment

In 1953, Stanley L. Miller, using the ideas and guidance of Harold C. Urey, applied an electric discharge (spark) to a mixture of ammonia, methane, hydrogen and water vapor for a week, obtaining a small amount of some amino acids. Since amino acids are the building-blocks of living things, the experiment made news as evidence for life arising spontaneously from non-living matter. Since then, many faults of the experiment were pointed out, so many other variations of the experiment were done to try to correct these faults and to get favorable results. These variations were generally either flawed as well, or unsuccessful. Lately, most evolutionists overlook the problem of getting primitive life from non-living matter, taking it for granted, and discuss evolution beginning from DNA or RNA. But if life cannot begin from purely natural processes, evolution has no foundation.

Miller’s experiment has been criticized as unrealistic, biased in favor of the desired outcome. Scientists now generally agree that earth’s early atmosphere was nothing like his ammonia-methane-hydrogen-water recipe. The oxygen in earth’s actual atmosphere would have destroyed the amino acids. His apparatus was something like a still, with an evaporator and condenser, but with a trap that isolated the amino acids as they were made, protecting them from the formic acid (as in bee venom) that was also made. The evaporator might be a model of the oceans and the condenser a model of the atmosphere, but what on earth does the trap represent?

But Miller’s experiment and its variations actually demonstrate the intrinsic difficulties of creating life from non-life. The biases actually help, because the experiments show that even with an artificial boost, life is nonetheless not produced. There are many principles of biology that are demonstrated by Miller’s experiment and its variations that explain why life cannot be produced from non-life by natural causes -- that all such attempts are intrinsically flawed.

Making Life

First, just making a few types of amino acids is not making life. Living things are made of enzymes and more complex organic molecules. To get life you need to at least connect a sequence of amino acids in a chain-type structure to get an enzyme -- and not just any sequence, but one that gives the enzyme a useful shape, because the shape is critically important to the function of the enzyme. An enzyme is an important, essential type of simple protein that is used as a tool to help construction and control of living things. Life uses more complex kinds of organic molecules, but to make life, you need to at least make enzymes.

Suppose someone told you that an earthquake or a tsunami could turn a forest into a pile of logs. You would probably find this plausible. But suppose he went on to say that this was proof that log cabins could be produced by natural causes. Surely you would object. How will the logs be cut to consistent lengths? How will they be notched to fit together? How will they be assembled into a useful shapes, with doors, windows, and roofs? Likewise, the amino acid building-blocks need to be assembled into enzymes with useful shapes.

Miller’s Experiment Examined

The following analysis of Miller’s experiment (and similar experiments) is based on a presentation by Timothy R. Stout of Creation Truth Outreach, Inc. and on other research that I did. I will use ‘plain English’ as much as possible, but will include the scientific terms in parentheses to make it easier for you to check my facts if you like.

Life is built from about 22 different kinds of amino acids -- 20 ‘standard’ kinds plus two variations used by a few unusual forms of life. Miller produced only four of these kinds in any significant quantity.

Miller’s experiment mostly produced tar (85%), a kind of chemical junk-yard of disorganized parts. He also produced formic acid (8%), which although an essential part of all amino acids, can be destructive, as mentioned earlier, and (about 3.5% of) other things. He also produced two of the simplest kinds of the amino acids (glycine and alanine, 2% each), which are water-repellent (hydrophobic). Two other, somewhat more complex amino acids (glutamic acid and aspartic acid, 0.02% each), which are water-attracting (hydrophilic), were produced. The other kinds of amino acids, which are mostly more complex in structure, were produced in only very tiny (trace) amounts, or not at all. There was no evidence that any of the amino acids had assembled into chains to form enzymes or any other sort of protein.

Problems, Problems, and More Problems

This was not a good mix for producing life. Enzymes need an amino acid sequence that generally alternates between the water-repellent and water-attracting types of amino acids. But because there was 100 times more of one kind than the other, half of the time when an amino acid needed to be added to a chain in progress (a polypeptide), there would be only a 1% chance of the correct kind. The simplest enzyme requires a chain of at least 57 amino acids, so the probability of successful assembly is 1% of 1% of 1% of 1% of 1% of 1% of 1% of 1% of ... 28 times, which basically translates to: impossible. Most simple proteins are chains of more than 100 amino acids.

With too many amino acids of the water-repellent kind, a forming chain of amino acids would be too ‘sticky’, causing tar to form instead of enzymes.

Another problem, of course, was that only four of the 20 'standard' kinds of amino acids were produced. This certainly eliminates many kinds of useful enzymes.

