It's Impossible To Love The Truth And Deny Evolution: Final Part - How We Know It's A Tree Of Life, Not An Orchard

We know that the evolution of life has been occurring on this planet for over 4 billion years, and that the underlying system is descent with modification. But even though we know that the nested hierarchy forms a tree of life, I've encountered creationists recently who say they believe in a common designer but not in common descent. Or to put it in their preferred language, they think evolution is like an orchard not a tree.

It isn't; and to see why it isn't, let me explain why the orchard hypothesis falls down. For starters, let's talk about alleles. If you recall from part 2 in the blog series, an allele is two or more alternative variants of a gene on the same place on the chromosome, that arise by mutation, inherited from two parents. We can study the correlation of pairs of alleles within populations and use the data to measure genetic distance between populations. This is called the coancestry coefficient. We know biological organisms are all related on a tree of life, because we can observe the comprehensive evidence for common ancestry by visualising the genetic relatedness explained by the coancestry coefficient of shared alleles and descent. Through the comprehensive range of multi-allelic genomic data, we observe that the evolutionary tree of life places every species on branches in terms of genetic similarity and relatedness. The genetic relatedness between two individuals is measured probabilistically regarding whether their alleles are identical by descent - that is, whether there is a matching segment of DNA shared by two or more individuals and inherited from a common ancestor (with the occurrence of no other recombination).

The coancestry coefficient is what predicts a coefficient of relatedness between two individuals - a genotype is observed at a locus in one individual x, and matched with genotype of another individual y at the same locus. While there are some misleading putative patterns of relatedness between individuals that share alleles that do not descend directly from a parent pair, just about every subset group of any population is measurable by its allele frequencies, where relatedness is characterised by their shared alleles that are matched by descent.

This is the exact same state of order in the animal kingdom; the greater genetic similarity between organism x and y than between x and z shows the last common ancestor between x and y is more recent than the last common ancestor between x and z. Using the formula, if you map the similarities and differences between any two species, you can place them on a family tree of biological evolution and know which species is more closely related to which. For example, there is greater genetic similarity between humans and gorillas than between humans and elephants, so we know that the last common ancestor of humans and gorillas is far more recent than the last common ancestor of humans and elephants. There is greater genetic similarity between tarsiers and guinea pigs than between tarsiers and kangaroos, so we know that the last common ancestor of tarsiers and guinea pigs is far more recent than the last common ancestor of tarsiers and kangaroos. Tarsiers, gorillas and humans all share a common primate ancestor, but the common ancestor between humans and gorillas (and chimpanzees, orangutans, gibbons and monkeys) is more recent than the common ancestor between any of those apes and tarsiers. Every time we apply this formula to any pair of animals by sequencing the genome, we can confirm how closely related they are in evolution's family tree.

The upshot is, the formula for the tree of life in evolution is that there is more genetic similarity between species more closely related (that is, the common ancestor between them is on a closer branch) than between species more distantly related (that is, the common ancestor between them is on a branch further back), and this is true with such predictability and evidential demonstrability that the tree of life becomes impossible to reasonably deny. By equal measure, the 'orchard' hypothesis completely falls down because this pattern would not be observed if every species or every taxonomic group (or however the orchard proponents define what constitutes a separate tree) was created as a separate tree in the orchard of life. The patterns are formed by genetic relatedness and distance, and they can be deciphered informationally like reading computer code, to leave us in no doubt that the orchard hypothesis is wrong.

From a Christian perspective, I believe we have a common Designer, but from a scientific perspective, I know all living things have common ancestry, and that the vast evidence accrued from sequencing the genomes of most living things confirms this beyond any reasonable doubt. It's not possible to make the square peg of the orchard hypothesis fit in to the round hole of common ancestry, because if the orchard theory was correct, we wouldn't have the genetic patterns we see when we sequence animal genomes.

On top of all the other evidence, there is another absolutely compelling predictive element to evolution too; if evolution is descent with modification in a tree of life, where organisms become more genetically distant from each other over time, then we’d expect to see more and more molecular convergence the further back in time we studied historical DNA. That is, if you could travel back in time a few million years, and find the ancestors of organism X and organism Y, you would find they are historically more similar to each other than modern Xs and Ys are to each other in the present. If you followed the same time line back a few tens of millions of years, you’d find even greater genetic convergence. This formula: more evolution, more genetic divergence; less evolution, more genetic convergence is such a robust predicative model, that it’s another one of those reasons why we can be absolutely confident that we are all ancestrally related.

This is precisely what we find when we compare the DNA of other species and place them in a nested hierarchy of relatedness. If you look at other primates (our most recent evolutionary cousins on the tree of life’s branches) we always find that when two distinct lineages have been evolving independently since their most recent common ancestor, the traces of common ancestry are there, but there are more genetic dissimilarities the further that line evolves. Humans are more closely related to chimps than to gorillas, we are more closely related to gorillas than to orangutans, and so on. In fact, chimpanzees and bonobos are more closely related to humans than to gorillas and orangutans, and gorillas are more closely related to humans than they are to monkeys. Everything fits exactly as we’d expect, given all the other evidence we have for evolution too. Perhaps, now, an illustration will help…..

