Monday, June 15, 2015


Neo-Darwinism is a theory that was first articulated in the nineteen thirties.  That was some sixty years after Darwin's 'On The Origin of Species' and the genetic discoveries of Gregor Mendel.  Mendel's work was not widely known or accepted, however, until the turn of the twentieth century. Neo-Darwinism was an attempt to meld Darwin's theories with Mendel's genetics.  The nineteen thirties was also twenty years before the discovery of the DNA double helix formation and the discovery a few years later that within the DNA were myriads of information arranged in coded sequences of nucleotides.  Our whole understanding of the replication process, the mixing of genes during sexual replication, the actual processes of mutations,  and the actual processes of how traits change from one generation to the next, has evolved exponentially since that time and continues to evolve.  Neo-Darwinian thinking has not.

Case in point is found in the writings of Richard Dawkins. It seems that Dawkins' main idea through all his writings is that things are not the way they seem.  Over and over we are taught that we cannot trust ourselves, our  perceptions, or our intuitive reactions to the world.  No!   That would be very ignorant and pre-Darwinian of us.  Well, if we can't trust ourselves, our instincts or our perceptions, then who can we trust?  Why, Richard Dawkins, of course!

In the Blind Watchmaker Dawkins tries to earn our trust by showing us the following example of how random mutations mixed with natural selection will yield remarkable results in very short order.  He takes a sentence from Shakespeare's Hamlet, "METHINKS IT IS LIKE A WEASEL."  Then he asks how many attempts it would take for a monkey hitting the keyboard of a typewriter, or any purely random banging of typewriter keys to come up with that phrase.  If the typewriter consists only of the twenty-six letters of the English language and a spacer,  then there are twenty-seven possibilities at each position (twenty-six letters plus the spacer).  Since there are twenty-eight letters plus spaces in the sentence, then you could calculate that it would take twenty-seven times twenty-seven times twenty-seven, repeated twenty-eight times, or one in ten thousand million, million, million, million, million, million tries, or one in 10 to the thirty-ninth power.   Good luck!

Now comes Dawkins' stroke of genius, borrowed from Darwin's stroke of genius.  With natural selection the chances are much, much better and the sentence can be achieved much, much more quickly.  How exactly?  He starts with a completely random twenty-eight letters:

     WDLMNLT DTJBKWTRZREZLMQCOP  but now he would 'breed' it.   In other words, knowing that he wants to get to "METHINKS IT IS LIKE A WEASEL," he selects  the letter group from the first generation of attempts that most closely resembles the target sentence.  He gets WDLMNLTDTJBSWIRZREZLMQCOP. He then does a second generation of attempts using this second arrangement and again selects the grouping that best forwards his progress toward the target sentence.  By the fortieth generation he has achieved...METHINKS IT IS LIKE I WEASEL, and then it takes him just three generations more to achieve the perfect typing of the sentence that he was trying to get to.  Does this seem fishy to you?  I know Dawkins doesn't want you to trust your instincts, but let's follow this 'fishy' impulse for a couple of minutes.  Look at his second attempt.  The only difference from the first attempt is that a K is replaced by an S, but this S is  the twelfth letter in the series, exactly like the S of IT IS in the final sentence.  If it were a random bang at the typewriter, wouldn't you probably have to have about twenty-six such bangs before you wound up with the right letter in the right sequence of letters?  Then, the last step takes just three attempts.  Three random attempts to replace an I with an A.  Very lucky!  Or was he just banging on one key and not the other twenty-seven?  Yes, he must have retained every key once it happened on the right letter and just randomly went after the remaining letters.  But why would he do that?  If the sequence is not yet functional, how would anyone, how would 'nature' know that those other parts of the nonsense sequence were potentially useful?  Those positions that had reached the targeted letters, not knowing there was a target, and still being non-functional, would be subject to mutation as much as the ones that hadn't already achieved the perfect letter.  The reason that there are so few steps is that Dawkins has, by his own admission, programmed his computer to seek out only those  letter changes that forward his agenda of changing the sentence to reach the final goal and, once achieved, removing them from further mutation attempts.  This is, of course, exactly the opposite of random evolution where there is no goal in mind at all.  So Dawkins says this is natural selection at work.  What is natural about it?  Every sentence, except perhaps the last few have no meaning at all.  Why would they be selected?  What possible advantage would one piece of gibberish have over the other?  There is nothing to select, nothing that could yield a possible advantage until we get to a meaningful sentence.  Natural selection begins when the process of random mutations creating a meaningful sequence ends. Neo-Darwinism and the natural selection process does not avoid the purely random process of mutations until after we wind up with something that is possibly functional.