Another problem -- no ‘molecular chaperones’. Chemists know that most enzymes require ‘molecular chaperones’ for correct assembly, to prevent making a jumbled mess (aggregation) -- that is, making tar. Molecular chaperones are proteins that interact with unfolded or partially folded protein subunits, working to stabilize them, unfold them, and/ or to assist in their correct folding and assembly. In other words, you need life to build life. This is what happens when plants build themselves from dirt, and when animals build themselves from dead plants. But until you create life, you don’t have molecular chaperones to help you create life.

Another problem is that it takes more energy to join amino acids into chains than to break the chains apart. A basic principle of physics and biology is that a system, left alone, tends to go to its lowest-energy state (equilibrium), which for amino acids is broken chains. When life exists, there are mechanisms to protect the chains (proteins) from breaking; but before life is formed, there is no protection. Again, life needed to make life.

Another problem is that there was too much formic acid. A formic acid molecule can easily connect to the end of a chain of amino acids, stopping the chain from getting any longer. Since there were four times as many formic acid molecules as amino acid molecules, there was only a one-in-five chance for the chain to continue growing at each step. The probability of getting a chain of 100 amino acids at this rate is so tiny (1/5 to the 99th power) that even if there were as many amino acid molecules in the experiment as the number of atoms in the Milky Way galaxy, there would be little chance of getting even one chain this long!

Another problem is that molecules can also connect on the side of the amino acid molecules, forming ‘side chains’ inside of building the chain only in the correct direction. This problem gets rapidly worse if the chain gets longer, because there will be more and more locations where side-chains can grow. Mathematically, the probability of getting a chain of 100 amino acids for this reason alone is one chance in 2 x 3 x 4 x 5 ... x 98 x 99 (99! or 99 factorial). Now, all the atoms in the entire universe will not be enough to get one accidental protein 100 amino acids long!

Another problem is that the mix of amino acids that Miller produced in his experiment did not have the correct ratio of fundamental properties to make viable enzymes. Half of the amino acids should be ‘non-polar’ (the water-repelling kind), and the other half should be ‘polar’ (the water-attracting kind). Of the polar kind, half should be electrically charged, and the other half uncharged. Of the electrically charged kind, half should have a positive charge, and the other half negative. So the proportions should be:
  • 1/2 (50%) non-polar
  • 1/4 (25%) polar, uncharged
  • 1/8 (12.5%) polar, charged positive
  • 1/8 (12.5%) polar, charged negative
So what mix did Miller get? He got:
  • 99% non-polar
  • 0% polar, uncharged
  • 0% polar, charged positive
  • 1% polar, charged negative
Just another reason why the experiment failed.

Another problem involves the symmetry (‘chirality’) of the organic molecules. Amino acid molecules can have left-handed and right-handed shapes, just as shoes and gloves do. But in the construction of life, only left-handed amino acids are used, except glycine, which is symmetrical -- neither left-handed nor right-handed. And life only uses right-handed sugars. And for good reason, because if you were made of equal amounts of both chiralities of proteins, your body would not fit together correctly, and you would die. (Think of the problem of mixing left-handed and right-handed screws in a complex machine.) Now suppose there was one man made of organic molecules of chirality all opposite to the rest of life. (He would look ordinary unless you looked at him with a powerful microscope.) He would have trouble digesting his food, because it would have the wrong chirality (for him).

Now it happens that amino acids have ‘unstable chirality’ -- that is, a left-handed amino acid molecule will occasionally flip (racemize) into a right-handed shape. This happens slowly, taking about 10 to 100 years for most of the molecules to change chirality. Our bodies can correct for this slow degradation by replacing cells of our body, although in some tissues, like teeth, this can be tolerated. Forensic scientists actually use this phenomena to measure the age of teeth.

So the chirality problem is this: If chemical evolution works, it needs to develop a construction of proteins with sufficient complexity to survive and reproduce. Until that critical point, we don’t have life -- just life-in-the-making. But along the way, ‘chiral instability’ will destroy the partly-made life before it has a chance to develop mechanisms for self-repair. Chiral instability may take perhaps as much as 1000 years to destroy the progress of evolution, but even evolutionists don’t believe evolution works anywhere near that fast. Until a mechanism for reproduction is developed, there is no way for evolution to randomly ‘try’ methods for combating chiral instability until it ‘accidentally’ finds a working method. It has to get this (and the survival and reproduction methods) right the first time.


