Wednesday, March 18, 2015

DNA, OUR MODERN REPLICATOR?


"Another rare voice of reason has entered the evolution debate. Matt Chait presents a very cogent explanation of a third option, that needs to be considered by anyone who is interested in the entire science vs. religion question. 
Chait's Blog, Beyond Evolution: Is There God After Dawkins? suggests an answer to the question that neither of the warring sides are likely to find appealing. Which means he's probably closer to the truth than either. Some of his posts are lengthy and involved, but it is a 'must read' for anyone who has given some thought to this issue."   Michael H., The Daily Grail                                                                                                                                    
Modern, neo-Darwinian evolutionary theory centers on the arrival on this planet of the replicator, defined by Richard Dawkins in his book, 'The Selfish Gene,' as a molecule that replicates by itself. This is the central creation miracle that starts the whole process of Darwinian evolution; an event so improbable that James Watson, one of the discoverers of the double-helix formation of the DNA molecule, declared it to be a 'miracle.' Watson's research partner, Frances Crick, contemplating the seeming impossibility of such a thing happening on earth, preferred to think of it as happening on another planet or moon and surviving, embedded in a meteor, an explosion that carried it from another solar system (ours was way too young, according to Crick, for such a pre-biotic evolution to have had the many millions of years necessary for all the separate and precise components of a replicating molecule to randomly assemble); so this pre-biotic evolution took place in another solar system, survived the enormous impact of an explosion strong enough to carry it out of the gravitational field of that solar system, survived a journey of many generations through unbearable heat, unimaginable cold, terrifying poisonous radiation, the complete lack of food sources, and the heat and percussion of an earth landing, to establish itself on this planet. This wacky scenario, called panspermia, was more plausible to Frances Crick than the current one being espoused by Richard Dawkins.

Let's put that aside for a moment and look at grammar. Grammatically, can a molecule replicate by 'itself'? Does a molecule have a 'self'? And what do we mean, mystics and materialists alike, when we use the word self?  The word self connotes a living being who is capable of initiating activity and experiencing desires. This is not my belief system, by the way. This is simply how we actually use the word. For instance if we have an infant, we, the parents, proudly tell our family and friends each and every activity that our young darling was able to accomplish by herself. "She stood by herself!" "She took her first step ('by herself' may or may not be included, but always implied)!"  He said "Dada!" Everyone who has kids has done this and everyone who hasn't has suffered through endless recitations of the accomplishments of other people's children. But the reason that the parents are thrilled is that their baby has just done something new and done it by her or his self.

Not true for the family car, the furniture, the house or any other inanimate object in one's possession. In fact if you have an acquaintance who begins bragging to you how their power mower started by itself, how their car just went for a drive by itself, how their house just expanded and built a whole new wing by itself, etc., that would be a good reason to call the proper authorities and send someone over to determine if your friend was now a danger to himself or others. I should mention here some modern technology that is advertised as doing things by itself. For instance, there are cars that may soon be on the public market that 'drive themselves.' This is true only in a limited sense. These cars do not drive themselves in the same way that we drive ourselves. Of course, we need equipment (a car) to drive ourselves anywhere. But we initiate that drive because we desire, for whatever reason, to get somewhere or just to have the pleasure of a drive. A car that drives itself, does not initiate the drive (thank God) but is merely the instrument for taking you where you want to go and when you want to go there. The car cannot take you where it wants to go, because the car, although it is a machine, is an inanimate object that does not experience anything, does not desire anything and does not initiate anything. Only living beings do that, and it is only of living beings that we can accurately say, " She did that by herself," "She always wanted to become a lawyer and she did,"or "He felt like taking a walk."  Living beings feel like doing things.  Inanimate objects, including machines, do not. It is only of living beings that you can ask why. "Why did you do that," would be a very natural thing to ask your roommate, but a very unnatural thing to ask a butterdish that just smashed to pieces on the floor. Animals also have selves; again not because of our belief system, but because of our grammar, because of the way we talk about them. "Snuggles doesn't like to be fed this early." "Fido always loves to go to the dog park." Rightly or wrongly, we talk and behave as if animals have feelings, experience things and desire things. And we can reasonably brag about how our pets did things by themselves. "Scruffy was lost for a week, but somehow he found his way back to our house, all by himself."

Now we do sometimes say of machines, our car for instance, "She likes to be driven at least once a week." What we mean by that is that if 'she' is not driven that often, then the battery will lose its charge, or something else will happen. But what we don't actually mean, unless we are ready for fifty-two hours in a mental institution, is that our car experiences things, is actually unhappy when it is idle, and in a much better mood when it is moving. What we really mean is that we like the car to be driven at least once a week because we don't like to call the tow truck when the car is not driven once a week.