This, I imagine, is Dawkins' way of suggesting how a functional protein can be created from a random sequence of nucleotides. Each three nucleotides in a gene code for an amino acid.  If a gene is on average a thousand nucleotides long, and the average protein sequence is over three hundred amino acids long, and there are twenty possible amino acids at each spot on the chain; then the chances of finding by random mutation a functional protein are one out of 20 to the three hundredth power, or ten to the three hundred and ninetieth power.  If you put that in perspective, 10 to the sixty-eighth power is the number of atoms in the Milky Way Galaxy and 10 to the eightieth power is the number of elementary particles in the known universe.  So is it as hard to evolve a functional protein from a random sequence of nucleotides as it is to randomly find "METHINKS IT IS LIKE A WEASEL" on a keyboard?  No.  It is 10 to the three hundred and fifty first power  harder!

Suppose, though, that somehow we got to a functional protein, and let's give Dawkins a break and say that this protein is an additional protein to hundreds of other proteins that had already gotten here by also beating these miraculous odds; and let's say that all the equipment for storing nucleotides and transcribing them and translating them, fabulously complex equipment that was here from the beginning of life 3.8 billion years ago; let's suppose that all of the proteins involved in that equipment had also beaten these miraculous odds and gotten here as well; and let's put aside such things as the construction of the double helix and the construction of a nucleus, and nuclear ducts and pores, and the dazzlingly complex timing system for the expression of proteins; that all these things had also beaten these incredible odds and managed to arrive here as well.  Okay, so now we have a new sentence, "METHINKS IT IS LIKE A WEASEL."  And never mind how it gets expressed, because in biological terms we have found a functional nucleotide sequence but we have no system of initiating the expression of this new code so that it can be translated into a meaningful sentence.  This brand new functional nucleotide sequence can not possibly be part of the timing sequence of gene expression in the organism in which it just emerged.  How or why does that timing sequence of gene expression change so that our new code can ever get translated into a functional protein?

For Dawkins' sake, let's just suppose it did.  Now let's look at the actual functionality of that new sentence.  If this sentence suddenly emerged randomly into the world of literature just like a new protein might suddenly emerge randomly into the world of functional biological organisms, what function would it serve?  The sentence "METHINKS IT IS LIKE A WEASEL"  is only 'functional' if it winds up in a Shakespearean play.  If it emerges into an Ellery Queen mystery or into a Walt Whitman poem it would be of no use at all.  In fact, it would ruin both the mystery and the poem.  Even if it emerged into the wrong Shakespeare play, it would also be ruinous.

"Friends, Romans, countrymen,  METHINKS IT IS LIKE A WEASEL!"


"Romeo, Romeo, wherefore  METHINKS IT IS LIKE A WEASEL?"

Even if by an absolutely amazing coincidence it emerged in the right play, in Hamlet, it would have to emerge in exactly the right place.

"To be or not to be,  METHINKS IT IS LIKE A WEASEL."

And even if it emerged in exactly the right place, there would be no place for it, because that phrase, Hamlet being already a highly functional play, is already there.  There are no gaps in meaning in Shakespeare's great play.  He did not write,

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:  (Mysterious pause.)

Polonius:  It is backed like a weasel.

No.  Shakespeare would never write a play with a hole in it, hoping that someone many, many years in the future will come up with just the right sentence to fill in that hole.  The play is a completely integrated unit, so the line, METHINKS IT IS LIKE A WEASEL, is already there, and all that work, all those absolutely uncanny and impossible strokes of amazing luck taking place over centuries resulted in nothing more than an awkward redundancy.

So we can either give Hamlet the line as in:

Hamlet: Do you see yonder cloud that's almost in shape of a camel?

Polonius: By the mass, and 'tis like a camel, indeed.

Hamelt: Methinks it is like a weasel.  METHINKS IT IS LIKE A WEASEL.

Which would make Hamlet a stutterer.  Or we could give Polonius the line, as in:

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.

