By Paul R. Martin

essay156

4/25/11

At times I have expressed my doubts about the ability of Darwinian Evolution to explain all of life. One of my earliest doubts was that I didn't think there was enough time. I had a vague idea about how to calculate the required time and to compare it with the time available, but I never did develop a case. Other doubts stemmed from the sizable gaps in the theory, such as the origin of life and the development of an individual organism, which aren't (yet) explained by the theory. I have also agreed with the arguments presented by Michael J. Behe in "Darwin's Black Box". I have not been impressed by Richard Dawkins.

And then there is the argument by counterexample. I think this argument should be compelling, but people don't seem to be interested enough even to consider it. The counterexample is that all animals, not just all species, but all individuals, sleep, not just occasionally, but regularly and for a sizeable part of each day. According to evolution, any species that regularly lost consciousness like that, and was thus vulnerable to enemies and unable to fight, flee, feed, or procreate, should have been selected out and gone extinct long ago. I won't continue this argument here because it would take us off the track. What I want to talk about in this essay is an argument from design, sort of an extension of Paley's and a little different tack from Behe's.

I'll call my argument the Analog-Digital Argument (ADA). In the light of all those other sources of doubt, it occurs to me that this is maybe the simplest and most compelling argument of them all.

The crux of the argument is that mind is required in order to produce a digital system, and we find digital systems in living organisms. Therefore mind was required to produce life.

To start with, let me explain the distinction between analog and digital systems. Most of the physical world behaves as an analog system. That is, the actions of the parts are determined strictly by physical laws and initial conditions. The planets and moons in the solar system proceeding along their orbital paths are examples of analog systems. The word 'analog' is used because the actual physical system has an analog in a mathematical system of laws and initial conditions, such as Kepler's or Newton's, or Einstein's.

The important feature of an analog system is that the actions proceed strictly according to the laws of nature without any involvement of or interference from any mind. We will ignore any possible mental involvement in setting up the initial conditions, or in formulating the laws of nature in the first place. A science experiment is an analog system only after the apparatus is all set up and the experiment is started and left alone.

Digital systems are different from analog systems in one key respect: digital systems contain symbolic information which has an effect on the behavior of the system. There is a lot of information present in an analog system, such as the positions of particles, the strengths of forces, etc. but none of this information is symbolic. A ten-kilogram stone "contains" or "carries around with it" the information that it weighs ten kilograms. That is analog information. By contrast, this string of thirty characters, 'The stone weighs 10 kilograms', contains the same information, but in this case the information is digital. To be symbolic, the information must be represented in some physical form, e.g. a string of letters, which has nothing to do with the physical system the information is about.

Digital information is commonly called "encoded information". That is because the information is represented by a code which can be thought of as a made-up arbitrary representation of the "real" information. Language is nothing but coded, or digital, information. The five-letter string, 'horse' is a code word representing a big familiar animal, but there is little resemblance between the string of letters and the animal itself.

The important question here is, exactly how is the correspondence between these code words and the things they represent made? Who or what dreams up and establishes the code? The answer is that some mind or minds established the code. For languages, this is obviously an extremely long and complex process, but in principle, it is easy to conclude that it was a series of human mental activities that developed each of our languages.

But let's take a much simpler example, that of Morse Code. Here is a code that was deliberately chosen and established by one person at one time and which was used for many decades to encode (secondarily) many millions of messages sent around the world. How and why did the letter 'N' get to be encoded as a dash followed by a dot? Did Sam Morse have some reason for choosing that pattern? He may have, but whatever his reasons, they don't affect the use of Morse Code in sending messages.

Now it is true that most use of Morse Code is to transfer information from one mind to another. With the use of Teletypewriters, or computers, the coded messages might be sent or received by physical, non-mental, systems, but this is not of interest to us now. We are not interested in the minds as senders or receivers. What we are interested in is the mind that originated the code in the first place. We are interested in the choices Morse himself made in establishing the code.