So let's get back to the creation event of neo-Darwinist thinking; the miraculous, random accumulation of a molecule that had the remarkable ability to replicate by itself. And, by the way, it is this replicating molecule that is not only the theoretical origin of neo-Darwinian evolution, but it is the entire reason for the existence of neo-Darwinian evolution. According to Dawkins we, that is living beings, are merely the temporary vessels for housing DNA. What we experience in this life and the way that we experience it doesn't matter a whit. What is of real significance are the genes that we have and how we are able to pass our genes on to the next generation (true success if we do; true failure if we don't).

To our knowledge, the only things that have selves, or, if you prefer different language, the only things that are capable of initiating, accomplishing and experiencing activity, are living beings. So when we say that a molecule began replicating by itself we are already conferring on that molecule the status of a living being. The Darwinian creation myth doesn't just begin with a molecule that could suddenly replicate by itself, it begins with a molecule that is suddenly alive. Now neo-Darwinian theorists will disagree. They will say that there was a very long evolution of replicating molecules before there was anything that we could call life. The truth is the earliest life forms that have been discovered by examining ancient rock layers for fossils or for traces of ancient life, were photosynthesizing and chemotrophic bacteria that lived very close to four billion years ago, when this planet had just cooled down enough so that the water on its surface was not boiling. Chemotrophs that lived way below the surface of the water near thermal vents are supposedly the very oldest living creatures. They survive in water that is way above the boiling point (but not actually boiling because the boiling point is much higher far below the surface) because of the extra bonding of their protein molecules. How could such a creature accumulate in an environment where each separate part would last no longer that the time it would take to boil an egg? In fact, exactly as long as the time it would take to boil an egg.

And speaking of time, when did this pre-biotic evolution take place on this planet? It seems like single celled life was already here and thriving the moment the surface water stopped boiling, just under four billion years ago.  Originally, Darwinists thought that this pre-biotic evolution must have taken place for fully half that time, two billion years, and the development of post-biotic evolution took place for the next two billion. When bacteria were found to be almost four billion years old, evolutionary theorists suddenly recalibrated and determined that pre-biotic evolution could have taken place in ten million years. Interesting.  When Einstein noticed that Isaac Newton's predictions were off a hair when light traveled in the vicinity of a large star, he came up with a whole new way of looking at space and time.  When neo-Darwinian evolutionists were off by 99.5%, they just slipped in a completely different number and no one blinked. In fact, it was evolutionists who determined that the early earth atmosphere had no oxygen. Was this based on any proof, any meteorological or geological evidence? No. It was merely based on the idea that pre-biotic evolution could not have taken place in an oxygenated atmosphere because the organic material that was supposedly floating around in these pre-biotic soups would have oxidized in the presence of oxygen. In other words, we readjusted our understanding of the early earth atmosphere to fit a theory rather than coming up with a theory based on the evidence. But now there is evidence, and there most certainly was, at least small amounts of oxygen, in the early earth atmosphere. There were also a whole raft of conditions that would have made pre-biotic evolution impossible, including ultra-violet radiation, continual meteor bombardments, hugely powerful and frequent volcanoes, etc. Also, there is absolutely no evidence that organic material ever existed on this planet prior to the organic material found within those first photosynthetic and chemotrophic bacteria.

Of course that was then.  What about now?  Is DNA our modern replicator? The whole neo-Darwinian theory is based on this assumption. But, is DNA a molecule that replicates by itself? Absolutely not! DNA replicates in conjunction with a whole cell's replication. Its replication is initiated by the arrival within the nucleus of certain very complex protein molecules that are released when a cell begins the replication process. Which brings us to another word whose meaning I would like to discuss before we go any further with the debunking of DNA as a 'replicator,' and that word is 'molecule.' A molecule is any stable grouping of two or more atoms. That is a category that is so broad as to be almost meaningless.  If we  consider the fact that in our everyday lives we rarely have any interaction with individual atoms, then every stable object we encounter could be considered a molecule, including iphones and the Taj Mahal. Of course it seems ridiculous to refer to something as technically precise as an iphone and something as exquisitely designed as the Taj Mahal as a molecule, but it is, I contend, equally ridiculous to refer to DNA, helicase, DNA polymerase, and many other mega protein molecules, whose exquisite precision of design and complexity surpasses both iphones and Taj Mahals, as molecules. 


