Intelligent Design Flaws: The Evidence for Natural Selection in Our DNA

Here in New Zealand the debate between religion and evolution is a muted affair, while news on the topic regularly makes headlines in the US, here it goes almost beneath notice. That is not to say the clash does not exist here, merely that it tends not to intrude into the public sphere. Over time the form of the argument has changed but at its heart the source of the conflict has remained the same, discoveries in science have unseated the traditional view of a divinely created world in which Humans are the pinnacle of creation.

At this point I would like to make it clear that the findings of science are not incompatible with such a view.  Even so, to accommodate the conclusions of scientific enquiries into nature certain tenets that were previously held to be literal truths (such as 7 day creation) must be reinterpreted symbolically. As in any human endeavour there exists a spectrum of approaches to the religious significance of science’s discoveries. To some, science represents the deepest truth we can know about the world, provisional as it may be, and as such must also inform the religious outlook. For others revealed scripture is the ultimate authority and where this disagrees with science, well, so much the worse for science. Most people fall somewhere between these two extremes.

I seldom wade directly into this debate but recently came across a paper that outlines some of the peculiarities to be found in our genome (in particular but multicellular life in general) which was framed in the context of refuting design. The paper is “Footprints of Nonsentient Design Inside the Human Genome” written by John C. Avise and published in Proceedings of the National Academy of Sciences. Before getting to the crux of his argument Avise spends some time to give a brief history of three concepts that have a bearing on the discussion of design in nature. Touching on Socrates, Reverend William Paley’s famous work “Natural Theology” and Darwin’s own thoughts on the topic Avise gives a primer on how the natural world was considered in pre-Darwin times. From here we move onto the rise of modern Creationism and Intelligent Design, charting it’s progression from the early 1980s to the more recent strategy of proposing the concept of “Irreducible Complexity“.

Finally there is a similarly brief sketch of Theodicy, or the attempt to reconcile the existence suffering in the world with the traditional view of an all-powerful and all-loving deity (if you are playing charades I recommend doing “sounds like” and then try acting out Odysseus’ journey following the fall of Troy). This last seems somewhat out of place in a paper such as this but the relevance becomes clear once the author begins to expound on the multitude of human ailments that are the result of imperfections in the architecture and the replicating processes of our genome.

The numbers involved and breadth of disease in this section are truly staggering, to quote from the paper itself:

Various mutations are known to debilitate the nervous system, liver, pancreas, bones, eyes, ears, skin, urinary and reproductive tracts, endocrine system, blood and other features of the circulatory system, muscles, joints, dentition, immune system, digestive tract, limbs, lungs, and almost any other body part you can name.

In covering the various methods we use to keep track of genetic diseases, one of which being the reference text “Mendelian Inheritance in Man” Avise notes that “the current version of which describes thousands of human genes, of which more than 75% are documented to carry mutational defects associated with a disease condition.” and concerning another effort at documentation the “Human Genome Mutation Database” states “recent versions of which describe more than 75,000 different disease-causing mutations identified to date“.

After all of this preamble we finally get to the design flaws we have been promised, the first being “Split Genes”. Here is where things get technical. A quick “Genetics 101″, while we may think of genes as being discrete entities in our cells that code for the proteins making up our bodies, one gene to one protein, things are actually a lot more complicated. What actually occurs for many genes is a long stretch of DNA, some of which is needed for the gene and some of which isn’t. These parts are called Exons (needed bits) and Introns (extra bits), imagine reading Harry Potter and finding someone had randomly glued in pages from the dictionary. This means each time our cells want to make a new copy of a protein the extra bits need to be chopped out and the needed bits stitched back together first.

This process is both wasteful (unnecessary copying and fixing of the gene coding regions) and harmful, to quote once again:

“An astonishing discovery is that a large fraction (perhaps one-third) of all known human genetic disorders is attributable in at least some clinical cases to mutational blunders in how premRNA molecules are processed”

Next up is is a section discussing gene regulation and surveillance of errors. I have to say, this part is too complicated for me to parse ant this late hour. So I’ll leave that one for the adventuresome. Suffice it to say that the regulation (turning genes on and off) and copying of our genes is a complicated and error prone business, too much so if we are to consider it the perfect solution to the problem of creating human life.

