Women In Church Leadership - A Novel Idea

In the UK, most Christians I know (myself included) support women in leadership, and by extension, women preaching. However, I do have quite a few Christian friends who don’t support women in leadership, and they attend churches that do not permit women to deliver sermons. They tend to base this on their interpretation of St. Paul’s teaching on the subject (notably, 1 Timothy 2:12 - “I do not permit a woman to teach or to assume authority over a man” and 1 Corinthians 14:34 - “Women should remain silent in the churches. They are not allowed to speak, but must be in submission, as the law says.”). But most Christians take those verses to be contextual admonitions directed at particular church cultures of the time, not blanket prohibitions of women’s roles in leadership to be religiously adhered to in perpetuity.

Certainly, the spirit of the Bible, and other verses, seem to indicate the acknowledgment and encouragement of the role of women in leadership. St. Paul, in Romans 16, speaks of Phoebe as a “deacon of the church”; Luke, in Acts 18:26, acknowledges Priscilla as a teacher; and in Acts 21, we learn that “Philip the evangelist had four unmarried daughters who prophesied.”. Moreover, great Old Testament women - like Rebecca, Leah, Deborah, Rahab, Esther, to name but a few - were given great authority and responsibility in furthering the Biblical story and enhancing God’s Kingdom.

Consequently, I think the correct Biblical interpretation is that it’s not just fine, but beneficial, to have women in leadership. But that said, those who disagree with me on this are probably just as confident that their interpretation is correct. And it has to be said, given debates like this one are long-standing, and given that the Biblical texts are too low-resolution for any of us to be certain what God wants for His church regarding women in leadership, there is no external metric to which we can assent to find out which group of Christians have got this one right.

My possibly novel idea
With this in mind, I have an idea that’s a bit off the wall, but is probably worth a moment’s consideration. Maybe we can’t know which option is right, but maybe God wants us to make a choice, and maybe God doesn’t mind all that much what we choose about women in leadership (as long as we are kind and conduct ourselves with goodness) because our subjective preference in this matter is a dignity He has bestowed upon us. In other words, as long as churches stick to the fundamental Christian tenets, maybe it’s fine to celebrate the diversity of church styles and denominations consistent with individual consumer preferences.

The church is broad and diverse; some people like to be monks, some like to be nuns, some people are Christian missionaries, some are business pioneers, some people prefer dancing in Pentecostal churches, some prefer quiet contemplative church services, and so on. Maybe it’s possible that that’s how God feels about our preference for leadership; for those men and women who prefer to be led by men, God is fine with a church that sets itself up with only male leaders; and for the rest, who value women in leadership, there are many churches for them too. 

Don’t get me wrong, if we had access to God’s perfect knowledge, and knew all the facts ourselves, there may be a definitive set of right answers about women in leadership that would make everything clear with that degree of hindsight. But given that we are imperfect humans, trying to do our best with limited information and our best efforts at scriptural interpretations, it may well be that God is perfectly fine with our a la carte model of individual preferences, where male leadership churches are fine for people who prefer that, and mixed leadership churches are fine for everyone else.

 

On The Economics Of High Oil Prices (And Why They Can Be Good)

As we’ve all seen in the UK recently, it costs a lot to fill up at the fuel pumps these days. And as most people are talking about it so much, it’s probably worth sharing a few thoughts.

Why so high?
First let’s examine why oil (and therefore fuel) prices are so high. It’s always largely down to supply and demand, but broken down, the Russia/Ukraine conflict is clearly a big factor, as is the transition from stringent global Covid restrictions to the new ‘living with Covid' phase, where demand shot up and supply couldn’t keep up with that demand. Also, the Covid years saw a reduction in fuel consumption, which hit income for fuel providers, whose increased prices are, in part, to compensate for the pandemic shortfall. Production volatility and capacity at the refineries are a factor, as are increased costs of distribution. The pound’s performance against the dollar is a factor for UK prices. And, also hugely significantly, the government imposes high taxes on fuel, which obviously makes it far more expensive at the pumps. Another significant factor is the ‘climate emergency’ brigade’s war on fossil fuels, which makes oil suppliers nervous about future investment for fear of more stringent green regulations/taxes, which would hit their capital assets.

Price dynamics
Given the foregoing, there are two further things that need saying here about the price increase. The first is that, except for taking off the tax, there is no real way to lower the price of fuel and make the situation better than doing nothing. The second is that, given the truth of the first point, higher prices increase efficiency of consumption. Beginning with the first point; rudimentary economics suggests we can't easily lower the price, because oil is a high-demand but an exhaustible resource. This means that every barrel must be sold at the optimum time for the supplier - if you sell a barrel tomorrow you can't sell it next week, and so on. Deciding when to sell barrels of oil is one of the key catalysts for determining current prices and future prices. And the key inputs to that decision are the current price and the expected future price.

Government activities will generally (but not always) either bid down current prices and bid up future prices, or they will bid up current prices and subject future markets to unwelcome volatility. If the government starts to bid down current prices and bid up expected future prices, they create an incentive for oil suppliers to sell less now and sell more in the future. But this, of course, reduces current supply and goes on to bid up current prices. As a rule of thumb, in a supply and demand free-ish market, the price of oil ought to rise at the rate of interest. This is because leaving oil in the ground is a kind of investment, and investments are generally actuarial analyses tailored to rates of interest. If governments artificially change the price path by reducing current output and increasing the current price, which is what is happening now, then the expected growth rate is diminished relative to projected future interest rates, inducing suppliers to sell more now and not leave it in the ground. Consequently, the very best thing the government can do as a temporary measure to help its citizens deal with the increase cost of fuel is to greatly reduce the fuel tax and offset the loss with temporary reduced public spending in another sector.

