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 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 you can get reports on the prime numbers that have been found so far. So I went to 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 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 "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: