Complexity_ A Guided Tour - Melanie Mitchell [132]
A single gene can code for more than one protein. It had long been thought that there was a one-to-one correspondence between genes and proteins. A problem for this assumption arose when the human genome was sequenced, and it was discovered that while the number of different types of proteins encoded by genes may exceed 100,000, the human genome contains only about 25,000 genes. The recently discovered phenomena of alternative splicing and RNA editing help explain this discrepancy. These processes can alter messenger RNA in various ways after it has transcribed DNA but before it is translated into amino acids. This means that different transcription events of the same gene can produce different final proteins.
In light of all these complications, even professional biologists don’t always agree on the definition of “gene.” Recently a group of science philosophers and biologists performed a survey in which 500 biologists were independently given certain unusual but real DNA sequences and asked whether each sequence qualified as a “gene,” and how confident they were of their answer. It turned out that for many of the sequences, opinion was split, with about 60% confident of one answer and 40% confident of the other answer. As stated in an article in Nature reporting on this work, “The more expert scientists become in molecular genetics, the less easy it is to be sure about what, if anything, a gene actually is.”
The complexity of living systems is largely due to networks of genes rather than the sum of independent effects of individual genes. As I described in chapter 16, genetic regulatory networks are currently a major focus of the field of genetics. In the old genes-as-beads-on-a-string view, as in Mendel’s laws, genes are linear—each gene independently contributes to the entire phenotype. The new, generally accepted view, is that genes in a cell operate in nonlinear information-processing networks, in which some genes control the actions of other genes in response to changes in the cell’s state—that is, genes do not operate independently.
There are heritable changes in the function of genes that can occur without any modification of the gene’s DNA sequence. Such changes are studied in the growing field of epigenetics. One example is so-called DNA methylation, in which an enzyme in a cell attaches particular molecules to some parts of a DNA sequence, effectively “turning off” those parts. When this occurs in a cell, all descendents of that cell will have the same DNA methylation. Thus if DNA methylation occurs in a sperm or egg cell, it will be inherited.
On the one hand, this kind of epigenetic effect happens all the time in our cells, and is essential for life in many respects, turning off genes that are no longer needed (e.g., once we reach adulthood, we no longer need to grow and develop like a child; thus genes controlling juvenile development are methylated). On the other hand, incorrect or absent methylation is the cause of some genetic disorders and diseases. In fact, the absence of necessary methylation during embryo development is thought by some to be the reason so many cloned embryos do not survive to birth, or why so many cloned animals that do survive have serious, often fatal disorders.
It has recently been discovered that in most organisms a large proportion of the DNA that is transcribed by RNA is not subsequently translated into proteins. This so-called noncoding RNA can have many regulatory effects on genes, as well as functional roles in cells, both of which jobs were previously thought to