What is a Gene? -- Nature

Here is a letter I wrote with Mike Snyder in response to this:
(It was never published.)

We read with great interest Helen Pearson's recent article on "What is
a gene?" It underscores the fact that we need an increasing amount of
space to describe the full complexity of genes, much more so than the
simple pictures we had in the past. It is worth elaborating on one
aspect of genes -- the interplay between living and dead genes,
between gene and pseudogene. Conventionally, pseudogenes were thought
of as non-functional remains of genes; however, increasingly, people
are coming to see that they may be active in different ways. In
particular, large-scale transcriptional studies from the ENCODE
consortium and others indicate that a substantial fraction of human
pseudogenes are transcribed, and a large-scale sequence analyses have
shown that the sequences associated with pseudogenes appear to be more
conserved (and under selection) than neutrally evolving DNA,
suggesting preservation for functional reasons. Moreover, detailed
biochemical experiments have illuminated functions for a few
pseudogenes (e.g. Makorin1-p1). Finally, recent studies of
polymorphisms indicate that in some individuals, pseudogenes are
actually functional genes (and vice-versa). In summary, many findings
have shown that line between gene and pseudogene is blurred, further
increasing the complexity of fully describing "What is a gene?"

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16724031&query_hl=3&itool=pubmed_docsum
NATURE|Vol 441|25 May 2006 NEWS FEATURE
What is a Gene?
Helen Pearson
‘Gene’ is not a typical four-letter
word. It is not offensive....
Rick Young, a geneticist at the Whitehead
Institute in Cambridge, Massachusetts, says
that when he first started teaching as a young
professor two decades ago, it took him about
two hours to teach fresh-faced undergraduates
what a gene was and the nuts and bolts of how
it worked. Today, he and his colleagues need
three months of lectures to convey the concept
of the gene, and that’s not because the students
are any less bright....

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