14. The DNA Enigma

by Blake

i.  The Biology

“The problem of the origin of life is clearly basically the equivalent to the problem of the origin of biological information.” – Bernd-Olaf Kuppers

DNA is found in every cell of the human body.  It has a double helix shape which is like a twisted ladder.  The rungs of that ladder are composed of pairs of nucleotide bases of which there are four types labeled A, T, C and G (A and T always pair together, and C and G always pair together).

In a process called transcription, the order of the nucleotide bases along the DNA molecule is transcribed onto an RNA molecule called mRNA (messenger RNA).  The way this happens is DNA unzips into its component strands while a single mRNA strand comes alongside and has one of the two DNA strands “transcribe” its bases onto the mRNA strand by pairing complementary base pairs.  Free nucleotide bases within the cell attach to the mRNA strand in an order that is dictated by the bases along the parallel DNA strand.  This process is extremely accurate in preserving the order of the original sequence of bases in the DNA molecule.

The mRNA which is now carrying the ordered string of bases, travels to a ribosome within the cell.  The mRNA strand then runs through the ribosome like ticker tape and the bases are “read” into groups of three, called codons.

tRNA (transfer RNA) is an RNA strand folded into a cloverleaf shape.  At one end is an anti-codon which is composed of three nucleotide bases and at the other end is a particular amino acid.  (There are 20 different types of amino acids).  The precise anti-codon of the tRNA match up with the complementary codons along the mRNA.  The amino acids at the other end of the tRNA connect to other amino acids and the tRNA then moves away, leaving its amino acid in the chain.  It becomes like an assembly line with the tRNA sweeping in, matching up codons, allowing amino acids to connect and then moving away.

As this goes on, a chain of amino acids is forming and the order of the amino acids causes the chain to fold into specific complex shapes.  These shapes are proteins.  Since the specialized function of each protein is determined by its shape, it is imperative that their component amino acids connect in the right order to form just the right protein.  If the amino acids do not connect in the correct order, the chain will not fold properly and will become useless to the cell.

Protein is a key component to life.  There are thousands of different kinds of proteins in the cell with all different functions.  Some catalyze metabolic reactions, some are involved in the transcription of DNA, some transport other molecules throughout the cell.  Proteins are incredibly complex, three-dimensional structures and their function is determined by their structure.

For example, there is one type of protein called a histone which is shaped to act as a perfectly sized and shaped spool upon which the DNA strand can wind around for compaction.  Cells contain almost 6 feet of DNA, but these histones greatly compact the DNA strands by spooling them into perfectly notched grooves on their surface that exactly fit the shape of the coiled DNA strand.  The irregularities in the DNA cord exactly match the irregularities in the notched grooves, making its precise shape integral to its ability to do its job.  These histones were formed by the process described above: each amino acid connecting in strict order until they fold into the spool shape (precise notches and all) necessary for the histone to do its job.  Sixty years ago, scientists believed proteins were ambiguous lumps that did simple jobs, but have since learned that they exhibit incredible complexity.  Their very specific structure allows them to do very specific jobs.  These proteins are how a cell lives which in turn is how all life lives.

This process of forming a protein all starts with the order of the pairs of bases along the rungs of the DNA molecule.  It is important to be clear that the order we observe in today’s DNA is no mystery.  Today’s DNA is sequenced in its particular order because it inherited its order from prior cells, and in turn prior life forms (previous generations) and in turn, according to evolution, prior species.  Life began on our planet three and a half billion years ago.  The 3 billion base pairs in a DNA molecule, in perfect order must have somehow begun.  This is the mystery.  We don’t know how this happened.  Even the simplest life requires 250 separate proteins to survive which would involve many base pairs in sequential order for each of these 250 individual proteins to form.  The ordering of these long arrangements of bases that provide instructions to build even a single protein is a mystery that continues to confound the scientific establishment.  It is our monolith – an inexplicable entity of great design that we find among the natural world.