Why were these marvelously complex creations referred to as molecules in the first place? I believe it is because of the schizophrenic attitude of the neo-Darwinian scientific establishment regarding biological complexity. On the one hand evolutionists don't want you finding out too much about the fantastic complexity of living bodies and living cells because that might lead you to the obvious conclusion that living bodies and their countless synchronous processes were the product of a transcendent intelligence and not the result of random copying errors and natural selection. On the other hand, evolutionary scientists take great pride and possessiveness about the complexity that they do understand, so they can brush off unanswerable questions about evolution with a "yes, of course I know the answer, but it's too difficult to explain to a layman like you" type of response.  Referring to enzymes, proteins and DNA as molecules makes them sound rather simple. I mean, if there are trillions of protein molecules in every lamb chop, how complicated can they be? On the other side is the obvious fact that molecular biology departments and graduate schools are springing up like weeds all over the planet, and their graduates are garnering the lion's share of Nobel Prizes every year. If it's all so simple, what's all the studying, all the research and all the fuss about? Here is a very 'simple' animation, simple because many parts are left out, of DNA replication in prokaryotic cells, the 'simplest' of cells; a process that has been going on for nearly four billion years: 




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Here is another animation, still simplified, but much closer to what the process actually looks like and in real time:


                                          video

As the narrator said, "numerous components have been deliberately left out to avoid confusion."  Among those components are: the laying down of starting stretches of RNA nucleotides to which the DNA nucleotides are attached, because DNA polymerase cannot start new chains, but only add to existing chains.  Then, the RNA stretches are removed and replaced with  new DNA stretches; also the proofreading of the new nucleotide strand as the polymerase doubles back to check on the bonding of the two strands.  If the bonding is off at any point, that means that the wrong nucleotide was placed on the new strand, so the polymerase backs up, enzymes are used to detach the wrong nucleotide from the chain and the correct nucleotide is inserted in its place; and disentangling, since all this work is done in the incredibly close confines of coils of DNA that are folded over and over each other.  When the coils get tangled an enzyme cuts one of the tangled strands, removes the other strand and re-attaches the strand that it cut.  And all of this, the laying down and removal of RNA stretches, the proofreading and the disentangling, plus many other functions, are all done at absolutely lightning speed.


I remind you that what you just watched is bacterial DNA replication; before there was man, before there were dinosaurs, before there were land animals, this is the exact same process that was taking place in photosynthetic and chemotropic bacteria almost four billion years ago at the so called 'simple' beginnings of life.  I could also show you equally remarkable animations of DNA transcription and DNA translation, but you can look them up yourself.  Just google DNA transcription animation and DNA translation animation.  All of these, at a level of complexity and precision that exceeds many times what you are able to see in the animation, were part of the precise, electronic equipment absolutely necessary to allow the first living beings to even have a life. How in the world can you imagine life 'beginning' as a competition among viable organisms, if the organism needs this much complexity and precision to become viable in the first place?

I remind you that if you call yourself an evolutionist then you believe that all living creatures from dragon flies to elephants to redwood trees to humans, and all the amazing organs and complexities within them, had their origin in copying errors made by this very equipment whose functioning you just watched.  (And I did not forget about natural selection.  Natural selection is, as the name implies, a selection process, not a creative process.  It selects among existing alternatives.  It does not originate or create anything.)  If you subscribe to such a theory that is your business, but after you have explained in detail how such a thing could have happened, which no one has ever even begun to have done on a molecular level, particularly when you consider that replication errors which take place on the molecular level  have absolutely nothing to do with the shapes of organs, organelles, or any visible contours of the body, both internal and external, but have to do only with amino acid changes within a protein molecule, supposed changes that take place within an existing gene with not even an attempt  to explain the formation of a new gene; even after you have explained all that, which you never will; then you would still have to explain how this fantastically precise and elaborate equipment got here in the first place.

We call DNA a molecule even though our DNA is composed of billions of individual nucleotide molecules strung together. A more accurate word would be an electronic component, a component of an amazingly complex charged system which supplies all the materials needed to grow, and all the equipment needed to maintain, a living body. The DNA is the component where all the coded recipes for the protein materials, at least the amino acid component of these materials, which we call genes, is stored. That is actually what DNA does. It stores the amino acid recipes for proteins, and it stores them passively, I might add. Other components are needed to copy these recipes, to select which recipe (gene) is to be copied and when, to direct the copied recipe to the equipment where the recipe will be translated into amino acids; components to link the amino acids into a chain, to add other molecules to the chain, to splice molecules from the chain, and components needed to fold the chain and to direct the finished protein product to the place in the body where it is needed.