The assertion in this argument is that when we find a system that uses encoded, or symbolic, information, then a mind was necessary at the beginning in order to establish the code. This should be obvious because of two facts. First, there is no physical reason for the particular correspondence between a symbol and what it represents, and secondly, there must be consistent agreement by parts of the system on what those correspondences are. In other words, the code was arbitrarily chosen and the code is instrumental in the functioning of the system.

Since this might be a little too complicated, let me use one other example of a digital system, a light bulb controlled by a switch on the wall. The symbolic information in this system is the position of the lever on the switch. If the lever is up, the light will be on. If the lever is down, the light will be off. There is nothing in the laws of nature that demand that correspondence. The correspondence was established by the manufacturer of the switch and its installation by the electrician. Together the two mental acts, of designing the switch and of installing the switch, determine how the physical world will behave in the presence of information encoded in the position of the switch lever. The behavior of the physical world follows strict physical laws, with no involvement of mind. The actual movement of the switch lever may or may not involve a mind. But the design of the system, in particular the choice of what position of the switch will mean what, necessarily required a mind in the designer and installer of the switch.

The key point here is that if digital, or symbolic, information is instrumental in the function of an otherwise analog physical system, then symbols must be associated with physical things. These associations require the decisions and choices of a mind to determine what is associated with what. So, mind is required in order to produce a digital system.

Next we turn to a familiar but absolutely marvelous digital system present in all known living organisms. It is the protein production system in living cells. As we well know, proteins are produced in cells by stringing amino acid groups together like strings of pearls. There are 20 different amino acid groups used by the cells and they are chosen in a sequence that is determined by information encoded in DNA (actually RNA but the information came from DNA). We won't get into the details of the mechanism of protein synthesis. That would be like getting into the details of the traffic in Morse Code messages around the world. We are going to focus on the very interface between the digital part of the system, the code, and the analog part of the system, the physical molecules which embody the code (like ink patterns embodying letters) and the physical molecules reacting to the coded patterns, or information about what amino acid group to take next.

We are going to look in detail at how the DNA code is established. That will be like looking at how and why Morse decided on his code, and how and why the code was accepted the way it was by all the many telegraph operators. In Morse's case, he chose the code strictly as a mental activity. He used his mind to do it. The code was accepted by everyone else simply because it wouldn't work as a communication code if they didn't.

We know that the DNA code is not binary, using the symbols 0 and 1, but quaternary, using symbols A, C, T, and G. (I am going to simplify and ignore U, which is used in RNA instead of G.). Similar to a binary byte as used in our computers, protein synthesis uses a "byte" consisting of a group of three of the symbols A, C, T, and G. This group, or "byte" is called a codon. A gene, which is a consecutive string of codons along the DNA strand, contains the information necessary to assemble one specific protein molecule. Each codon specifies a specific amino acid group, and the sequence of codons specifies the sequence of amino acid groups.

What we want to zero in on here is the association of a specific codon pattern with its specific amino acid group. The codon, being a string, for example 'ATG', is digital. The associated amino acid group is a chemical molecule which simply obeys the laws of physics and chemistry. It is analog. This association, or really this set of associations (there are 64 of them), is the focal point of what we want to understand. How is the digital-analog association between codon and molecule made? It's like asking how were the dot-dash combinations assigned to alphabetic letters in Morse Code.

The actual code itself is not important here. It is a little complicated, with two or more codons usually coding for the same amino acid, and with some codons serving as "punctuation" and not coding for any amino acid. (The amino acid Tryptophan, coded by TGG, and Methionine, coded by ATG are the only ones with only one code.) For our purposes we can simply think of a group of three letters like CTT, or GAT, as picking out, or being associated with exactly one of the 20 amino acids.

Now let's look at the mechanism of using the coded information from the DNA to choose the right amino acid to add to the growing protein molecule. That is done by a huge molecule, or group of molecules, called a ribosome. The ribosome reads a strip of RNA, which is a copy of the gene from the DNA, and advances along this strip three letters, or one codon, at a time. When a new codon appears on the strip, it is exposed to the soup of molecules floating around in the cell on the outside of the ribosome. Let's say that the codon contains TGG. This is digital information that means "the next amino acid to grab is Tryptophan." What happens next is amazing (as if any of this is short of amazing).

