April 28, 2017

Adam and the Genome 3: Chapter 2- Genomes as Language, Genomes as Books (Part 1)

Adam and the Genome 3: Chapter 2- Genomes as Language, Genomes as Books (Part 1)

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.”

Now consider that verse in Anglo-Saxon from around the year 990 AD:

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:

OOPS, sorry, I meant 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.

Comments

  1. Goatse McGoatface says:

    So what about the soul? Do humans have souls? Do apes? Did our common ancestor? Or is this kind of talk meaningless and out of step with the times?

    • Good questions, but why hide behind the sparky pen name?

    • This is another subject fraught with controversy and subject to multiple interpretations. Nevertheless, it is a good discussion to have, as Chaplain Mike showed in his post, “Just a Shell?” Genesis 2:7 (KJV), says, “7 And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.” The Hebrew words for “living soul” are nephesh chayah, translated elsewhere as “living beings” and sometimes as “persons”. In the New Testament Greek, for example, 1 Corinthians 15:45 “And so it is written, the first man Adam was made a living soul; the last Adam was made a quickening spirit.” The word “soul” is psyche from which in the English tends to mean “mind”. Spirit is “pneuma” which as in the Hebrew “ruach” means breath, wind, or spirit. I’m trying to run the references in the Bible, but the search isn’t returning what I’m looking for, but basically, Ecclesiastes states animals have spirits that return to God and it says something similar in Psalms. What most Americans mean when they say “soul” is that immortal part of us that survives death and is given to us by God.

      So, and this is strictly my personal opinion, spirit (ruach or pneuma), meaning breath or life, plus matter (dust, dirt, flesh) equals living being or “souls, persons” in the ancient understanding. In the modern understanding, life is an emergent property, so a soul is also an emergent property as well. In my opinion, animals have souls i.e. are living beings, the difference between animals and us are; we are made after the “image” of God. So we are rational and, most importantly, morally and spiritually accountable to God, especially to be his “priests” in the “temple” that is His creation. That is my take, YMMV.

      • Goatse McGoatface says:

        Just humans? Not other apes?

        Or to look at it another way–all humans?

        (Notice that we have the same argument about human fetuses.)

        I think you’ll find that the Bible contains various views on death, not all of which involve personal immortality. Not that there is any reason to give any special credence to the Bible’s views of such things. Today, we understand that we are animals, and that the gods are created in our image rather than vice versa. The “soul” concept (understood as some sort of vehicle for preserving human consciousness forever, and / or distinguishing those with “human” rights from those without) makes no sense, and has no place in modern scientific thinking.

        • Adam Tauno Williams says:

          But we do have concepts of sentience, self-awareness, theory-of-mind, narrative memory – ideas far more specific than our ancestors had at their disposal.

          Research indicates this is a bit of a sliding scale. The average humans check all the boxes. Cetaceans and apes check most of the boxes. Dogs check a few of the boxes. Mice fewer. Lobsters … Of course – all these are averages; exceptional high and low performance in individuals are demonstrable.

          And sometimes it is hard to tell – quite possibly a cat simply has no interest in participating in our stupid test. You need to be very clever to test some things.

          This sliding scale of soul-ness does not bother me in the least [but it does seem to get some people into a tither]. Life is complicated – not tidy – … but didn’t we already know that?

          • “quite possibly a cat simply has no interest in participating in our stupid test…” So true. Are cats interested in anything, really?

            • Cats are definitely interested in many things. Or they are doing a good job of faking it, but then so are we.

        • “The “soul” concept (understood as some sort of vehicle for preserving human consciousness forever, and / or distinguishing those with “human” rights from those without) makes no sense, and has no place in modern scientific thinking.” Well, sez you, I don’t agree. We certainly are animals, as even the Bible says (Ecc 3:18), “I said in mine heart concerning the estate of the sons of men, that God might manifest them, and that they might see that they themselves are beasts.” The whole point of this particular post is how close, in modern scientific thinking, we are to the other beasts. And note I said “soul” was an emergent property, a concept of modern scientific thinking, but you blew right past that, in your haste to lecture this poor deluded Christian on modern scientific thinking. Thanks for playing.

