Sunday, 30 November 2008

The Idiocy Of Creationism (part 1)

For anyone wanting to earn an easy 100,000 lira, Old Earth Creationist Harun Yahya is offering a prize for the best paper on why evolution is invalid. At first I was excited because I thought that by writing a decent paper I could swindle some creationist cash and put it towards real science, but reading the entry page was a list of every fallacious argument that Creationists come up with. So instead I felt it best to debunk the frivolous claims in my own words, even if Talk.Origins counters all these arguments and more.

(1) Life cannot emerge by chance...
Firstly, evolution does not try to explain the origin of life. Evolution is a process which acts on life that is already there, it's like complaining that plate tectonics is invalidated because we don't have an adequate theory of planet formation. How life came about certainly does need an answer, but even if that answer is Goddidit the diversity of life in it's present form can only be explained by evolution.

As for abiogenesis being a matter of chance? While Einstein was wrong to say God does not play with dice, to put life down to an expression of quantum physics would be an inadequate explanation. Instead life would need to come about by a set number of steps that have to be in the realms of possibilities of what that organic matter can do. No theory of abiogenesis is down to chance, each one is a series of steps that start with but a few chemicals and a catalyst and result in replicating organisms.

As for the probability given on their site (1 in 10950,) an explanation can be found at There will not be one single step that will lead from inanimate matter to fully-replicating cells. It may be hundreds of steps all requiring certain conditions in which to happen. It could take thousands or millions of years for the process to take, we simply don't know. But no scientists are alleging that the first cells will look anything like modern cells we have to work with. What survives now 3.5 billion years later would look nothing like the primitive cells that would have started the process.

(2) There is not a single intermediate fossil...
This is a flat-out lie. Firstly every fossil is an intermediate form, life keeps changing generation to generation so life can be nothing but intermediates. But that's not really the point Mr Yahya is getting at, so I'll directly address the idea of transitional forms.

Each fossil is going to be it's own complete form, it's going to look like the species of which it is. But it's the relative transition of the form in regard to older fossils and younger fossils that gives us the understanding of evolution. In our own lineage, Homo Erectus is much like us but not quite. It's probable that we are descendants of Homo Erectus, just as Neanderthals were. But it's unlikely that we are descended from Neanderthals, the DNA support just isn't there. Going back further we have Homo Habilis and even before that Australopithecus. By sorting the fossils in order, we can see a pattern of transition.

An intermediate in this case would play the role of the "missing link", an intermediate between Australopithecus and Homo Sapien is Homo Erectus. Between Australopithecus and Homo Erectus is Homo Habilis. Each is their own species, but they become intermediary forms when put in context. Humans are not the only species where we have a good fossil record of the transition. The horse and the whale both have a strong fossil record supporting the gradual transition. We have intermediaries of the fish to tetrapod transition, of the reptile to mammal, of the dinosaur to bird.

(3) “Living fossils” are a response to evolutionary myths...
Evolution is not destroyed by the idea of "living fossils", all that matters is when the species first appears in the fossil record, not when it last appears. If rabbits appeared in the fossil record long before any other tetrapod, common descent would be wrong. But a 200 million year old rabbit is not a problem at all for evolution provided there are other species before it that show a transition from reptiles to mammals, and non-rabbits to rabbits.

It all comes down to a matter of selection. If a species like the Coelacanth is in a successful form, then any variation on that form may not be as advantageous and die out. It comes down to a matter of survival, so if any macroscopic mutations aren't successful then there is no reason why we should expect change. It's a shame we can't compare the DNA of a modern Coelacanth to one from 400 million years ago, because that should highlight the difference.

(4) The unimaginable information in DNA...
Again with the "it's all too complicated to be formed by chance" argument. All that's needed to show this argument to be false is to show how information can be added. And there is such a mechanism: gene duplication. There are several thousand scientific papers explaining this phenomenon (go here and search for gene duplication). Once there is a mechanism of increasing information, combined with a process of selection on said information, the size of any genome presents no problem given enough time.

(5) Organs with irreducible complexity...
Two things here come to mind: firstly irreducible complexity is not a problem for evolutionary theory, secondly the eye and wing are not irreducibly complex. The problem of irreducible complexity was solved almost a century ago, decades before it became the new calling cry of creationists. All it takes is for an additive part to become a necessary function of the system, as soon as that happens taking away that additive part would make the system non-functional.

