The challenge to the modern evolutionist is how to conceptualize fitness in the realm of transmission and heritability so that the units of selection, as they are involved in a choice, do not turn out to be a poor Neo-Darwinian description of the actual dynamics involved in the transition from single cells to multicellular organisms. The hypothesis that the germline and the self-policing system evolved a progressive adaptation of reducing and controlling withinorganism change, because this orthoselective mechanism presumably served to facilitate the transition between cells and multicellularity, should be seriously considered. Genetic homogeneity reduces selection. Early germline sequestration would reduce the opportunity for conflicting genomes and at the same time would get out of selection’s reach because cells would tend to be homogeneously cooperative and cell duplication would be limited or would produce similar cells. Moreover, intracellular or intercellular mechanisms tending to reduce within-organism change will be favored not by selection but by the intercellular mechanisms that promote fusion through cohesion and cooperation as in Myxobacteria and slime molds. In fact this new mechanism may be considered an organismic-multicellular-organization, non-Darwinian, but only while homogenous cooperation lasts or exists to promote a higher level system (e.g., a tissue, organ, etc.) necessary for higher-level-system survival. This latter is a more inclusive evolutionary unit. Clearly, "jumping" to cooperation through conflicting genome modifiers of various types means reducing the fitness of lower-level units but at the same time increasing the fitness of the multicellular "group". There may be moments between unicellular cooperations and the new higher-level-system in which multicellular organization has not yet set in, in which case the evolutionary transition is left without selection of the lower level or without the higher more inclusive evolutionary unit. There, we will have "blanks" and no evolution. How long these "uncertain" periods will last, no one can predict, simply because they will depend on nature’s circumstances. Since desertion from cooperative arrangements may result from mutation among conflict-gene-modifiers, the transition has to wait for the mechanism of cooperation to initiate the reduction of fitness of lower level units. Mutation rate and the frequency-dependent advantages that result within the population of cells have to be at a minimum and reduced to just some cells, but not all. Frequency-dependent selection within the population will always boycott the maximization of group fitness. The transition period cannot be bountiful in its new fitness function with those mutation-based frequency-dependent selection individuals. Their rapid elimination will make way for the higher level unit. Adaptation as viewed by traditional Neo-Darwinism (although not by Darwin) (e.g., Williams, 1996) is set to produce only better-designed individuals (the phenotype) sacrificing the other levels of organization where conflict mediation made life so bountiful in many directions.

The past 45 years have seen an explosion in our knowledge of basic molecular genetics and this recent revolution is transforming our view of the mechanisms of inheritance and the evolution of life on Earth. The time is now ripe to see and analyze the implications to the basic tenets of evolutionary theory. The scientific revolution initiated by Charles Darwin, that natural selection is the driving force in evolution, has become stagnated with Neo-Darwinian thinking. We believe the dogma requires updating with the new perspectives of the molecular revolution in the immune system of animals with backbones, the vertebrates. Therefore, it is now reasonable to entertain previously heretical concepts and questions such as: Is there a Lamarckian principle at work in the immune system? Is Weismann’s Barrier permeable to some extent? In other words, can some acquired characteristics be inherited? Can we describe the process in molecular terms?

The key conceptual point is this: mutations in genes of somatic cells of an animal can possibly be transmitted to the genes of germ cells and passed on to offspring of future generations. This is a molecular update to the original idea of the inheritance of acquired characteristics presented by Lamarck and later accepted by Darwin in his Pangenesis theory.

We therefore introduce the two, not necessarily incompatible, concepts: 1) the traditional Neo-Darwinian that evolutionary genetic variability pre-exists before the selective force acts (natural selection); versus, 2) the Lamarckian view of the generation of genetic variability at the same time as the selective force acts. This latter concept is singularly relevant to the immune system, where the selective force/environmental stimulus, the infectious disease, exists at the same time as the appearance of new somatic genetic variability (the mutated genes encoding antibodies against infection).

Just as it is for the immune system, the modern Lamarckian molecular process might explain why some species have been able to undergo an apparent rapid genetic transformation when sudden environmental changes, or catastrophes have occurred in nature.

