Gene is the natural unit of genetic information. A gene is traditionally understood to be genetic information that affects a discernable property of the individual, i.e. the occurrence of a certain trait or its particular form. A trait can consist in the presence or absence of certain morphological structures, just as it can correspond to the presence or absence of a certain pattern of behaviour. If two organisms differ in a particular gene, i.e. if they have a different variant of a particular gene, i.e. a different allele, then they can differ in the relevant trait. In some cases, the carriers of different alleles differ under all circumstances; in some cases the differences are manifested only in a certain specific environment, either external or internal – under conditions with the presence of quite specific variants of the other genes in the genome of the individual. It is necessary to be aware that the relationship between the gene and the trait that it determines is actually quite the opposite than would follow from the above definition. The existence of a genetically determined phenotype difference between the individuals of the particular species is the primary feature. Only on the basis of identification of this difference is it possible to identify the specific trait and to postulate the existence of the particular gene. The relevant methods, whether genetic methods (search for the gene for the known phenotype manifestation through crossing) or the reverse genetic method (looking for the phenotype manifestation of a known gene through targetted introduction of the DNA section into the genome of the individual or targetted removal or damaging of this section) can then be employed to locate the particular gene in the overall genome of the studied organism, i.e. to determine the locus at which this gene is located.
Although the gene is delimited through its functional manifestations, this does not mean that it evolved in evolution precisely because of selective pressure on this function. A gene is apparently very frequently defined and named according to a phenotype manifestation of a mutation that the particular gene inactivates. This type of phenotype manifestation need not have any connection with the actual function of this gene and can be a quite random side product of its damage. The familiar joke about how pulling all the legs off a flea leads to its becoming deaf (because it then fails to react to the instruction “jump, flea!”) could be retold as an excerpt from a concluding grant report. “We have fulfilled the main target of the project, we have discovered the gene controlling the function of hearing in fleas. Using the technique of gene targetting, we have unambiguously demonstrated that the gene Hear 1 is responsible for the ability to hear acoustic signals in fleas. Fleas with both copies of this gene inactivated ceased to react to acoustic stimuli. Footnote in small print: An additional result of the project was the discovery that limbs are not formed in these fleas. However, research on the ontogenesis of limbs was not part of the original grant plan and thus this potentially interesting phenomenon was not studied further.”
Modern molecular biologists almost universally employ the term gene to denote a cistron. Cistron was originally defined in terms of the “cis-trans-test”(see Cis-Trans-Test). When a gene is identified with a cistron, a gene basically corresponds to a continuous DNA section coding, for example, a certain RNA chain, e.g. ribosomal RNA or mRNA coding a particular protein. The particular DNA section can be subsequently modified, e.g. at the level of mRNA, by cis-splicing, i.e. splicing and reconnection of its individual sections, but not by trans-splicing, i.e. connection of RNA sections derived from other RNA molecules that are rewritten from other DNA sections.
The concept of a gene as a cistron is very practical from the viewpoint of molecular biology. It permits more or less exact and particularly unambiguous delimitation of the genes coding the individual molecules that participate in the life processes of cells and multi-cellular organisms. As, at the present time, the study of these molecules forms the major content of the work of the greatest number of scientific workers in the field of biology, this conception of a gene quite predominates. It is seen by a great many biologists as quite obvious, correct and, in fact, the only possibility. However, this concept of a gene is quite inadequate for the purposes of evolutionary biology. It is apparent that two independent mutations at two places on a single cistron can have different, mutually independent phenotype manifestations. In sexually reproducing organisms, i.e. in most of currently known species, genetic recombination can occur at any time between these mutations in this section, which would physically separate not only the two mutations, but also the evolutionary fates of these mutations. Basically, every nucleotide in the DNA, to be more exact in the regulation and coding areas of the DNA, can thus act as an independent gene, can have a phenotype manifestation and can be transferred from one generation to the next. Whether two mutations in a single DNA chain will behave in evolution as two independent genes or as a single gene is decided by their mutual distance, or rather by the probability of their separation as a consequence of crossing-over, the probability that they will be passed down to the next generation, determined most frequently by the intensity of selection against their carriers or to their benefit, and also by the effective and nominal size of the population in which the evolution is occurring.