In my first post on Meyer’s Signature in the Cell I discussed information theory, and claimed that the cell exhibits functional information—information that cannot be explained in terms of the physical machinery of the cell.  In this post I want to provide some background on the machinery and inner workings of the cell to provide evidence for the claim that the cell contains complex specified information (functional information), and explain why biologists have come to recognize that DNA stores and transmits “genetic information,” contains a “genetic blueprint” with “assembly instructions,” and expresses a “digital code.” 

The two most basic components of the cell are DNA and proteins.  DNA is made up of a 4 character chemical alphabet: adenine, thymine, guanine, cytosine (these are called nucleotides).  These nucleotides always appear in complimentary pairs: adenine is paired with thymine, and guanine is paired with cytosine. 

Proteins—the workhorses of the cell—are composed of amino acids.  The cell contains 20 different kinds of amino acids.  To create functional proteins, these amino acids must be sequenced together in a specific order, forming a “chain” of amino acids (proteins come in varying lengths, with shorter proteins consisting of ~100 amino acids, most proteins consisting of several hundred, and some as large as 34,350 [titin]).  While there are a number of ways in which amino acids can be sequenced, the vast majority of combinations are functionless.  They sequence must be specified if the protein is to have function (functionality also requires the protein to be folded into a particular shape).

In 1958 Francis Crick proposed that there exists a relationship between DNA and proteins: DNA builds proteins.  Crick suggested that the sequence of nucleotide bases along the spine of the DNA molecule determines the arrangement of amino acids in proteins.  But how does a 4 character genetic alphabet determine the sequence of a 20 character alphabet?  Crick said it must utilize a digital code to translate one biological “language” into another.  He postulated the existence of several biological entities he thought would be necessary to explain how genetic information could be converted into proteins, all without any observational evidence.  Within five years, not only was Crick’s theory of a digital code within the cell proven correct, but the biological entities he postulated were discovered as well.  What exactly did biologists discover?

The process of protein production involves unwinding and transcribing a portion of the DNA molecule.  RNA polymerase is responsible for unwinding the section of DNA that needs to be copied, and then carrying out the transcription process.  RNA polymerase attaches itself to the binding site of the gene—a site that specifies where the gene begins.  This is necessary to prevent RNA polymerase from beginning its transcription in the middle or end of the gene, and thus missing important genetic information.  Then, the RNA polymerase directs and positions RNA nucleotides present in the cell’s nucleus to pair with their complimentary partner on the DNA template.  As the RNA nucleotides pair with the DNA nucleotides, the RNA polymerase binds the RNA nucleotides together to form a long chain called Messenger RNA (mRNA).  The finished product is a strand of mRNA that is the exact compliment of the DNA.

mRNA is then is transported outside the cell nucleus to the ribosome to undergo translation to create a protein.  Since mRNA copies sections of DNA that code for proteins as well as sections that don’t (introns), however, the mRNA must be edited prior to its arrival at the ribosome.  Enzymes in the cell carry out the editing process by splicing the mRNA, cutting out the non-coding regions, and then reassemble the coding regions in their proper order.  Once editing is complete, mRNA enters the ribosome.

Once docked inside the ribosome, transfer RNA (tRNA) shows up to carry out the process of translating the mRNA sequence to create a protein.  tRNA molecules are short strings of (ribo)nucleotides[1] looped together to form a cross-like shape.  On one end of the cross there is a sequence of three ribonucleotides (called an anti-codon) that allows tRNA to bind to mRNA, and on the other end is an amino acid.  There are many different types of tRNA molecules (31-61 depending on the cell), each of which carries a single, specific amino acid.[2]  tRNA molecules can be thought of as the personal chauffeurs and matchmakers of amino acids, transporting them to the ribosome and linking them together with other amino acids to form proteins. 

Once a tRNA molecule is found whose anti-codon corresponds to the first three nucleotides (called a codon) in the mRNA sequence, it attaches itself to the beginning of the mRNA molecule (the mRNA codon pairs with the tRNA anti-codon).  This is followed by the arrival of a second tRNA molecule.  It attaches itself to the next triplet of mRNA nucleotide sequences.  Once attached, the amino acid it carries will bond to the first amino acid,[3] linking them together like box cars of a train.  Once bonded, the tRNA molecule drops off, leaving its amino acid behind.  This is followed by the arrival of yet another tRNA, and the process continues until the entire strand of mRNA is translated by tRNA, producing a chain of amino acids (protein). If you are not a biologist, this process may be hard to imagine. A wonderful video animation of the process can be viewed at www.signatureinthecell.com (lower right corner).

This simplified version of protein production presents us with a window into the complexity of the cell.  Life requires a great number of interacting and matching parts, as well as biological information:

  • Phosphate, ribose, oxygen, hydrogen, and nucleotide bases to form DNA
  • A complex and specified arrangement of nucleotides to form biological information
  • RNA polymerase to unwind and transcribe that genetic information into mRNA
  • A transport system to move mRNA from the nucleus to the ribosome
  • Enzymes to edit the mRNA
  • Ribosomes to synthesize proteins
  • 20 different amino acids to construct proteins
  • At least 20 different kinds of tRNA to translate DNA into proteins
  • 20 aminoacyl-tRNA syntheases to bind amino acids to tRNA
  • Peptidyl transferase to bind the amino acids together in the ribosome

It also presents us with a chicken-and-egg dilemma.  As Jacque Monod wrote in 1971, “The [DNA] code is meaningless unless translated.  The modern cell’s translating machinery consists of at least fifty macromolecular components which are themselves coded in DNA: the code cannot be translated otherwise than by the products of translation”[4] (note, we now know that more than 100 proteins are required).  David Goodsell wrote that this “is one of the unanswered riddles of biochemistry: which came first, proteins or protein synthesis?  If proteins are needed to make proteins, how did the whole thing get started?”[5]

Biologists and origin of life scientists, then, must explain at least four things: (1) the origin of the system for storing and encoding digital information; (2) the origin of the digital information itself; (3) the origin of the components necessary for unwinding, transcribing, editing, transporting, and translating the information; (4) the origin of the functional interdependence of the various parts required for processing this information.

How is the origin of these things to be explained?  Before we evaluate various proposals, we need to take a look at how scientists who study the past go about their work; specifically, the method by which they determine what it was in the past that caused the effects we observe in the present. 

[1]Between 73-93, although I’ve read 74-94 as well.

[2]An enzyme called “aminoacyl-tRNA syntheases” is responsible for attaching amino acids to tRNA molecules.  There are 20 different enzymes, one for each of the twenty different kinds of amino acids. 

[3]A protein in the ribosome called peptidyl transferase is responsible for binding the amino acids together.

[4]Jacques Monod, Chance and Necessity, 143 in Meyer, 133-4.

[5]David Goodsell, The Machinery of Life, 45 in Meyer, 134.