Cluster analysis carried out with 16 ecotypes of Hydra collected from 15 widely separated and ecologically distinct localities in India has revealed that local adaptation is simply the result of switching specific genes, depending on the ecological requirements (Rastogy and Pandey, 1992). This unicellular animal has a tremendous regulatory machinery of structural reorganization that constitutes a challenge to traditional taxonomy (Ewer, 1948; Grayson, 1971; Campbell, 1983). As with protozoa, Hydra resort to sexual reproduction only under unfavorable environmental conditions (Prasad and Mookerjee, 1986). Hydra’s universal adaptation forces the experimenter to adopt an L system model in view of the fact that gene frequency changes are not a prerequisite to adaptation. A single individual can do it with an extranuclear trigger superadaptability that probably retained the ancestral form of modern marine larvae that have "type 1" development, which is a widespread and basic mode of embryogenesis in modern animals.

In type 1 development cleavage begins immediately after fertilization and proceeds for a number of cell divisions, as in sea urchin embryos. By the end of cleavage, all the blastomeres have been specified; the resulting embryo has one thousand cells and is divided into a group of polyclonal lineages in which each element gives rise to a certain differentiated cell type. Following Blackstone and Ellison (1998) one can interpret type 1 development as a means of reducing the time for development and the intercellular variability through defecting cells, by way of maternal control. Maternal control of cell behavior (first proposed by Buss, 1987) in the transition of unicellular Hydra-like animals to multicellular ones retaining L type extranucleic inheritance can be a way of reducing conflict among cells, thereby making cooperation possible.

Thus, Hydra’s L type superadaptability could be the origin of multicellular life that went through an evolutionary transition to a new higher-level unit of individuality.

There have been cases in Drosophila in which the comparative genetic structure and spatial patterns of cosmopolitan and local species have shown rapid genetic changes among profoundly isolated local demes that cannot be interpreted with the usual Neo-Darwinian theory (Hoenigsberg and Parkash, 1995). Jenning’s (1940, p. 48) clearly stated that: "The doctrine of the inheritance of acquired characteristics finds its last refuge in the genetics of Protozoa. It is a fact that Protozoa are modified in many ways by the action of environmental conditions, and it is known that the modified characteristics so induced are inherited for long periods in vegetative reproduction for hundreds of generations" (quoted from Sapp, 1987). Moreover, some authors have analyzed epi- and extranucleic inheritance, and have found it necessary to postulate Lamarckian inheritance and non-Mendelian inheritance (Landman, 1991; Hoenigsberg, 1992).

The Somatic Selection Hypothesis, first proposed by Steele (1979), is a modern molecular counterpart of the Pangenesis idea. This hypothesis proposes a mechanism to explain the genetic evolution of variable antibody genes (V genes) via a soma-to-germline gene feedback system. The mechanisms allow for the creation of new genetic variant animals in response to microbial invaders from the external environment. There is now no doubt that the DNA sequences which encode the proteins for the recognition of foreign invaders (antibodies) undergo rapid somatic gene mutation as a result of being activated by the antigens of the invading infectious agent. The most recent data strongly support the theory that antibody gene mutations are passed back to germline DNA in a process involving reverse transcription. Reverse transcription, after a stormy reception, has been accepted after a Nobel Prize was awarded to Temin and Baltimore (1975) and it has now become widely recognized as an essential process in the replication of retroviruses (such as HIV) and other cellular events. Retroviruses are so-called because genetic information flows from RNA to DNA, the reverse of the normal direction, DNA to RNA, in all living cells.

For a general summary of the essential points concerning the immune system as a Lamarckian process in the Darwinian controversy we offer Rothenfluh and T. Steele (1993); Rothenfluh and E.J. Steele (1993); Steele et al. (1996, 1998). Most of the detailed molecular evidence can be found in Rothenfluh et al. (1995). To analyze Weismann’s barrier we offer Pollard (1984) and Buss (1987).

The evidence points to the operation of the gene feedback loop involving the flow of genetic information from somatic cells (lymphocytes) into the germline genes.

The appearance in the germline of a gene structure (a specific gene sequence) thought to be present only in the soma cannot be ignored. Now that the human genome sequencing has been completed, we would not be surprised if the gene structure found in the soma is also found in the germline of all vertebrates. Lamarckian possibilities will have to be admitted as a general scientific interpretation in biology.