        • Kinda related, here’s a question that came up in a men’s group I was at yesterday…

          Do demons have souls? When they stumbled across Jesus (or vice versa), were they “redeemable”? They certainly understood who Jesus was…so were they “save-able” from a spirit standpoint? Seems like all Jesus ever did was cast them out.

          Same with Satan. Is/was He redeemable? Does he have a soul that can be saved?

        • Clay Crouch says:

          Thank you for settling all the big questions for us in one short comment. You is smart. You is kind. You is important. You is da goat-man.

    • Adam Tauno Williams says:

      > So what about the soul?

      Define “soul”.

      • Exactly.

        My current thought on this – changeable at a moment’s notice, if someone offers a better “definition” – is this:

        A spirit created for communion with God.

    • What’s the first chronological biblical reference for a soul?

  2. Mike, your beginning paragraph seems to contradict what your first quote says.

    “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 the book you quote says:

    “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.”

    Now I think you were wanting to emphasize that evolution can be gradual, but in your opening statement you seem to rule out the possibility of substantial change within a generation, which the book, if I’m understanding this quote correctly, does not. Or is the book saying that evolution of an organism can be very slight over time while other organisms change substantially over time?

    • Mike the Geologist says:

      I think what Dennis is trying to say, and I am poorly conveying, is that incremental change occurs from generation to generation but is not noticed until the changes accumalte over many generations and result in a major shift in average population characteristics… or something like that, I am but a lowly geologist 🙂

  3. Adam Tauno Williams says:

    > “So how did we go from zero (humans) to thousands” is that we didn’t

    Some of this misunderstanding comes from the notion of “Extinction”. People very often speak of a species “dying-out”, being “replaced” by something else. In essence creating a cycle of extinction and replacement. Extinction->Replacement feels/sounds punctuated rather than incremental.

    But it rarely works that way.

    Generally one line gradually supersedes *itself* into one or more lines. Canis Mosbachensis [arguably the great^1000 grand pappy of the modern “dog”] no longer exists – it is extinct. But it did not “die out”. Some of its progeny, nearer to human populations [and the kind of climate humans like], trended one way, and other of its progeny, isolated from human populations [and in climates humans like less], went another way. The form identifiable as Canis Mosbachensis faded away – became extinct – but that did not happen via death, it happened through birth.

  4. Mike, I LOVED the take on how textural language has changed/evolved. Thanks for bringing that element into your post. It might not be a perfect analogy, but it certainly is worthy of contemplation and consideration in describing the potential for animal evolution/change.

    • The analogy is Dennis’, and is, in my opinion, brilliant. The change from old Anglo-Saxon to Modern English was gradual from generation to generation. Each generation understood their older generation, and were in turn understood by the next generation. But the overall transition resulted in a new language– Modern English, that barely resembled the ancient Anglo-Saxon from which it descended. It might not be a perfect analogy, but it is a darn good one. Just like a blue whale hardly resembles Indohylus, if you can grasp the language transition, you can grasp evolutionary transition.

      • Indeed.

        Hey, think about how cellphones have changed the way we communicate via visual “text”. You’ve got LOL and OMG and IMHO. And then you have all these:
        🙂
        😉
        😮

        More evolution, right under our eyes!

      • An extension of that language analogy that Dennis mentioned briefly but didn’t delve into, but I think might be interesting if someone were so skilled to elaborate (I am not) is the effect of isolating/blending particular languages/dialects/etc. through migration and other human movement over time and then apply that to the genetic effect of populations being isolated and/or blended

  5. Stepping back a bit from all the other conversations related to this…but, if large parts of Genesis are theological narratives telling a story of ancestry and/or Israel’s place in the world…

    Where does this leave the “God-breathed” aspects? From what I’m seeing, that’s just as much legend/theological statement as anything else. There was never a single instance where a deity breathed life into inanimate or animalistic objects, creating ‘souls’, especially immortal ones. That concept would have been foreign to OT Jews, introduced with Plato, and sharpened with NT Christians.

    We can see throughout history and philosophy how our concept of the soul developed, but a bigger question is how did sentience or logic and reason develop over time, creating all the underlining structures that later people called “the soul”.

    https://en.wikipedia.org/wiki/Soul

    Surprisingly, as always…I’m ok with all this, of knowing there is no such thing as a sou, of knowing God didn’t breathe life into man. 100% ok with it, it’s rather freeing and liberating, and in no way prevents anyone from ever living their life as Jesus instructed.