Efficient consumption
In the meantime, I said that higher prices increase efficiency of consumption, and here’s why. When the price of a good increases, the people who value it most tend to be the ones who buy it, where the people who don’t need or want it enough to pay the higher prices will either go without or look for a substitute. Suppose there’s a shortage of fuel, and the prices go up because the quantity demanded exceeds the quantity supplied. These price rises discourage casual consumption, and they encourage more production until fuel is readily available again at a more affordable price for more people. If Jeff fills up his car with 60 litres of fuel and sits idly for 2 weeks, and Bob has no fuel and can’t drive his taxi, then the 60 litres have been sold inefficiently. While market volatility isn't a good thing for consumers, if it does happen, like it has in the oil industry, then price increases that reflect the reality of the supply and demand curves are a blessing not a curse, because they cut inefficient consumption (like Jeff’s), safeguard efficient consumption (like Bob’s), and spur on increased production.

Five Reasons Not To Commit Suicide: Why Life Is Worth Living

I just felt a strong nudge from the Holy Spirit to articulate these thoughts, to share the reasons why you shouldn’t commit suicide, and put them on video, for some future good out there. I don’t know whether its impact is for this week, next month, or for years later – just that someone might need to hear these words at a crucial time in their life, so better that it’s out there for anyone in need.

It's Impossible To Love The Truth And Deny Evolution: Part VII - On Interpreting Scripture

 

In recent articles, I've talked about the undeniable evidence for evolution over billions of years, and I did so to encourage Christians to come together and love the truth and elegance of evolution. Here I’d like to pay attention to what is perhaps the main reason that some Christians are creationist - taking the Bible too literally in the places when other interpretations are more accurate and enriching. Some of the most powerful truths the Bible conveys are far beyond the mere literal interpretations of the creationists. The Bible verses are not always literal, but they are always true, and that is the key distinction.

One of the most powerful methods of storytelling is through metaphors and analogies. And what I want to show in this article is that metaphors and analogies are more than just stories conveying simple truths; they are intricately woven into the very fabric of what mind is. It is no wonder that God used the powerful metaphor of marriage to speak of our relationship with Him. The central narrative – that God emptied Himself by coming into nature to incorporate Himself on our journey - is itself both literal and metaphorical; it is literally true because the person of Christ lived as a man, and it is metaphorically true because it infuses an abstract metaphysical power into the entire human history, making the journey and the destination a real tangible goal for every one of us

Let me suggest how we can manage our reading of the Old Testament and conceptually demarcate our history from our non-history - a suggestion that points to a few truths that are bound to seem utterly strange to a post-Enlightenment person steeped in the logic of the Greeks and the empiricism of Bacon, Locke, Berkeley and Hume. Part of the understanding required is the understanding that in ancient traditions, particularly oral traditions, the narrative being conveyed is a blend of fact and fiction, where profound truths are disseminated in a way that requires interpretative qualities beyond the headlights of the kind of rigorous historical and scientific analysis we moderns are used to. Given that life itself is so richly analogical, metaphorical and narrative-laden, it is no wonder that we are insistent that a deep understanding of the Bible won't come to anyone who trivialises its dynamic nature and is blind to its analogical, metaphorical and narrative-laden power.

Old Testament figures like Adam, Eve, Cain, Abel, Noah, Jacob, Joseph, Abraham, Moses, Joshua, Samson, Samuel, Saul, Job, Jonah, David and Solomon are such an agglomeration of history, myth, legend, analogy, metaphor and theological aetiology that we can't hope to pin them down to simple historical/non-historical analyses. That's not to treat them all the same, of course - there are evidently different extents to which the above applies to Adam, Jonah and Job than, say, David and Solomon. What's clear, though, is that while God 'breathed' His influence onto the writing of scripture over the many centuries of its composition, He allowed His word to be subjected to the limitations of creation, and for the narrative to be absorbed into a blend of the literal and non-literal in order to convey the power of the gospel of grace. These Old Testament stories are so psychologically deep and theologically complex that it's not even possible to justifiably approach them through a simple binary literal or non-literal lens of analysis.

The writer of Genesis would have been a significantly different person to any kind of person a contemporary person living in the post-scientific revolution era would have ever encountered. The writer of Genesis would have no apprehension of a global concept, or the size of the world, solar system or universe; he’d have no concept of what a billion is, and no experience of prescribed philosophical investigations or formal empirical procedures associated with the science of the past few hundred years. And it’s highly likely, given what we know of the formal development of human thought over the past two and a half millennia, that he wouldn’t even understand what modern people are probing when they debate whether the Genesis 1 text should be taken literally or not. The concept of demarcating recorded literal history from symbolic theological expressions would be alien to the man who wrote Genesis 1, and to the New Testament figures too, which is why, when Jesus talks about Adam, He is speaking theologically in a way that the audience of the day would understand. When talking about Adam, Noah, Jacob, Jonah, Abraham, etc Jesus is talking about such deep and profound truths, so far transcendent of actual historical events, that those speaking about them in scripture would be quite aghast at how far many modern people had departed from its tenor in applying banal scientific metrics to the literalism text.

