April 19, 2019

Faith Across the Multiverse, Parables from Modern Science- Part 3, The Language of Biology, Chapter 7: The Genome Made Flesh By Andy Walsh

Faith Across the Multiverse: Parables from Modern Science

Part 3, The Language of Biology, Chapter 7: The Genome Made Flesh

By Andy Walsh

We are blogging through the book, “Faith Across the Multiverse, Parables from Modern Science” by Andy Walsh.  Today is Chapter 7: The Genome Made Flesh.  Walsh begins this chapter with a description of the TV show Orphan Black.  Orphan Black is a Canadian science fiction thriller television series starring Tatiana Maslany as several identical people who are clones. The series focuses on Sarah Manning, a woman who assumes the identity of one of her fellow clones, Elizabeth Childs, after witnessing Childs’ suicide. The series raises issues about the moral and ethical implications of human cloning, and its effect on issues of personal identity.  Different mothers gave birth to them, different families raised them, but they all start out from the same genes.

This clone narrative is a useful device for exploring the roles of nature and nurture in human development.  In this fictional realization, the characters are nearly identical physically and significantly divergent in personality and behavior.  Reality doesn’t split so neatly into nature determining biology and nurture determining psychology, as anyone who has known identical twins can testify to.  I have a friend who had triplets, two boys and a girl with identical genes, raised in the same family under the same Midwest, small-town Indiana environment, but each child had their own unique personality.

In the last chapter, Walsh talked about symmetry and asymmetry.  A fully symmetrical system has everything interchangeable, so nothing changes.  Asymmetrical systems have differences, gradients, structures, some aspect that has the capacity to meaningfully change.  All of us start out in a relative symmetrical place, as a single cell.  Then that cell begins to divide into two, four, eight, and so on.  Still, all those cells have the same DNA, which creates another sort of symmetry.  Eventually, we wind up with a wide assortment of cells, tissues, and organs, none of which are interchangeable. How does that happen?

Well, cells have membranes, barriers that keep the insides on the inside and outsides on the outside.  There are two layers of molecules called fatty acids making up the membrane.  The fatty parts face each other in the middle portion of the membrane; they would feel oily or greasy if we got enough together for a macroscopic amount we could sense.  Like oil, they don’t mix with water, and a significant portion of us is water.  The acid parts of the fatty acid in one layer of the membrane face the outside of the cell, and the acid parts of the other layer face the inside.  Thus we have our first biological asymmetry.  Asymmetries will play a key role in allowing our cells to differentiate into different parts as we develop.  Since what goes into a cell from the outside affects how it develops, so controlling the flow in and out is important.  That concept will also be relevant to the metaphorical application Walsh is trying to make.

Cells have gates that permit transit.  The gates are proteins and the “keys” are molecules with specific chemical signatures.  Think of a door with a fingerprint scanner, the key is not a separate thing that you carry, but an integral part of who you are.  Once inside the cell there are other membranes and protein scaffolds that serve as conduits along which other proteins carry inbound and outbound “payloads” e.g. food and wastes. The most relevant compartment for our purposes is the nucleus, which stores the DNA representing a complete copy of our genome.  That DNA represents information that the cell needs to carry out its various functions.  This includes information to guide development from a single cell to a ten-trillion-member strong community known as you.  So we need to understand how the information in DNA gets put into action.

A DNA molecule is a twisted ladder-like stack of building blocks called nucleotides. There are four types of DNA nucleotides-adenine, cytosine, guanine, and thymine-or A, C, G, and T, for short.  If you could peer into any one of your body’s 50 trillion cells, you’d find a fantastically complex and busy world. At the center of this world you’d find a nucleus containing 46 molecules called chromosomes-23 from your mother and 23 from your father. These chromosomes are basically an instruction set for the construction and maintenance of… you.

These two long stacks of building blocks fit together like two sides of zipper, but there’s a rule involved: adenine only pairs with thymine, and cytosine only pairs with guanine. So each rung in the DNA ladder is a pair of nucleotides, and each pair is either an A stuck to a T or a C stuck to a G.

You’ve got six billion of these pairs of nucleotides in each of your cells, and amongst these six billion nucleotide pairs are roughly 23,000 genes. A gene is a distinct stretch of DNA that determines something about who you are.  Genes vary in size, from just a few thousand pairs of nucleotides (or “base pairs”) to over two million base pairs.

