We continue our review of the book, Adam and the Genome: Reading Scripture after Genetic Science, by Dennis Venema and Scot McKnight . Today, Chapter 2- Part 1.
Most people do not understand how evolution purports to work. They think it involves substantial changes in multiple organisms in the same generation for a change to pass down over time. Such changes are wildly improbable and so they conclude evolution is wildly improbable. If evolution worked that way, they’d be right. But evolution involves the shifting of average characteristics of populations over long periods of time. Individuals DO NOT evolve, populations do. As Douglas J. Futuyma (in Evolutionary Biology, Sinauer Associates 1986) said:
“Biological evolution … is change in the properties of populations of organisms that transcend the lifetime of a single individual. The ontogeny (developmental history) of an individual is not considered evolution; individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are inheritable via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportion of different alleles (different forms or groups of genes) within a population (such as those determining blood types) to the successive alterations that led from the earliest proto-organism to snails, bees, giraffes, and dandelions.”
The answer to a previous blog comment, “So how did we go from zero (humans) to thousands” is that we didn’t. There was always a population of thousands. As the average characteristics of the ancestral population to humans and chimpanzees changed, the group of thousands that eventually became human became more human-like generation after generation. The change from one generation to the next would not be immediately recognizable as it would be a subtle shift in the AVERAGE characteristics of the population as a whole. It is a continuum over millions of years, and most people cannot imagine the time frame. There was NO one point where daddy and mommy were apes and the little baby was a human.
Dennis puts this in perspective by using the analogy of the evolution of the English language. Consider the familiar verse in modern English from John 14:6—
Jesus answered, “I am the way and the truth, and the life. No one comes to the Father except through me.”
Even knowing what we are supposed to be reading, we can barely make out the sense of the words. Besides the spelling and grammar, there are letters that are no longer in use. It’s a stretch to say they are the same language, and yet, Anglo-Saxon incrementally became modern English over generations. If we were to view snapshots of this transition over time, that is to say, sample the “fossil record” of language, we would see the following “transitional forms” from the Middle Ages to the present:
Jhesus seith to hym, Y am weie, treuthe, and ye lijf; no man cometh to the fadir, but bi me. (Wycliffe Bible, 1395)
Iesus sayd vnto him: I am ye waye ye truthe, and ye life. And no man cometh vnto the father but by me. (Tyndale Bible, 1525)
Iesus saith vnto him, I am the Way, the Trueth, and the Life; no man cometh vnto the Father but by mee. (King James Version, 1611)
Jesus saith unto him, I am the way, the truth, and the life; no man cometh unto the Father, but by me. (King James Version, Cambridge edition, 1769)
This is a brilliant, and fruitful analogy. As Dennis says:
“As we know, these various translations are not instantaneous changes from one to the next. Rather, they are samples drawn at intervals from a continuous process. All along the way they remained the “same language” in the sense that each generation could easily understand their parents and their offspring. Over time, however, changes accumulated that gradually shifted the language. Word spellings, grammar, and pronunciations changed. Given enough time, it becomes more and more of a stretch to say the languages are the same—such as Anglo-Saxon and Modern English. Despite the striking differences we see now, the process that produced them was gradual. Additionally, there is no convenient point where we can say Anglo-Saxon “became” Modern English; the process was a continuum.”
The analogy of the way the average characteristics of a species can shift over time is apt. The total genetic instruction for building an organism is the genome. Our genome resides on 46 chromosomes, 23 from our father, and 23 from our mother. Females have two X chromosomes and males have an X and a Y chromosome. Each chromosome is a long string of DNA “letters”. There are four letters in the DNA alphabet. These letters are organic chemicals called: adenine (A), cytosine (C), guanine (G), and thymidine (T) linked together in a long string. The human genome has about 3 billion of these letters in each set of 23 chromosomes or around 6 billion “letters” altogether. In the analogy Dennis is making, we can consider the human genome to be a ‘language” shared by a population of “speakers”.
The DNA language changes over time in slight variations like treuthe > truthe > trueth to finally truth. Like in English, any change in one word is not that significant, the combined shifts of many words over generations is enough to radically change a language. Likewise, for a population of organisms; a shift from one allele of a gene to another will not have a large effect. The combined action of many such changes will significantly shift the characteristics of a population over many generations. Over time the genetic changes accumulate to the point where generations far removed from each other would not be considered the same species. Anglo-Saxon and Modern English then are like Indohyus and a blue whale.