It's obvious why we don't need the story of Adam and Eve to be literally true to understand its real meaning of ourselves in relation to God. Literalists insists on reading Genesis 1 to be 6 x 24 hour days, but when we get to Genesis 3, they suddenly stop reading that literally, because if read literally then only the serpent, Adam and Eve receive some consequences for their actions, not the rest of humankind. To see the story of the fall as being about human sin, you have to extend beyond the purely literal. The literal story of two humans and a snake sinning in a garden and everyone else becomes cursed because of it is beyond silly unless we give it its full allegorical due, which is what Paul does in Romans with a figurative truth where they represent all of mankind. Similarly, there is no such thing as a literal tree of the knowledge of good and evil - it makes no sense except as a story conveying deep symbolic metaphysics. But when we see the tree of knowledge and the Fall as allegorical stories about the human capacity for moral agency, and the ability to make choices when measured up against their moral consequences, including the ability to choose God over self, or self over God, we then get to understand what those theological symbols mean. The tree of knowledge of good and evil is meaningless without an already evolved moral awareness and conception of free will in acting on that awareness.

It's absolutely absurd to me that anyone could be so misjudged as to think of Genesis as being science - but to compound the point, here are just some of the scriptural errors that emerge when we try to align it with known science. In Genesis 1, the earth is created before the sun, which is the wrong way around scientifically. Light is created on the first day (Genesis 1:3), but the stars that emit light aren't created until the fourth day (Genesis 1:14). These stars on the fourth day are said to be made to let them shine on earth (Genesis 1:15), but yet on day 1, God had already created the light and called the light “day,” and the darkness “night". And if three days had already passed without stars, those days couldn't have been measured if the stars weren't created until the fourth day. This gets even more bizarre when we see that our sun and moon weren't created until day 4 (Genesis 1:16) and yet we'd already had three days of evening and morning before that point in the creation story. Moreover, if we want to be scientifically technical, the moon isn't a lesser light, it merely reflects the sun's light - which means Genesis 1:16 is wrong when it says " God made two great lights" - He actually only made one great light, and one smaller celestial object (the moon) to reflect it.

The writer of Exodus refers to God "showing steadfast love to the thousandth generation of those who love Him" (Exodus 20:6), but according to literalists Exodus documents events only a few hundred years after Adam and Eve. For a thousand generations to occur, it would take 25,000 years. Now obviously, we can say this doesn't have to be read literally, but that goes against the creationist wishes, so they can't really have it both ways.

If taken scientifically, the Genesis account actually distorts the truth of the genetic mapping even further; for example, reading Genesis scientifically we would see that fruit trees appear before marine life, which is known to be wrong, and can easily be observed on the genetic map. Reading Genesis scientifically, we have whales and birds created at the same time, but this is also far from accurate, as birds were here millions of years before whales. Reading Genesis scientifically we have insects, spiders, reptiles and amphibians created at the same time as mammals, which is wrong by a factor of several hundred million years. So even if one questions the genetic sequencing I mentioned earlier (and there is absolutely no reason to do so) a scientific Genesis account would actually contradict the genotypic mapping with which creationists say God endowed creatures – it either has God as a master deceiver or as an incompetent Creator who cannot even create a blueprint to match the genotypic order.

Furthermore, the ordering of the appearance of phyla is scientifically incorrect with a literal interpretation - fruit and seed bearing plants came after the water was teeming with life. Even dinosaurs are long before seed bearing fruits, yet Genesis says otherwise, showing it is not a scientific account. Moreover, human evolution has been going on for hundreds of thousands of years, and given that any so-called speciation that would make proto-humans distinct from humans would have occurred at the population level not at the individual level, the Genesis account that there were two first humans is not scientifically accurate as a literal interpretation. Forming a man out of the dust and breathing life into him through his nostrils is not a scientific reality for making him 'a living being', but it's a powerful spiritual image, conveying how God imparts spiritual extras into human beings that make them over and above the rest of the animal kingdom. A woman cannot literally come from a man's rib. Biblical figures like Adam, Noah and Methuselah cannot live for over 900 years, and Sarah could not conceive Isaac at 90 years old. No human being has ever lived hundreds of years, and no woman could ever become pregnant at 90 yeas old. There was not one world language at the time of writing (Genesis 11:1) and the whole variety of world languages did not literally suddenly appear in one fait accompli moment by being scattered all over the earth, as conveyed in Genesis 11:8.