The eye will still work if one takes away components, so it's not irreducibly complex. One can be born without lenses in their eye and still have sight in some form. Some people are born partially or wholly colour blind, yet the eye can still serve a function perfectly well. In this case it's mistaking complexity for irreducible complexity, and that is the more important question: how did the eye evolve? The answer is through a gradual set of stages, from simple light sensitive cells all the way to what we have now. Each of these stages can be seen in the animal kingdom, it's not hard to make the link from one to the other. A wing is much the same, through gradual stages wings have evolved into what they are now. The same can be said for any complex function, the gradual stages are seen throughout nature.

(6) All the variety of life on Earth appeared suddenly 530 million years ago...
Suddenly? Well on a geological timeline, suddenly sounds right. In reality the Cambrian explosion happened over a period of tens of millions of years. There is also evidence of multi cellular life going back at least 50 million years earlier, the explosion itself is not a sudden outburst of life. There is a good run-down of the gradual timeline here. Even the rapid state of emergent life as seen in the Cambrian explosion can be seen in other points of earth's history as well.

It's also important to understand that events like the Cambrian explosion are macroscopic expressions of life. Early evolution of complex creatures would have been on the microscopic level and would have simply been too small to see. Whatever events transpired to allow for macroscopic creatures doesn't mean that all phyla came to be at that point, it just means that it's the point where they are visible in the fossil record.

Tuesday, 25 November 2008

Book review: A Short History Of Nearly Everything

I really wasn't sure what to expect when I picked up Bill Bryson's book on science, I'd heard good things about it but wasn't sure really what I would get out of it. It was something I wanted to read before getting into other books that detail the specifics, that way I wouldn't be reading over the same kinds of information. What I discovered, however, was that what I did know enhanced the learning experience.

A Short History Of Nearly Everything achieved what it set out to do, explain the basics of science in a manner that is understandable for the layman. As a rough guide to science, it's hard to think of any resource better. It's the kind of book I wish I had in high school, maybe it would have kept me in the science lab instead of the computer lab.

The manner in which the science is laid out is well presented, it ties together the many different facets of knowledge well. It not only tells the stories of the information we know now, but also goes to great lengths to tell the story of the history of knowledge and the progression of ideas. That understanding of the context is vital to understanding the information.

The book was not only about the science, but the scientists behind it. Scientists are fascinating people, and at each step of the way the scientist behind the discovery had an interesting tale to tell. From egotistical narcissists to paranoid eccentrics and all the lucky or unlucky moments that befell them, each discovery was accompanied with a mini biography of the discoverer. Most of the time this was entertaining, but occasionally dragged on for too long and left me thinking "Isn't this supposed to be a science book?"

Overall it was a thoroughly entertaining read. Bryson did a superb job of pacing this book out, he made otherwise dull areas of science seem exciting, and was able to make every chapter both entertaining and informative. What most impressed me was the humility in it all, he went to great lengths to stress the unknown and where conflict exists in the scientific community on certain issues. It was very refreshing to see a pop-science book that was so willing to talk about what is still yet to be discovered, it's a softer stance that when talking to the general public is needed. Read this book!

Next book: Stephen Hawking - A Brief History of Time

The Problem With The Christian Doctrine

While scanning newspapers online recently, I came across this article about a Baptist pastor saying that the Jews would burn in hell because they didn't accept Jesus. While he's somewhat apologetic at causing offence, his comments are still indicative of his views on the matter. The more damning aspect of the Christian Doctrine is that one needs to accept Jesus as a personal saviour in order to be spared an eternity of torture. This archaic and draconian tenet is to me the most disgusting element of the Christian doctrine.

The fall of Adam
In the beginning, there was an answer: 42. But what was the question? God didn't know so he made the earth to calculate the ultimate question. From the earth came all life, but for his greatest creation he used his pottery skills to craft it out of clay. And low and behold, there stood Adam. Adam was lonely as all golems are, so God created Eve who had the pleasure bits that would occupy Adam's mind. But like all woman who aren't confined to the kitchen, Eve went rogue and took advice from a talking snake. After all, she had no knowledge of good and evil. So Adam and Eve were cast out into the world, knowing they had condemned mankind for all eternity.