In other words, chemical evolution (if it works) needs to create potential life ‘designs’ over and over and over until one of them ‘works’ (actually lives and reproduces). But we have presented a long list of problems, each one of which prevents the production of even a small scrap of one enzyme, let alone a construction of various proteins with sufficient complexity to survive and reproduce. The problems presented don’t involve imagining what might have happened long ago. All of these problems (for getting chemical evolution to work) are based on facts and principles of organic chemistry that have been, and can be, demonstrated in a laboratory, coupled with mathematics and logic. Yet ALL of these problems would need to be overcome (contrary to the facts and principles of organic chemistry) to make chemical evolution work!

Those who patiently wait for SETI or experiments such as Miller’s to prove that life can arise spontaneously from non-life are ignoring logic and the facts of organic chemistry. Why are they such patient believers? I am convinced that they are biased by a fervent desire to deny a Creator, who they are afraid might require something of them.

P.S. If you would like to learn more about these and similar reasons why known physical principles prevent life from arising by natural causes, read Timothy R. Stout's pamphlet online.

P.P.S. I neglected to explain that when left- and right-handed versions of an organic molecule are possible, chemistry unguided by information (generally in the form of the design of other organic molecules), that is, when the chemical components are simply jostled by random motions, you will get equal numbers of the left- and right-handed versions, because the laws of physics alone show no preference for one over the other. It takes actual information to make a choice for the kind needed for the over-all design.

I also neglected to point out that for energy-efficient construction and functioning of life's various organic molecules, information in the form of specialized tools are needed. For example, tools called enzymes are designed to fit certain kinds of organic molecules. efficiently accessing the energy in them. For example, the enzyme lactase operates on lactose, pectase on pectin, lipase on glyceride, etc. The DNA information creates these tools to operate the machinery of life.

Monday, February 11, 2008

Why the Search for Extra-Terrestrial Intelligence (SETI)?

In a previous post, I described how I developed a computing methodology that I called 'multiprocessing', and how a similar, but more elaborate and expansive methodology appeared later on the Internet generally called 'distributed computing'. Distributed computing allows any researcher around the world to set up a research project, one that requires huge amounts of computing, so that volunteers worldwide can easily contribute some of their computer's time to work on the project. Volunteers can elect to contribute to multiple projects.

Just as operating systems such as Microsoft Windows or Linix allow multiple programs (also called applications) to share the resources of one computer, BOINC (Berkeley Open Infrastructure for Network Computing) allows multiple research projects to share the resources of multiple computers worldwide over the Internet. Currently there are 1,269,740 volunteers with 2,688,370 computers around the world that are connected by BOINC to hundreds of projects (as reported by boincstats.com).

http://setiathome.berkeley.edu/ is the leading project. About 61% of the volunteers run SETI@Home as one of their projects, and SETI@Home uses about 67% of the computers, generating 51% of the credits for work done. If the credits are proportional to the work done as they are supposed to be, than more than half of the BOINC computing is supporting the SETI@Home project.

Most of the other projects are biology research (mostly drug and disease research) or in the fields of climate, cosmology, and mathematics. But SETI is the Search for Extra-Terrestrial Intelligence. The SETI software downloads and analyzes radio telescope data, trying to find signs of extraterrestrial intelligence.

Most BOINC projects have web sites that provide reports on the progress of the research. For example. on PrimeGrid.com you can get reports on the prime numbers that have been found so far. So I went to http://setiathome.berkeley.edu/ to find out what progress has been made on SETI. All I found were discussions about 'progress' meaning the amount of searching that has been done, but nothing about progress finding anything. So I did a more general Google search for SETI progress, and found things like:

We've done a lot of searching ..

We're improving our methods ..

We've found a lot of exo-planets ..

We have detected minerals on Mars that on Earth protect the process of photosynthesis.

Not very impressive. I already knew that many planets orbiting other stars have been found, but nearly all of these are judged unable to support life, and they are too distant for detection of life anyway. And that last one is like finding a sharp knife in a house and concluding that a murder was possible. So I kept searching for SETI progress.

On the web site http://openseti.org/Read6.html I read:

At an August 6, 2004 symposium organized by The Planetary Society, titled The Significance of Negative SETI Results, leading SETI experts scratched their heads over the meaning of their failure to receive signals from Extraterrestrial Intelligence.

As a quick summary, this is what the panel of experts said:

There is no news.

We haven't done very much.

We should search vast numbers of stars...

We've thus far probed only a hundred-trillionth of the search space. We still need to cover the other 99,999,999,999,999 hundred trillionths before we can say there are no alien signals to be found.

We'll detect an alien communique within the next two decades.

Maybe within 100 or 200 years.

Maybe 50 or 100 years.

If they really want to contact us, they can.

Think serendipity. We should all be looking for little glitches in our data.

On the web site http://www.setileague.org/photos/hits.htm "What we've seen so far" I found:

Since the launch of The SETI League's Project Argus sky survey in April 1996, our members have detected a few interesting signals. They are depicted here, along with noteworthy results of some prior SETI experiments.