Let's turn to Noah’s flood as another example; creationists believe that the world really was flooded in its entirety and they believe the Bible says that when the ark rested on a mountain in the Middle East it contained every human and land animal in the world, and that they were the only survivors on the plant. Even if we put aside the mass of evidence of human evolution throughout the world and the copious amounts of art and artefacts that give evidence of their uninterrupted evolution, the land animals issue, if taken literally, amounts to one of the oddest stories the world has ever seen. For example, a literal interpretation means we have to believe that the voluminous amounts of species indigenous to one part of the world all made their way from the Ark’s resting place, residing in their place of provenance, travelling through conditions under which their phenotype wasn’t built to survive, and avoiding all predation along the way (never mind that many would require other animals for food in a world in which all other life had been destroyed). We are supposed to believe that the kangaroos, koalas, and wombats made their way across Asia through the Indonesian islands and over the east side of the Indian ocean to Australia. We are supposed to believe that the Arctic walruses, polar bears and caribous survived the warmer climate of Europe as they all found their way northwards. We are supposed to believe that anacondas and capybara found their way to South America and the giant tortoise found its way to the Galapagos islands, all from the Middle East. It's beyond silly to attempt to take this as a literal event in history - and the author of the flood story in the Bible would think it preposterous if he could fast forward in time and see that some Christians had become so detached from the symbolic and metaphysical theology of the story and its concomitant archetype that they were actually considering it as a literal global event.

Sticking with South America, take (for example) sloths, armadillos, spider monkeys, poison arrow frogs, jaguars, opossums, electric eels, chinchillas, guanacos, caimans, and hoatzins (to name but a few) - it is now possible to draw up maps based on chromosome painting where, with observing genomic sequencing, we can establish the relationship between DNA sequence variations among all these animals, and all other animals linked to them in one big family tree. We can locate the syntenic segment associations as well as the molecular markers within the major clades which delineate families, orders, who evolved from who, where this evolution took place, and the length of time animals have been indigenous to a particular place. Not surprisingly, in our studies of genomes across the world with thousands of species in virtually every location, we found that the genomic studies, DNA sequence variations, and markers within the major clades give exhibition to evolution over billions of years. All the data fits, and we have not one case where a particular genomic sequence has been discordantly out of place on the family tree - everything fits together, and when we conduct new tests on unsequenced genomes we find that they match our predictions without fail, giving us a consistent map of evolution. If the animals had been only a few thousand years old, or had all converged upon their destination from one Middle Eastern centrepoint (which in many cases geography prohibits due to oceans) the genomic sequences would be very different – not matching the evolutionary history that they do.

The upshot of all this is, with regard to the Bible, the intention of meaning shouldn’t be confused with science, and it is for the same reason that the intention of meaning of the works of Keats or Tennyson or Blake should not be confused with the works of Newton or Kepler or Maxwell - different expressions are being conveyed through different types of language. On hearing that a wife's love for her husband "Lifts her high above the clouds", only a very foolish man would say 'No it doesn't, because that contradicts Newtonian laws'. Yet some Christians too often fall into the mistake of doing something similar with their Biblical interpretations.

The Bible contains everything one needs for having a relationship with God. It won't tell you about the age of the earth or evolution or gravity or electromagnetism because those subjects weren't studied in depth by the men of the day who wrote scripture. It’s not as though one needs to put God aside to study science; people just need to stop looking for scientific answers in scripture, because by doing so they skew God's intention, and miss the power of meaning contained in books like Genesis. Don't put God aside when studying science; rather, look at science as the tool with which we assess the finer details of the beauty of God's 'physical' creation.

The Foolish 'Windfall Tax' Idea

 

Of course, everyone with even a sketchy understanding of economics knows already that the ‘windfall tax’ is a bad idea. But for those who don’t yet know it, here are a couple of pointers. There are three main things we can do in an economy to make the world a better place; the first is waste fewer resources, which means consuming as optimally and efficiently as possible (which also includes allocating those resources in line with the information signals generated by prices in accordance with supply and demand curves). The second is work harder to provide more goods and services that people want and need, at better prices, using resources most efficiently. The third is to keep increasing our knowledge and our technological capacity so that the things we want and need become cheaper, easier and quicker than they were for previous generations. Whether in times of prosperity, in a pandemic, in a war, or whenever, there is nothing better that we can do for humans in an economy than those three things.

Perhaps now you can start to see why capital taxes like this (which includes tax on capital gains, interest, shareholder dividends and corporation income), dressed up as the ‘windfall tax’, are inimical to the threefold progress of the above. If you tax capital, you disincentivise saving and increase consumption, and if you tax capital, you disincentivise investment and innovation. If you increase consumption artificially, you decrease efficiency in point 1; and if you disincentivise investment and innovation, you tax (in the long run) labour, growth and innovation, which decreases the efficiency in points 2 and 3. 

Taxing capital disincentivises capital accumulation, and therefore negatively affects investment, production and labour. But it’s worse than that, because in the current tax systems money is taxed multiple times, which produces even greater inefficiencies and retardation of economic development. Taxing your earnings and then your capital amounts to double taxation, because capital gains are the fruits from the income that has already been taxed once. Taxing both income and capital is like fining a pedestrian for being drunk and then fining him again half an hour later for having too much alcohol in his bloodstream. Finally, taxing capital is also a deferred tax on labour, because capital is earned by past labour that has already been taxed at the point of earnings, and is therefore the deferred benefits of past labour. Tax the capital that is the present reward for past labour and you’re double taxing the original labour.

The upshot of all this is that a windfall tax is a terrible idea thought up by people who don’t understand economics, for the persuasion of people who are impoverished by listening to those people who don’t understand economics. 