Floating around in the cell soup are molecules of the 20 amino acids, each one attached to a molecule of tRNA. That stands for Transfer RNA and it is these molecules that we want to concentrate on. They are the physical connection between the digital and analog information in the system.

There is roughly one specific type of tRNA for each code combination, so there are about 60 different types (some combinations are used for punctuation which we will ignore). Each one has a specific amino acid attached to one end, and it has a codon of three letters exposed on the other end. The codon is the complement of the code for the amino acid it is connected to. That is, a tRNA for Tryptophan will have the codon ACC. That is because A and T stick together and C and G stick together. So when the ACC end of the Tryptophan tRNA happens to bump up against the TGG codon being presented by the ribosome, it will stick and the ribosome has thereby grabbed the right amino acid. No other combination will stick. The ribosome then proceeds to connect the Tryptophan to the growing string of amino acids. It then cuts the tRNA strip loose and sends it back out into the soup, and then clicks along to the next codon on the RNA strip. But let's look at that tRNA strip in more detail.

We can think of RNA molecules in a cell like 2x4s on a construction site. On a construction site, 2x4s are cheap handy parts that can be used for many different purposes. Similarly, RNA is used in the cell for many different purposes. Most of the molecular building blocks in organisms are made of protein. But a lot of them are made of RNA. Protein molecules are big and complicated by comparison to RNA. Proteins are made by the complicated process using ribosomes as we have discussed. RNA, on the other hand, is produced by a much simpler process. To make a strip of RNA, the double helix of DNA unzips and opens up for a section. This means the rungs of the DNA consisting of pairs of A-T and C-G are broken apart exposing half of the rung on each side like the two sides of an open zipper. What happens next is that individual A's, T's, C's, and G's floating around in the soup bump up against these exposed edges. When an A bumps into a T, it sticks. Similarly with C's and G's. Pretty soon, both sides of the open zipper are filled back up. These peel off and are the new RNA molecules. (We'll ignore the complexity of the two RNA strips being different ). The point is that the cell can make RNA strips to order simply by having the pattern, or information, for the RNA encoded in a length of DNA and then having that length replicated. It's like having a mill producing 2x4s right on the job site.

Next, let's look at the structure of the tRNA molecule. It looks sort of like a twisted rubber band that forms a scarecrow looking structure. There is a pumpkin shaped head, two outstretched arms with catcher's mitts on the hands, and two skinny legs taped together with one leg shorter than the other. That's the image you should have in mind when we go through this. Bear in mind that this entire molecule is made of nothing but A's, T's, C's, and G's attached to a spiral backbone strand made of sugar. The sequence of these nucleotides (that's what the A's etc. are called) is important for several reasons. One reason is that to make and keep the shape of the scarecrow, the strip must stick to itself on sections like the arms. The strip goes over the top of the arm, for example, then loops around to form the baseball mitt, and then back along the underside of the arm. Here it sticks to the upper part of the arm, by As sticking to Ts and Gs sticking to Cs, and that holds the thing together. Very clever.

There are a couple of even more important reasons why the sequence is important. The first is a particular codon right on the top of the pumpkin head. This codon is the one that this particular tRNA codes for. That is, if this tRNA codes for, and carries a Tryptophan molecule, then there will be an ACC on the top of the pumpkin head.

The second important sequence of nucleotides in the tRNA is on the longer of the two legs. The chemical structure of this string of nucleotides is such that it sticks onto a certain place on the exact amino acid that matches the code in its pumpkin head. And, this sequence sticks to none of the other amino acids, nor does it stick to the correct one at any but the correct site on the molecule. Truly amazing.

So what we have is 60 different kinds of tRNA, each one grabbing and holding its specific amino acid, and in due time, getting snagged by a ribosome which separates the tRNA and sends it back into the soup to get another amino acid.

