“We Are All Mutants”: Mutation Basics

In The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution (2016), Richard Dawkins writes:

The word ‘mutation’ conjures up images of grotesquely distorted creatures, perhaps generated by unscrupulous experimenters, or springing up as a consequence of some radioactive catastrophe. The truth is somewhat different. We are all mutants. The DNA passed on to us from our parents contains novel changes—mutations—which were not present in the DNA that they inherited from their parents. Fortunately so, for mutations provide the raw material, sculpted over millennia by natural selection, used to build the bodies of all the pilgrims on our journey. (126)

I’ve wanted to understand the basics of such a process that provides the “raw material” for evolution as well as a share of diseases and disabilities.  Explaining it here is a step in that direction, so here’s my version of Mutation Made Simple—very simple. I’ve omitted RNA, base pairs, and gene recombination, and I’ve compressed and approximated.

Despite simplification, though, the basics of mutations remain difficult to grasp initially for two reasons. One is that DNA duplication, even when it is on track, takes place in several steps that are difficult to visualize and it does so with four kinds of chemical players of whom three bear unfamiliar names. They are nucleotide, codon, and amino acid; the familiar fourth one is protein. Many mutations start with a miscopied nucleotide, which leads to an error in a codon, which corresponds to the wrong amino acid, which may screw up the protein. Simple.

The second difficulty is that there is “slack” in these steps. That is, many of the missteps that could lead to an actual difference in a body are corrected by the cell or produce no  result or produce a result that is harmless. A built-in “forgiveness factor” prevents every single mistake in DNA copying from invariably leading to potentially risky changes in an organism. Such a buffer in the genetic system is an important piece of its complexity.

dna and codons (www2.le.ac.uk)

From the top: the double strand of DNA; the three-letter codons from one of the strands; and the necklace of amino acids designated by each codon. (www2.le.ac.uk)

That said, let’s look at the normal duplication sequence. Mutations exist because cells require replacement. The first step in making a new cell is for the old one to make a copy of its DNA. DNA strands themselves consist of a line-up of basic organic molecules, the nucleotides. There are only four nucleotides, with names that are abbreviated A, C, G, and T. This is the DNA “code,” somewhat like the dots and dashes in Morse code.

The cell reads the nucleotides in groups of three. That is, the nucleotides constitute a kind of small alphabet that spells out a vocabulary of 64 three-letter “words.”  Each word or triplet, which is the codon, designates one of twenty amino acids.  (So here is one “slack” point: twenty amino acids designated by three times as many codons means each amino acid may be designated by not just one codon but by several. The result is a buffer: An incorrect codon doesn’t necessarily call up the wrong amino acid. )

Cells then build the protein molecules that will form the new cell by reading each codon, bringing the appropriate amino acid molecule into place, and stringing it like a bead on a necklace in the proper sequence. The finished molecule is the necklace of amino acids, a particular and complex protein.

But sometimes over billions of nucleotide duplications, a nucleotide miscopies; what should be a copy of an A is a T instead, a C miscopies as a G.

sickle cell (sicklecellanaemia.org)
Sickle cells among normal red blood cells. (sicklecellanemia.org)

Take the codon TTC, for example. Let’s say that a copy of it comes out as TTA, one letter off. When this TTA later comes up in the protein production line, which amino acid does it designate and what will the impact be? Is TTA one of the few “nonsense” codons that match no amino acid all and stop the copying process before the protein is complete? Or, if it does result in a changed protein and gene, will the change be limited to one organism, or has the error occurred in a gene for sperm or the ovum that will carry it to offspring?

Point mutation (Pinterest)

The GAG codon, when it miscopies as GTG, puts into the hemoglobin protein an amino acid that creates sickle-shaped cells can bring on painful anemia but also protection against malaria. (Pinterest)

TTA, it turns out, has no such harsh consequences. The amino acid it calls up has the same function as the one that the original TTC corresponded to. The final protein functions normally. No harm, no foul—another bit of “forgiveness” in the replication process. But see the illustrations for the much less neutral mutation that produces Sickle cells in the blood.