The next stop on our curious ride is the mitochondria, or more specifically mitochondrial DNA. You may recall the oft repeated refrain that the mitochondria is the “powerhouse of the cell”, not to be confused with midichlorians which mediate the power of the Force. The mitochondria contain the reactions that allow us to extract energy from our food, without them you would die in very short order. It is one of the more intriguing facts about our cells that the mitochondria are equipped with their own DNA, and yet this DNA does not contain all of the information required to carry out the life giving energy reactions, it is supplemented by the DNA contained in the nucleus of the cell, your genomic DNA. Not only this but the interior of the mitochondria is a poor place to keep DNA, it is after all where energetic reactions are being carried out and toxic waste products are produced. Would you keep a valuable library in a working furnace?

These facts are all but inexplicable (and a great many more are mentioned in the paper) by appeal to a perfect designer but they are relatively easily dealt with via the paradigm that mitochondria are the remnants of a symbiotic bacteria. One which long ago insinuated itself into our cells and over the millennia has shed much of it’s own genome while housed in it’s comfortable new habitat. An analogy might be the loss of certain mathematical abilities in modern students who rely on electronic devices to to the hard work of calculation for them.

The paper goes on to deal with repeating sections of DNA, the existence of duplicated genes and pseudogenes and roving DNA that copies itself around the genome. But you can read about those for yourself, this post is already more than typically verbose. I would just like to sum up with the final hopeful run-on sentence (cousins of which plague my own writing) of the author:

“The evolutionary-genetic sciences thus can help religions to escape from the profound conundrums of ID, and thereby return religion to its rightful realm—not as the secular interpreter of the biological minutiae of our physical existence but, rather, as a respectable philosophical counselor on grander matters, including ethics and morality, the soul, spiritualness, sacredness, and other such matters that have always been of ultimate concern to humanity.”

Not exactly an uncontroversial sentiment itself.

Avise, J. (2010). Colloquium Paper: Footprints of nonsentient design inside the human genome Proceedings of the National Academy of Sciences, 107 (Supplement_2), 8969-8976 DOI: 10.1073/pnas.0914609107

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Backing Up Evolution

I’ve said it before and no doubt I’ll say it again but we know science works because it makes predictions that we can then measure against the universe and determine if the models we have created to describe it are accurate or not. One of the more successful models is the theory of evolution by natural selection. A criticism levelled against the theory of evolution by detractors is the claim that new information can not be introduced into the system, only taken away. This is actually false but lets consider how we might tackle this question scientifically

First, the underlying assumption here isn’t unreasonable, let’s explore it. The accepted mechanism of introducing change in an organism, change that natural selection can then act upon, is mutation. Mutations involve a mistake in the copying of an organism’s DNA, this might consist of a change in a single base of a gene (an insertion of an extra base, deletion of an existing base or swapping one base for another) or it might involve large stretches of DNA. The basic principle that is relevant here is the same, a change is made to the blueprints of life in our cells.

As you might expect there are many more ways of being wrong than there are of being right, any random change is more likely to introduce a defect in the complicated machinery of life than it is to create an improvement (bearing in mind that “improvement” is a value judgement that really cannot be applied here but don’t focus on the wrong part of the story). So on the surface it would seem that random change is very definitely a bad thing, mutations would likely lead to loss of gene function, and by extension, loss of information and specifically death of the individual.

How might evolution get around such a problem? One solution would be to make copies of critical genes, this way is one copy is damaged through mutation the other can still function and produce a viable organism. The “spare” gene would then be free to mutate and the resulting gene may be selected for or against by natural selection (or human breeders).

If you have been reading closely you will have picked up on our prediction, the genomes of organisms should contain copies of various genes that allow mutations to occur without harming the individual that accumulates them. It turns out this is exactly what we find.  A recent study found a significant amount of redundancy in the genome of Zebrafish which allows mutations to occur in genes critical to development without lethal consequences to the fish.

The researchers intentionally gave mutagens to populations of Zebrafish and looked for changes in fish morphology indicative of mutations. In particular they created a mutation that lead to the loss of most of the fish’s scales, similar to that of Mirror Carp. The mutation was traced to a gene critical to normal development, further investigation revealed that the gene existed as a redundant pair, only one of which being required for normal development.