Polonius: METHINKS IT IS LIKE A WEASEL.  It is backed like a weasel.

In which case we have made Polonius an impudent mimicker of Hamlet, or a mumbler,  repeating Hamlet's words to himself.  Whether we make Hamlet a stutterer or Polonius a mimicker or a mumbler, we have diminished the quality of the play and in neo-Darwinian terms, we have created something that, after overcoming all these impossible odds for more years than there are in the life of the entire universe, and finding ourselves with absolutely inconceivable good luck to be in the one literary (biological) context where we could be of any possible use, we wind up diminishing the value of the play (organism) and becoming a prompt candidate not for retention but for elimination and can expect to no longer be around after the first encounter with a good editor (natural selection).

It is not only Dawkins, but all neo-Darwinists and even many of the biologists who question neo-Darwinism who  make this assumption:  that the path of evolution is the creation of an 'improved' protein.  Improved for who?  For which organism?  Each organism has the suite of proteins that is perfect for it.  Replacing one of those 'inferior' proteins in any healthy organism with an 'improved' protein would do nothing but wreak havoc and probably cause the death of that organism.  Living organisms are not Tinkertoys or Lego sculptures.  They are exquisitely synchronized, electronically, chemically, mechanically and metabolically coordinated machines, and the proteins that they have are the perfect proteins that work in perfect synchronicity with all the other proteins of that organism and within all the organs and organelles and tissues and systems of that organism.  The introduction of a new, 'improved' protein would be not an advantage but a disaster.

And where has this nucleotide sequence that has been slowly and randomly mutating into a functional protein, where has this sequence been for all these centuries?  According to neo-Darwinists it could have been a sequence that is part of 'junk' DNA,  so that it can mutate over time without causing any effect to the organism since this 'junk' DNA sequence is not expressed anyway. This brings up two problems.   If it is part of the junk DNA that is not fired, then how does it suddenly become fired?  How does it work itself into the dazzlingly complex and precise system of gene firing that is already in place?  Also, if the neo-Darwinists are keeping abreast of current scientific events, they should know that we are running out of 'junk' DNA.  Scientists are discovering that much, if not all, of the supposed junk DNA is not junk at all, but is either used for the manufacture of RNA sequences, or is  part of the incredibly elaborate firing system of genes used during embryosis or is useful in many as yet undiscovered ways.  So there may very well be  no stretches of 'useless' DNA that can be mutationally tinkered with over the centuries without a negative effect on the organism.  Another neo-Darwinian scenario is that a protein that was used for one purpose, gets mutationally converted over time to another protein with a different use.  The problem with this scenario is that scientists have not been able to find one scenario of any protein changing mutationally into another protein of a different function without the first protein becoming non-functional.  That means that in the process of mutation changes to the individual nucleotides of the sequence, the sequence would quickly reach a point where it could not form a protein at all (a protein is a three dimensional molecular machine, so the nucleotide chain, after it has been translated into an amino acid chain, must be folded into a stable three dimensional machine or it can do no work.  There are strict rules for these foldings and they require the curling back and binding of amino acids with others in the sequence which in turn depends on the chemicals of the different nucleotides and their spatial relation to each other.)  A few random changes in nucleotides and the sequence is no longer foldable; therefore no longer functional.  The organism without the benefit of that mutated protein would either die immediately or, being in a severely diminished state, be quickly eliminated (selected out).  The final scenario is that the whole process begins with a duplication mutation, where a section of DNA is copied twice onto the same chromosome.  This would mean that we start the sequence of impossibly rare mutations with a barely possible mutation. A mutation where enough DNA is copied twice so that it could convert, by itself, into a functional protein, is so rare, that I don't think that any researcher can point to one example of such a mutation occurring naturally. And from there we have to begin a process of thousands of impossibly minute chance occurrences to then wind up in an organism which just happens to be 'waiting ' for this perfect protein.  The problem is, organisms aren't waiting for proteins, just like great Shakespearean plays are not waiting for missing sentences.   They already have the exact right ones that they need in exactly the right order and in exactly the right number.

I am not saying that evolution doesn't happen.  It just doesn't happen one protein at a time, and it doesn't happen even close to the way that Dawkins thinks it happens.  If you want to know how I think it happens, please read my post, 'Evolution.'  Thanks.

Your comments are always welcome.