I spent the last few chapters getting into a little math, to give you a sense of what nature needs to do to evolve new protein sequences from scratch, or to stitch together smaller ones into larger ones. My purpose was also to heighten our intuition for what is and isn’t possible in nature. I showed that we can get a rough estimate of how likely it would be for ten nucleotides in a sequence to be deleted from the genome of a real organism, through random mutations. Based on a few simple assumptions, we could consider it to be a “One In A Trillion” event.
This might sound rare, but we also need to put it into perspective. We just need a bacterial colony to perform a trillion trials, and it will likely happen at least once. In other words, a One In A Trillion event isn’t necessarily a problem by itself. The problem is that it has to occur in the context of other low probability events.
Unfortunately, the probability of many of the things that are said to happen in evolutionary stories are almost impossible to calculate. Even so, it’s useful to try and get a better sense of scale for the probability of a particular event, even if we can’t get the numbers precisely right.
Now, when telling their stories, evolutionary theorists tend to credit nature with the ability to do extraordinary things, to explain how certain DNA sequences evolved. I will refer to these as “serendipity wands.” They are like magic wands, but instead of magic, the power behind them is incredible luck. However, I prefer the word serendipity, even though it means basically the same thing, because “the wands of serendipity” has a nice ring to it.
The first serendipity wand is called “duplication.” This is where just the right sequence of nucleotides gets duplicated right next to the original, often more than once, in just the right quantities. This wand is the equivalent of using the “copy” and “paste” functions in a word processor, with the pasted text placed next to the original. For example, if you were typing out directions for someone, and you wanted them to turn right three times, you could type “TURN RIGHT,” then select the text, copy it, and paste it two times next to the original text.
In nature, duplicates are accidents, blips in the machinery that copies the cell’s genome, and this is how many proteins are said to have evolved. A new protein supposedly starts out as an accidental duplicate of an existing one, and gradually the code for the duplicate protein mutates so that the protein somehow finds a new function.
Now, I don’t think it’s unreasonable to say that duplication happens from time to time. Maybe the copying machinery stutters, and spits out the same sequence of letters a few more times than it should, although we should be curious to know how these mistakes make it past the built-in error correcting processes, which we’ll discuss in a later chapter. But this isn’t the reason I call it a serendipity wand.
Evolutionary theorists say that duplication events are common. However, there is a certain amount of circular reasoning here. They argue this is the way many proteins evolved, and so by definition, it must be a common event, because there are a lot of proteins. There are also a lot of repetitive sequences in the genome, so it is assumed they came about as a result of duplication events.
You will also find a lot of repeats of the word “the” in this letter, and their existence could be explained by the repeated stuttering of the copy and paste facility in my word processor. I suppose this is a possibility, but as the author of this letter, I know there is also a very different explanation.
I call “duplication” a serendipity wand because, in evolutionary stories, it isn’t about random sequences being duplicated. Instead, a specific sequence is “copied,” and then “pasted” exactly the right number of times. If you use copy and paste in a document, you don’t choose random letters and words. You first select the exact text you need. If you want someone to turn right three times, you can’t have your instructions say “TURN RIGHT, NRIGHT, GHT.” This wouldn’t make any sense.
You need to select the exact text “TURN RIGHT,” copy it, and then paste it exactly twice, right next to the original without any distracting or ambiguous text in-between, apart from spaces. If you pasted it just one extra time, the person following your instructions would find themselves right back where they started!
In the stories of evolving sequences as told by evolutionary theorists, the evolving item, whether a developing protein or something else, gets lucky because just the right sequence gets copied and pasted the right number of times. If even one extra letter is included or missed out in the copying process, the sequence could lose the desired function. The evolving sequence also gets lucky in that the duplicates somehow get past the mechanisms built into the system to prevent errors.
The second serendipity wand is called “translocation,” which is a term used by biologists. This is where genetic sequences are moved about through the genome, or perhaps even brought over from other organisms. On the other hand, if two sequences are very close, they can be brought together with a few convenient nucleotide deletions.
This wand is the equivalent of using the “cut” and “paste” functions in a word processor, except unlike the previous wand, you can cut the text from the same document or a different one, and paste the text into wherever you want it to be in your document. What‘s more, the pasted text will just happen to follow on perfectly from the text that already existed in your document.
I think this is by far the most extravagant serendipity wand in evolutionary theory. I have already shown that to get ten nucleotides in a row deleted is the equivalent of a One In A Trillion event, and this was simply to get two sequences next to each other that were separated by those ten nucleotides. It might happen, although lots of other things are also much more likely to happen.
But what are the odds of any two specific sequences far away in a genome coming together, while remaining intact in the process? The probability decreases by orders of magnitude, the further away the two sequences are. Yet with the “translocation” serendipity wand as waved by theorists, it doesn’t matter. No matter how far away, no matter how improbable, it can happen with a wave of the storytelling wand.