Genes are often called the blueprint for life, because they tell each of your cells what to do and when to do it: be a muscle, make bone, carry nerve signals, and so on. And how do genes orchestrate all this? They make proteins. In fact, each gene is really just a recipe for a making a certain protein.

And why are proteins important? Well, for starters, you are made of proteins. 50% of the dry weight of a cell is protein of one form or another. Meanwhile, proteins also do all of the heavy lifting in your body: digestion, circulation, immunity, communication between cells, motion-all are made possible by one or more of the estimated 100,000 different proteins that your body makes.

But the genes in your DNA don’t make protein directly. Instead, special proteins called enzymes read and copy (or “transcribe”) the DNA code. The segment of DNA to be transcribed gets “unzipped” by an enzyme, which uses the DNA as a template to build a single-stranded molecule of RNA. Like DNA, RNA is a long strand of nucleotides.

This transcribed RNA is called messenger RNA, or mRNA for short, because it leaves the nucleus and travels out into the cytoplasm of the cell. There, protein factories called ribosomes translate the mRNA code and use it to make the protein specified in the DNA recipe.

If all this sounds confusing, just remember: DNA is used to make RNA, then RNA is used to make proteins-and proteins run the show.

The point Walsh is making is that developmental biology has features of chaotic dynamics and strange attractors that he talked about in Chapter 3.  Complex systems often seek to settle in one specific situation. This situation may be static (Attractor) or dynamic (Strange Attractor).  Recall this quote from Walsh in Chapter 3:

This tendency of certain dynamic systems to stay with certain bounds despite perturbation, or what might be seen as bumps in a predetermined road, helps me to think about grace. More precisely I find it easier to believe that grace can coexist with God having a purpose or will for how the world turns out.  The metaphor of a bump in the road, a little deviation from the expected before returning to the intended path, conveys a similar idea.  At the same time, a road is static; these strange attractors are dynamic.  The stability of the pattern emerges out of the dynamic activity of the system, not in contrast to it.  Thus I find strange attractors a useful additional metaphor when thinking about grace.

As with chaotic dynamics, there are certain degrees of freedom; for example, each skin cell has the opportunity to respond or not to the “call” of becoming a follicle.  Development does not require that any one cell make a particular choice in that regard.  And yet the interplay of positive and negative feedback provides some high level stability of outcome and structure, just as with strange attractors.  Once again, Walsh says, the emergence and continued existence of life thrives on grace.

So now Walsh wants to consider the implications of all these biological ideas for how we are able to function together as the body of Christ, after Paul’s use of the body metaphor in 1 Corinthians 12.  The first thing that stands out to him is the pattern of growth.  The church began with a single individual, Jesus.  Just as the single cell represents all of the necessary potential to become a fully formed human, so Jesus represents the fullness of human potential that he wants his church to realize.

To realize that potential, Jesus began his ministry by recruiting a small group of disciples to labor with him.  It was these twelve who would spread out and start churches elsewhere, which in turn sent missionaries out to start more churches, and so on.  These subsequent movements replicated this same pattern of growing from individuals or small groups that expanded as circumstances allowed.  Walsh says:

There are clear advantages to this approach, in the sense that often one or a few can go places and do things that a large group cannot.  The challenge is for those folks to be flexible and able to do many jobs, because they are all that there is.  The apostle Paul captured this idea when he wrote, “I have become all things to all people” (1 Corinthians 9:22).  In the same way, your cells can’t specialize too quickly in development; they need to be able to maintain that potential to do a wide variety of jobs in the future.

As the churches spread in the first century, there began to be specialization in response to context.  The church is Jerusalem among the Jews had one context.  Other groups were developing in Turkey, Greece, and Rome, in the context of the Greek, Roman, and other cultures of those nations.  The practices of those churches began to diverge, since communication was slow, making it logistically difficult to keep synchronized.  The local environment was bound to be influential.  When the leaders of different churches discovered that they had different practices the human tendency was to think one group had to fall in line with the other group.  Ultimately, however, those leaders mutually decided to recognize that their core principles could in fact be expressed in different ways depending on the context.  Walsh says:

This does not mean, however, that anything goes.  Think about our cells; they have a wide latitude to express different genes in their particular contexts, but they can’t just invent new genes on the spot.  For the church, the Bible serves the role of the genome.  Even as those early churches were discovering how to best express their principles in their different contexts, they agreed on the texts that would guide them in their decision making.  Everything that they did had to arise from those texts and be consistent with them, otherwise they could not claim to be part of the Christian church, the body of Christ.  But they had freedom to determine what that looked like in their environment.

