It's Impossible To Love The Truth And Deny Evolution: Part IV - On Speciation

As we've seen in the last three blog posts, it's impossible to have even the sketchiest understanding of biology, seek the truth, and fail to observe that genes provide an undeniable map of evolution. In biological evolution, we know that taxonomic ranks are consistent (kingdom, phylum, class, order, family, genus, species) and we know that genetic sequencing and our observations of the tree of life are also consistent with each other, where every species that is supposed to have evolved from its ancestors fits into the tree of life exactly as is expected if we are genetically related – there are no inconsistencies or anomalies. The computational information within every piece of DNA contains the history of the mutations of each generation, where every single living thing fits into these nested hierarchies of similarities and differences. And the pattern of relatedness that can be observed between any pair of living things through genetic resemblances, and the fact that every single time we do this they fall consistently and hierarchically within a family tree of relatedness, means evolution is as undeniable a fact as there is.

With this in mind, be wary of one trick creationists play when hearing this. They'll say they admit that there are genetic changes within species, but God created all unique species in their 'kind' and no single species ever evolved into another distinct species. Here is an example of the kind of thing they say, from the execrable Answers In Genesis site:

"As creationists, we must frequently remind detractors that we do not deny that species vary, change, and even appear over time. The biodiversity represented in the 8.7 million or so species in the world is a testament, not to random chance processes, but to the genetic variability and potential for diversification within the created kinds."

Let's not focus on the long-standing misunderstanding about evolution being "random chance processes" (it is not), as I've covered that in other blog posts, but instead focus on the attempt to mislead by denying that creatures can evolve into different species. The first thing to point out here is that just as God gave Adam the dignity of naming the animals - which is not a literal story, of course, but a story that conveys the sovereignty and responsibility God has given humans over the planet. It is also humans who get to name creatures according to markers, and it is those markers that we've called 'species', based on our empirical observations in biological evolution. 

We have classified two organisms as being different species if they will not or cannot produce fertile offspring together. That is how we've defined species - it has nothing to do with how different things look. Two organisms can look very similar and be a different species, and they can look quite different and still be the same species. Speciation is usually the consequence of gradual change in isolation from the species from which it departed. So as the progeny of each generation accumulates more and more slight genetic differences, at some point there is enough distinction so that some of them will not or cannot produce fertile offspring. At that point, it is not hard to understand that the future generations of these two different species will be growing farther and farther apart in whatever changes happen in them because they will not interbreed.

At this point you have two separate branches on the family tree that constitute two different species. Some species adapt to live so closely together that they cannot survive without one another. We, for example, cannot live without bacteria in our guts. There are also conditions under which two species have merged, and the genome of one has been almost completely transferred into the other, such as when bacterial consortia are found. A consortium is a group of different bacteria where the waste product of one, be it ammonia or oxygen or hydrogen sulphite, etc, is the food of another. The material coming into the consortium is recycled, often leaving a very efficient colony. The transfer of materials between consortia members is limited by the surface area that they can share. If only one member could get inside another then the whole process would be even more efficient. This has happened at least twice in the history of life (although probably much more often), including in our lineage. Once one species is inside the other, a strange situation occurs. Both have separate genomes that compete with one another, yet they still rely on one another. It is like a battle between co-dependent friends.

As natural selection tends towards survivability on a fitness landscape, and as interbreeding has now ceased, new species will gradually become more and more genetically different over time from the creatures with which they were once more closely related. It is perhaps difficult to imagine how those gradual changes could produce so many diverse creatures in the animal kingdom, and why it can be hard for creationists to believe humans are genetically related to chimpanzees, elephants, cats and fish. But if you think of the rich diversity of domesticated dogs in just a few thousand years of artificial selection in dog breeding, and a few tens of thousand of years since their descent from grey wolves, then it should be possible to contemplate how much diversity of change can occur with the animal kingdom over millions and billions of years.

This is a passage from Francis Collins’ brilliant book The Language of God, in which he sums up the sheer magnitude of time that we are considering:

“If the 4.6 billion years of the earth’s existence from initial formation to today were compressed into a twenty-four hour day with the earth being formed at 12:01am - life would appear at about 3:30am.  After a long day of slow progression to multicellular organisms, the Cambrian explosion would finally occur at about 9pm. Later that evening dinosaurs would roam the earth. Their extinction would occur at 11:40pm, at which point the mammals would begin to expand. The divergence of branches leading to chimps and humans would occur with only one minute and seventeen seconds remaining in the day, and anatomically modern humans would appear with just three seconds left. It is not surprising that many of us have a great deal of difficulty contemplating evolutionary time.” 

