And Slaters Go Plop

Hamlet: Do you see yonder cloud that’s almost in shape of a camel?
Polonius: By the mass, and ’tis like a camel, indeed.
Hamlet: Methinks it is like a weasel.

In attempting to discredit evolution by natural selection, creationists have often described the impossibility of random mutations in DNA being capable of anything beneficial as the equivalent of a tornado in a junkyard accidentally building a 747 or a group of monkeys bashing the keys of a typewriter to successfully write the works of Shakespeare.

And they’re right. If evolution was merely random mutations then it would be unfathomably impossible for life to evolve as it does. But here’s the rub: no evolutionary biologists claim that random mutations alone cause the diversity of life we observe. This is where the crucial natural selection part comes in. Evolution occurs by random mutations, most of them neutral, where any beneficial mutations are selected for by the environment and those successful mutations go on to have more children who will likely inherit those beneficial mutations. And so on and so on.

To illustrate the point, back in 1986 Richard Dawkins in his book, The Blind Watchmaker demonstrated a simple program which he named ‘Weasel‘ as a reference to the concept of monkeys and typewriters and the above quote from Shakespeare. ‘Weasel’ starts with a jumble of letters, spawns ‘children’ from them (i.e. multiple copies), each with slight mutations and selects whichever ‘child’ is the most similar to a target phrase to spawn a new generation of children.

The point of the program was not to demonstrate every aspect of evolution by natural selection (that’s rather too much to ask of a small page of code), just the power of mutation when combined with a selection process as opposed to brute-force random chance.

Below I’ve created a simple version of Dawkins’ program that is limited to a single word and which will, due to the limitations of Javascript and browsers, only attempt a maximum of 500 generations. Have a play around to get a feel for how random mutations can result in very non-random outcomes when there is a selection criteria combined with heritability.

Full screen version

If you know how to run Python and want to check out a version closer to that of the original ‘Weasel’, take a look at the one created by fellow blogger and PhD student in evolutionary genetics, David, over at The Ativism. His is not limited to 500 generations like mine and he includes the newer concept of the option of ‘locking’ successful mutations.

The lecture lasts around 40 minutes and the rest is questions and answers.

In our bodies we contain two different types of DNA. There is the bog-standard (or, nuclear, because it’s in the nucleus) DNA which is a combination of half of your mother’s and half of your father’s DNA which you inherited when one of your father’s sperm fused with one of your mother’s eggs. And then there is Mitochondrial DNA which is different to nuclear DNA in that we inherit it directly from our mother alone as a part of the egg which is swarming with hundreds of thousands of mitochondria . Nuclear DNA fulfils the role of building our bodies and mitochondrial DNA provides the means for mitochondria to generate the energy a cell needs to do the things it does (i.e. dividing or making stuff). When cells divide they make a duplicate of your DNA and, inevitably, the mitochondria end up dividing themselves up between the newly-formed cells where they will recombine with each other to keep the numbers up.

If you are a mushroom, a plant, or an animal (from jellyfish to wetas to elephants) you will have mitochondrial DNA and if your species uses sex for reproduction you will likely have inherited it from your mother.

Every time nuclear DNA is recombined during procreation and every time mitochondrial DNA is recombined within the cells of your body little mutations can occur. Most of these mutations are neutral in that they don’t inhibit or enhance the functioning of the DNA.

What this means is that, while our nuclear DNA will pick up on average 128 mutations (out of ~3,000,000,000 base pairs) during sexual reproduction, mitochondrial DNA have more mutations (out of only ~17,000 base pairs in mammals) without the added complication of sexual recombination and this makes it much easier to compare mitochondrial DNA between people and, therefore, make reasonably accurate predictions for just how closely maternally related they are by comparison of their mitochondrial DNA alone.

Let’s say we take your mitochondrial DNA and compare it with your sibling’s. We will find that the two samples are almost, but not quite, identical. This is because there have been a handful of mutations in the time that you’ve had your mitochondrial DNA to yourselves. Now if we take your sample and compare it to a maternal cousin (i.e. you mother’s sister’s children) you will find that, while still almost identical, a few more changes will have crept in. You will notice a pattern of increasing change occurring as you compare the mutations of maternal second cousins, third cousins, fourth cousins and so on and so on.