Genetic analogy
Earlier in the series, I explained that the genetic code comprises DNA made up of a simple alphabet where the order of these letters across the genome creates a unique organism with a unique genetic code. I also posited the analogy of a genome being like a book, consisting of chromosomes, which are like paragraphs, made up of genes (which are sentences). Sometimes it's hard to visualise systems like genetic algorithms and common ancestry if you're not familiar with what biology 'looks' like - so to make this even clearer, let me develop the illustration of books to show how certain this genetic relatedness is in terms of common ancestry within a tree of life.

Let us suppose a highly sophisticated supercomputer could map the genomes of all the species in existence and assign unique combinations of letters of any unique common ancestor algorithms that could be represented with words and then literary sentences. Imagine that as evolution begins, from the crude biochemical stages into creation of the genetic code shared by all living things, we reach a point on the tree of life in which any of the genomes of the last common ancestors of a particular set of branches of different species is represented by a literary work. Imagine too that similarities in literary types and evolutionary branches follow similarities between morphological phylogenetic trees and molecular phylogenetic trees, in that the genes that code traits in terms of size, shape, and structure of an organism are consistent with how those traits are observed both phenotypically and genotypically. In other words, in this computer program, a Jane Austen novel is more like a Charlotte Bronte novel than it is an Arthur C. Clarke novel or a Philip K Dick novel, similar to how a guinea pig is more like a squirrel than it is a chicken or a snake, and so forth. In this illustration, the branches on the tree of life would resemble a literary library in terms of genres, authors, books and styles. 

In reality, analogies are limited, and we have many more pages of text on the evolutionary tree, because genes expand across species in a non-linear way too, and each species has thousands of protein-coding genes - but a literary illustration will suffice to convey the broader point. Evolution works by shuffling the letters (sexual recombination of genes) where the exchange of texts (the genetic material between different organisms) produces the offspring with combinations of traits that emerge from either parent. We are using a literary library to illustrate the trajectory evolution follows, where each successful recombination of genes over populations goes on to produce the vast diversity of animals we see in evolution, each with their own unique sequences of DNA.

Now, suppose we zoom in further on a particular sequence of, say, a mammalian genome and find that it contains the following sentence: 

“I hope no one who reads this book has been quite as miserable as Susan and Lucy were that night; but if you have been - if you've been up all night and cried till you have no more tears left in you - you will know that there comes in the end a sort of quietness. You feel as if nothing is ever going to happen again.”

Let’s say that this sentence, From C.S. Lewis’s The Lion, The Witch and The Wardrobe, is found on the guinea pig genome. We’d expect to see on other rodent species quotes in the genome that resemble these works from Narnia (or, at least, the same author); for example porcupines are closely related to guinea pigs, so we wouldn’t be surprised to find something like “Awake. Love. Think. Speak. Be walking trees. Be talking beasts. Be divine waters.” (from The Magician’s Nephew) on a porcupine genotype. Perhaps on beavers we’d find texts from Lewis's The Great Divorce, whereas on rabbits we might find texts by Tolkien (because rabbits are not rodents but they are similar). We’d find nothing from Ayn Rand or Phillip Larkin in the rodent group, and likewise, if John Donne and George Herbert were found on marsupial genomes, then we’d find quite a genetic distance in our library between them and something by John Paul Sartre or Albert Camus, who might be sharks or swordfish. We’d find Dostoevsky and Tolstoy on closer branches than we’d find Evelyn Waugh and PG. Wodhouse. Dickens would be closer to Hardy than he would Burgess; bonobos would be closer to gorillas than they would wombats - the tree of both biology and literature form a compatible nested branching structure.

Evolution here looks like a library. And extending the library analogy to all biological life, we can read the genomes of most species that exist in a similar way to how we can discern patters in text sequences (it’s not quite the same, but the library analogy is to make it easier for you to visualise). That is, we can read the DNA of any 2 species (or as many as we choose) and plot the genetic relatedness and get exactly what you'd expect from common ancestry and a nested hierarchy within a tree of life.

And here the story goes deeper, because every literary sentence we could read on genes, whether it's from Hemingway, Homer or Hugo, would itself be subject to mutations within species, where we could map which lines come from which branch, and observe how they've evolved too. Take the line from Narnia again, which appears on a particular gene sequence on a particular guinea pig: 

“I hope no one who reads this book has been quite as miserable as Susan and Lucy were that night; but if you have been - if you've been up all night and cried till you have no more tears left in you - you will know that there comes in the end a sort of quietness. You feel as if nothing is ever going to happen again.” 