The human genome project has provided for us accurate information about the whole history of evolution through analysis of DNA and the chain of events which led to ourselves and other primates. Scientists are even very sure that they know at which point in the tree of evolution the chromosomal fusion occurred in our ancestors for Homo-sapiens to evolve. 

I am certain that most of the Christian objections to the long history of evolution on our planet are psychological objections; after all, we are so used to seeing that if the devotional aspect of our inner-self has planted a tree of Divine hope in our hearts, the harsh realities of a long protracted ‘tooth and claw’ evolutionary process tend to wave a threatening axe in front of the tree. But it is not so.

It's Impossible To Love The Truth And Deny Evolution: Part III - Assigned DNA Codes

 

Evolution-denying creationists actually believe that God created every single species as entirely distinct from every other species, so that there is no evolutionary connection at all. That's why they say misinformed things like they believe in microevolution but not macroevolution (note: this bogus distinction as an argument against evolution is not one that anyone who understood science would ever make). If God had wanted to create all species as entirely distinct, not giving the appearance of having any evolutionary connection, then the genetic relationships between species is not something you'd expect to see in a single act of creation. All of the world's organisms (with the exception of a few bacteria and archaea strands) use the exact same set of 20 amino acids to code for their proteins. And with that set of 20 amino acids, they use the same specific 3-bit DNA sequences to code for their specific amino acids. 

Why would God do that if we are not genetically related to all other species, and they to each other? It's especially strange when you look at the genetic sequence for these same-function genes in a bacterium and then at the genetic sequence for the same protein in a human - they have a remarkable similarity. In fact, some of the genes are almost identical, despite being hundreds of bases long. In a special act of creation, like the one to which the Genesis 1 literalists subscribe, would God really have wanted to create a system in which we share the blueprinting for the same proteins with the bacteria in our mouth?

But it gets even deeper. If each of the world's creatures were all created in a single act of creation, this 3-bit DNA sequence could have easily been assigned to code differently for the 20 common amino acids between groups; and furthermore the DNA sequences themselves could have been radically different between groups, or radically unique to species. God could have shuffled it around and made every species different for these attributes; with a 3-bit system of 4 varying nucleotides, and with a total of 64 different codons being issued across 20 different amino acids independently, there are literally enough combinations of codons and amino acids to assign each living species its own unique genetic code. In other words, there is absolutely no reason for God to give each organism the same genetic coding blueprint, and exhibit the computations of the relational distance of every species to each other, unless He wanted to make it look like all evolved in the same family tree of life over billion of years. Creationists are encouraged to go figure that one out! 

Why Did God Use So Much Space & Time?

A conversation came up the other day, in which I was asked why I thought God decided to spend such an inordinate amount of time and space to do His creating. Here are my thoughts on the matter.

Given that the universe is 14 billion years old, and that life has been evolving on this planet for over 4 billion of those years, one might reasonably ask why God chose to create nature over such vast expanses of time and space when He could have wrapped it up a lot sooner. I think the first thing to note is that in doing it this way, God has created a universe with lots of information that gets rinsed out in the mathematical wash. In other words, the notable things in the universe - like stars, planets, chemistry, biological life and, ultimately, humans - are highly unrepresentative of the exceeding mathematical profligacy in the rest of the universe.

This seems to be a truth reflected in the natural order of things: there is a plethora of thermonuclear spillage when planets are created; there are dozens of thorns for every rose; there are many more non-beneficial mutations in DNA than beneficial ones; there are millions of sperm that are unsuccessful alongside the one successful one that engenders a fruitful union in fertilisation. Even in the arts, or the economy, or in trade-based competition, or in sport, or in epistemology, the winners are far outnumbered by the losers.

How much truer that is of life in the universe too. To consider just how vast even our galaxy is; if you shrunk our galaxy to the size of the earth, then the solar system we inhabit within that galaxy would be about the size of a bowling ball. And as far as we know, we are the only life in that whole galaxy, maybe even the whole universe (a remarkable fact if it's true, given that there are around 1 billion trillion stars in the observable universe). One thing is abundantly clear: the special things in nature are very very rare and highly unrepresentative of the rest of the mathematical baggage in it.

The upshot is, there are many patterns in physics that are mirrored in human behaviour too, especially when it comes to power laws, and Pareto distributions. Perhaps the nature of the universe is some kind of symbolic representation of deeper truths related to God's creation story. Perhaps it's a part of the 'all good things to those who wait' philosophy, or a 'big rewards to those who work hard' philosophy, where value comes at a cost, and takes time and effort. All the most impressive designs in human terms require prodigious amounts of planning, foundational work and intricately executed design techniques that factor in the complexity of the whole project, not just individual parts.

