On the strongest proof that all living things on Earth are related through evolution

According to polls in the US, about 50% of all Americans do not believe that evolution created life on Earth as we see it today, from bacteria to blue whales. Indeed, many do not believe in evolution at all. Let me begin this Substack article, therefore, with two questions for you. 1) Do you believe that all living things on our planet are related through evolution? There are only three possible answers: “yes”, “no”, and “don’t know”. Let us leave aside the “no”s and “don’t know” replies for a moment and focus on those who said “yes”. Here is question 2: What is your evidence? Why do you believe in evolution? 

One possible answer is: the fossil record. With its succession of seemingly related forms over successive rock strata over millions of years, does it not prove the general role of evolution? In fact, no.  It certainly indicates many, often profound, changes over time in the detailed forms, the “morphologies”, of animals and plants but it does not show that one form ever evolved into another. What the fossil record is good at is showing extinctions, where a particular kind of animal present for a long time disappears from the fossil record and never appears again.  What it could do, in principle, but has not, is disprove evolution. One of the most brilliant 20^th century biologists, the British geneticist J.B.S. Haldane, was once asked if there was anything that could make him disbelieve in evolution. His instant reply was “A rabbit in the Ordovician”. What he meant was a rabbit’s fossil skeleton in rocks dating from the Ordovician period (485 to 444 million years ago), a time that is more than 400 million years prior to the immediate ancestors of rabbits. If such a rabbit fossil was found to be genuine (not a planted fake) that would indeed be a fatal blow to our concept of evolution.  

What about morphologies themselves? It is easy – at least once you know a lot – to group animals by degrees of resemblance and that is the basis of taxonomy, the classificatory scheme of living things. For instance, lions resemble tigers much more closely than they do elephants or apes. Do not such resemblances provide strong evidence for evolution? Again, not really. Those resemblances are perfectly consistent with evolution but do not prove it to be the source of changes in living things over time.  

If neither the fossil record nor taxonomy supplies proof of evolution as a general shaper of life on Earth, what does? My suspicion is that many people would, after struggling with this question, reply to the effect of “well, the biologists who study these things have lots of evidence”. That is true (see last two references, below) but, clearly, is a weak answer. Wouldn’t you want to have a better argument than that? 

Most of those who deny evolution’s power in shaping life on Earth do not totally deny the power of evolution; they concede that it can produce small changes, “microevolution” (though that word is used in a somewhat more technical sense by evolutionary biologists). The existence of antibiotic-resistant bacteria would be an example of this kind of evolution. However, evolution skeptics or outright deniers balk at the possibility that the big changes in shape and form and mental traits in animals were generated by evolution. Furthermore, it is true, as many such skeptics note, that no one has ever observed any such big changes take place. So, to return to the question: is there a kind of evidence that indicates that this huge diversity was produced by evolution?  

Here, I will argue that the answer is “yes” and that it comes from study of the large molecule uniquely made by living things and which carries biological heredity, namely deoxyribose nucleic acid or DNA. It is the basis of heredity for all organisms on Earth except for certain viruses (whose hereditary material is the related substance, ribonucleic acid, RNA.) My claim (not original to me of course) is that the DNA molecules of living animals and plants and microbes, including viruses (except for the RNA viruses), when analyzed appropriately, provide the essential evidence for evolution.  

We must avoid getting deep into the biochemical weeds but we can describe DNA sufficiently to see the gist of the argument. Briefly, DNA is a long molecule, consisting of two intertwined strands, each of which consists of a long polymer (long strings) of repeating units termed nucleotides. The two strands link up in the center via smaller parts called “bases”, each such conjoined couple of bases being termed a “base pair”. Skipping the details of the chemistry, the key point is that there are four kinds of base pairs, each one constituting a chemical “letter”. A DNA sequence is a sequence of these letters, where any letter can, in principle, follow any other. For our purposes, let us just label the four kinds of letters as A, B, C, and D.  

Each “gene”, a “unit of heredity” (we will return in this newsletter to what this means) has its unique sequence of such letters, which defines it and whose sequence gives it its ability to do its individual thing. In the mid-1970s, two scientists (Frederick Sanger in the UK and Walter Gilbert in the US) and their laboratory colleagues figured out ways to deduce the complete sequence of the letters in a DNA molecule. By the early 2000s, this could be done for all DNAs, no matter their length.  The human hereditary material, termed its “genome”, is present in all the cells of the body except red blood cells and has a total of about 3 billion nucleotides. That sequence has been known to near completeness since 2003. 