But the mystery alone is not the reason for the intelligent design theory.  This is not an argument from ignorance, concluding “God” because of a lack of any other explanation.  Instead, the information itself is examined and understood to be of a particular type that can tell us something about its origins.

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Below is a video showing the process of transcription (DNA to RNA).

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Below is a video showing the process of translation (RNA to Protein).

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Below is a diagram of the process of gene expression outlined above.  It follows what Francis Crick referred to as the “Central Dogma” of Molecular Biology: information passes from DNA to RNA, and then from RNA to Proteins.

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ii.  The Information

“DNA is like a computer program but far, far more advanced than any software ever created.” – Bill Gates

There is clearly information within DNA.  The question is what type and can its type tell us anything about its origins.  Stephen Meyer, in his book, Signature in the Cell, compares the process of gene expression to the manufacturing process that goes on when engineers at places like Boeing use CAD-CAM (computer aided design and manufacture) software to make precise parts for airplanes.  This process uses digitally coded information as instructions to manufacture the parts with extreme precision.  Just like the information in DNA must be transcribed onto RNA before the proteins can be made, there is an analogous step within the CAD-CAM process where the digital information in the CAD software is changed into another type of machine code before directing the manufacture of the parts.  One distinction Meyer makes between the CAD-CAM process and gene expression is that the process of gene expression not only produces the “machines” that are proteins, but it also reproduces itself.

Consider three sequences of letters:

1.  CATCATCATCATCAT

2.  IBVNEMDKGJRMLSE

3.  TAKEOUTTHETRASH

Sequence (1) follows a specific pattern but contains very little meaning.  If you wanted to compress the string, you could write, “REPEATCAT5X” and the exact same message would be conveyed using 11 characters instead of 15.  Its regular, repetitive pattern is what allows it to be compressed so efficiently.  This property of compressibility is related to another property of information: complexity.  The more compressible a sequence is, the less complex the sequence is.  Patterns like what we see in (1) are found throughout the natural world because the natural world follows the order found in the laws of science.

Sequence (2) appears to be random and lack any specificity.  Random sequences are the most complex sequences there are since they cannot be compressed at all.  The most compressed way to write a random sequence is to simply write that sequence itself.  Random sequences are incompressible because there is no pattern at all to their order.  Just like we find patterns within the natural world, we also find randomness, for example the way seedlings fall onto the ground or the distribution of stars in our sky.

You can view the property of complexity as a spectrum, with sequences of low complexity such as (1) at one end of the spectrum and sequences with high complexity such as (2) at the other end.  (1) has the property of specificity but not complexity.  (2) has the property  of complexity but not specificity.

Sequence (3) is different.  Sequence (3) contains a certain amount of specificity since it clearly follows a pattern (the English language), but it also contains a certain amount of complexity since it can only be compressed to a moderate level (long strings of written text can be compressed by about 50%).  Sequence (3), therefore, lies somewhere in the middle of the complexity spectrum.  But sequence (3) is special for another reason: it has meaning.  It conveys a message – in this case, a command.  Upon reading the three sequences it is only sequence (3) that has a message to understand.  This type of information that falls roughly in the middle of the complexity spectrum is also special in that we never find this type of information without a mind behind it.  It is nowhere to be found in the nonhuman, natural world.  This type of information is imbued with intention and has an intentional mind as its source wherever we observe it.  We see this type of information in written text, in paintings, signs, spoken language, ancient hieroglyphics, integrated circuits, machine codes, computer hardware and software – but nowhere in nature.  This is repeatedly confirmed and never disconfirmed.

To an alien civilization who didn’t speak English none of the three sequences above would have meaning.  If these aliens were studying humans as a species, though, they would find that we behave differently when we read sequence (3) versus when we read  (1) or (2).  When we read sequence (3), we do something specific each time that we read it.  We do the same thing each time we read it – we take out the trash.

This is similar to what we experience when we look into the process of gene expression.  The arrangement of the base pairs appears random to us (just as sequence (3) appears random to the aliens).  But what we find is that their arrangement causes a rich array of specific actions to occur: the manufacture of all the diverse proteins that are necessary for the cell.