It is tempting to talk about this phenomenon in terms of intention, the gene was duplicated so that it could mutate and provide raw material for evolution. This is a mistake however, evolution can not move towards any putative desired future state. the genes that are duplicated in this way will be random and the mutations that affect the genes will be equally random, there are likely many genes in the Zebrafish that are not duplicated and would cause death to the individual if they were to change. This does not detract from the fact that a proposed mechanism for introducing new information into an organisms genome has proven correct.

Science is Awesome.

Designing Babies, like Designing Women only smaller.

“Keep in mind this child is still you, simply the best of you. You could conceive naturally a thousand times and never get such a result.”
- Geneticist, Gattaca

Gene Eye View

The gene centered view of evolutionary change is a useful way to visualize how the processes work and to come up with explanations of why things happen the way they do. I have already mentioned concepts like genetic fitness, genetic lines and goals of an individual and this is where those concepts are grounded. This way of considering things was not originally put forward by Richard Dawkins but he certainly popularized it in 1976 with his book The Selfish Gene.

Gene

The usefulness of this method becomes apparent when you consider that we are use to thinking of species as individuals, discrete in time and space that act upon the world and are in turn themselves acted upon. But evolution doesn’t happen on the scale of individuals, a particular animal does not evolve the population does, and what produces this change in population characteristics? alterations in the genes. If we reverse our point of view and consider the genes as the primary actors in the evolution games things start to make more sense.

Genes are the true replicators in biological systems, while we may consider reproduction to be about continuing the legacy of an individual into the future in actuality it is the genes that are really being propagated. In addition it is the genes that change over time, not individuals even though in conversation it is useful short hand to refer to, say rabbits, evolving over eons it is really the genes and gene frequencies in the population that we are  discussing.

Given that it is the genes that evolution is really concerned with we can start to put into context the concepts that we have been talking about up until now. In other words when we talk about behaviours or physical characteristics benefiting an individual what we mean is that it helps the individual’s genes survive and replicate and eventually spread through the species. More specifically the gene for that trait is selected by the environment of the individual to continue into the next generation.

In this way when a mutation alters the expression characteristics of a gene (eg making brown eyes blue for instance) it introduces variation in the population of genes and this new variant must compete against the other versions (alleles) in order to continue to exist (be passed on to the next generation). So when we consider how an adaption aids an individual we also need to think in terms of what activity is best for the genes because that is what will be maximized and optimized by nature, that’s just the way it works.

Raphael from TMNT

Yesterday: Kin Selection Tomorrow: Molecular Evidence

Kin Selection

Do you spend time with your family? Good. Because a man that doesn’t spend time with his family can never be a real man.
-Don Corleone (The Godfather)

It’s all about family, kin selection is the explanation given for behavior that decreases the ability of an individual to have offspring while increasing that of the individual’s family. The most extreme examples of this is found in eusocial insect species such as ants and bees where entire segments of the population give up their “reproductive rights” in order to tend to those who do the reproducing for them.

Of course the ants don’t get together and decide who gets to breed and who doesn’t, that decision is made by the interaction between their genes and the environment they are exposed to. The point is those genes can be selected for under the right circumstances. In species like bees where the colony is mostly composed of the progeny of a single queen the population are essentially all siblings each sharing a significant amount of their genome. In this case they are more closely related to each other than they would be to their own offspring whom would only share 50% of their genes. From the point of view of continuing the genetic line therefore their efforts are better spent raising more siblings than going off on their own to have children outside the colony.

For other animals the genetic payoff isn’t as high but the same principles still apply, why do some animals invest time helping to rear the young of brothers and sisters or children? Because it serves their genetic interests to do so. There is an hypothesis that male homosexuality in humans is this sort of kin selection trait. There is evidence that the genes that confer homosexuality on males increase fertility when they are in a female host, and having homosexual relatives may (there isn’t much evidence for this) increase the pool of helpers mothers can draw on to raise their young. Speculative but fascinating.

So in light of kin selection it becomes less mysterious to explain concepts like altruism, fundamentally altruism means performing actions that benefit another individual at a cost to yourself. If in the environment your genes evolved the individuals you are most likely to meet are your own family members then it is not really a cost to your genetic line to help them. So it makes sense that even though the human population of the Earth has reached the point were you are much more likely to interact with complete strangers on a day to day basis we embody behaviours that compel us to act compassionately towards those around us, that’s the way we evolved and I wouldn’t have it any other way. (Of course I would say that, I’m programmed to)

Yesterday: Sexual Selection Tomorrow: Gene Eye View