Now, once you have established what rate of change you can expect between maternal relatives you can go ahead and test your neighbour. If you find that your neighbour’s difference in mutations are only about those of, say, your maternal second cousin then you will be able to fairly confidently predict that you have just met a previously unknown second cousin. If, however, you compare you neighbour’s mutations and they are larger than what you would expect from a close relative you should be able to make a prediction for how many generations ago it was that you shared a common grandmother based on the rate of change.

You may have heard before of a ‘mitochondrial Eve’ that was talked about a few years back. They got to this conclusion by testing as many diverse people in the world as they could think of and compared their mitochondrial DNA to see what was the greatest difference they could find. It turns out that the most remote common maternal ancestor they could identify lived around 8000 generations and perhaps 170,000 years ago. The exact numbers are, understandably, still hotly disputed but the fact of the genetic relationship is sound.

Some people have taken this to mean that this ‘Eve’ was actually the first human but they’ve missed the point. We could have done a ‘mitochondrial Eve’ analysis for just the people of a particular village in South America and found that their mitochondrial Eve was only 50 generations ago. Conversely, we could have done a mitochondrial Eve analysis of humans and chimpanzees and discovered that they are around 250,000 generations and 7 million years ago (as, indeed, they have found).

There are many other ways to measure the relatedness between animals including the Y chromosome (which is passed exclusively from father to son) and a plethoria of nuclear DNA comparisons. But I’ll leave those explanations to people who actually know what they are talking about. If this kind of stuff interests you like it does me, I wholeheartedly recommend The Ancestor’s Tale by Richard Dawkins.

Dawkins’ series The Genius of Charles Darwin is currently showing on the History Channel on Sky here in NZ. Omitted from the series was this insightful interview with Father George Coyne on the subjects of evolution, cosmology, science and faith.

Source

If you have a moment and you feel so inclined, please take a minute to fill out a survey on the public understanding of evolution which is being run by Michael Shermer & co. I’m not sure what data they hope to garner or for what purpose but they provide you with the opportunity to be emailed the results once they’ve finished.

I love these t-shirts! I’m going to have to order a couple.

Check out the full range here.

In celebration of the World Youth Day in Sydney and of the recent “Academic Freedom” law changes in Louisiana I’d like to present Galileo Galilei’s confession for the “absurd and philosophically false” notion that “the earth is not the center of the world, nor immovable, but that it moves”:

I, Galileo Galilei, son of the late Vincenzio Galilei of Florence, aged 70 years, tried personally by this court, and kneeling before You, the most Eminent and Reverend Lord Cardinals, Inquisitors-General throughout the Christian Republic against heretical depravity, having before my eyes the Most Holy Gospels, and laying on them my own hands; I swear that I have always believed, I believe now, and with God’s help I will in future believe all which the Holy Catholic and Apostolic Church doth hold, preach, and teach.

But since I, after having been admonished by this Holy Office entirely to abandon the false opinion that the Sun was the centre of the universe and immoveable, and that the Earth was not the centre of the same and that it moved, and that I was neither to hold, defend, nor teach in any manner whatever, either orally or in writing, the said false doctrine; and after having received a notification that the said doctrine is contrary to Holy Writ, I did write and cause to be printed a book in which I treat of the said already condemned doctrine, and bring forward arguments of much efficacy in its favour, without arriving at any solution: I have been judged vehemently suspected of heresy, that is, of having held and believed that the Sun is the centre of the universe and immoveable, and that the Earth is not the centre of the same, and that it does move.

Nevertheless, wishing to remove from the minds of your Eminences and all faithful Christians this vehement suspicion reasonably conceived against me, I abjure with sincere heart and unfeigned faith, I curse and detest the said errors and heresies, and generally all and every error and sect contrary to the Holy Catholic Church. And I swear that for the future I will neither say nor assert in speaking or writing such things as may bring upon me similar suspicion; and if I know any heretic, or one suspected of heresy, I will denounce him to this Holy Office, or to the Inquisitor and Ordinary of the place in which I may be.