As another analogy, consider three factories that are each manufacturing certain articles.  Factory one produces well defined cubes, one after the other.  Factory two produces amorphous gobbledygook – random parts thrown together.  Factory three, though, appears special because out of factory three comes all sorts of fine, individual sculptures: a sculpture of a woman, a sculpture of a tree, a bust of a man and so on.  Inside factory three you would not see a random process going on as you would in factory two.  Nor would you see a set rule being followed as you would in factory one.  What you would see is a sculptor creating different forms based upon his own intentions and will.  This is apparent because neither a random process nor a process governed by rules can produce the originals that he comes up with.

Some have argued that there are, in fact, examples of this type of information within nature.  Salt crystals are a counter example sometimes given.  Salt crystals are extremely intricate forms that have a highly repetitive structure of sodium and chlorine atoms arranged in a three-dimensional grid; a pattern in which one type of atom always has six of the other type surrounding it.  While this structure has a highly impressive order to it, it is still just a pattern with relatively low complexity.  It was formed following the simple rules of Chemistry.  It has low complexity because you could compress its pattern into a simple direction such as: “surround each type of atom with six of the same other type of atom” and the structure would be duplicated from this simple algorithm.

You can see how different the information within a salt crystal is from something like Tolstoy’s War and Peace.  The book, War and Peace, exhibits an irregular and non-repeating design that comes from a mind which has intention.  Given the patterns within the English language, War and Peace can be compressed to a certain degree, but not nearly so much as if you were to follow a simple algorithm like: repeat “WARPEACE” for the equivalent number of characters that the book contains.  While the text of  War and Peace follows the common patterns of language, it does not follow any algorithm, nor is it random.

Regardless of the particular patterns that naturally emerge due to the trends we find in all language, the fact remains that the ideas behind the patterned language in War and Peace are at the whim of Leo Tolstoy.  We don’t know what idea Tolstoy will convey next – say on page 568 – because there is no rule for what Tolstoy will decide to say.  The ideas come from a mind and so although they are not random, they are also irregular and non-repeating, indescribable by any algorithm.  The sequence of bases along the DNA molecule are like this.

Skeptics have claimed it is biased to call the resulting protein output “significant.”  They say that it is only “subjectively significant” since it is the source of our own life.  If the bases were sequenced differently, they say, it would just be an alternate structure that is built.  But compare the actual proteins made to these other possible outputs whose sequences are misordered and you see a clear difference in form.  There is an obvious difference between an amorphous “pile of parts” versus a structured, working thing.  One can objectively be called “significant” and the other not.

Intelligent design has only really begun to be accepted as a possible theory within the last twenty years.  The earliest theory for the origin of life, of course, was chance.  This was before scientists understood just how complex proteins and protein formation are.  It is now estimated that for the origin of life to be just a chance accident, the probability would be somewhere around 1 chance in 1041,000.

Another possible explanation claims that perhaps the nucleotide bases in DNA somehow “self organized” according to some undiscovered natural law.  After all, there are other cases within nature (like the salt crystal example cited earlier) where laws of nature produce a certain kind of order and self organization.  In Signature in the Cell, Stephen Meyer gives the example of a vortex that forms when water drains.  The ordered shape that the water forms as it drains is due to gravity and the Coriolis force and other physical forces.  It is claimed that maybe certain underlying attractions cause the nucleotides of DNA to fall into the particular order that they do.  If the nucleotide “A” has a certain proclivity to be next to nucleotide “G” along the DNA strand, then maybe this underlying pattern could explain the sequence of the bases.  This seems reasonable at first look, but to understand the impossibility of this solution, you must examine the structure of the DNA molecule itself.  The nucleotide bases are attached to the sugar-phosphate backbone, but not to each other.  Therefore, there is nothing between them that places them in order.  Meyer makes the analogy of a magnetic board with magnetic letters.  When you arrange a word on it, you can arrange any word you choose because the letters are not connected to each other, but are only connected to the board.  Just like magnetic letters on the magnetic board, the nucleotides can be connected in any way since they are only connected onto the sugar phosphate backbone and not to each other.  Beyond the reason cited here that involves the structural mechanics of DNA, there is a more overarching problem with this alternative explanation: if there was some underlying tendency causing certain nucleotides to be arranged next to certain other nucleotides, this would only result in an information-poor pattern that was merely repetitive rather than actually conveying information.  Again, it would be like trying to write a rich and brilliant novel using a repeating algorithm.