To be clear, certain pieces of the genome can definitely be moved about. But this usually happens for very specific reasons that involve strictly regulated control mechanisms and markers. In other words, it’s one thing to say that translocation happens, which is true in certain limited circumstances. It’s a completely different thing to say that specific sequence A gets moved to a specific region B of the genome, just because this is needed for an evolutionary story to work.
If a parcel was delivered to your door, and a friend said that “parcels get transported,” you wouldn’t consider it a good explanation for why it arrived on your doorstep. If the parcel was addressed to you, and contained gold bars worth a million dollars, you would probably find your friend’s explanation a little lame.
Yet this is what evolutionary theorists do in their stories. Since parcels get “translocated” across the world all the time, this is apparently sufficient to explain how you got a parcel on your doorstep, addressed to you, containing gold bars worth a million dollars.
The third serendipity wand involves what I call “magical steps.” To explain this one, let’s take a closer look at how some proteins are said to have evolved, according to evolutionary theory. One way is through a process called “gene duplication.”
The word “gene” usually refers to a genetic sequence that codes for a protein or perhaps an RNA sequence, although sometimes it is used more loosely to refer to any genetic sequence that does something useful.
In “gene duplication” a gene gets accidentally duplicated. The cell can still use the original sequence to make the protein, while the copy is then supposedly free to mutate; and somehow, the copy gradually finds a new function. This is the basic idea, which might sound reasonable on the surface, although it requires a whole lot of luck for the gene to be duplicated intact in the first place. But it also begs several questions.
First of all, if a new gene starts off as a duplicate of an old one, which one does the cell use to make the protein? If it only uses one of the genes, then the other doesn’t get produced. But if it’s not produced, it won’t evolve through natural selection.
To explain why, it helps to think of mutations as designers in a factory, constantly tinkering with the design plans, and to think of natural selection as the factory testers, the ones who get to test each tweaked design before it gets rolled out for mass production, to see if the tweak is better, worse or the same as the previous design. Mutation is the tinkerer, and natural selection is the tester. According to evolutionary theory, you need both, in order for evolution to happen.
But a gene that doesn’t produce a protein or something useful, can’t be tested in the real world, and so isn’t subject to natural selection. Rather than evolving into a sequence that does something different and useful to the cell, it is likely to lose its information over time, becoming what is called a “pseudogene,” which usually has similarities to a known gene, but with some or even a complete loss of functionality.
However, let’s say that after the duplication of a gene, the cell produces both the original and the duplicate, because it can’t tell the difference. Let’s label the original gene A, and the duplicate gene A1. Gene A already has a function. According to evolutionary theory, duplicate gene A1 could eventually evolve into a new gene, which I will label as gene B, with a new or related function, through a series of evolutionary steps that I will imaginatively label as A2, A3, A4 and so on.
Ideally, each of the steps A2, A3 and so on should give the organism an advantage, so that natural selection can work cumulatively toward gene B. I suppose an individual step might be neutral, neither an advantage nor a disadvantage, and the gene might drift somewhat randomly towards the next step.
Individual steps probably shouldn’t be a disadvantage, because then natural selection would work against it. However, I suppose a temporary disadvantage might slip through the cracks once in a while, if an advantage is just round the corner. However, no step should break the gene, so that the protein it codes for loses its useful function, because then natural selection won’t have a need to preserve the sequence.
To sum up: each evolutionary step from duplicate gene A1 to new gene B needs to be viable. In other words, intermediate genes A2, A3 and so on should still have a function, and be turned into a protein by the cell, so that the function can be tested in the real world. If not, it can’t be tested and will probably devolve into a pseudogene. Many or all of the intermediate steps should also give the cell an advantage, so that natural selection can propel the evolving gene forward on the path to finding a new function.
However, in their stories, evolutionary theorists rarely spell out the exact mutational steps gene A1 would need to go through to become gene B, while also showing the effect each step would have on the organism. Admittedly, it’s probably difficult to do this, but surely it isn’t impossible, if this really is a major way in which new proteins evolve.
Scientists have the ability to knock out whole genes, and edit single nucleotides within a gene to test its effect on an organism. Evolutionary theorists can supply biologists with a viable functional and chemical pathway from gene A to gene B, and researchers could test this through many experimental rounds.
But obviously it’s much easier to simply assume it happened, and write, “gene A evolved into gene B through duplication followed by a series of mutations,” without any detailed proof or testing of the supposedly functional steps in-between.
This is why I call it a serendipity wand. In evolutionary storytelling, proteins find their functions almost by magic, going through a series of “magical steps” that might be discussed in vague theoretical terms, but are rarely spelled out in detail and then tested in the real world.
I call the people who write such things “evolutionary theorists,” because this is what they are. They often take valid processes such as horizontal gene transfer, which bacteria use to exchange genes, and then apply it universally, to any piece of the genome they want to move around. As long as scientific language is used and the story sounds plausible on the surface, when they wave the serendipity wands of duplication, translocation and magical steps, anything is possible.