For the variable genes of the immune system one can say: How do we explain the presence of highly non-random patterns in the germline V gene DNA which can only arise through direct antigen-binding selection mechanism acting on the protein product of the gene (the antibody) instead of the DNA?

Steele’s group at the University of Wollongong in Australia, ask the question of whether the DNA sequences of germline V gene benefit in any way from the antigen-driven somatic mutation and selection events that have occurred in previous generations. The question is: How many new V region mutant DNA sequences appear in B lymphocytes during immune responses and are subject to selection in view of the success of the encoded antibody in competing for antigen. Steele’s group asks if these new sequences can pass over the germline DNA (Steele et al., 1998).

The Somatic Selection Theory predicts the germline transmission of acquired somatic mutations of antibody V region genes. This stunt could be effected through the enzyme reverse transcriptase (copying somatic RNA into DNA) mediated by naturally occurring endogenous RNA retroviruses (lymphocytic ones) acting as "gene shuttles" which transport mutated V region gene sequences into germ cells. The next step would be the physical integration of this somatically derived hereditary information into the germline DNA so as to replace the pre-existing sequence.

It maybe interesting to remember that in the Proceedings of the National Academy of Sciences of the United States, Bartl et al. (1994) speculated that genes could be transmitted between species by viral infection, thus contributing to the evolution of the vertebrate immune system. Thus, last century, Weissman’s barrier was already penetrated. This statement in the prestigious Proceedings is even more daring than Ted Steele’s idea in the Somatic Selection Theory.

Let us mention a few examples of acquired characteristics:

Animals such as the ostrich and the African warthog have large callosities in parts of the body (sternum, forelimbs, hind limbs) as a consequence of their resting. The strong horny calluses appear to protect the skin surfaces upon which the animal kneels. Ostriches rest by squatting on their legs and their breast-bone (sternum). In these and in other animals, callusing can also be induced to occur if surfaces are subjected to frequent rubbing. Therefore, they can be classed as an "acquired" somatic adaptation. What is particularly interesting is that all those prominent natural calluses found in ostriches and warthogs are already well formed in the embryo in the absence of friction or rubbing. This means that these strategically located callosities are germline encoded. The skin pads of the soles of the feet of the newly born humans can be placed in this class.

Traditional Neo-Darwinian explanation (not by Charles Darwin but by his followers) is that these are peculiarities of a germline origin brought about by the natural selection process. Evidently to solve the issue between Neo-Darwinian explanation and the Lamarckian one requires experimentation with the genes involved. This is a very difficult and complex phenomenon, certainly more complex than the antibody V genes of B lymphocytes.

Steele and Cairns (1989) and Howard Temin (1989) reviewed the evidence for the existence of reverse transcriptase enzymes in bacteria.

Without going into the details, John Cairns and co-workers of Harvard University were able to produce gene mutations in bacterial cultures in a directed fashion. They showed that certain mutations only appeared if chemical substrates related to the enzyme-encoding genes that mutated were present in the growth medium. Although controversial, John Cairn’s original explanation made it necessary to invoke a reverse transcriptase-based gene feedback loop. Previously Steele (1979) used the same explanation for his soma to germline theory for the antibody V genes of the immune system.

What about acquired inheritance in plants where there is no "Weismann Barrier" separating the soma and the germline. Acquired somatic modifications in plants which are the result of somatic mutations can be propagated to progeny when the seed is formed from that part of the plant that developed the somatic mutation. Therefore, Lamarckian evolution is and has been a fact in plants.

Phenomena such as induced heavy metal tolerance as acquired inheritance have been routinely demonstrated (McClintock, 1978; Cullis, 1984; Pren Das et al., 1990; Rothenfluh, 1995).

This example may not be a so very special scenario because it is known that mouse sperm cells maturing in the epididymal canals of the testis have the spontaneous ability to take up exogenous DNA which can be integrated into the genomic DNA of the sperm nucleus.

Spadafora and colleague’s work (Zoragi and Spadafora, 1997) has been controversial but now they are defining many of the steps of the DNA-uptake pathway.