As a quick summary, this is the sort of "interesting signals" that they found:

"HAARP signals reflected not off the ionosphere, but rather off the lunar surface"

"the NASA Stardust spacecraft's re-entry into the Earth's atmosphere"

a possible black hole

"Hydrogen clouds drift[ing] around in the interstellar medium"

".. the signal was most likely terrestrial interference."

".. have not seen a signal like this."

".. Computer interference is suspected."

It is clear that the SETI project is a dismal failure, because if they found something, they would be loudly bragging about it, and even if they were on the track of a good possibility, they would be talking hopefully about it. So why is half of the BOINC processing resources still aimed at SETI after all these years? Why is the SETI project so popular in spite of its persistant failure to find anything significant?

The usual defense is that it is not impossible to find signs of extraterrestrial intelligence -- it is just a hard problem that needs more time. (This in spite of such a large-scale effort since 2002.) It is surely a matter of faith to keep believing, to keep hoping, in spite of such a huge failure.

The foundation of the search for extraterrestrial intelligence is the premise that life can arise spontaneously from non-life. Since no one has been able to demonstrate this in the laboratory (although many have tried), it is hoped that SETI will show that it has happened elsewhere.

Of course, the SETI faith denies the traditional faith in the Biblical account -- that God created all life. But, ironically, finding life elsewhere in the universe would not disprove the Biblical account, because the Bible tells of created life other than that in this earth. Although the Bible doesn't indicate whether these living creatures reside in this universe or another, it does tell of occasional visits to earth.

The more important issue is whether life arises spontaneously or whether life requires a creator. There are other scientific avenues for examining this issue that are more convincing than the SETI research. One avenue is based on information science -- see my blog articles:

Information From Randomness?

In The Beginning Was Information

Is Encoded Information an Essential Part of the Universe?

Another avenue is biology, which I may discuss another time.

Saturday, February 09, 2008

Multiprocessing, or Distributed Computing

When I worked for ITT, sometimes I investigated new methods of sending military radio signals to improve resistance to enemy interference. To evaluate these methods without needing to build new radios, I simulated the communication process with software. It took a huge amount of computer time to try many different design values and to average the results of many experiments.

To get more experimental results faster, I decided to take advantage of the facts that (1) the company had hundreds of computers connected by a local area network, and that (2) most of the time, these computers were either idle or working at only a fraction of full capacity. So I devised a system whereby the idle time of most of these computers could be used to work on my research project.

I organized my software so that the work could be done by small tasks needing from half an hour to two hours of computer time each; and so that the results of these tasks could be consolidated to complete the work. One part of the system doled out these tasks to computers that volunteered to do work. Another part collected, checked, and reported the results, and determined how much work each volunteer computer did.

To promote the project and solicit volunteers, I sent out emails and provided a web page. The emails explained how easy it was to volunteer (just one click), and how each volunteer could enable and disable the contribution of his computer whenever he wanted. The web page displayed project progress and volunteer contributions, and provided answers to frequently-asked questions. Since origami is one of my hobbies, I offered an origami prize for the biggest contributor.

I ran several projects this way, and usually got about 100 volunteers, with about 60 to 80 computers working at one time. A project generally ran for three to four weeks. So each project was about four or five years of computing for one computer.

Most volunteers let their computer run the project overnight, and some would volunteer other computers when colleagues left on vacation or a business trip. The 'multiprocessing' (as I called it) had to shut down every Friday night, however, because that was when the entire computer network was shut down for data backup. I fixed it so that the multiprocessing would automatically restart on Saturday mornings.

I created my 'multiprocessing' system in 1998 and used it for a few years. Another division of ITT that wanted to do something similar for evaluation of weather satellite data processing asked my advice to set up their system.

But now this kind of computing is done world-wide on the Internet on a much larger scale, and it's now called 'distributed computing'. United Devices established their distributed computing system in 2001. University of California, Berkeley launched BOINC (Berkeley Open Infrastructure for Network Computing) in 2003. BOINC has over 540,000 active computers worldwide working on hundreds of projects.

Now my computer runs BOINC in its spare time, supporting four projects:

PrimeGrid: prime number research

Cosmology at Home: cosmological research

Rosetta at Home: protein folding research

World Community Grid: drug research

Most BOINC projects are non-profit, and there is no monetary compensation to those who volunteer their computer's run-time. But all BOINC projects issue credits as a kind of thank-you that is proportional to the amount of work contributed. And there are web sites that provide statistics and graphics that summarize a contributor's credits and ranking, like this: