In an article written by Paul Haggarty, a recent study published in Science was explained concerning the idea of epigenetics, the information in the genome aside from what is contained in the DNA sequence. The most popular form studied by scientists relates to the chemical modification, acetylation and methylation, of DNA and histones. The information can be expressed, or used, or hidden, but always existing in a person's cells and tissues.
The study in Science claims to have shown that manipulation of the epidenetic process during the production of sperm in mice influences the development of their offspring over many generations.
We already know specific signatures in the fathers sperm have been linked to autism or the susceptibility of the child to certain diseases. In the new study, scientists at Mcgill University altered the activity of a histone protein that controls epigenetic processes during sperm production in mice. It was shown to affect the health of the offspring and it persisted over generations.
In addition, it is suggested that if certain environmental factors disrupt this epigenetic process, there could be birth defects that can be traced back to the father. For example, there is a certain possible evolutionary utility of the milder effects of this which may allow offspring to sense the metabolic environment, whether it may be famine or plenty, and to program its own metabolism to respond accordingly.
I am of the opinion that these kinds of factors must be due to something specific, we just haven't discovered it yet. It is impossible for these effects to be transferred without some kind of information holding material, and if it is not DNA, it must be something else, or it may be all coincidence.