To make these 60 different types of tRNA there is for each of the 60, at least one section of the DNA that has the pattern for making it. Now let's think about the two important "business ends" of the tRNA. The pumpkin head contains the digital information identifying the particular amino acid. ACC for example in the case of Tryptophan. And the other important end is the long leg which actually binds chemically with the real Tryptophan molecule. The pumpkin head is digital and the leg is analog. This molecule of tRNA makes the association and it is the only thing that makes the association. It is the digital-analog link. It is equivalent to one entry in Samuel Morse's chart linking letters with patterns of dots and dashes.

Now, to help illustrate how this all works, let's compare the action of a ribosome with the action of a belt-fed machine gun. There are a lot of similarities.

The purpose of a ribosome is to spit out protein molecules. The purpose of a machine gun is to spit out bullets. The machine gun takes in a belt of ammunition one cartridge at a time. It spits out the bullet, discards the cartridge casing and belt link, and then advances to the next cartridge to do it all over again.

The ribosome takes in a belt of RNA (this is not the tRNA we have been talking about) which specifies which tRNA to grab from the soup. The tRNA is like the cartridge and belt link but they are not linked together to start with. When the ribosome grabs the right tRNA, the left hand catcher's mitt grabs the right hand catcher's mitt of the previous tRNA and forms a link on a chain. This chain is similar to the ammunition chain of the machine gun. It travels a short way down the ribosome until the amino acid group gets hooked up with the previous amino acid group, and then the tRNA is broken loose and ejected sort of like the cartridge casing and the belt link.

Now let's compare a tRNA molecule to a cartridge. The business end of the cartridge is the bullet and its charge of gunpowder. The business end of the tRNA is the amino acid molecule. At the other end of the cartridge is the primer. At the other end of the tRNA is the codon on top of the pumpkin head. The codon is digital information specifying what amino acid is attached. The primer could be thought of as digital information too, in a way, but it does not specify whether there is a tracer or an armor piercing bullet attached. Instead it relays information about exactly when the bullet is to leave the chamber. The decision is really made back in the firing pin mechanism, but when the firing pin lets the primer know that it is time, the primer sets the powder off and the bullet is on its way. It's a stretch to consider that as digital information, but it doesn't matter. This is an inexact analogy which is only meant to give you something to visualize.

Now, finally, we are ready to ask the really important question. How did the assignments in the genetic code get made? What is the equivalent of Samuel F.B. Morse assigning dot and dash patterns to letters? The answer is easy if some mind made those assignments. It is simply a matter of filling out that 64 position grid. For each of the 64 combinations of A, T, C, and G, choose one of the 20 amino acids. Just make sure you use each amino acid at least once. I suppose this could be done by some mindless mechanism, but I don't know where that grid is, or was, nor can I imagine how any physical process could make use of it if it did exist. After all, the filled out grid is digital and its representation has nothing to do with any physical processes.

What about making the tRNA molecules themselves after the code has been decided on? Well, what you need are about 60 different sections of DNA each one containing the sequence of nucleotides whose complement will fold up into one of those pumpkin-headed scarecrow configurations. That part wouldn't be too hard because the same sequence would serve to make the overall scarecrow structure for all 60.

But to get it right, halfway down each of those sections needs to be the specific three letter codon that is specified in the assignment table. And that is different in each of the 60. The whole section is made of nucleotides (A's, T's, C's, and G's) but these three are very special. They contain the digital information that identifies this particular tRNA molecule and distinguishes it from the other 59.

In addition to these special letters in the middle, there is a special sequence at the end of what will become the longer leg of the scarecrow. This needs to be the specific sequence of nucleotides that will form the physical binding site for the specific amino acid that matches the codon in the assignment table. Getting those two sequences right seems to be tricky without a mind.

The difficulty is not just in getting the codon and the tail to match up according to the assignment table, but to get 60 different ones right at the same time. "Right" meaning that the codon and the binding site are consistent with an arbitrary assignment of the 60 or so combinations.

The problem for evolution is to explain how this comes about by a mindless process. How does the information in those sixty different stretches of DNA get established without a mind?