 

It's Impossible To Love The Truth And Deny Evolution: Part VI - The Origin Of Life

Abiogenesis is the process whereby once upon a time life arose from non-life. We are not entirely sure how this process arose (although we are not entirely unsure either), but given that God has created a universe of such ingenious proportions, it's not difficult to accept that bringing life from non-life is well within the scope of His cosmic narrative. What we know this far is that all physical things that exist are made from a finite set of constituents called the elementary particles. The manner in which these elementary particles interact with each other is well known; quarks come together to form nucleons, nucleons come together to form nuclei, nuclei combine with electrons to form atoms, atoms combine with each other to form molecules and materials, and so on.

We know about the compounds that pervaded the early solar system, because we know what comes out of stars and what can be carried in by comets. We know this because we can do astronomical spectroscopy and observe the contents of newly formed solar systems. We even know that amino acids, the constituents of proteins (life’s 'workhorses'), are found in space and can be synthesised in a lab by mimicking lightning striking the earth’s primordial oceans. We also know that ancient clays can catalyse the reaction of some of the early compounds on earth into nucleic acids - which are often touted as the 'building blocks' of life. Not only that, but we also know that nucleic acids can spontaneously form the molecule known as RNA. RNA can not only speed up chemical reactions which could confer a biological advantage, but it can work as a template for itself - perhaps the first mechanism of reproduction. However, not all these environments are conducive to the forming of life - in fact, many are impossible incubators. As none of the elementary particles, nor their simplest combinations, can self-replicate in an evolvable way, life can only spontaneously form in environments that enable life to retain its specific configuration of elementary particles that allow reproduction.

We have a universe that is more than 14 billion years old - most of which cannot produce life. However, the elements of the periodic table still allow a rich range of chemistry to emerge; so rich, in fact, that many complex chemicals do exist and undergo reactions. We know that the vast majority of these compounds cannot reproduce under any known environment, but the underlying engine of our physics and chemistry shows that reproduction (self-replication) can happen - it is just such a rare event that it needed a molecule to form a template of itself, against which the compounds in the environment spontaneously formed a copy of the template. Even though our universe has approximately 100 billion galaxies, each with around 100 billion stars in it, nucleotides bonding to create the first RNAs would still be an amazingly rare event in our universe.

What we can extrapolate about the origin of life question is this. In this world, the common states are liquid, solid and gas. We know such incipient life could not exist in solids, because things in solids cannot diffuse around, and atoms vibrate around an average position with too much restriction for life to flourish. Equally, life isn't likely to exist in the gas phase, because the replication machinery has a necessary complexity and weighs too heavily to thrive in the gas phase. The fact that life exists in liquids is because liquids allow signal transduction by diffusion and can act as a suitable solvent for bio-machinery. Life was unlikely to exist in any other state apart from liquid - hence the ‘primordial soup’ metaphor.

The high surface tension, the low viscosity, the boiling point, the melting point and the fact that water expands upon cooling can all be explained by the way water molecules interact with each other - namely that it is capable of making four hydrogen bonds. Why it does this ultimately lies with the laws of quantum mechanics. The Schrodinger equation, when solved for a given collection of atoms, tells us the properties of that collection of atoms. It tells us how much energy we need to pull it apart, or equivalently, how much energy is released when it forms. The same can be said for collections of water molecules. The solution to the Schrodinger equation is found using the same methods, whether we are dealing with water, or ammonia, or caffeine or any other compound we care to study. The properties of water and all other molecules are the inevitable outcome of the natural dispositions of electrons and nucleons. The properties of water aren't arbitrary; they are emergent phenomena of the properties of the universe - just one of a myriad of consequences of the laws of physics.

That fact that life on earth depends on water is a testament to how life has adapted to the aqueous environment found on the planet on which it arose. It seems true that many of water’s special properties played a significant role in allowing life as it is to exist - however, given that the properties of water are just a consequence of the combination of fundamental particles from which it is made, it is no surprise that we complex beings find ourselves on a planet which has this life-enhancing molecule in abundance, as opposed to anywhere else in the universe.

As I recall, biologist Nick Lane has a theory that proton power is no late innovation, but evolved much earlier in the tree of life than we first thought. The first branch in the tree is between the two great groups of simple cells, bacteria and archaea, and Lane reminds us (rightly) that both of these groups have proton pumps and both generate ATP from proton currents, using a similar protein. It seems very likely indeed that both inherited this machinery from a common ancestor, and that this source was the progenitor of all life on earth, including you, me and the oak tree down the road.

It must be said, though, that although traits found in both the archaea and bacteria are most likely inherited from the common ancestor of all life, a few must have been acquired later by gene exchange, thus giving credence to our belief that ‘distinct’ means, in many cases, ‘evolved independently’. We know that this common ancestor possessed DNA, RNA and proteins, a universal genetic code, ribosomes (which are protein-building mechanisms), ATP and a proton-powered enzyme for making ATP. These intricate mechanisms for reading off DNA and converting genes into proteins are rather like a modern cell. Yet there are nuanced differences as well - in particular, the detailed mechanics of DNA replication would have been quite different. Moreover, it looks as if DNA replication evolved independently in bacteria and archaea; that is, most scientists seem to agree that the defining boundaries of cells evolved independently in bacteria and archaea.