Without this entire network of synchronous components, DNA is useless; a computerized library of recipes with no one or nothing to read these recipes, no one or nothing to copy them  and bring them to the larder where the coded recipes could be translated into amino acid ingredients; in fact there are no amino acid ingredients; no larder where the ingredients would be stored, and no kitchen or kitchen equipment to prepare the recipe if there were ingredients. 
To think of DNA as having an independent existence, as replicating by 'itself;' a molecule, if you like, of stored coded recipes for proteins, of this helpless molecule spreading through the 'pre-biotic seas,' when it has no way of manufacturing proteins and no body to manufacture the proteins for, has got to strike even the most dyed-in-the-wool evolutionist as absolutely ludicrous. That is why it is so much better to refer to DNA as a component, because it communicates the accurate meaning that DNA is electronic, is an enormously complex piece of equipment and depends for its functioning on a whole system of other charged and enormously complex components.



I should mention the other part of this neo-Darwinian fantasy.  The 'replicator' is floating in a pre-biotic pool of organic molecules, including protein molecules.  It is in these imaginary pre-biotic pools (no evidence of any such thing, of any organic material on this planet prior to the arrival of bacteria has ever been discovered) that the 'supposed' replicators competed and evolved.  Competed for what, I would venture to ask?  For food sources?  Do molecules eat?  Do molecules need to eat?  How in the world do we suddenly have hungry molecules?  And what do they need food sources for?  Do they have systems to break down and digest these food sources?  To convert them into what?  Into replacement cells for a body that they don't have?  Molecules continue to exist as long as their bonds are not broken.  Are these replicating molecules trying to become better survivors?  In order for them to become replicators, as the fantasy goes, they had to have stayed in tact for millions of years, the exact same molecules; because, don't forget, this is prior to life, so there are no new generations.  These would have to be the exact same molecules that started accumulating millions of years ago and somehow survived countless volcanoes, meteor bombardments and tectonic plate shifts. How much better at surviving could they get? 

And exactly what is floating in these pre-biotic pools?  Are there protein molecules there?  How could that possibly be?  Every naturally occurring protein molecule that we have ever encountered has been manufactured through the genetic processes of transcription and translation with the components of DNA, RNA, RNA polymerase, DNA polymerase, helicase, TRNA molecules, ribosomes, and others.  Every protein molecule is a three dimensional machine whose shape, series of charges and chemical make-up are designed for a specific function within a living body and are manufactured specifically to fulfill that function, and that includes the proteins that are stitched together in laboratories in the hopes of being re-inserted into a living body and fulfilling a specific function there.  


Amino acids cannot form chains in water, yet the belief is that that is exactly what was happening in these pre-biotic tide pools.  They cannot survive in sunlight, in the presence of oxygen, cannot withstand heavy jostling (first think of whipping a meringue from egg whites, which quickly denatures all the proteins in the egg whites and makes them stiff, then gradually work your way up to volcanoes, meteor bombardments, and tectonic plate shifts).  The more familiar you are with the complexity, delicacy and specificity of design of protein molecules and the ingeniously protected, metabolized, homeostatic environment in which they are manufactured, an environment as different from the environment of the earth outside of living bodies and the environments created in high tech laboratories as the environment of Jupiter differs from the environment of our own planet, the more laughable this fantastical theory becomes. 

Why would people adopt such an absurd theory of a creation and evolution based on replicators, and why would so many people readily accept it?  It is because they have been so indoctrinated in the idea that evolution equals science, that anyone who questions evolution, who even thinks about it deeply rather than blindly accepts it, has to be either a fundamentalist knuckle dragger or delusional in some profound way.  Yet if they believe in such an obviously nonsensical theory, it is they who are delusional; they who are so committed to not seeing transcendent intelligence, unfathomable beauty and precision in the world around us, that they seek desperately to adopt any belief system that portends to explain the origin and development of life without the intercession of intelligence, no matter how ludicrous those explanations are.  

If you have taken the time to seriously consider the above paragraphs, then you have to conclude that Richard Dawkins, the Emperor of Neo-Darwinia, has no clothes; that his evolutionary  pronouncements on the origin and development of life are as fanciful as any other creation myth or fairy tale, whether a religious fairy tale or a scientific fairy tale.   

I know that hundreds of you read these words every day.  There must be some Darwinists among you.  I have just ruthlessly attacked your belief system.  Aren't there any among you who will defend yourselves and show me the error of my ways?  I look forward to your comments.


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