I also swear and promise to adopt and observe entirely all the penances which have been or may be by this Holy Office imposed on me. And if I contravene any of these said promises, protests, or oaths, (which God forbid!) I submit myself to all the pains and penalties which by the Sacred Canons and other Decrees general and particular are against such offenders imposed and promulgated. So help me God and the Holy Gospels, which I touch with my own hands.

I Galileo Galilei aforesaid have abjured, sworn, and promised, and hold myself bound as above; and in token of the truth, with my own hand have subscribed the present schedule of my abjuration, and have recited it word by word. In Rome, at the Convent della Minerva, this 22nd day of June, 1633.

I, GALILEO GALILEI, have abjured as above, with my own hand.

On Saturday I trundled along to Academy Cinemas in Auckland to watch a documentary on the life and achievements of Allan Wilson, a NZ-born molecular evolutionary biologist.

Allan Wilson was born in Ngaruawahia in 1934 and died of leukaemia in 1991. He spent most of his life in the United States where he formed the Allan Wilson Centre for Molecular Ecology and Evolution at Berkeley.

So what was so special about Allan Wilson that a documentary was made about him?

At the time that Wilson was studying, the theory of evolution didn’t really have much objective data to go on regarding the differences between species. People could look at the size and shape of a bone and compare it with other species (across the outside of the tree of life) and they could see back down inside the branches by digging up old bones to see if modern species might share common ancestors. Going by morphology (i.e. how things look) is a fairly inexact science and while it might point you in the right direction it would have been nicer to be able to use numbers to be able to make mathematical and statistical predictions.

We take DNA for granted these days but in Wilson’s time very little was known about these building blocks of life.

Wilson straddled a path between zoology and molecular chemistry which were both tackling the problem of evolution from quite different angles. He caught a bit of flak for his attempts to marry the two but he drew the most fire from creationists – surprise, surprise – when some of his later experiments began to show the true, measurable relationships between humans and other species, namely the great apes.

He was heavily involved in the concept of the molecular clock, which is a way of finding how closely related one species is to another at the genetic level without necessarily being able to read the genes themselves. You may have also heard of the Mitochondrial Eve hypothesis – that’s his too.

Since his death both the human and the chimpanzee genomes have been read and have further bolstered the conclusions he was able to make by merging two seemingly disparate sciences. And also, sadly, since his death advances in diagnosis as well as treatment of leukaemia have been made due to the methods he and his team pioneered.

The film-maker went so far as to say that in the years to come Allan Wilson’s name will become synonymous with some of the other pioneers in the theory of evolution by natural selection. And everyone seems to agree; just about everything that present-day evolutionary biologists are working on stems from the advancements of this one bloke from Ngaruawahia.

Today I was asked by Rhett, a Christian pastor-to-be,

“Where would you say your concern for human suffering comes from in that you are an Atheist evolutionists. Forgive me for simplifying things terribly here, but do you see the moral compass as having evolved? And isn’t evolution all about survival of the fittest, might is right etc? How does concern for others suffering coming into you worldview?”

Evolution is a scientific observation about how life works. How living organisms change through the generations and the mechanisms that cause those changes. Many people see evolution as anti-Christian because the evidence claimed by the theory of evolution by natural selection (the proper name for the theory) flies in the face of a literal interpretation of the creation story in the Bible. Evolution is only anti-Christian if you define Christianity in such a way that it relies on an explanation that contradicts the scientific findings – in the same way that the theory of gravity would be anti-Christian if one of the core tenets of Christianity was that the spirit of God is what keeps planets in their orbits.

Many Christians have no issue with evolution and any controversy about the fundamentals of the theory is within Christianity itself and stems from a multitude of interpretations of scripture.

Atheists are people who don’t believe that there is a God. I’m the kind of atheist who thinks that the question “Is there a God” is one that is as unprovable as the question “Is there an invisible pink unicorn” because most people’s definition of a God seems to entail the same, non-observable or non-testable properties. On the question of whether it’s possible to prove God exists or not I’m an agnostic but my conclusion after looking at the arguments and the evidence is that there is none.