So the question ‘what sort of a cell was this common ancestor?’ is, as Nick Lane concedes, a difficult question. Clearly not a cell with no boundaries, that would defy every known chemical law – but seemingly it was a very simple yet sophisticated entity in terms of its genes and proteins, and was powered by proton currents rather than fermentation, but with membranes that are no longer seen in cells today. To compound the point, back then the oceans were very different to what they are now; the primordial oceans were saturated with carbon dioxide, making them acidic, whereas the seas today have more alkaline. Also there was practically no oxygen, and without oxygen, iron dissolves readily – and we can see from our geological studies that the vast banded-iron formations around the world are a result of iron that once dissolved in oceans. As oxygen levels slowly rose, billions of tonnes of iron precipitated out as rust. This almost certainly means that the interface between the alkaline vents and the primordial seas would have been much more conducive to biochemistry than they are today – in fact scientists have found ancient vents with a similar structure and even reproduced them in the lab.

So the theory that ancient alkaline hydrothermal vents were the incubators for life looks very plausible, particularly if hydrogen and carbon dioxide did in fact react in those vents to form simple organic molecules and also release energy. But we still might be wise to proceed with some caution, because although hydrogen with carbon dioxide may well be central to life, energy is still required in the first place to engender this process, so much so that it is probably nigh-on impossible for bacteria to grow by chemistry alone without the catalysing energy. Let me offer an analogy. Think of the energy stored by ATP as equivalent to £1. If it takes £1 to kick-start a reaction, which then releases £2, in theory a cell has gained £1. However, if the only way a cell has to store energy is to make ATP, it can make only one molecule; to make two new ATPs would cost £2. So one ATP would have been spent to gain one ATP, and the spare change wasted as heat. That's not consistent with being alive. Yet Nick Lane is suggesting that the hydrothermal vents would provide a good explanation to this problem, claiming that::

“The fluid from the vents would have contained reactive molecules such as methyl sulphide, which would generate acetyl phosphate, a molecule that some bacteria today still use interchangeably with ATP. What's more, the natural proton gradient would have supplemented this energy source by spontaneously generating another primitive form of ATP called pyrophosphate. Pyrophosphate also acts in much the same way as ATP and is still used alongside ATP by many bacteria and archaea. These bacteria speed up its production using a simple enzyme called pyrophosphatase”.

So the common ancestor of life could harness the natural proton gradient of ancient vents to produce energy, and by some reversing process store energy too, as this system seems to allow cells to save up small amounts of energy, much the same as we save up our loose change and buy something so it no longer becomes waste. This is equivalent to saying that the proton gradients enable cells to grow and then, by their accumulative energy, leave the vents. This means it may well be true that the last common ancestor of all life was not a frivolously spending cell at all, but a thrifty rock riddled with bubbly iron-sulphur membranes that engendered the energy for primordial biochemical reactions. This natural flow reactor, power-driven by hydrogen and proton gradients, catalysed organic chemicals and brought about proto-life (both bacteria and the archaea) that would become the first living cells – eventually producing you, me and the oak tree.

Given the intractability of this subject and the vast domains of time, it may never be possible to know for sure whether or not life evolved by this mechanism, or whether the initial elemental organism with the properties of self-replication happened just once (maybe only once in the entire history of the universe) or several times. But a good case may have been made that hydrothermal vents had the answer. It's worth adding a point I made in my book The Genius of the Invisible God:

"I won't even bring to bear the complication that the tem 'life' is a human construct, upon which we have created a descriptive term for the purposes of classification. The emergence of life is referred to as abiogenesis - which is the point at which the earth's chemistry evolved into a self-replicating system. But the point at which chemistry becomes biology is not an instantaneous moment (and even if it were, it would be an arbitrarily defined human classification). But let's pretend there is one single point in history when we can say that life began - an A to B event of causation.  The putative conclusion begins with 'Therefore, all life is designed' - and from what I've said it is self-evidentially obvious that there are no philosophical conditions under which one can identify a particular point in history as being the beginning of the design of life. All one is doing is looking for the transition from chemistry to biology, but they overlap, and they give no exhibition to any kind of process of divine choreography, because they can be reduced to particles that simulate mere possibility as fluctuations in a quantum field."

The upshot is, the abiogenesis that brought about early life isn't a direct object of empirical study for us - it is probably a one-off or exceedingly rare event that we may only simulate in the lab, where the exact conditions of the actual event are always likely to elude us. But whichever way we cut the cloth, when describing creation - from abiogenesis all the way through to the rich and diverse complexities of life we see after a few billion years of natural selection - we are describing how God has engineered the laws of physics to behave so that it administers His grand narrative.

 

It's Impossible To Love The Truth And Deny Evolution: Part V - How & Why We Evolved Two Sexes

 

In this blog post, I thought I'd offer a brief explanation for how evolution came to produce two sexes within the species of most organisms. The mixing of genetic material has great advantages. Genetic tricks can be shared between simple life forms to create better adapted life forms. Sex overcomes many genetic problems because a good copy of the mutated gene can be inherited from the parent without deleterious mutations. Mixing of genetic information over populations is a mechanism that has been retained throughout the majority of evolutionary history, because it is so beneficial in washing out deleterious genes.

This mechanism is also part of the reason why distinct sexes evolved in the first place in multicellular organisms - they constitute an advantageous breeding strategy. Imagine that the genetic information is mixed together by the combination of two identical sex cells (these are called 'gametes'). Now, offspring with more nutrients available during development will have a greater change for survival than their more nutritionally impoverished peers, so sex cells would evolve to get bigger, in order to contain more nutrients (these are called 'eggs'). However, the bigger they get, the more cumbersome they are and the smaller the chances of two meeting and exchanging genetic material, so sex cells that are small and quick will have an evolutionary advantage as cells grow (this is one of the reasons why sperm cells are so small).