If we push a little further on the idea of the Bible as the genome of the church, we come to an interesting observation.  There is no single cell that expresses every single gene in your genome.  There are some core genes that they all use, such as the ones that are involved in making proteins form DNA.  Every cell needs to be able to do that.  But other sequences are only used by certain cell types.  And even then, they aren’t all used all the time; some play a role at one stage of development, while others are relevant to mature cells, and still others only come into play in response to a certain external signal or condition.

Likewise, the church, rather than the individual Christian, is the unit that expresses the entirety of the Christian genome.  After all the Bible is pretty big book, making it practically challenging to keep the whole thing in mind all at once.  Even when we are trying to live according to the Bible, we tend to be thinking about a few verses or a group of ideas rather than the entire Bible.  Rather than trying to pretend that we can do otherwise, we can embrace that arrangement as the way things are meant to operate.

I think Walsh displays his Evangelical Protestant roots here.  Remember, he is a writer for Intervarsity Christian Fellowship and Christianity Today.  I expect some pushback today from our Catholic and Orthodox commenters.  I think he has the cart before the horse here.  The Church isn’t what the Bible says it is, the Bible is what the Church says it is.  I used to believe the Evangelical position; the New Testament defines what the Church is, we have to get back to the plain reading of the Bible, if one wants to be the New Testament Church.  I idealized the early Church as some kind of pure entity that existed in the pages of the New Testament.  One needed to distill one’s experiences and ideas from the encrustations of man’s traditions and Constantine-polluted apostasies of the Nicolaitanes and Laodiceans until one reached the 7-times distilled pure essence of the New Testament Church.  Except, of course, no such thing ever existed.

But still, Luther had a point; the first followers of Jesus witnessed to all succeeding followers.  And that witness, oral at first, was eventually written down by faithful, Holy Spirit inspired followers so it would not be lost, and we would have a reliable and authoritative guide.  As Luke said, in the beginning of his gospel:

So many others have tried their hand at putting together a story of the wonderful harvest of Scripture and history that took place among us, using reports handed down by the original eyewitnesses who served this Word with their very lives. Since I have investigated all the reports in close detail, starting from the story’s beginning, I decided to write it all out for you, most honorable Theophilus, so you can know beyond the shadow of a doubt the reliability of what you were taught. (Luke 1:1-4, the Message).

And Walsh does say this:

The role of context and heritage in the development of our church bodies helps to explain why we don’t all wind up looking the same, either individually or as congregations and denominations, even though we read the same Bible.  At the same time, it highlights the reality that the Bible does not fully determine everything about our Christian practices and beliefs, just as our genome does not fully determine our biology.  That doesn’t mean any aspect of our Christianity that is not fully determined by the Bible is wrong.  It is simply a recognition that the Bible isn’t a complete rule book for every decision we might have to make, which is fine since it neither claims to be nor needs to be.

I don’t think Walsh is too off base here.  Even given his obvious Protestant perspective.  For instance, read this article by Father Stephen Freeman, my go-to Orthodox guy.

The money quote from Father Stephen (in my opinion):

Yes, the Scriptures are theopneustos (“God breathed”), but so is every human soul. The God-breathed character of the Scriptures does not exalt them over us but raises them up to the same level as us. For ancient authorities (and the Orthodox faithful to this day) were Baptized into the death and resurrection of Christ and were thereby united together with Him. The Church was not and is not “under” the Bible, for it cannot be. Christ is Head of the Church, part of His Body. Is Christ “under the Scriptures?” All of the “lists” that are cited in the notion of the evolution of the Canon are lists of what the Church reads. And the Church reads them in her services as the Divine Word of God, just as the Church herself is the Divine Body of Christ, just as the Liturgy is the Marriage Supper of the Lamb, etc. The “Canon” of Scripture is as much a statement about the Church as it is about the Scriptures.

I can get on board with Father Stephen and Andy Walsh here. I think they are both basically saying something similar.