If each nucleotide position can be occupied by one of the four letters, then even in a relatively small gene of, say, 1000 nucleotides, there are 4 ¹⁰⁰⁰  possible different sequences (of A, B, C, and Ds) for that gene.  This is already a vast number! but the key fact is that each gene has its distinct chemical identity, written in its sequence. Furthermore, all genes must reproduce themselves very accurately, during cell divisions in the body and in sexual reproduction as one generation gives rise to the next. If they did not, heredity could not work. Hence, each copy in your cells of each gene inherited from your mother is very likely to be essentially identical to her copy, just as each gene inherited from your father is likely to be essentially identical to his copy of that gene in most cells in your body.  

Yet mistakes, for instance the substitution, of a B by a D (in our simple labeling scheme) at a particular place in a particular gene, do happen though they are relatively rare. Over many generations these mistakes can build up and the versions of a gene that many people may have inherited from the same ancestor – for instance, someone in your family line two centuries previously -- will generally have more differences from the ancestor’s DNA than those inherited by their immediate offspring. Yet, and this is a key point, not all those differences really matter, many of the changes have very little to zero effect. The term for this lack of effect is “neutrality”.  (Why and how neutrality occurs is something we will return to in another article.) The upshot is that most change in the letters of the DNA script accumulates over time and generations, without causing harm and at a fairly regular rate. This phenomenon has been termed the “molecular clock”, because the extent of mutational change is roughly parallel to the passage of time over many generations. The changes do not occur with metronomic regularity but they build up over time. (Of course, changes that have a positive effect, selected changes, also build up over long times but neutral and “near neutral” changes provide most of the tickings of the molecular clock.)  

Hence, the closer two organisms are believed to be in their relatedness, the more similar in sequence their genes will be. Conversely, the more distant they are (as judged by taxonomy) the more dissimilar their DNA molecules will be.  An example: all domestic dogs are believed to have descended from wolves some 20,000 to 30,000 years ago. In contrast, as inferred from the fossil record, the line of animals that became apes separated from that which became carnivores (including dogs) 70-100 million years ago, a much longer time interval. The prediction is that the DNA sequences of the genes of all domestic dog breeds will be generally more alike than any will be to that of chimpanzees or humans, despite all the visible differences in dog breeds. That is what is found: the DNA sequence of the genes of your Labrador retriever will be much more like those of your friend’s bulldog than either will be to the DNA of sea lions or aardvarks in your local zoo.  

There are complications in this story of course. For instance, the closer two species are related to each other the less reliable inferences from the molecular clock are but on the scale of major taxonomic differences, the molecular clock works, when you compare truly equivalent sequences, that is from the same genes. Thus, the picture of evolutionary relatedness we deduce from morphologies is mirrored in their degree of DNA sequence differences! This makes perfect sense in terms of what we know about evolution and DNA sequences. But, and this is the crucial point, it would not be expected if organisms had been created by an Intelligent Designer. Why should such an all-powerful being bother to make the DNA sequences resemble each other in rough quantitative parallel to the morphologies of the organisms? This would be micromanagement on the part of the Deity to an absurd level. The next time an evolution skeptic or denier attempts to put you on the back foot by arguing that there is no tight evidence for evolution, try this argument on them and put them on the back foot.

Supplementary Reading

1. Zuckerkandl, E., Pauling, L. (1965).  Molecules as documents of evolutionary history. J. Theor. Biol. 8: 357-366. (The first detailed statement of why there should be a molecular clock and how it can be used to study evolutionary history.) 

2. Pace, N.R. (2009). Mapping the Tree of Life: Progress and Prospects. Microbiology and Molecular Biology Reviews. doi.org/10.1128mmbr. (A very good review of how DNA sequence information can be used to create a picture of Life’s evolutionary history, “the Tree of Life”.) 

3. Mayr, E. (2002). What Evolution Is. Weidenfeld & Nicolson, London. (The final big statement on evolution and how it works from one of the great 20^th century biologists.) 

4. Coyne, J. (2010). Why Evolution is True. Oxford University Press, New York. (A slightly later, and of course different statement from Ernst Mayr’s book, on the wealth of evidence for evolution.)