Consequently, identical members of the same multicellular species will almost invariably evolve into two forms. This asymmetry results in a fork of two reproductive strategies; a multicellular species will have a 'sperm'-strategy from which we call male, and an 'egg'-strategy form which we call female. Sperm combining with sperm do not have enough nutrients to support a developing offspring, and eggs are too bulky to meet one another. One sperm and one egg, however, will form a viable offspring, so that is why there has been an evolution of males and females over the years emerging from those tiny gradual changes in the genetics of the organisms. Male and female evolve concomitantly because two-sex sexual reproduction produces more viable offspring than both asexual reproduction and single-sex sexual reproduction.

Conversely, single-celled life has no need for distinct sexes, as there is no need for nutrient stores for development. All mono-cellular cells can reproduce, and one main motivation for doing so is to obtain good versions of damaged genes. In fact, single-celled organisms have machinery that can detect damaged genes, and that machinery starts a cascade of events which result in sex with the nearest available cell that can respond to those signals. Multi-cellular life reproduces with specific sex cells, and only those specific cells are used for reproduction. Because of the increased utility of the process of recombination of genes, it is unsurprising that over time a mechanism which suppresses the growth of non-sex cells in multi-celluar life would have taken precedence. Evolution works by small increments, and we would therefore expect that the signals for reproduction in single-celled organisms, which detect DNA damage, would be used for exactly the opposite function in multicellular organisms - to suppress their growth and division. This is exactly what we see. The same molecules (caspases, cytochromes and others) are involved in initiating sex in unicellular life and in initiating DNA repair and cellular suicide in multicellular life. Moreover, when this particular mechanism is damaged, single cells in multicellular life are likely to grow out of control, and this is what we see with cancer. These same molecules are very frequently in a mutated form in cancer tissue.

The upshot is, all organisms have a limited lifespan and all reproduce themselves to create offspring. The traits of an organism, called the phenotype, are determined by a heritable mechanism, called the genotype. The genotype is passed on to organisms' offspring through a process that creates randomly imperfect copies of the genotype. Therefore the offspring of an organism demonstrates variability in their phenotype as compared to each other and the offspring's parent. The varied phenotype of each offspring creates a varied probability of survival to reproduction age within that competitive environment. Those offspring that do survive to reproduction age pass on their more heritable phenotype to the next generation.

The laws of physics and chemistry completely determine the mutations and subsequent selection process, just like the laws of physics determine the outcome of a spinning roulette wheel, rolling dice, or where water runs when it lands on the ground. From the fact that all organisms are modified descendants of their parent(s), and that any two organisms, whether living or dead, have a common ancestor, we can infer the primary axiom discussed earlier in the series: that evolution produces a nested hierarchy. As we've seen, since each generation of offspring produce their own generations, organisms can diverge from each other in their succession of traits, especially when they are geographically isolated from each other. When plotted on a graph, this nested hierarchy forms a tree-like structure where the branches are the separate paths that come about as the traits diverge.

We have already covered the fact that, in evolutionary history, millions of traits and genetic differences have been evolving gradually slowly over the course of 4 billion years, so the tree like structure has a huge number of branches on it. Everything that has ever lived fits somewhere on that nested hierarchy, and where it fits can be evidenced by studying the configuration of its genotype to such a precise degree that evolution is as demonstrable a fact as any fact we know. 

We also talked about how all life belongs in a nested hierarchy resembling a tree of life. One caveat though, the roots of the tree, the early formations of life, are not quite hierarchical in the same way - they are more like an intertwined network rather than a hierarchical tree, and it's for reasons I'll explain. Firstly, there are a few of examples when branches on the tree fuse - such as the mitochondrial merger and subsequent endosymbioses, which resulted in the evolution of eukaryotes; or the later merger which resulted in chloroplasts. Horizontal gene transfer is quite common in bacteria, but there is still a core set of genes for each species which can be used to define the species and place it on the tree of life. However, to place a branch on the tree requires a lineage from which it can branch. This is fine for all recent life - tracing back gives three clear lineages from which all modern life arose: prokaryotes (bacteria), archaea and eukaryotes. But the meeting point of these three lineages is where the problem arises.

Simplified, we can't say that archaea split from bacteria and eukaryotes then split from archaea, because there are some eukaryotic 'core' genes which are also present in bacteria, but not archaea. We can't say that eukaryotes split from bacteria then archaea split from eukaryotes because there are genes shared with bacteria and archaea but not eukaryotes. Eukaryotes and archaea couldn't have split from bacteria separately because they share core genes which aren't in bacteria. The only reconciliation is to assume that all three lineages (or at least two of them) were rapidly exchanging genetic material. Generally, the tree of life genes are transferred predominantly by inheritance, but horizontal gene transfer also played a major role in shaping these three lineages from which all life is derived.

