Epigenetic mechanisms are increasingly being accepted as an integral part of normal science. Earlier genetic studies appear to have assumed that the only changes were ‘mutations’ as a result of a change in the DNA sequence. If any such changes altered the amino acid sequences then it was effectively a mutation, and if it occurred in a germline cell (including in unicellular organisms) then it could be passed on to subsequent generations. However, it is increasingly apparent that other changes are also important, for example, changes to methylation patterns, and to the histone proteins. Epigenetics was sometimes consider ‘additional’ to classical genetics, but it is still fully dependent on DNA, RNA and protein sequences, and at least since  it has been considered a part of normal science. A richer way is to expand classical genetics to include transfer of information between cellular generations. Indeed, it is hard to imagine a unicellular protist that does not modify some of its protein expression levels as a result of environmental changes-gene regulation is integral to biology. There is a very general question about the regulation of gene expression levels in both unicellular and multicellular organisms. Unicellular organisms are interesting in that they have different levels of gene expression, depending on their environment. For multicellular organisms (say, plants and animals) there is the very important issue that all cells are considered to have the same genetic information, yet the proteins they are expressing is different. For example, plant cells in roots do not normally express the large numbers of chloroplast proteins; this is a fundamental example.
First we should mention that there are several processes that regulate epigenetics, and that they are widespread in nature. There are at least three classes of responses that modify gene expression, small RNAs, methylation (and hydroxymethylation), and protein modifications (in eukaryotes at least). These organisms have several (five) histone proteins attached to their DNA in pairs, and these form regular structures along the DNA – the nucleosomes, and the tightness of these nucleosomes affects gene expression. There are several interesting modifications to the histone proteins that are found in a very wide variety of deeply diverging eukaryotes [2-4]. We consider these to be present in the universal ancestor of eukaryotes , that is, they are general (but not necessarily universal) because they are found in Excavates, which many people consider are ancestral to other eukaryotes [6, 7]. Similarly, an important point is that methylation, phosphorylation, etc. of the DNA and of the histones is a part of normal evolution (at least in eukaryotes that have the nucleosome structure) . One of the most interesting aspects is methylation (and hydroxymethylation) of cytosine, and this is found in many deep branching eukaryotes . Typically there is methylation of cytosine molecules, especially in CpG (cytosine followed by guanine) regions. The role of small RNAs in helping regulate the levels of protein expression is discussed in . The main point here is that protein expression levels are very variable in all cells – it is not just classical genetics that is important; there are many epigenetic mechanisms affecting the differences in protein expression. Epigenetics is a unifying force in biology.
One of the main conclusions/recommendations that I have is that we should insist that anyone should actually have read Lamarck’s book who wishes to suggest that the ‘inheritance of acquired characters’ is some sense Lamarckian. Yes, Lamarck was one of the early evolutionists, and should be well recognized as such. However, nowhere in his book does he indicate anything about the mechanisms of evolution, or of the potential of an increase in numbers. We have to accept standards of evidence. It appears that the inheritance of acquired characters it was a general assumption at the time, and Lamarck assumes it, but never really discusses how it might occur.