Let’s look more closely at the building blocks of DNA – the nucleotides.
Notice that it is more complex than an amino acid, where three complex chemical groups are covalently linked together. And unlike amino acids, nucleotides are not recovered in Miller-Urey type experiments. In fact, Robert Shapiro, professor emeritus of chemistry and senior research scientist at New York University, notes:
And no sample of a nucleotide, the building block of RNA or DNA, has ever been discovered in a natural source apart from Earth life. Or even take off the phosphate, one of the three parts, and no nucleoside has ever been put together. Nature has no inclination whatsoever to build nucleosides or nucleotides that we can detect, and the pharmaceutical industry has discovered this.
What is also remarkable about nucleotides is that it is possible to connect the sugar, phosphate group, and nitrogenous base together to form different structures.
We’ve seen that the logic of protein structure entails the covalent linkage of a pattern of noncovalent interactions. This is how we encode a three-dimensional reality in one-dimensional terms. And all of this was made possible by the fact that amino acids are linked together in a way where their side chains were not involved in the linkage and thus served more like appendages.
But we have also seen this very logic is at play when it comes to the formation of a chain of nucleotides. As with the side chains of amino acids, the nitrogenous bases can interact with each other through noncovalent forces causing the nucleotide chain to fold into a three-dimensional structure. This is what happens with a lot of RNA and explains its ability to function as a catalyst. But let’s turn to DNA.
We’ve seen that a protein is formed by covalently linking amino acids, yet in a fashion where the diverse side chains do not participate in this binding. This frees them to function elsewhere. So what do the side-chains do? In short, they interact with each other. Through electrostatic interactions, they fold most proteins into a compact, globular shape and it is the shape that is at the very heart of protein function (if you disrupt the shape, you disrupt the function).
What I’d like to do now is impress upon you the very brilliance of this design, as it goes a very long way in explaining why proteins have been so useful for evolution.
To make a protein, we simply covalently link individual amino acids together via a peptide bond. The figure below shows the formation of a peptide bond.
I’d like to draw your attention to two things. First, note that the carboxyl group of one amino acid reacts with the amino group of the second amino acid to form the peptide bond (highlighted in the orange box). This creates a dipeptide with differing ends. At the N-terminal end, there is a free amino group and the C-terminal end has a free carboxyl group. This simply means we can attached a third amino acid to the C-terminal end of the dipeptide with the very same reaction. And if we can add a third, we can add a fourth. Etc. Thus, the structure of the amino acid is perfectly poised to create a growing chain whose length would be determined by factors other than amino acid structure. We can thus begin to catch a glimpse of one reason why proteins are so versatile, as the relative ease of construction is coupled to an ability to vary the length.
Since we have been talking about proteins, let’s back up to say a few things about their building blocks – the amino acids. Below is a figure of an amino acid.
Note the central carbon atom and how it is covalently bonded with four different groups. Three of these four groups are always the same in every amino acid used by life: the amino group (orange box), the carboxyl group (blue box), and the hydrogen atom. The R signifies the side chain, which differs for each amino acid.
Let me summarize some of the observations I have made with my recent focus on proteins and their role in the success of evolution. Consider the following:
To what degree is the design of a designer constrained by his/her building material? For example, imagine that we enlisted the service of the worlds most creative and brilliant engineers and tasked them to design a space craft that will carry men to Mars and back. Now, let’s add one constraint – the only material available to the designers is concrete. Would these brilliant designers be able to meet the design objective?
Below if a nice video about our modern understanding of evolution.
I especially enjoyed the comments from Sean Carroll (according to Michael Ruse, “Of all the scientists in the world today, there is no one with whom Charles Darwin would rather spend an evening than Sean Carroll.”):
So what this means is in some ways, some sense, evolution is a simpler process than we first thought. When you think about all of the diversity of forms out there, we first believed this would involve all sorts of novel creations, starting from scratch, again and again and again. We now understand that, no, that evolution works with packets of information and uses them in a new and different ways, and new and different combinations, without necessarily having to invent anything fundamentally new, but new combinations.
My, that’s a pretty radical change in the way we view evolution. The old way was far less friendly to teleology and also failed to prepare scientists for the more accurate understanding of evolution, an understanding that is now much more friendly to teleology.
This all raises some interesting questions. For example, without proteins, and their manufacturing process, what becomes of the blind watchmaker? Without proteins, and the latent functions contained within, might not the blind watchmaker exist as the impotent, crippled, blind watchmaker with no one to notice its existence? If so, how much credit does the blind watchmaker really deserve?
The vast and immense Tree of Life is a protein-dependent output. Point to
some evidence of evolution and I’ll point to the proteins that underlie it.
Without proteins, would there be a Tree of Life 3.5 billion years after the
RNA world took root? How do we know? If we believe so, would the Tree be
as immense and vast as it is today? A life form composed of nucleic acids,
carbohydrates, and lipids would suffice for the purposes of the blind
watchmaker. But could the blind watchmaker turn this material into
something that is analogous to an Ash tree filled with squirrels, beetles,
and birds?
May 25th, 2008 by 
Mike Gene 
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