God gave mankind free will, yet not the knowledge to exercise free will. Ironically enough, by eating from the tree man gained knowledge of good and evil and would have been able to make an informed choice. Adam may have had free will but without knowledge of right and wrong it's hard to exercise free will properly. One might even conclude that to punish someone who was God-given ignorant for an action that was well beyond their control is extreme, and that to punish all mankind for that moment of judgement he never had.

So now everyone is a sinner and has to atone for that absence of judgement on the account of Eve. If only God didn't put that talking snake in the tree, or he didn't put the tree there at all. God's supposedly omniscient so he would have known what was going to happen before it happened. There was no need to have anything there at all. But of course any rationalisation on why the tree was there is post hoc reasoning on account of us. Maybe the tree was there so man could exercise free will, maybe it was there because it was part of a divine plan. That's the great thing about theology: it doesn't matter what the justification is because it can be justified in any way. After all, we can't know the mind of God and hell is reserved for anyone who bothers to question Him.

Now of course, Adam and Eve is nothing more than an allegorical tale. There was no creation, no garden of Eden and no fall from paradise. The whole story is downright silly, and I really can't understand how anyone could think it's a literal story of human history. But it's central to the Christian doctrine of original sin, without it there is nothing that Jesus needs to atone for.

The resurrection of Jesus
So after four millennium of punishing people through genocide, and other atrocities, God decides that the vile corrupt creation deserves a chance to atone. So his plan? He comes down to earth to impregnate a virgin so she can give birth to God. Only it's not God, it's God in human form. Now in human form, Jesus becomes a cult leader, saying a few profound things (and a few inane things as well, but it's not like he's God or anything) and getting a bit of a following. He eventually gets punk'd by Judas so he can get tortured and die in order to redeem mankind for the sin that he put on them in the first place. There's only one condition: you have to believe in God in order to be saved.

Why God had to come down in human form is again a matter of theological interpretation. Why couldn't God just have atoned mankind with the raising of an eyebrow? Why did God have to come down in human form in order to do so? Again, we can't know the mind of God so any questioning as to why is blasphemy. It's another post hoc rationalisation of the content, any interpretation we give of the gospels is nothing but post hoc reasoning. How is a modern interpretation by a liberal Christian sect any better or worse than the Catholic interpretation or a Baptist one? They all claim that their interpretation is the correct one, yet they all suffer from pushing their own biases into their interpretation.

When it comes down to it though, most of these interpretations have one central tenet: atonement through faith. So it doesn't matter what you did in life because we are all sinners, if there is a belief in Jesus then one will be saved. Not about works, not about being a good person, but when it comes down to it faith is all that matters. This fundamentalist interpretation is quite a frightening prospect, it ties non-belief with eternal punishment and all those who don't accept Jesus into their heart will suffer the consequences of the fall.

Most people throughout history have not heard of Jesus, they would all be condemned. In a Christian society making a choice is possible, but for those who have never heard of Jesus are condemned to suffer for all eternity for the crime of simply being born in the wrong place and time. But it's God so we can forgive him for infinite punishment of people who had no choice in the matter and still call God all-loving. After all, those who question whether God is all-loving will feel the wrath normally reserved for the children of the Nile.

Non-literal interpretation
It must be recognised that there are as many interpretations of the afterlife as there are those who believe in the afterlife, and there are many sects of Christianity which don't hold the fundamentalist interpretation that is part of Evangelicalism. The main argument here is a rejection of the central tenets that are most amplified in Charismatic circles; the absolute nature of the belief is at odds with a secular multicultural society. As the good pastor found out, saying that those who don't accept Jesus will be eternally tortured doesn't make for good interfaith relations.

Monday, 24 November 2008

Arguing Theology

Religion has come under a lot of criticism in recent times, it's moved beyond factional wars and now it's come to the point where the institution itself is being questioned. Why do we need religion? What purpose does it serve? What positives and negatives are the outcomes? These seems like legitimate points of contention, but the mere expression of scepticism is met with immense hostility. It's no surprise, any idea that has some personal significance is going to be defended with absolute conviction. What does surprise me is some of the tactics for apologetics is the appeal to the scriptures, that one must be an accomplished theologian in order to criticise any and all aspects of religious belief.