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

 

It's Impossible To Love The Truth And Deny Evolution

Since the genomes of hundreds of animals have been sequenced, it is impossible to grasp even the basics of genetics and deny the fact that evolution happened over millions of years, and to deny the fact that every species is genetically related to each other in a tree of life. These are biological facts that are impossible to reject. Don't get me wrong, evolution denial has never been in the least bit credible, and always shameful and intellectually repressive, but these days it's so abundantly and incontrovertibly clear that evolution by natural selection is the correct explanation for the diversity of life on this planet that the remaining attempts to persist in its denial are merely cases of scraping the barrel and feeding a scientifically and theologically impoverished minority.

The story of evolution over four billion years is this; all organisms can be traced back to a common ancestor, and so all of the diversity in life we see today is due to common descent with modification, through natural selection, genetic mutation, and genetic drift. We have a lot of evidence to back up this theory, including the fossil record, geologic evidence, and most comprehensively, genetic data. There are three mechanisms for evolution: natural selection, genetic mutation, and genetic drift.

Natural selection: Organisms who are better suited for their environment have a higher probability of surviving long enough to reproduce and pass on their genes. This is pretty much common sense.

Genetic mutation: Changes in genetic code occur naturally during reproduction, and at random. There are several types of genetic mutations, including the insertion of a base pair, the deletion of a base pair, and the switching of positions of two pre-existing base pairs. These mutations occur all the time.

Genetic drift: This is the relative frequency of how often an allele (a specific genetic trait) appears in a population, based on how many currently-existing organisms contain that trait. Over time, some alleles that are not well-suited for the environment may become less common and eventually disappear completely. This can reduce genetic variability.

The axioms of evolution claim that all life evolved slowly and gradually from the first life forms. Traits are inherited from one generation to the next with slight variations. This being true, we should be able to create a kind of family tree of organisms and their traits, just like we create a family tree for our human ancestors. If you hired a professional genealogist to study your genealogical tree, you'd find the branches form nested groups of families based on the name of the husbands. As new generations marry, the daughter lineages create branches with the names of their new husbands, and the sons simply create newer and more complicated branches with the same name. In my father's and mother's family tree, for example, even in just a few generations we have family members with over a dozen different surnames.

In biological evolution over 4 billion years, traits in organisms evolve in the same way. If you replace the new family line where the husband's name comes in with a new novel trait in an offspring, you find the same thing. That organism with a new trait creates a new branch where the descendants keep that trait and also accumulate new ones as they go along, much like how all the grand-daughters will take on new marital names and form their own branches. This is what is called in biology a "nested hierarchy".

The genome of every single organism contains the totality of genetic information within that organism – we each have a unique one (it’s mostly the same, but every individual has slight variations). A genome is like a book, consisting of chromosomes, which are like paragraphs. These paragraphs are made up of genes (sentences in this book analogy) and they act as instructions to make molecules. Each gene is like a sentence that defines its protein structure, and the letters in the sentence convey the building blocks of the DNA strand (a subset part of the gene). DNA is a molecule in the shape of a double helix, which is a long spiral staircase made up of nucleotides – and it is these that determine the genetic code of all living things.

As the genomes of so many animals and plants have been sequenced, we have a picture of evolution so clear that we know where every living thing appears on the tree of life. We know this because the information available to us from genome sequencing is computational – that is, from the sequences we can compute the relational distance of every species to each other, just as if we subjected books to a computational process and saw them undergo mutations, we would track the computational steps at every part of the journey and know which copies of books emerged from which other books and so forth. This is because genes are best thought of as passengers that use bodies as vehicles for propagation – just as in this analogy, letters and sentences would be using the book structure to get themselves passed on. The DNA code is a digital code that has no non-trivial difference from computer coding that can be mapped in precise accordance with the journey its constituent information units have taken. A gene is a sentence that conveys the structure of a protein, and just as would be the case if we subjected books to the same kind of evolutionary process and read every intermediary stage as the sentence structures changed bit-by-bit over time, the same computational process is analysable when it comes to code read in the cells of every living thing.

We can look at the rich diversity of species and map the phenotypic variation – variation due to underlying heritable genetic variation. We know from our genetic story that we are equally related to dogs as we are whales, and bats as we are hippos, and hedgehogs as we are deer, because the last common ancestor we have with, say, the dog, is the same as the last common ancestor shared with, say, the whale – even though regarding the appearance of an organism, characters and traits, the difference between a dog and a whale, or a bat and a hippo, is immense. Because we can read the code in the cells of every living thing, we also know that regarding the genetic distance on the phylogenetic tree, we are more closely related to mice, rats, rabbits and guinea pigs than any of the animals of the previous list (take most other animals and we’d know the genetic distance too). And genome sequencing shows us, beyond any doubt, that we are most closely related to other apes (chimpanzees, orangutans, gorillas, bonobos, etc) and all primates diverged from a common ancestor.

These studies show other conclusive evidence too. For example, inherited strands of past viruses (called endogenous retroviruses) show clear relatedness between species, and in a way that is exactly consistent with the tree of life. So too do the homologies – the common features and traits shared by organisms also matches both the genetic data of the family tree of all species, and the data that shows the trajectory of endogenous retroviruses.

The upshot of all this is, if you reject this as conclusive evidence for evolution, and remain unwilling to reject creationism and embrace these facts as instruments of God's creative genius, then you don’t understand how significant and decisive these data are, and how deep and wondrous the theology can get. There is simply no way of denying the fact of evolution and living with a clear conscience and a content mental state.