Knowing how we emotionally and intellectually engage with reality at a human level, I can conceive of what might be behind the Divine wisdom of a vast, lengthy creation story, in which the banality of the gas, dust, rocks and gravitational and magnetic fields could represent a symbolic demystification of creation as a fait accompli event spanning much shorter execution time. Perhaps the vastness of creation is God's way of illustrating just how much cosmic magnitude went into the intellectual process - and how comparably meagre our own intellectual prowess really is in trying to fathom such a mind. Intelligence is, after all, the ability to explore avenues of possibility by sifting and selecting - so why should we be surprised if God exhibits this with the creation of the universe, like all artistic geniuses do? Perhaps we shouldn’t expect anything less.

We are told two big things about this creation in terms of God's cosmological masterwork: in Romans 1:20 we are told that "Since the creation of the world, God’s invisible qualities—His eternal power and divine nature—have been clearly seen, being understood from what has been made, so that people are without excuse." And in Psalm 19, we are told that "The heavens declare the glory of God; the skies proclaim the work of His hands". That is perhaps a good conclusion one can draw for why God used such vast amounts of time and space: they are the revelation of the huge mathematical permutations in designing something so complex: a design that has His fingerprints on it in the constitution of the mathematical bias written into nature's fundamental blueprint of a biased random walk. And if you don't understand how amazing a fundamental blueprint of a biased random walk is, you don't understand it at all. Consequently, a signature from God of that level of mathematical genius is going to require a physical substrate spanning vast stretches of time and space, just as a painter would require a vastly spacious canvas in order play out the exhibition of his artistic genius on a grand, iridescent scale.

Linking those two concepts together: the vastness of space and time, and the highly unrepresentative pockets of order painted onto a giant canvas of disorder - ask yourself this. Don't we feel that bit more special being one in a billion than one in a small group? If Jack says to Jill "I love you more than anyone in our social group" or "I love you more than anyone in our church congregation" we all know that that is not anything like as powerful as saying “I love you more than anyone else in the world”. The more unrepresentative a love is when it deviates from the mean of weighted experience, the more it is treasured as something amazingly rare, special and wondrous. Perhaps God’s capacious expanse of the skies and His chronologically extensive timeframe for dong His creation is an illustration of just how exorbitantly rare, special and wondrous we are.

Or maybe think of it in terms of the mathematically biased random walk - perhaps as redolent of our two beloveds, Jack and Jill, having no chance of meeting without their mutual friends getting together and making special arrangements for that to happen. Perhaps those two beloveds would have been lost without the intervention of those that loved them. And perhaps when we think of the vastness of the matter in the universe, that those particles would be 'lost' in the interstices of a prohibitively large search space without God’s intervening genius to bring them together with the blueprint of a biased random walk. The vastness of the universe and the broad timescales could well be an exhibition of the Divine genius (Romans 1) unlocking the vastly complex combination lock that helps gritty 'lost' matter 'become 'found' - like two beloveds finding each other against all the odds. God’s story is, after all, a love story between Creator and creation.

That’s my best conjecture for why God used an enormously complex, spatially vast, chronically extensive canvas to demonstrate His artistic genius: it is the genius of a rare, unique, profoundly beautiful, deliberate love story where that which is lost becomes found, and is embraced by the Creator through the Incarnation, just as when the father embraces his prodigal son on his return from the doldrums. The grandeur of the universe may well be a simulacrum of the entire gospel story: that the whole creation narrative is based on Christ dying for our salvation - and the mathematical cost of life, represented in the vastly expressive canvas of mathematical and physical nature, may be an illustration of the cost of life in terms of salvation - the price God paid for the creatures He loves. That is to say: our Father God has shown through His Son Jesus that He is willing to bear the greatest costs imaginable (Philippians 2:7, 2 Corinthians 5:21) for the things He loves - and that may be as true of the universal nature of things as it is the individuals He created, and for whom He died.

It's Impossible To Love The Truth And Deny Evolution: Part II - Alleles & Genetic Algorithms

As we observed in the last blog post, the nature of genetics is that genes are transcendent - and this is what is meant by the notion that genes are like passengers using bodies as vehicles. Genes are contained within individual organisms, but because they are duplicated in numerous offspring they can propagate themselves even at the cost of host agents. Individual alleles can manifest unique attributes greater than the sum of their parts, thereby ensuring information is spread throughout the nexus of the biological landscape.