The Courtier's Reply
In response to criticism of The God Delusion, the Mr Pharyngula PZ Myers came up with a great counter called The Courtier's Reply. It's just a fantastic counter to the claim that one cannot dismiss God without being an accomplished theologian. It seems an obvious point, one does not have to be versed on eastern European folklore in order to dismiss the concept of vampires. The realm of studying reality is the scientific realm, and the construct of religion as an explanatory mechanism and the wider effects of the social construct on a population throughout time are best studied with the best tools available.

Modern interpretations of God are nothing more than putting lipstick on a pig, while theologians trump these new philosophical interpretations of God, it's still the same biblical-based entity as before with no evidential backing. No matter what new philosophical justification there is for God, the tenet of the resurrection still remains central to the Christian doctrine. Whether God exists is not going to be determined by philosophical constructs, rather it will be determined by evidence.

To understand the effects of religion on a wider scale, it's absurd to think that reading a holy book would indicate anything beyond a peripheral understanding of the text itself. For behavioural effects, it's best to look at neuroscience and psychology. For societal effects, there's sociology and history. Being an accomplished theologian won't teach anyone about the influence of religion on society, but the social sciences will and that's the place to look to.

Now consider the parallel with something I actually do care about: gaming. One might ask the question "what are the wider effects of gaming on the individual and their role in the community?" Now if there was a study that showed a trend of violence among gamers, would it be more pertinent to question the controlling factors of the study or whether the psychologist in charge had ever beaten Quake on Nightmare difficulty? If there was a sociological study showing anti-social behaviour increasing among online gamers, would the controlling factors of the study be under question or whether the sociologist's World of Warcraft character had reached level 80?

The parallel with gaming is there to show that knowing the content of a subject is not an adequate resource to deal with questions not relating to that content. Knowing the back-story of Zelda universe does not make that person any bit qualified to answer questions on behaviour associated with playing the game. Theology won't answer questions of individual behaviour, it won't answer question of the wider social effects of group behaviour and how that has happened throughout history. The best way to study the inquisition is to look at the historical evidence, not the bible.

Middle-Earth scholarship
What does reading the bible actually tell us? It's like any other piece of literature, it has a message that the author(s) intended. Those who are adept at literary analysis would see even further into the book and be able to understand the authors themselves. But for the layman, the bible is a chance to get immersed in the world of the mythology. They are able to emotionally connect with the characters involved and try to understand the motivations associated therein. In essence studying theology has the academic scholarship of studying Lord Of The Rings.

J.R.R. Tolkien wrote a masterpiece in the fantasy genre, it's influence today is seen transcending literary fantasy and into the pop culture. Admittedly the adaption to the silver screen helped bring it into the consciousness of an otherwise ignorant mainstream, but it's success still speaks volumes for it's quality. It doesn't stop there either, the appendices, and further books all bring Middle Earth to life and give it a complete mythology.

Now if one were to argue the meaning of Frodo's journey, it would help to read the book. It would give an even better picture by reading the appendices, and given greater context of it's magnitude by delving into the Silmarillion. One who has read the books several times and studied the key passages and themes would have a greater understanding than someone like myself who has only read the book twice. Sure I'd be able to argue a few points on an equal footing, but for most things they would be able to teach me so much.

And in the end that's what being a theologian amounts to. They could tell me so much about the way the bible is presented, they could tell me about what each passage means in the greater context of the whole. But when they do so from a theological perspective, they can only give me theological answers. To read the book as a quasi-historical document would give us an accurate representation of what the bible is. But to read it as the divine word of God, there's as much in theological scholarship as there is in Tolkien's classic. Only Middle-Earth scholars aren't deluding themselves into thinking they are understanding Eru.

Thursday, 6 November 2008

Shannon Entropy

I've been challenged by an ID advocate in order to explain away a certain element of information theory in regard to evolution. When most people refer to entropy, it's to do with the second law of thermodynamics. But in the case of this particular person, he refers to Shannon Uncertainty - a system in information theory. Now I was very confused as to just what this had to do with evolution, but DNA is a coding sequence so maybe there needs to be some explanation for how evolution overcomes the problem of a loss of information over a long period of time.