Comments

  1. Asymmetry systems are par for the course of human experience; some things are evidently closer to being symmetrical, but none meet the criteria for perfection that symmetry implies. All other things being equal, there are all kinds of ways for a thing or event to be asymmetrical, but only one way of being symmetrical. Do we ever encounter a truly symmetrical thing or event in human experience, or is symmetry an abstract idea not actually encountered in nature? Does science know any phenomenon that are (perfectly — but it seems to me that you can’t have a little symmetry– it’s either there or it’s not) symmetrical? Or is perfect symmetry like a perfectly geometrical object, not existing in nature; i.e., all existent things are more-or-less asymmetrical? If real symmetry does not exist in nature

    • Adam Tauno Williams says:

      > If real symmetry does not exist in nature

      There is a bit of fast-and-loose with the meaning here – which is OK, he’s making a point. Just like most talk of DNA/RNA skips over the terrifyingly complex Ribosomes and their “DNA” [the things that do that zipping and unzipping].

      Scientifically, or at least in terms of Physics, “symmetry” means stable/no-change under variant conditions. Which is pretty far from what he is talking about.

      Then Quantum Chemistry [yep, that is now a thing] has its own meaning for “symmetry”. Thier symmetry is used, somehow, I don’t quite get it, but I don’t know if the notion of “perfect” is even applicable. Mostly QC is [I think] about creating crystalline structures on a molecular level that are deviant from something-like-perfect in some very precise way – – – superconductor research does a lot of that kind of thing.

    • Mike the Geologist says:

      “Does science know any phenomenon that are (perfectly — but it seems to me that you can’t have a little symmetry– it’s either there or it’s not) symmetrical? Or is perfect symmetry like a perfectly geometrical object, not existing in nature…”

      I’m hard pressed to think of perfect symmetry existing in nature, it is most likely as a perfectly geometrical object, more of an ideal. However, the example that came to me immediatley were aquifers that can be modeled as obeying Darcy’s Law. The conditions to apply Darcy’s Law are that the aquifer must be homogenous and isotropic in its properties. Think sandbox with uniform grains of sand. Some glacial aquifers approach this well enough that the flow and contaminant tranport equations work as very useful approximations. In other words, close enough for government work 🙂

  2. senecagriggs says:

    My take on nature vs nuture

    70% nature; in other words, 70% of who you are – including personality are established in your genetic code. 30% is the environment you were reared in [nuture].

    For instance; are you a restless, fidgety type of individual [ such as I am ]. You were born with that propensity. It cannot be nutured out of you though it may become somewhat more disciplined.

    Obviously, IQ is established at birth but one child with an IQ of 110 might master Algebra with excellent teaching and another might not master algebra due to inferior teaching.
    [ Personally I think there’s a math gene – it missed my train.]

    70%

    Believing in “tabula rasa” is believing in unicorns. No one is born a “blank slate.”

  3. Burro (Mule) says:

    For the church, the Bible serves the role of the genome.

    Irenaeus seemed to think differently. I am not a patristics scholar, but enough of a veteran of the Internet apologetics wars of the early 00s to remember this quote from Irenaus:

    Rather, the canon of truth expresses the correct hypothesis of Scripture itself, that by which one can see in Scripture the picture of a king, Christ, rather than a dog or fox.

    Is there anything in the biological mechanism that guides how an organism is created from the template implied in the DNA/genome? I am thinking it is the RNA. If this is the case, then it would be perfect to consider the Scriptures as the DNA/genome of Christianity and the Apostolic tradition as the RNA. Or, in another metaphor, as a diamond in its setting displaying far more brilliance in the correct setting than it would sitting on a mechanic’s oil rag.

    Then He went down with them and came to Nazareth, and was subject to them, but His mother kept all these things in her heart. . It is this contemplation of Christ by the Blessed Virgin that appears to me to be the root of all Christian epistemology.

  4. Christiane says:

    ” I expect some pushback today from our Catholic and Orthodox commenters. I think he has the cart before the horse here. The Church isn’t what the Bible says it is, the Bible is what the Church says it is.”

    Yep

    The early Church was strangely consistent in its ‘Euangelion’, it’s ‘proclamation’: CHRIST IS RISEN

    And the early Church which flowed out from Jerusalem had established Apostolic traditions that were similar in all the first major centers of Christianity: Jerusalem, Rome, Antioch, Alexandria, Asia Minor, etc. . . . ways of praying, oral ministry based on the teachings of the Apostles . . . in the earliest days, even the Holy Gospels were not yet written down, BECAUSE THEY THOUGHT OUR LORD WOULD RETURN IMMINENTLY