There is even a formula Pn=P0e^-nu to measure the allele frequency in a population of organisms - where Pn is the frequency of an allele in a specific generation of your liking, P0 is the frequency of the original gene you are mutating, -n is the generations passed, u is the mutation rate, and e is the mathematical constant, an irrational number of a value of roughly 2.7. The formula accounts for mutations from the wild type allele to the mutant variant, and it accounts for reproduction, assuming the fitness is indiscriminate between the wild type and the new mutant. It's very useful for assessing the changing allele frequency in a population - assuming no natural selection - but when the changing allele does have an impact on fitness, you can integrate the new information in the form of a fitness coefficient (w), which takes into account for the new rate of faster or slower allelic spread into the formula following the mutation rate, u.

So, for example, suppose every 100 wild types develop with no mutant alleles, (or Aa) where out of the individuals that reproduce successfully only 80 of the aa individuals succeed in doing so. The fitness (w) of the recessive phenotype would then be 80% or 0.8. So you would put in a 0.8 at the end and this will correspondingly slow allelic spread.

The formula then becomes Pn=P0e^-nuw

Anyone can try out a calculation on a hypothetical allelic frequency change, although bear in mind mutation rates vary between organism to organism, and even gene to gene. In a human cell, the average mutation rate is something to the tune of 1 mutation in every 30 million base pairs, per generation.

As I've said in previous blog posts, a system contains information by virtue of its relation to another agent or system capable of perceiving, interpreting and responding to that information. The biological substrate is a system whereby we've delineated terms like 'law' and 'disorder' and actively played out those delineations through the fundamental dialectic of structure, mechanism and function. This process has active information that gets scrambled by the second law of thermodynamics under severe mathematical constraints and, after enduring biochemical facilitation, gives rise to the biological landscape we see before us. Under these conditions, and mathematically speaking (which is what the universe is - one big mathematical object), new information is being created all the time, where under these conditions the amount of information in a system is quantified by how much it reduces the uncertainty for the receiver.

The genetic algorithms in biology are implicitly part of the whole constraining process; they are informationally connected through interconnected mathematical pathways. You can take any two distinct species and chart their evolutionary relationship through the similarities in their genetic sequence. Differences vary depending on which two species in particular you select, but they all share something in common. Even between the two most distantly related groups, such as between a bacterium and a human cell, you'll find the groundwork for many similar genes and genetic sequences - which play crucial roles in cell maintenance and reproduction - has already been laid out. Genes and regions of DNA responsible for carrying out the process of DNA replication, of coding, regulating, and carrying out the process of creating proteins, are present in both taxonomic groups more or less in nearly the same DNA sequences between groupings.

The genome is suffused with self-replicating elements, known as transposons, which are regions of the gene that are highly mobile elements, often cutting themselves out of a region of the gene, or copying themselves and migrating elsewhere. One class operates by cutting and pasting itself around, with minimal duplicating activity. But in cutting in pasting itself around, it often leaves broken edges of DNA where it comes and goes, which, invariably, is going to be identified and filled by DNA polymerase and its coenzymes. Because DNA polymerase in this instance is working blind, so to speak, it has no idea what nucleotides to use to glue the broken pieces together, so it will use random ones. This chain of events gives transposons of the cutting and pasting class an innate property of causing mutations at the joining sites of wherever they go and leave.

There is second class as well - known as retrotransposons. They are more like 'copy and paste' to the transposons' 'cut and paste' - and they are a large source of new genetic information, because in their very nature they carry genetic regulation sequences responsible for making certain proteins (without which they would be inefficient self-replicators) and regulatory sequences for initiating the production of the aformentioned proteins. They copy themselves, and the translocated copy is carried about by proteins and randomly inserted at a new site on the genome. Since there is no natural selection acting on them - because they don't play a vital role in survival - the copies are free to mutate and mutate successively through generations. And with those promotion factors already in place, whatever the DNA sequence happens to mutate into will engender a new gene. If it turns into something biologically ineffectual, it will just keep mutating until its regulatory sequence is destroyed. If it mutates into something useful for the genotype/phenotype, then voila, here is the new gene. This process plays a big role in the formation of new genes.

Another mechanism of gene duplication comes from what's called 'meiotic recombination', wherein chromosome pairs adjoin to one another and transfer genes between themselves. The net gain of the genes is always zero; there are only two to work with; one per chromosomes, and generally, the recombination yields an equal count of genes between chromosomes when they are done trading. But sometimes an unequal number of genes may be traded; one chromosome may get both genes, and the other none. If the chromosome with both genes becomes a gamete that merges with another gamete to form a new lifeform, then you have a net gain of one gene for every generation following that lifeform to come.

And this is just one aspect of it in genetics - compound it with other discoveries, with the observation of gain of function mutations, of emergence of new traits, new behaviours, homologies in anatomy and physiology, and so on, and there is a picture so comprehensive that it cannot be denied by a genuine truthseeker.

More to come in Part III