You're neglecting the fact that those 300 proteins that check for DNA mutations reside mainly in the cells of the body, not in human eggs and sperm cells. What about meiosis and the crossover that takes place during that process? Many times crossover occurs without a hitch, but such a process sometimes creates massive instability in the embryo that it can't survive out of the womb. Women have many more miscarriages than they think. Biologically, that's an expensive way to create a baby. Why don't we have a mechanism that will prevent that? Because in the long run, it's benifical to the species, not in just the shuffle of genes, but also in the potential mutations that can form from them. Yes, mutations are deadly. Very deadly. If we really knew the number of embryoes that never made it outside their mother's wombs because the chormasomes they inherited were defective, it will surpass the number that have evermade it outside the womb with "pinpoint" mutations! This is where nature's genetic experiment really takes place. Outside of the womb is just the testing ground for the individuals that survive.

You're also forgetting that DNA can be altered in many different ways. Genes can be duplicated, deleted, inserted, and if master genes get mutations, whole limbs can grow strange places! Haven't you ever seen those wacky genetic defect pictures? A riot! Yes, many of them won't confer an organism evolutionary advantage, but you don't always need to start from scratch if you want to have a new tissue or a new organ. Most of the basic celllular process have been established eons ago. Most of the time, if a tissue, organ or molecule becomes extremely useful in one organism, evolution uses that (or variations thereof) in a different organism, which are much simpler to get. Also, I recommend looking into the evolutions of rudimants, animals with four stomachs (cows, sheep, goat, etc.). Fantastic story there.

Gotta run. Thanks for starting this discussion. I could go on for hours, but I have to eat breakfast. =)

Bah. As long as my last reply was, I didn't seem to capture any of the ideas I wanted to express.

I don't really have time to continue writing at the moment, but if mutation is not the basis of diversity, I would be interested to know your theory as to the development of novel tissues since ID did it's work - are you putting forth the argument that current organisms exist in the same state as the point of 'ID', or that ID is in fact ongoing and benevolently gives novel characteristics to some organisms?

Having only a relatively basic knowledge of the processes discussed here, I can follow the majority of the examples but don't know enough about the background research to form an argument for or against specific cases. However, what seems to be more and more evident in your blogs is that you have a clear opinion about this debate and you are presenting your arguments in a non-objective way. This reply is a pretty disorganised spiel but hopefully there are some points of worth in there.

As plunge has pointed out, there are some significant omissions in your posts. These tend to lead to the conclusion that chance or evolution could not have brought about the living phenomenon we see today, implying Intelligent Design.

I believe that your mutation argument presented in this blog challeges the very nature of genetic expression itself. You seem to argue that mutation is not the cause of evolution - that mutation is, in fact, detrimental to organisms. While this may be the case in many instances, plunge explained the idea behind evolution and natural selection driven by mutation, which I am certain you are very familiar with. If mutation did not occur - and I am not talking about on an individual level, but on a scale of populations, which need to be large for evolution to noticeably occur - then the continual fluctuation in environmental factors on Earth would lead to severe genetic homogeneity, with a population having had genetic characteristics continually selected against and removed - WITHOUT new characteristics emerging. Eventually each population would be exposed to an environmental factor for which there was no 'beneficial' characteristic present, creating an evolutionary dead-end. This is natural, and throughout history, has been approximately balanced by the rate of creation of new species. So where have these new species come from? Spontaneous creation? Or gradual divergence in net characteristics originally derived from mutation?

Without some mutation, there would be no ongoing diversity, and without diversity, a population exposed to fluctuating stresses would eventually become extinct.

Your question - "If mutation is the process by which we evolve; why would we evolve a system to prevent further evolution?" - is flawed and biased. Continual mutation would cause severe damage to the basic nature of a macropod, and the undesirable effects you described in your blog. Some kind of system must be in place to stop heat, radiation or other effects from continually damaging cells IN THE SHORT TERM so an individual organism can function. However, small variations on a long timescale (by which I mean a handful of heritable variations per generation in millions of individuals), with altered characteristics present on recessive alleles, would be sufficient to promote genetic diversity over thousands or millions of years.

You express your belief that it is impossible for complex systems or material to spring into existence. I agree with this in a general sense. However, I don't see any logical progression from this belief to intelligent design or creationism. While science does not yet provide an infallible theory for the initiation of life on Earth, the knowledge of genetics and life processes is increasing exponentially. The advent of religion was to explain the unfathomable, and since Science has proven Creationism according to the Bible incorrect, ID is the new security blanket of those not willing to accept or consider the immensity of the Universe and the probability of the development of life.

To claim impossibility of the spontaneous creation of life requires an understanding of the nature of first life, which science is yet to determine. Evolution is a mechanism that is currently operating, but we don't know how it has operated in the past or what form organisms took billions of years ago. Writing off spontaneous creation and implying ID in the same breath is inherently hypocritical. Please step back and look at your 'objectivity'. Science has holes in its knowledge. Faith fills those holes, but it is a temporary faith with the belief that those holes will be filled with evidence. ID and creationism rely on groundless faith that will never be proven.

