The Origin of Genes

AN EVOLUTION FOR EVOLUTION THEORY (Written in 1993)

Though the name of Charles Darwin is now almost irrevocably associated with evolution theory, his contribution was only a development of the existing ideas of Jean Baptiste Chevalier de Lamarck, Thomas Malthus and Edward Blyth. The main difference between Lamarck's theory and Darwin's development lay in the question of whether an organism could change during its own lifetime in response to environmental circumstances and pass those changes on to offspring or whether all changes were random and became established only if they were beneficial. The rediscovery of Mendel's observations on the laws of inheritance pointed the finger in the direction of Darwinism. By the time DNA had been pinpointed as the chemically coded carrier of inherited characteristics, Lamarckism became officially discredited and denounced as heresy by most molecular biologists on the grounds that acquired characteristics could not be translated into chemically coded inheritable characteristics. The further discovery that DNA is susceptible to random mutations led those biologists to study DNA extensively as the assumed source of all evolutionary change.

The Darwinist theory accounts beautifully for many observed phenomena, such as sub-specific variation and the unique results of mixing genes through sexual reproduction. Natural selection, which was always the cornerstone of Darwin's theory, provides an entirely logical system of criteria for determining success or failure and consequent ability to pass on inherited characteristics. What neo-Darwinism has never adequately explained is how those characteristics got there in the first place. In recent years there has been a growing body of evidence which is at odds with the neo-Darwinist theory, producing nagging doubts about its ability to account for other factors such as the variable amounts of DNA in the chromosomes of different species, the existence of so-called "junk" DNA (which amounts to 97% in humans), the improbability of a one-off mutation becoming established across a widespread species and the phenomenon of parallel (or convergent) evolution, which seems to be the opposite of random.

The main attraction of Lamarckism is that it allows organisms to adapt responsively to the actual environments they inhabit rather than rely on luck to prepare them for an unknown future environment. Time and time again, observations indicate that organisms can adapt remarkably quickly to changes in their environment. Indeed, evolutionary scientists regularly refer to selection pressure causing the necessity for change. On a neo-Darwinist interpretation, that means that supposedly random beneficial mutations happen exactly when they are needed. The main problem with Lamarckism is that no satisfactory mechanism has ever been proposed for it. My purpose in this article is to propose a mechanism for genetic change which fits in with Lamarckism and avoids many of the pitfalls of neo-Darwinism.

At the heart of my enquiry lies the question, "What is DNA and what, exactly, does it do?". Essentially, it is an easily replicated, long-chain carrier of chemically coded information which transcribes the exact amino acid sequence in enzymes and other proteins. Each cistron within a DNA stand contains the almost unique sequence of nucleotide bases (running to thousands or millions in length) which codes for a particular enzyme or other protein molecule. What any organism inherits from its ancestors is effectively an instruction manual for making specific proteins. Therefore genetic change means a change in the ability to make enzymes and specific proteins. That change may be a gain or a loss.

So the next question is, "What are enzymes and what, exactly, do they do?". An enzyme is a three-dimensional protein molecule, composed of a long chain of polymerised amino acids, which fits snugly round a particular type of molecule, known as its substrate. Each enzyme is specific to its substrate. The enzyme holds its substrate in a position where other chemicals can attack it, or flexes so as to create stress in the substrate's chemical bonds, and the substrate becomes chemically altered or split. The exact nature of that reaction is specific to the enzyme, which is said to catalyse that specific chemical change. Different enzymes can catalyse different changes to the same substrate. Thus, enzymes determine the cell's abilities to carry out chemical reactions and DNA determines the ability to make those enzymes.

Neo-Darwinists would have us believe that a cistron of DNA, thousands or millions of bases long, can come into existence by random mutations and code for a protein which, by staggeringly good fortune, happens to be the specific enzyme for a substrate which is present in the cell. The odds against any particular sequence of bases in an average cistron are astronomical, which is a very appropriate word since a one atom stake at such odds would stand to win the entire known universe as merely a tiny deposit on the ultimate payout. Since there is a correlation between the base sequence in DNA and the specific properties of the protein for which it codes, the possibility that a protein coded from randomly produced DNA might be the specific enzyme for any substrate at all (let alone one which is present in the cell that produced it) can be totally discounted within any finite time. The only way to make a specific enzyme, which fits snugly round a substrate, is to make it in situ from its component amino acids, like making a plaster cast of a footprint.

Amino acids are abundant in all cells and experiments have shown that they may have been abundant in the primordial soup, before life began. If an alien molecule enters a cell (or any enclosed space where there are lots of amino acids), it should come as no surprise that the amino acids would cluster around it, since amino acids have an internal bi-polarity (from the amino group to the carboxyl group) which causes them to be attracted to other polar molecules.