    • Mike the Geologist says:

      The way I see it Stuart, is that God-Breathed means God gives life. The Scriptures are God-Breathed because if you put your trust in them they lead you to Jesus, who gives you life. The ancients understood if you quit breathing you no longer had life. Same way if you bled out you were dead i.e. the life is in the blood. Its an ancient understanding that still has theological truth. What’s the difference between a self-replicating agglomeration of organic chemicals and YOU. Nothing, except you are alive and you are still you. What’s the dividing line between life and non-life, there isn’t one, its a continuum or as I like to put it; it is an emergent property. You are more than the sum total of the physics and chemistry and biology of the material that makes up you body. The whole is more than the sum of the parts. So our souls are us. We are embodied, yet more than just the body. The more is the emergent property. And if Jesus (and Paul) are to be believed, the MORE will be reunited with the body, and then a new property will emerge: the resurrection life. Jesus is the template for that emergent property, if it was not so, he would have told us so. I don’t need to figure it out, I just need to trust Him.

  6. As probably most readers/commenters here, I closely identified with Dennis’s Christian school experience, up through college and some grad school for me. Particularly disheartening, now at least, is the straw man caricature that was presented as evolution and those who accepted evolution, and for that matter was evolution was. I still remember evolution=a printing press explosion and a Hemingway novel is the result–and every evolutionist believes in evolution BECAUSE they don’t want to be told what is right and wrong by God. How I wish I could be back in time….

    • Headless Unicorn Guy says:

      But you took the red pill and are seeing how deep the rabbit hole goes.

      And looking around, you see Christians gobbling the blue pills like M&Ms.

    • It’s true. Once you confront the fact that you were lied to or misled by literally everyone in your surroundings, people for whom truth and honesty are top virtues…it’s a tough thing to overcome.

      • Nah, most are just clueless. That is my observation. Evolution isn’t a make or break issue. I mean, you will never be confronted with a Neanderthal walking into church one Sunday and throwing the whole congregation off kilter. A gay couple or a co-habiting couple could walk in (depending on denominational line drawings) and force everyone out of their neatly constructed paradigms at once. But Evolution, it isn’t something anyone has to deal with in the course of their life, except scientists and biblical scholars and those studying those things. The average church-going Joe doesn’t really deal with these issues and is quite comfortable to trust the real deceivers and maintain there is no Evolution, but they, themselves are not really able to discern the truth of it all, and, frankly, don’t really need to. You can be a doctor and just avoid the whole evolutionary issues, a chemist, a welder. It is only Scientists who are left struggling. And churches often have precious few scientists.

        • Depends on what you mean by “make or break issue.” While I agree with your basic premise, when the congregation makes even considering the option of evolution, yet alone accepting it, a mark that you can’t possibly be a Christian because you have given in to the devil and his thinking, then it isn’t a non factor.

  7. Burro [Mule] says:

    It seems to me that linguistic change is built into language to create the isolated populations needed for genetic drift to work properly. Yeah, I know. I’m a Nazi and a Trumpite, and such a one is not fit to live, but I have a sneaky feeling that I, and Freeman Dyson, are right about this.

    • …huh?

      • Burro [Mule] says:

        “…there is strong evidence, in our history and prehistory…to support the hypothesis that plasticity and diversity of language played a essential role in human evolution. It is not just a an inconvenient historical accident that we have a variety of languages. It was nature’s way to make it possible for us to evolve rapidly. Rapid evolution of human capacities demanded that social and biological evolution go hand in hand. Biological progress came from random genetic fluctuations that could be significant only in small and genetically isolated communities.”

        Freeman Dyson, “Clones or Clades?“, in Disturbing The Universe, 1979

        In linguistics as in biology, empires are suicide.

  8. God made man, but he used a monkey to do it…

    Devo

    https://www.youtube.com/watch?v=5JdS-sSKsBc

  9. The first set of images is pretty much how I picture this group at Saturday brunch except that we have more, and presumably better looking, women.

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