February 24, 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.

Klasie Kraalogies: As Mist Before the Sun: The Slow Relief of Unbelief (2)

The Anatomy Lesson of Dr. Nicolaes Tulp, Rembrandt

AS MIST BEFORE THE SUN: THE SLOW RELIEF OF UNBELIEF
By Klasie Kraalogies

Part 2

They say a little knowledge is a dangerous thing, but it’s not one half as bad as a lot of ignorance

• Terry Pratchett, Equal Rites

The great difficulty in telling a long and meandering story is knowing what to leave out. But what I can’t leave out in my story is the impact of learning – partly getting a university education, but also making a greed for knowledge and understanding a major driving force in my life.

I went off to university, and completed a B.Sc. (Hons) with Geology and Mathematics as majors. Geology quickly showed my that even with a lot of standing on one leg, squinting with one eye while singing the Paternoster, there is no way I could make the evidence of the world around me fit into the narrow, Young Earth Creationist view I had been taught. But what I did was to shelve matters, trying to see if maybe I can hit upon a previously unconsidered idea with which to make things work.

Then, two things happened. At the head office of the sect, I picked up a copy of a magazine emanating from a fringe Calvinist group. Also, I attended a lecture by a Bulgarian maths professor that introduced Gödel’s Incompleteness Theorems. The former opened my mind (if “opened” is the operative word?) to other types of theological thinking. The latter provided a way, at least temporarily, whereby I constructed what I thought was a clever way to reconcile my difficulties. I thought I was being clever – what I was doing was succumbing to sophistry, a postmodernist escape. Which is really funny in retrospect, because along with the rest of the Young, Restless and Reformed Crowd, I loved making fun of postmodernists.

I left the sect. Married by now, I had my children baptised in a Dutch Reformed Congregation, while also attending some other Calvinist churches. I learnt to get irritated by loud Young Earth Creationists, Baptists, and most Evangelicals. I started to appreciate Catholicism and Orthodoxy. Also during this time, I discovered Internet Monk. This was in the early 2000’s.  Under various pseudonyms I developed a presence online, including Michael Spencer’s old Boar’s Head Tavern and that other site, which some here might remember, Reformed Catholicism (I think that was the name). I was appointed to the board of a small Christian Classical School. Yes, all of that. My unrecognized postmodernism allowed me to work in geology, and still confess a lot of other things that just didn’t quite fit.

But, one can only deceive one’s self for so long. Shortly after immigrating to Canada (2007), I realised that I really couldn’t reject the scientific evidence anymore. This was at the time of the discovery of the Denisovan subspecies of the human evolutionary branch. I mention that, because as with many events, there is a particular final straw that makes that happen (I checked the dates – the article that caught my attention came out in 2010).  I admitted that to be consistent, I must admit to being a Theistic Evolutionist. You see, I quickly recognised the fact that acceptance or non-acceptance of evidence has epistemological consequences. If, like some Christians I know, I refuse to believe evidence, saying it is a lack of human understanding, or more common still, how can we know what is the truth, it also implies, explicitly, that we cannot absorb any other true information through our senses. Therefore, unless we are all gnostics, we must deny all knowledge. Epistemology is dead. Hence, either we follow the evidence, or we through all knowledge out, including the very Scripture we read. If you can’t trust your eyes, how can you trust words on a page?

This produced some peace for a period. Arriving in Canada, and looking at my local ecclesiastical options, we joined the LCC (Lutheran Church Canada, sister-church of the LCMS). Even there it wasn’t long before I was invited to join church council. Enthusiastic people soon get noticed. Of course, like the LCMS, the LCC is essentially a YEC-church. But I was prepared to live with that. At least we had a very liturgical congregation. That was fun…..

Next time: Crisis – Reason, Sociology and Information

• • •

Previous Posts

Just a “Shell”?

Vermont Skies 2014

I heard it again today, while attending the death of an elderly woman.

“This is not her. What we see here is just the shell. The real her is now in heaven with Jesus and with grandpa.”

And again a little later.

“It’s amazing to me how little seeing her shell bothers me. That’s not her. Everything that was truly her is now in heaven.”

Like it or not, this is what is understood at ground level as the Christian hope. One day we’ll cast off the shell of our body and go to our true home, where we’ll be free to be who we really are.

Problem: “everything that is truly who we are” includes our bodies. Right? We are embodied, vivified creatures. Dust and breath together, as Genesis 2 metaphorically affirms. In fact, I would argue it is impossible for us to imagine what human life is, what a human being is, without having some sort of physical, materialistic picture in our heads.