    But when Our Lord tarried, the ‘deposit of faith’ began to be written down, and shared, and eventually collected, from which the Councils formed the ‘canon’ . . . . and in the ‘canon’ was the Book of Acts, written long after the early Church had begun its mission

    so yes, ‘push-back’, but not adversely so much as wanting Bible-believers to understand that there were many who came before them who worked hard to see that the sacred Scriptures would one day be delivered to future members of the Body of Christ . . . and that long effort is another story in itself;
    but without doubt, the Apostolic Church existed prior to the selection of the canon

    • Headless Unicorn Guy says:

      “You adapt and go on. Like the Jews after Rome destroyed their Temple and scattered them over the Empire. Like the Church after the last Apostle died without Christ returning and they realized they had to dig in for the long haul.”
      — from “Dyads”, by Ken Pick and C Alan Loewen in Infinite Space, Infinite God II

  5. Headless Unicorn Guy says:

    I idealized the early Church as some kind of pure entity that existed in the pages of the New Testament. One needed to distill one’s experiences and ideas from the encrustations of man’s traditions and Constantine-polluted apostasies of the Nicolaitanes and Laodiceans until one reached the 7-times distilled pure essence of the New Testament Church.

    Wahabi Islam also has this obsession with returning to the Original Pure Islam As It Was In The Days of The Prophet.

    Look where it got them.
    Just as real-world experience starts debugging their religion (as it has ours), they wipe it and reinstall the 1.0 Beta version.

  6. Dana Ames says:

    Well done again, Mike the G. Grateful for your clear summaries, and that your go-to is Fr Stephen. You will not be steered wrongly from that source.

    I don’t have too much pushback, only to reiterate some of what Christiane said. The quote from Luke’s gospel says something: …”so you can know beyond the shadow of a doubt the reliability of what you were taught.” What Theophilus was taught wasn’t “the Bible” as we know it, because it didn’t exist yet. The early Church had the Jewish scriptures, and its teaching was largely the interpretation of those scriptures through the lens of the death and resurrection of Christ – reading backwards, so to speak, as Christ explained it on the road to Emmaus. So the reliability noted is about the teaching, not “the Bible.” Again, back to interpretation…

    And this: “Jesus represents the fullness of human potential that he wants his church to realize.” Yes, Yes, Yes! Christ is the first Truly Human Being. This is how he created us to be: able to develop in virtue in order to act in self-giving love toward God and others. Jesus did this not only from his divine nature, but also from his human nature, always open to the Father and the Spirit. He could not have loved from his human nature – or even become incarnate in the first place – if that nature was in essence a “sin nature”, or if it was hopelessly broken beyond repair (“totally depraved” or some like supposition). Becoming virtuous isn’t some way to circumvent Christ’s “finished work on the cross” – it’s what baptism into his death on the Cross is supposed to enable. It’s not about building up some kind of merit in order to persuade the Father to let us into “heaven” – it’s learning how to be formed in order to have a basis from which to live in the manner in we were created to be as humans.

    One of the things about Evangelical theology, and western theology in general, that made no sense to me was that I couldn’t find anything good about being human, even after having prayed to acceptJesusChristasmypersonalLordandSavior and “received forgiveness.” (Doesn’t that make my salvation dependent upon MY decision and subjective feelings rather than Christ’s work? But I digress…) There was no point to humanity except to show God’s glory (so is God some kind of a narcissist?), or so that we could go to “heaven” and perpetually worship, or some other such abstract purpose not ultimately related to our complete healing; we might have just as well been created as a different kind of beautiful plant,or gemstone… I couldn’t find a satisfying answer to the question, “Why did God create humanity?” Sorry Lutherans, but Luther’s image of humanity as “snow-covered dung” never ever worked for me. The value of humans was that we were created in the image of God, but again, the usual descriptions of what that meant didn’t go far enough for me – certainly not far enough to justify or even connect with the purpose of Jesus’ death. It was a big, fat dead end, with no understandable basis for the dignity of humans in the big picture of things. In the east, it’s way different…

    Not sure if “To realize that potential, Jesus began his ministry by recruiting a small group of disciples to labor with him” is supposed to be an analogy for cell division/differentiation. If it is, I’m not sure it’s an apt one. Maybe I’m misunderstanding.

    Dana

  7. . i have an interesting argument about the existence of god: what if we will see a self replicating robot ( lets say even with dna) on a far planet? do we need to conclude design or a natural process in this case? remember that according to evolution if its made from organic components and have a self replicating system we need to conclude a natural process because it has living traits. but we know that even a self replicating robot is evidence for design. therefore a penguin for instance need design too

    check also this evidence against evolution

    https://answersingenesis.org/evolution/

    have a nice day