Besides such mutations that start with the miscopying of a nucleotide, mutations can also occur in another way: through the insertion or deletion of nucleotides and codons, sometimes one codon, sometimes hundreds.

Codons are read in threes. So the insertion or deletion of even a single nucleotide changes all the codons coming after it in what’s called the frame of the gene, the full sequence of codons. To see the effect of such a seemingly minor change, delete just the first letter, t, from the following sentence of three-letter words:  “the man won the bet” becomes “hem anw ont heb et…”.  And if you inserts a single letter instead of deleting one, the chaotic effect is the same.

In other mutations, a codon or group of codons goes manic and repeats far in excess of the usual number. A gene for brain development, for example, includes from six to fifty repetitions of a CGG codon. That’s normal for that gene. But in a mutation that leads to a form of retardation called Fragile-X Syndrome, the gene repeats the CGG codon from 200 to 1000 times.

So mutations start with nucleotides and codons but may end by altering genes. Some changes are disastrous, some have little or no effect, some are passed on through generations, most are not passed on at all. But in the background, behind the grim or the helpful outcomes, mutations keep bringing forth a trickle of variations of all sorts, in all species—the modest but persistent originality of organic life itself. Untypical coloration in an insect or a flower or an animal’s fur may start out as a minor difference. But over generations, if the individuals with the coloring are a little healthier, evade a few more predators, attract more mates, or produce more offspring, the color mutation will take its place in the species.

 

Darwin and the Buddha

The teachings of Charles Darwin and Gautama Buddha are worlds apart. Yet their descriptions of life bear similarities to each other and even interlock in ways that expand my view of each.  I’ll focus this comparison on  On the Origin of Species and the Dhammapada, a widely read collection of the Buddha’s sayings.

The differences are straightforward enough. Darwin’s eye was mainly on the past. In Origins, he observed the characteristics of successive generations of plants and animals—except for humans, whose evolution he discussed in other books—to show how natural selection and fertility served as the sources of the variation of species.

The Buddha, on the other hand, focused on humans, on the pain of our disappointments and the ease that disciplined renunciations could bring. And in contrast to Darwin’s focus on ancestry, the Buddha’s eye was on the future, on each person’s potential path forward out of suffering. Finally, while Darwinian evolution moved on inexorably, the Buddha convinced his followers that their future was in their own hands, that if they turned inward to grasp the nature of change and expectation, they could calm their cravings.

Yet beneath these distinct differences, both thinker followed a logic built from the same pieces.

buddhistchannel.tv

buddhistchannel.tv

First, for both Darwin and the Buddha, the struggles of ordinary life make up the starting point for the consequences and possibilities that followed. As different as their two works are, taken together they rest on the premise that for humans, animals, and plants alike, life is stressful, sometimes dangerous, and often unpredictable. Whether in a plant stunted by inadequate sunlight or a woman in conflict between family and her career, it is everyday obstacles and threats that drive the changes that the thinkers explored.

Such changes consisted of a series of steps, the other great commonality between their views. For Darwin, the steps were those small, random variations which, if they benefited an organism consistently, took their place among its inherited traits. Though each step was small, the end result could be a new, better-adapted species. For the Buddha, the steps consisted of a discipline in correct understanding, the extinguishing of selfish desires, and future rebirths. As they were in Darwinian evolution, the steps to enlightenment took time but led to relief from pain.

Combined, these variations on the themes of struggle, gradual change, and final resolution offer a rich vision: living things experience conditions that are not easily or perfectly satisfied, but the future offers steps from pain towards peace, though not necessarily within an individual’s lifetime. In place of a deity to oversee the the fate of living things, both men saw a reality in which ordinary life and an organism’s response to it were sufficient to drive changes sooner or later.

I and most people and animals tend to fix our gaze on those satisfactions and dangers that we see a relatively short distance ahead—the state of our income, our health, our children, our security, predictable weather, unpredictable disasters. I wonder what it was like to have the mindset of Darwin and Buddha, tuned to long spans of steady transition in which a being’s every moment is a step towards elsewhere.

 

My thanks to Elaine Smith for her assistance.