Parts 2 and 3 of the volume Biological Information New Perspectives cover “Biological Information and Genetic Theory” and “Theoretical Molecular Biology,” respectively. Various papers from that volume explain how the origin of biological information challenges neo-Darwinian thinking. But two papers by Discovery Institute senior fellow Jonathan Wells help set the stage by investigating where functional information resides in living cells. Of course everyone agrees that gene-coding DNA is an important source of functional information in living organisms which neo-Darwinism must explain. But what about non-protein-coding DNA? Is there functional information in DNA outside of the genes? And how about epigenetic information that exists outside of DNA entirely? Wells finds that both non-protein-coding DNA and epigenetic information are important sources of functional information that need be explained under any viable evolutionary model.
Is the Genome Full of Junk?
Wells’s first paper, “Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information,” opens the second part of the volume. Citing numerous examples of functionality for non-coding DNA, he argues that “the notion of ‘junk DNA’ is obsolete, and the amount of biological information in the genome far exceeds the information in protein-coding regions.” Wells uncovers various lines of evidence in support of this claim.
First, there are the conclusions of the ENCODE project which suggest that there is “widespread transcription of non-protein-coding DNA.” According to Wells, “Widespread transcription suggests probable function; so does sequence conservation.”
This evidence, however, is somewhat circumstantial. Thus Wells observes as a second point that “[t]here is also direct evidence for specific functions of non-protein-coding RNAs.” He then gives many examples of how non-coding RNA performs specific functions in cells, including:
- Regulating gene expression.
- Alternative splicing, allowing the construction of many new transcripts. As Wells explains, “Alternative splicing plays an essential role in the differentiation of cells and tissues at the proper times during embryo development, and many alternatively spliced RNAs occur in a developmental-stage-and tissue-specific manner.”
- Introns not only regulate gene expression, but “also encode many of the small RNAs essential for the processing of ribosomal RNAs, as well as the regulatory elements associated with such RNA-coding sequences.”
- “Non-protein-coding RNAs are essential for chromatin organization, and non-protein-coding RNAs have been shown to affect gene expression by modifying chromatin structure [54,55].”
- “Pseudogenes are transcribed into non-protein-coding RNAs that in some cases regulate the expression of the corresponding protein-coding genes”
- Long Interspersed Nuclear Elements (LINEs), and Short Interspersed Nuclear Elements (SINEs), such as Alus, can have many functions. As one set of researchers that Wells quotes observed, “Finding… that these SINE encoded RNAs indeed have biological functions has refuted the historical notion that SINEs are merely ‘ junk DNA’.”
Wells also observes that the nucleotide sequence of DNA is not the only way that non-coding DNA can have functions:
The genome functions hierarchically, and the order of nucleotides in protein- coding and non-protein-coding DNA constitutes only the first level of that hierarchy. The length of DNA sequences (even non-protein-coding ones) is a second level; chromatin organization is a third level; and the position of chromosomes within the nucleus is a fourth. There is evidence that DNA functions at the second, third, and fourth levels in ways that are independent of the precise nucleotide sequence.
He concludes that even as we find more and more functionality for non-coding DNA, other non-DNA-based sources of information are being discovered in living cells:
non-protein-coding regions of DNA that some previously regarded as “junk” turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life.
The latter argument is elaborated in another article by Wells in the third section of the book, “The Membrane Code: A Carrier of Essential Biological Information That Is Not Specified by DNA and Is Inherited Apart from It.” According to Wells, “a genetic program is not sufficient for embryogenesis: biological information outside of DNA is needed to specify the body plan of the embryo and much of its subsequent development.” Wells explains:
Some of that information is in cell membrane patterns, which contain a two-dimensional code mediated by proteins and carbohydrates. These molecules specify targets for morphogenetic determinants in the cytoplasm, generate endogenous electric fields that provide spatial coordinates for embryo development, regulate intracellular signaling, and participate in cell-cell interactions. Although the individual membrane molecules are at least partly specified by DNA sequences, their two-dimensional patterns are not. Furthermore, membrane patterns can be inherited independently of the DNA.
Does this epigenetic information pose a problem for neo-Darwinism? Jonathan Wells thinks it does:
One could speculate that accidental changes in membrane patterns — analogous to accidental mutations in DNA — could provide the missing raw materials for evolution. Yet two- and three-dimensional information-carrying patterns are likely to entail more specified complexity than the one-dimensional information in DNA sequences, making beneficial “mutations” in such patterns much less probable than beneficial mutations in DNA. At the very least, calculations of the time required for evolution will now have to take into account these higher dimensions of biological information.
Thus, any viable model for the origin of biological information must explain not just the information in gene-coding DNA, but also the origin of the information in non-coding DNA, and the origin of epigenetic information. That, as even some evolutionary biologists are starting to acknowledge, is a tall order.