This is not necessarily what an atheist wants however. I would personally like to carry on after I die and the thought of bad people getting their comeuppance in the end is pretty appealing.

The link between atheists and evolution only really exists because there really is no other plausible explanation for how life develops. Evolutionists are not necessarily atheists but atheists are unlikely to be anything but evolutionists because of the lack of rival explanations that don’t include a god.

The theory of evolution by natural selection makes the observation that the offspring that are best suited for the environment they find themselves in are going to be more likely to have more offspring themselves and this will cause more of the population of their species to have similar traits because children inherit many of their parent’s genes.

This is sometimes termed as “survival of the fittest” which some people take to mean that “only the bullies win”. But to be successful as a species it’s not necessarily the strongest and most aggressive that do well. Being small and agile is a popular survival mechanism. So is being good in the dark or being camouflaged or being able to fly or being able to eat lots of grass or plankton and so on and so on. Another trait that has proved extremely useful is the ability to cooperate with other members of your species and this leads me to the core of Rhett’s question; Morality.

Altruism is defined as looking after the interests of others over your own. Reciprocal altruism is looking after the interests of others with the expectation that they will repay the favour. Reciprocal altruism has always been easily explained in evolution; if a species develops a trait that will allow individuals to help each other out not only will those members of the species do better than their siblings but the species as a whole is likely to do well as a result. At a simple level genuine altruism is also easily explained because a species that develops the tendency to be willing to die to help the survival of your direct offspring or of members of your family group is going to be more likely to pass that tendency on. Your children who survive because of your altruism will more than likely carry the same genes and close relatives have a higher chance of carrying that same trait. For an excellent discussion of this topic read Dawkins’ The Selfish Gene.

So, self-sacrificing behaviour is very much a part of evolution and easily explained in even relatively simple creatures. Where it gets really complicated is with the likes of humans who not only inherit genes but have the hardware (brains and language) to spread memes (ideas).

We get much of our morality from our culture. Memes are spread around from person to person and from culture to culture. Some memes are bad, some good, others neutral – just like genes. Some people think our morality comes from God and struggle to understand how someone who doesn’t believe in a God (or, specifically, their God) can have morals. But morals are really just memes for how to best live in a society. Some morals are built into us at the level of our genes (a parent who will fight to the death for their child) and some are developed by trial and error or even by reason and passed from person to person as a meme (washing your hands after defecating – a reasonably recent meme). Often morals are encapsulated in the form of a religion and passed from person to person that way, perhaps because religion has been an excellent medium for spreading memes with its use of repetition, documentation, authority and so on.

“Do you see the moral compass as having evolved?”
Yes, absolutely. Most of the core behaviours of morality can be explained by way of genes (especially if we can observe them in species that don’t spread memes – i.e. ‘learn’) and the rest in humans have been able to be propagated due to the fact that we have the hardware which allows us to be really good at spreading memes. And even memetic morality evolves, just not by the same mechanism as genes. In our current society it’s immoral to prohibit a woman from voting but our ancestors thought it perfectly reasonable.

“Isn’t evolution all about survival of the fittest, might is right etc?”
Nope. It’s all about how well suited you are to the environment you find yourself in. Also, please notice the difference between observing the process and mechanisms of evolution and believing in evolution (as if it were some kind of ideology).

“How does concern for others suffering coming into you worldview?”
Like most people I inherited my morality from my family and from the culture I was brought up in. I’ve also read a lot of literature on different people’s opinions on how to best live as a society since then.

Morality is a game we all play and it’s a function of society. Pretending that morality comes to us by divine revelation is a form of exclusivism and I would have thought that in this day and age we’d be smart enough to see beyond that. 

Most of us will have heard of vitamin C. It’s in oranges and tablets that taste like oranges right? But what is it? And what’s it got to do with orangutans, the Royal Navy and rose hips?

Well, I’m glad you asked; grab a coffee and come on in…
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