That’s why people say such mixed up things in the presence of death. On the one hand they express gladness that their loved one is free from “the shell,” out of their mortal body, that their “spirit” is in heaven. On the other hand, without any conscious regard for the inconsistency, they talk about how grandma is now “up there” dancing with grandpa or playing cards with Uncle Jack or holding the little baby she lost as a young woman. They simply can’t conceive of their loved in any other terms than what is familiar to them — this earthly, embodied life.

Let’s consider again what I consider to be a much more coherent and satisfying understanding of the full Christian hope. This is by N.T. Wright, from Rethinking the Tradition:

We should remember especially that the use of the word ‘heaven’ to denote the ultimate goal of the redeemed, though hugely emphasized by medieval piety, mystery plays, and the like, and still almost universal at a popular level, is severely misleading and does not begin to do justice to the Christian hope. I am repeatedly frustrated by how hard it is to get this point through the thick wall of traditional thought and language that most Christians put up. ‘Going to heaven when you die’ is not held out in the New Testament as the main goal. The main goal is to be bodily raised into the transformed, glorious likeness of Jesus Christ. If we want to speak of ‘going to heaven when we die’, we should be clear that this represents the first, and far less important, stage of a two-stage process. That is why it is also appropriate to use the ancient word ‘paradise’ to describe the same thing….

…In the New Testament every single Christian is referred to as a ‘saint’, including the muddled and sinful ones to whom Paul writes his letters. The background to early Christian thought about the church includes the Dead Sea Scrolls; and there we find the members of theQumran sect referred to as ‘the holy ones’. They are designated thus, not simply because they are living a holy life in the present, though it is hoped that they will do that as well, but because by joining the sect — in the Christian’s case, by getting baptized and confessing Jesus as the risen Lord — they have left the realm of darkness and entered the kingdom of light (Colossians 1.12-14).

This means that the New Testament language about the bodily death of Christians, and what happens to them thereafter, makes no distinction whatever in this respect between those who have attained significant holiness or Christlikeness in the present and those who haven’t. ‘My desire’, says Paul in Philippians 1.22, ‘is to depart and be with Christ, for that is far better.’ He doesn’t for a moment imply that this ‘being with Christ’ is something which he will experience but which the Philippians, like Newman’s Gerontius, will find terrifying and want to postpone. His state (being with Christ) will indeed be exalted, but it will be no different, no more exalted, than that of every single Christian after death. He will not be, in that sense, a ‘saint’, differentiated from mere ‘souls’ who wait in another place or state.

…Nor does Paul imply that this ‘departing and being with Christ’ is the same thing as the eventual resurrection of the body, which he describes vividly later in the same letter (3.20-21). No: all the Christian dead have ‘departed’ and are ‘with Christ’. The only other idea Paul offers to explain where the Christian dead are now and what they are doing is that of ‘sleeping in Christ’. He uses this idea frequently (1 Corinthians 7.39; 11.30; 15.6, 18,20,51; 1 Thessalonians 4.13-15), and some have thought that by it he must mean an unconscious state, from which one would be brought back to consciousness at the resurrection — so much so, perhaps, that it will seem as though we have passed straight from the one to the other. The probability is, though, that this is a strong metaphor, a way of reminding us about the ‘waking up’ which will be the resurrection. Had the post-mortem state been unconscious, would Paul have thought of it as ‘far better’ than what he had in the present?

This picture is further confirmed by the language of Revelation. There we find the souls of the martyrs waiting, under the altar, for the final redemption to take place. They are at rest; they are conscious; they are able to ask how long it will be before justice is done (6.9-11); but they are not yet enjoying the final bliss which is to come in the New Jerusalem. This is in line with the classic Eastern Orthodox doctrine, which, though it speaks of the saints, and invokes them in all sorts of ways, does not see them as having finally experienced the completeness of redemption. Until all God’s people are safely home, none of them is yet fulfilled. That is why the Orthodox pray for the saints as well as with them, that they — with us when we join them — may come to the fulfilment of God’s complete purposes.

Finally, lest you think I would rudely insist upon doctrinal precision when I’m visiting with grieving families and try to convince them, in the midst of fresh loss, that they should change their thinking about the future hope, let me assure you that I usually just stay silent and focus on being present and providing appropriate comfort. The last thing they need is a lesson in eschatology.

I may cringe when I hear them call the body of their deceased loved one a mere “shell,” but I don’t say anything. I just gather them at the bedside and lead them in prayer:

God of life, at this important moment we thank you that ______ is safe in your care. You tell us that to depart this life and be with Christ is far better, and so we pray that you would take _______ into your care and give her that joy and peace in your presence. May she rest in your love until the day of resurrection, when this mortal body will be raised and she will be remade, complete and new, in a whole new creation, where we will be reunited and there will be no more sickness, separation, and sorrow. Thank you that, whether we live or die, we belong to the Lord and that nothing can ever separate us from your love. Hold ______ and her family in your love until that day. In your holy name we pray, Amen.

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