A few hundred or thousand generations down the line of breeding, we might find this: 

“You would not have called to me unless I had been calling to you," said the Lion.” (From The Silver Chair) 

And we might have got there on a journey like this:

1) "You one who looks this book unless been quite as miserable as Susan and Lion"

5) "You would not looks this book unless been quite as calling as Susan and Lion"

10) "You would not looks this book unless I had as calling as Susan and Lion"

15) "You would not have this me unless I had as calling as said and Lion"

20) "You would not have called to me unless I had been calling to you," said the Lion.”

That is, not only can we observe different authors, works and genres in our library of life by significant changes in the genome at the level of species, in which splits into more genetically distinct descendant populations isolates groups so they can no longer breed successfully, we can see the gradual accumulation of genetic differences along the way, as books by single authors evolve into new books, and eventually brand new authors, and brand new styles and genres. That's one of the profound things about both evolution and literature - there is so much distinction and at the same time so much similarity and relatedness and common ground.

As we saw in part 4 in the series, speciation begins when a population of interbreeding organisms divides into two populations of different species. At the point of speciation, there has been a recent divide from common ancestor (or really it's a population of ancestors), which means the two new species will have close to identical genes in the early stage. As time goes on, those organisms will begin to develop grater differences in their genomes. Returning to our literary library analogy, as the genomes evolve, they are a bit (although not entirely) like texts of novels being copied but with copying changes (mutations), where once a change has occurred, that becomes the new text from which future copies will be made (and so on). Let's take this passage from C.S. Lewis's The Voyage of the Dawn Treader, and imagine it is found on the genomes of a species of rodent that is about to divide into two sub-populations. 

“A powerful dragon crying its eyes out under the moon in a deserted valley is a sight and a sound hardly to be imagined.” 

Now consider two independent copies are made of that gene, with the following coping error in each, respectively:

Copy A (49) -“A powerful dragon crying its eyes out under the moon in a dewerted valley is a sight and a sound hardly to be imagined.”

Copy B  (2) - “A bowerful dragon crying its eyes out under the moon in a deserted valley is a sight and a sound hardly to be imagined.”

Copy A has the first copying error on letter number 49 in the sequence, and Copy B has the first copying error on letter number 2 in the sequence. Now observe when both Copy A and Copy B are copied a further time, and these are the results.

Copy A1 (49, 10) -“A powerful cragon crying its eyes out under the moon in a dewerted valley is a sight and a sound hardly to be imagined.”

Copy B1 (2, 15) - “A bowerful dragob crying its eyes out under the moon in a deserted valley is a sight and a sound hardly to be imagined.”

Copy A has a further copying error on letter 10 in the sequence, and Copy B has a further copying error on letter 15 in the sequence. Let's observe two further copies that emerge from each:

Copy A2 (49, 10, 54) -“A powerful cragon crying its eyes out under the moon in a dewertef valley is a sight and a sound hardly to be imagined.”

Copy B2 (2, 15, 20) - “A bowerful dragob cryihg its eyes out under the moon in a deserted valley is a sight and a sound hardly to be imagined.”

Copy A3 (49, 10, 54, 4) -“A poqerful cragon crying its eyes out under the moon in a dewertef valley is a sight and a sound hardly to be imagined.”

Copy B3 (2, 15, 20, 63) - “A bowerful dragob cryihg its eyes out under the moon in a deserted valley is s sight and a sound hardly to be imagined.”

A bit further down the reproductive line, you see a genome with the following sequence:

Copy ?? (49, 10, 54, 4, 17, 26) -“A poqerful cragon ctying its eues out under the moon in a dewertef valley is a sight and a sound hardly to be imagined.”

Just one look at the sequence shows beyond any reasonable doubt that this is the progeny of the A lineage and not the B lineage. You can see the sequence consists of past mutations and two new ones, making it obvious to which text (genome) it belongs. Imagine what the biological world is like, where we are analysing whole books of thousands of related species that have been copied over and over again, with small changes in text every time it is copied in a fertile sexual union. This is what we see in evolution's tree of life. Genomes that are similar, with chapters and paragraphs and sentences that have undergone mappable changes, telling a story of evolved genomes. This literary-like biological story doesn't just give us an observable trail of evidence for common ancestry, it also equips us with robust predictive power about the data and patterns we should expect to observe when we analyse the genomes in the biological sphere.

Be careful not to take analogies too far though. The library of evolution has been to convey that the entire tree of life can be read as though it is journey of evolution, where text-like information shows common descent, and a nested hierarchy of relatedness. Studying genetics confirms beyond any reasonable doubt that all species evolved from at least one early common ancestor, and that the further we observe along the evolutionary tree the greater the genomic similarities occur in exactly the places we would expect if evolution really happened.

Be wary, you will meet creationists who proclaim that these similarities in DNA are simply the result of God's 'common design' not descent with modification in separate species in a tree of life. But common design is not sufficient to explain the patterns of relatedness observed with the comprehensive studies of genetic relatedness, and how the chapters, paragraphs, sentences and copying changes are expressed in line with the ancestral pattern predicted in the tree of life.