Natural selection is a harsh mistress
Firstly, let's take the assumption that mutations are random. There's no way of knowing what mutations will happen in an individual. If there were no copying errors, there would be no modification through successive generations as our DNA is the only material that is passed down from parents to children. It's also important to note that while mutation happens on an individual level, evolution takes place in a population. All children we have will still be homosapien, it's just that given enough genetic isolation that my descendants may be unable to breed with your descendants and from there homosapien becomes two species.

Our genetic code is passed down through sexual intercourse, 50% comes from the male and 50% from the female. Each baby is born with a mixture of traits and some errors in copying. These mutations can be harmful, but most are neutral. Occasionally some can be advantageous, and the theory of evolution stipulates that these advantageous mutations would mean that descendants of that organism would be better at surviving and thus produce more future offspring, eventuating in those successful traits being passed through the whole population. So what of Shannon Uncertainty?

Let's make a hypothetical gene, call it VENTER1. Now this hypothetical gene is vital to the animal COYNORR. It contains 100 coding characters all of which need to be exact in order for Coynorr to survive. Any change to the code would mean that the baby Coynorr would not develop successfully. Without successful embryological development, the baby Coynorr would not be able to pass on the fatal mutation. So the gene while being subjected to random mutation would pass down generation after generation because any modification to that gene would stop the self-replicating process.

That was a very extreme case, what about a non-fatal hypothetical gene, we'll call this one COLLINS1. Now this gene determines the leg strength of the Coynorr, it's a creature that needs to be able to run fast in order to escape predators. While the weakened form of this gene could be passed down through generations, it giving the Coynorr a slight disadvantage against it's predator means that it's less likely to be carried on than those faster Coynorrs. Over many generations, descendants of Coynorrs that don't mutate would have more successful offspring.

So that covers the slightly negative and the severely negative, but what of positive mutations? Now take the hypothetical gene MILLER1. It has a mutation in copying that allows the individual to have a selection advantage over it's rivals. The advantageous mutated gene will become more frequent in the population over time than the same gene without mutation. The Coynorr population would over time have the superior MILLER1 gene, because any born without would be at a survival disadvantage.

And for the final mutation, a neutral mutation. What if the gene WATSON1 had a mutation that could mutate in certain ways without being detrimental? If the mutation changed the functionality but offered neither survival advantage or detriment, then there's no problem. What does it matter if a species has neutral mutations? Each one of us has hundreds of mutations in our code (it's important to remember that there's over 3 billion base pairs in our genetic code) and most of us walk around fine. Indeed some changes would have no effect at all on the organism given that some amino acids can be coded by multiple sequences. Alanine will be coded by any of GCA, GCU, GCG or GCC, Leucine can be coded by any of 6 combinations.

He's a perfect clone
The more and more I've thought about this question, the less it's made sense to me. There's really no way this could apply to evolution at all. When language is transmitted there is specified meaning. If I were to take this post and put it under a modifier, over time the meaning would get lost as mistakes creep in. This is the loss in information theory, but DNA is not specified information in the way language is. There's no one code for any particular species, and variation through generations is not only inevitable but advantageous!

Each generation any one individual passes on only half of their DNA in a child, the other half coming from their sexual partner. So in two generations, a grandparent will only have 25% of their DNA passed on and in three a great grandparent will only have 12.5% passed on. Over time there's very little chance of anything unique to you being passed on, but that doesn't matter. It's the survival of the genes that matters and we are just one transitional form.

And that we are, an intermediary carrier of genes. There's no such thing as the perfect design that is getting lost in transmission over time, a design is as good as it's ability to survive and reproduce. Species live in an ever-changing environment so variation needs to occur for successful adaptation. This is why sex is such a powerful survival strategy in the animal kingdom, it allows for a greater mix of mutations into an offspring. Species are always in evolutionary arms races, sometimes in the macroscopic world and other times in the microscopic world. Those in the old world became resistant to smallpox, but it's introduction to the new world was devastating for the indigenous population.

Mutations in our DNA is not only inevitable, but it's necessary for evolution to occur. Natural selection weeds out the negative mutations and promotes the good mutations, while over time genetic drift with population isolation leads to speciation. What's lost, what's gained, what changes over time, all these are part of the natural process of life. Life simply exists and in this brutal chaotic struggle for survival, any change that can help with that is more than welcome.