From the point of view of evolutionary history, most amino acid clusters probably amount to nothing (and the invaded cell may die as a consequence) but, every now and then, the conditions will have been right for the amino acids to polymerise in situ around the alien molecule, forming a three-dimensional protein. That protein may have catalysed some chemical change to the molecule, converting it into a molecule (or molecules) that the cell could already cope with, eject or beneficially use. If, having done that, the protein releases the product(s) and retains its three-dimensional shape as a free molecule, it is, from the point of view of the cell, a useful novel enzyme. Although the polymerisation of amino acids under such circumstances may never have been observed, I am sure it will turn out to be a predictable example of cause-and-effect cell chemistry when scientists do discover how it happens.

What I am now asserting is that the cell can back-transcribe that enzyme to form a new strand of DNA which is the cistron that codes for that enzyme. (I use the term back-transcription to cover the entire reverse process of transcription and translation). A free strand of DNA within a cell can easily become incorporated into a virus. That virus would be able to replicate and spread itself through the body of any multi-cellular organism in which it found itself, just like any other virus does. It has been experimentally demonstrated that viruses can insert their DNA into the chromosomal DNA of their host cells. Indeed, genetic engineers use viruses to purposefully insert DNA into cell nucleii. There is no reason to dispute that the chromosomes in the gametes (or sex cells) are susceptible to viral insertions, especially since meiosis is known to be a time of chromosomal changes. Hence, any virus can be passed on to future generations as part of the chromosomal DNA rather than as a free agent. If that virus contains a cistron which is beneficial to the organism which catches or inherits it, natural selection does the rest.

Since a virus can spread throughout a localised population, the gametes of many individuals could be affected, which would cause many of the descendants of that population to have that novel addition to their chromosomal DNA within a few generations. This process circumvents the problem of the improbability of a one-off change becoming established throughout a widespread species and it also fits in well with punctuated equilibrium theory, which holds that evolution takes place in short bursts within geographically isolated populations. Since viruses are indiscriminate in terms of destination, it follows that a virus containing a novel cistron could spread through many different species and be carried by birds to other locations. The consequence is parallel (or convergent) evolution. Many neo-Darwinists have accepted that viruses may have played a role in evolution without having taken that idea to its logical conclusion. The reputation that viruses have for being exploitative parasites is due to the fact that those are the ones that we are most aware of and know most about.

The most contentious aspect of this theory is undoubtedly the hitherto unobserved ability of cells to back-transcribe the amino acid sequence of a novel enzyme into a new strand of DNA. However, it should come as no surprise that we haven't seen it since the formation of a novel enzyme will be a very rare event which takes place in only one cell and may now be limited to a small number of species. Only one molecule of that novel enzyme is produced initially and it back-transcribes to form only one strand of DNA (via m-RNA). The technology simply does not exist to observe (or work with) single molecules. Such circumstancial evidence as there is for this theory has usually been assigned to the "weird inexplicable phenomena" file and ignored. The process of back-transcription is mechanistically no more complicated or unlikely than the forward transcription that undoubtedly occurs. Given that most organic reactions are equilibrium reactions whose direction of flow is determined by the circumstances, it seems inevitable that the ability to back-transcribe is there.

In nature, all coding systems have an entry and an exit, such as a transmitter and a receiver, a microphone and a loudspeaker or a mouth and an ear. Each does the reverse process of the other. Why should DNA be different? A piece of magnetic tape, which is the closest analogy to DNA, does not acquire its recording through random alignment of its magnetic particles; a recording is put onto it (once) and then it can be played back or dubbed (repeatedly). If a machine was set up to emit random dots and dashes, the resultant Morse code message would undoubtedly contain occasional words but it would never give a grammatical sentence - let alone a meaningful paragraph - in any reasonable finite time. Therefore, I see it as a theoretical necessity, which cannot be disproved in practice, that DNA can be formed from protein.

What this theory means is that evolution does not proceed through random mutations in DNA but through systematic additions of DNA, which are originally produced as the stored coding system for enzymes that are spontaneously produced in response to particular problems. In life, we do not try to find solutions to problems that do not exist (though we do invent problems that won't exist) and it is ludicrous to suppose that DNA undergoes random mutations in order to be accidentally ready to solve a problem if it arises. Yet that is what it would have to do since a mythical, beneficial mutation would actually have to be the last of an accumulation of thousands (or millions) of beneficial mutations within one cistron-length of DNA.  Natural selection could play no part in guiding those mutations towards a goal since a stretch of DNA either does code for a useful protein or it doesn't. If it was half way there or three-quarters of the way there (or even 99% of the way there) it would still be effectively not there and would confer no benefit on the organism that possessed it. A further complication for mutation theory is that, if mutations did produce a useful cistron, they would also have to produce Start and Stop codons at either end of the cistron.