Dennis then notes that another analogical way of thinking about the genome is that it is like a book. A genome has specific genes in a specific order, just as a book has specific words, paragraphs, and chapters arranged in a sequence. And now, dear blog readers, we are about to thrash about in the tall weeds of Genetics 101. It is very tempting to just quote the chapter at length. Though the book analogy is helpful, we should examine some differences between books and DNA sequences to better appreciate how geneticists compare two genomes to each other. This is where it gets a bit technical.
- Each DNA letter has a partner that it pair up with.
- Each chromosome has two long strings of letters
- These two strings twist around each other to form the “double helix” structure that Watson and Crick solved in 1952.
- The two strings separate during replication.
- Each is used as a template to make a new complimentary string.
- Imagine a long stack of children’s building blocks on its side.
- Imagine four shades of blocks corresponding to the four DNA letters—A, C, G, and T.
- Each shade of brick has magnets attached in a specific pattern on the side.
- C matches to G and T matches to A.
- Though DNA copying is highly accurate, it is not perfect, and copying errors arise.
- Copying errors arise through mismatched letter pairs i.e. a “mutation”.
- The next time the chromosome is copied, the mismatched pair will correctly specify its proper partner.
- The mismatched pair (the mutation event) becomes locked in for one of the chromosome copies.
- The result is a new variant in the population.
- Recent studies indicate that out of 3 billion letter pairs, about 100 mutate every generation.
- Like treuthe > truthe > trueth > truth, these subtle changes enter the population and may become more common over time.
- The properties of DNA make it a great way to store and replicate information, but not much else.
- Proteins are useful molecules made up of 20 (instead of 4) building blocks called amino acids.
- Because of their structural diversity, proteins are great at most biological functions but don’t transmit information well. So both DNA and proteins are needed.
- Since there are 20 amino acids and only 4 DNA letters, sets of 3 DNA letters are “read” to specify amino acids. There are 64 possible combination of DNA-three-sets called codons.
Most amino acids can be specified by more than one codon. For example, the amino acid, glycine, can be coded for by four different codons: GGA, GGC, GGG, and GGT. All four codons are equivalent in that they specify the same amino acid. Other amino acids can be coded for by up to 6 different codons. In other words, the amino acid codon code is partially redundant.
Dennis then gives a real example of a gene; the DNA sequence that codes for the insulin protein. Insulin being the protein hormone that regulates blood sugar in animals. So in Figure 2-5 the first 90 nucleotides and 30 amino acids for humans and dogs are compared.
Note we observe many correspondences and a few differences. Some DNA differences result in amino acid differences and some don’t. As Dennis says:
Now, in both species these “words” have the same “meaning”—both the human and canine genes produce a functional insulin hormone that regulates blood glucose levels. The fact that slightly different sequences can have the same function should not be a surprise; in many ways it is like the words treuthe, truthe, and truth, all of which carry the same meaning, despite their subtle differences…
In looking at the sequences above, we can see that there is good evidence to support the hypothesis that these two present-day genes come from a common ancestral population in the distant past… they are far more similar to each other than they are functionally required to be.
We can test this hypothesis further by looking at a larger data set. Humans are not thought to have shared a common ancestral population with dogs for a long time. When Linnaeus (1707-1778) drew up his taxonomy of animal life (prior to Darwin BTW) he famously placed humans and great apes in a category he called “primate” because of the close anatomical similarities. Consider these images:
While Linnaeus certainly was not thinking common ancestry, he naturally recognized that these species have a closer anatomical affinity to humans than other animals. So evolutionary theory predicts that these ape species share a more recent common ancestral population with humans than non-primate species such as dogs, do. If that is so, then their gene sequences should be a closer match to human sequences than what we observe in dogs. So let’s look at the example of insulin gene and include chimpanzees, gorillas and orangutans. What do we see?
What we observe for this short segment is that the gorilla sequence is identical to that of humans, except for one letter; the chimpanzee is identical except for three; and the orangutan is identical except for five, while the dog is different by 14. This level of identity far exceeds what is needed for functional insulin. We have failed to reject the hypothesis that humans share a common ancestral population with apes.