“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.

Such simplification notwithstanding, though, the basics of mutations can be difficult to grasp at first 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 with four kinds of chemical players of whom three bear names unfamiliar to many people. 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. Such a chain of effects is a lot to wrap one’s head around.

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 kind of 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 part 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 simply A, C, G, and T. This is the DNA “code,” 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. 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 in turn, bringing the appropriate amino acid molecule into place, and stringing it like a bead on a necklace in the proper sequence. The finished molecule, the necklace of amino acids, is 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 instead, 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 example 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, delete just the first letter, t, from this sentence of three-letter words:  “the man won the bet” becomes “hem anw ont heb et…”.  And like such a small deletion, the insertion of a nucleotide has the same chaotic effect.

In other mutations, a codon or group of codons 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 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 more predators, attract more mates, or produce more offspring, the color mutation will take its place in the species.

 

Dawkins: Not One of Our Ancestors Was a Failure

Richard Dawkins’s theme is upbeat:

All organisms that have ever lived—every animal and plant, all bacteria and all fungi, every creeping thing, and all readers of this book—can look back at their ancestors and make the following proud claim: Not a single one of our ancestors died in infancy. They all reached adulthood, and every single one [allowing for the inclusion of such outliers as in vitro fertilization] was capable of finding at least one heterosexual partner and of successful copulation. Not a single one of our ancestors was felled by an enemy, or by a virus, or by a misjudged footstep on a cliff edge, before bringing at least one child into the world. Thousands of our ancestors’ contemporaries fail in all these respects, but not a single solitary one of our ancestors failed in any of them.…Since all organisms inherit all their genes from their ancestors, rather than from their ancestors’ unsuccessful contemporaries, all organisms tend to possess successful genes. They have what it takes to become ancestors—and that means to survive and reproduce…That is why birds are so good at flying, fish so good at swimming, monkeys so good at climbing, viruses so good at spreading. That is why we love life and love sex and love children. It is because we all, without a single exception, inherit all our genes from an unbroken line of successful ancestors. (River Out of Eden)

Many readers love this passage. Its any-organism’s view backwards along the unbroken line of forebears celebrates the successes and joys of being alive. And it explains this success not as the result of human uniqueness or a generous deity but as nature’ own selection process. The same pride and pleasure we take in hearing about a great-grandmother who struggled, travelled, settled, and raised a family, Dawkins extends to all ancestors of all species, without exception. Any reader who may have earlier viewed evolution as alien and godless might feel a little less resistance now.

But other readers may take exception to the passage for other reasons. Some of that inheritance from our successful ancestors, we wish we would be spared. Down Syndrome, Cystic Fibrosis, some cancers, and other diseases are inherited to a degree. So are mental illness and violent tendencies. For those suffering from such inheritances today, the genetic filter has not been effective enough.

And then there’s bad luck. Many organisms that were as well-endowed genetically as “successful” ancestors might also have left offspring had it not been for factors beyond their control. The twin of that pioneer grandmother may have died in battle, gone down with the ship, succumbed to an earthquake, or starved in a drought—childless.

Last but not least, many people today are able to have children but choose not to. They may remain, though, no less “successful” in every other sense of the word.

In the end, I think these exceptions, instead of weakening Dawkins’ point, strengthen it—as if each living organism could say with conviction, see, so many different pieces, not only the genes but the circumstances too, had to fall into place for me to be here. And they did.