Undoubtedly, random mutations in DNA do occur but they are, as many people have always suspected, invariably destructive or neutral. If they are destructive, they cause the organism in question to be unable to do some chemical reaction that its ancestors could do, which may result in the immediate death of that organism or it may cause congenital disorders. If mutations are neutral, they either cause no change to the actual amino acid sequence in the protein for which the affected cistron codes or the change is so insignificant that it has no effect on the function of the protein.

Alternatively, and more usually, mutations will have affected stretches of DNA which were no longer used or needed by the organism. Evolution has been composed of a steady increase in DNA through viral additions which, at the time they were added, were potentially useful to the organisms to which they occurred. As environmental circumstances changed, some of those abilities became unused and hence susceptible to mutations, without harmful effect, to the point where they became "junk" DNA. Once a stretch of DNA has become "junk" DNA, it remains "junk" DNA for ever. It cannot become a useful cistron through mutation. The only way an organism can acquire a new cistron is through viral addition. Viruses are the carriers of cistrons - the messengers of evolution. The ancestors of all existing strands of naturally-occurring DNA were originally produced by back-transcrription from proteins (or from RNA), though many of those strands have become mutated out of all recognition during subsequent replications. Hence my use of the term back-transcription has been thoroughly inappropriate since the first transcription was always from protein to DNA.

It is possible that a point mutation could lead to an enzyme becoming more efficient or stable (but not to a change of function) and chromosomal mutations (inversions and translocations) may bring co-operative cistrons closer together, but an accumulation of mutations can never be constructive. One way in which an apparent mutation could be beneficial to an organism is through the duplication of cistrons as a result of crossover of DNA strands during meiosis. This could easily lead to the offspring having an enhanced ability. Evidence shows that there are many copies of some cistrons within an individual's DNA, which probably got there through crossover during meiosis. Duplications may have played an important role in evolution. However, it must be stressed that those extra cistrons were not produced by mutation but by addition of replicas.

In this theory, mutations can be viewed as one of nature's culling techniques while evolution is a positive adaptive response to environmental conditions through viral additions and possible subsequent duplications. In a wider context, what this theory means is that the early history of evolution was determined by the spontaneous ways in which organisms coped with microscopic aliens, waste products and other hazards that were inflicted on them by their environments.

Any self-replicating or sexually reproductive organism is unlikely to change if it can extract sufficient energy, minerals, organic chemicals and water from the environment to which it has become adapted, if the environment does not change. The changes must come when it encounters a new hazard caused by a change in the environment or diet. Different organisms may produce different enzymes which catalyse different reactions to the same substrate. The ways in which different organisms have, in practice, coped with the same (and different) hazards, has given rise to the vast diversity of plants and animals that we see around us.

If a cell's spontaneous chemical response to a new hazard gives rise to a novel protein which helps the cell to overcome that hazard, the information pertaining to the manufacture of that protein can be stored in the DNA and passed on to subsequent generations, who will benefit from already "knowing" how to cope with that hazard. As I said before, I have no quarrel with natural selection as the criterion by which advantages become established. The greatest advantages came from responses which not only coped with hazards but also turned them to the organism's benefit. Examples include plants utilising light as a direct source of energy (while other organisms merely shielded themselves from it) and animals using oxygen to carry out selective oxidation reactions, which also provide energy. It is quite conceivable that bones and shells may have originated as the result of the disposal of unwanted calcium. As well as enzymes, structural proteins were also originally formed by in situ polymerisations of aminoacids and subsequently coded into DNA. Thus the whole subject of body-building becomes incorporated into this theory as well as the spontaneous responses to aliens and waste products. However, the subject of morphology is one that biologists have yet to understand. It is by no means certain that it is determined by DNA.

It can easily be seen that this theory relies far less upon luck than the neo-Darwinist mutation theory and consequently would require far less time to occur. The current controversy amongst scientists of many disciplines over the reliability of radioactive dating techniques, and the growing body of evidence that the earth is much younger than is generally supposed, were the factors which led me to develop this theory. I am indebted to Richard Milton, whose book, "TheFacts of Life", provided me with much of that evidence. The fact that this theory makes sense of the known facts, in those areas where neo-Darwinism does not, leads me to believe it will be shown to be essentially correct. I am not a molecular biologist and I do not have the means at my disposal to test out any aspect of this theory scientifically. Consequently, I present it now for others to criticise, support, disprove or confirm. I am certain that the last-named of these will eventually be the case.

Hugh Dower M.Sc. (Chemistry)

 

Wonderful featured pages

Darwin

One of the common myths of our present society is that evolution theory was invented in the 19th cen…

Lamarck

The sentences that 20th century history gave to Jean-Baptiste Pierre Antoine de Monet, Chevalier de …

Haeckel

As the birthplace of Protestantism, Germany had a tradition of questioning authority and tolerating …

Butler

Living in New Zealand as a sheepfarmer at the time of publication of Darwin’s "The Origin of Species…