A couple comments I would add to this:

Regarding your proposition that the development of new tissues would require the spontaneous development of signaling molecules, transcription factors and signal transduction pathways: I'm amazed you would even suggest this. Do you not realize this is just another version of the mousetrap argument? It's silly to suggest these things must all happen at once. Have you even discussed this with a good evo-devo biologist (who disagrees with your view?) Again, there's plenty out there who would love to correspond with an eager young biologist.

Regarding the comment on DNA error correction: Yes, precisely as stated above, this implies that evolution somehow "knows" mutations are good or bad. I see similarities between this and asking why early whales returned to the ocean when their distant ancestors had forsaken water for land.

"To meet criteria number one were are looking for the ever elusive “beneficial mutation”; one that could give a selective advantage to the organism."

You left out a crucial piece of the concept (I wonder why people always do that?): a selective advantage _in a particular environment_. There is no such thing as a purely, universally beneficial mutation. Leaving out that piece is a big flaw in your later discussion.

"Antibiotic resistance clearly occurs, however, in all studies, when the original bacteria are reintroduced they quickly out compete their resistant counterparts for resources."

Think about this for a second. The situation you describe is precisely what I noted: there is no universal definition of a beneficial mutation. It depends upon the environment. If you create a strain of bacteria that thrives in an environment in which regular bacteria can't cope as well, and then dump the resistant strain back into a regular environment with the original bacteria line, there is every reason to believe the more general strain will have the advantage, largely because it doesn't expend resources dealing with a non-existent problem. It is the environment that gives the resistant strain an advantage, not the strain itself. In the abscence of a particular pressure, adaptations are costly to maintain. But it is precisely because pressures appear and then do NOT disappear that particular traits continue to be selected for and more lasting progress occurs.

And of course, saying that this proves that mutation has a "cost" is unacceptably vague to a scientist (how much is the cost, exactly! What's the percentage! THAT is what scientists ask and specify in these sorts of issues). This is not how actual geneticists discuss the subject of mutation. Not all mutations provide such a cost on top of the original strain. The fact that you haven't read enough biology journals to be well read in the field is certainly no crime, but pretending that a discussion of two simple examples commonly described to laypeople makes you capable of generalizing about mutation is just plain silly.

"Caused by a single point mutation, hemoglobin can change to a “sickle cell” conformation and block the possibility of contracting malaria. However, individuals with this mutation also incur a cost of “Sickle Cell Anemia”, which can be unbearable and typically leads to an early death. After reviewing the symptoms for both malaria and sickle cell anemia decide for yourself if this is an example of a beneficial mutation."

First of all, beneficial mutations aren't beneficial because they are enjoyable, they are beneficial because they confer reproductive advantages. Obviously, all things equal, having a recessive trait that when activated causes horrible symptoms ain't much fun. But in a malaria-heavy environment, it does seem to provide some serious protection against mortality, and that's what matters.

But second of all, you've totally mangled the description of what sickle cell anemia is! People with the mutation do NOT get full-blown sickle cell anemia! It is a recessive trait, not a dominant one: you need two copies, one from each parent. As a trait, sickle-cell is a trade-off for a _population_ (remember them? They are what evolution ACTUALLY happens to, as opposed to this constant creationist straw man that it happens to individuals): roughly (and somewhat abstractly), in order to get more resistance to malaria in 50% of the population, you incurr the cost of having a 25% chance that an individual will get two copies of the mutation and suffer the anemia.

"Consider what it would take to evolve a novel tissue type. Not even the entire organ and it ability to function, just the tissue that it requires."

What it would require is a REASON to evolve a new tissue type: an ongoing pressure that consistently shades particular modifications to keep going in a particular way. At no point in the process would we expect there to be any obvious target goal: a "final" tissue type. What we would expect would be ongoing advantages for small changes to certain cells in certain areas, including adding things like signalling, transcription factors, and so on that at any particular stage of development are never make or break necessary, but gradually become more and more central to the emergent system (emergent only in hindsight, remember). If you are incredulous that complex, interworking systems can evolve, then how to explain the evolution of blood clotting (to pick a trendy example)?

"Lastly, note that cells have over 300 molecular machines patrolling the DNA strand to check for errors (mutations). If mutation is the process by which we evolve; why would we evolve a system to prevent further evolution?"

Because its advantageous to keep changes below the level of an error-catastrophe. I'm not sure I really understand the point of this little aside. Desipte all those machines, we still have tons of mutations: are you claiming that we don't? What's the point? Maybe you are assuming that evolution is a process that THINKS, that goes "oh, mutations are good, therefore, I should never bother to protect against them!" In addition to being grossly simplistic, that just isn't how it works. Preventing or allowing mutation to a greater or lesser degree is ITSELF something that is only good or bad in context (as you should know, different species have different rates of mutation). So it is no surprise that there should be mechanisms that regulate mutation.