In the final analysis, each theory lacks in one respect where the intelligent design theory does not: they cannot explain the origin of the information.  Intelligent design theory contends that the reason the scientific establishment has continued to be confounded by this problem is because they search for a non-mind cause to this information type that we only ever see come from a mind.

While intelligent design does claim that some kind of intelligence is behind the design of the first life, it makes no mention of what type of intelligence it is.  Since Intelligent Design fits well with the beliefs of Christianity, many of its proponents are Christian, but not all.  Many secular philosophers have been impressed by the criticisms that the intelligent design movement has had against the orthodox reductive view of the origin of life.  Thomas Nagel is a renowned atheist philosopher and while he does not subscribe to intelligent design, he does agree with its powerful criticisms of the orthodox scientific world view.  He actually rocked the boat a bit a few years ago when he recommended Meyer’s book, The Signature In the Cell to the “2009 Books of the Year” supplement for The Times.  Nagel later wrote in his own book, Mind and Cosmos:

“Even though writers like Michael Behe and Stephen Meyer are motivated at least in part by their religious beliefs, the empirical arguments they offer against the likelihood that the origin of life and its evolutionary history can be fully explained by physics and chemistry are of great interest in themselves….I believe the defenders of intelligent design deserve our gratitude for challenging a scientific world view that owes some of the passion displayed by its adherents precisely to the fact that it is thought to liberate us from religion.”

David Berlinski, a respected philosopher, is another non-Christian who finds some truth in the arguments of intelligent design.  In spite of being agnostic, he is a senior fellow of the Discovery Institute, a think tank that advocates intelligent design.  He similarly finds serious problems with the “orthodox reductive view” of the origin of life.

Francis Crick, the co-discoverer of DNA (and a staunch atheist) has even gone so far as to claim that perhaps the information of the first life on Earth came from intelligent beings in outer space in a process he called “directed panspermia.”  He said in 1980, “An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.”

Next to the origin of the universe, the origin of life is the ultimate mystery and this question leads right to the edge of where science operates.  In fact, you could say it bumps its head against the far wall.  This wall represents a boundary between science and religion and philosophy.  Going further, as the evidence leads us, makes many people uncomfortable.  This has resulted in a court case over whether Intelligent Design should even be mentioned in schools as a proposed theory.  It has also caused editors of peer reviewed journals to be fired for publishing papers on intelligent design.  Many opponents of intelligent design don’t just disagree with it – they actively seek to silence it from even being considered in the public domain.

In 1967, two scientists observed consistent, uniform pulses that came from the same location in the sky.  Jocelyn Bell Burnell, one of the scientists later said, “We did not really believe that we had picked up signals from another civilization, but obviously the idea had crossed our minds and we had not proof that it was an entirely natural radio emission.”  Those pulses ended up being a new discovery: a pulsar, which is a type of collapsed star that rotates while emitting an intense beam of radiation like the rotating spotlight of a lighthouse.  The resulting effect is a pulse of radiation that repeats at incredibly consistent intervals.

Upon detecting these uniform pulses, the scientists were coming face to face with an extraordinary pattern that was so conspicuous that they actually considered the idea that a mind (aliens) might be responsible for them.  They later learned that it was merely the same type of strict pattern that we observe throughout nature.

In the case of the billions of nucleotide bases appearing in an irregular, non-repeating order, shouldn’t a mind at least be considered?