Re: mutation rates
Mon, 24 May 1999 20:07:12 EDT

Because of my debating style, I have caused some confusion in this thread and
I need to clear it up before I address Rich's specific comments, so please
bear with me.

Whenever I present an argument I try not to be pedantic and explain
everything in excrutiating minute detail in order to cover every possible
contingency. Hence I tend to leave out concepts or ideas I feel should be
assumed based on the thread topic. In this thread, we are debating whether a
lack of constancy in the rates of molecular clocks means that the rates of
mutation are also not constant. I have argued that they do not, because
there is experimental evidence that demonstrates that mutation rates are
largely constant. Because of the nature of the thread topic, I did not feel
it necessary to add "mutation rates **that form the bases of the molecular
clocks** are largely constant." I had assumed that this would be implicitely
understood since we were discussing molecular clocks and not all processes in
general that are based on mutational events. However, Rich's comments
suggest that I have given the impression that I was claiming that **ALL**
mutations occur at a constant rate.

Therefore let me clarify my position. First, not all mutational events occur
at a constant rate. As Rich pointed out a significant block that do not are
those caused by mutagenic agents. As I explained this is because the rate of
occurance is directly proportional to the amount of exposure to the mutagenic
agent. So Rich has a valid point. It is, however, moot, because mutations
that are caused by mutagenic events do not appear to have any significant
effect on molecular clocks based on current experimental evidence. This is
for two simple reasons. First, to my knowledge no molecular clock is based
on a mutational event that is known to be caused or significantly influenced
by a mutagenic agent. Secondly, the mutational events that do form the bases
of the known molecular clocks are known to be caused by internal rather than
external mechanisms. That is, they are known to be caused by replication and
proofreading errors caused by the relative inefficiency of the replication
and proofreading enzymes rather than by externally acquired (or even internal
manufactured) mutagenic agents. Also these internal mechanisms are not known
to be significantly affected by mutagenic agents. Though the incident of
replication and/or proofreading errors is not absolutely constant (there is
some minor variability based on chance) we know that statistically speaking
over a long period of time these kinds of errors do possess a largely
constant rate of occurance, just as a coin flipped many times that starts out
with more heads than tails will over time acquire the normal statistical
50:50 pattern.

So to conclude, while it is true that the various forms of mutagenesis do
have variable rates of mutation, the mutational events that are linked to the
known molecular clocks are not themselves mutagenic and are known to be

In a message dated 5/24/99 3:51:27 AM Mountain Daylight Time, writes:

> > > It can also change if the cellular environment changes. The presence
> > > chemical mutagens in the cell will change the mutation rate. Not to
> > > mention X-rays or even UV light. A reduction in the ozone layer could
> > > conceivably increase mutations significantly.
> >
> > True, but that's because mutagenesis is an "artificial" form of mutation
> > compared to the normal way mutation occurs, ie replication errors...
> I don't see what's artificial about it.

I admit that that was a poor choice of words, but I was trying to point out
that the mutations linked to the molecular clocks are not known to be caused
or influenced by mutagenic agents. They are instead caused solely by
inherent molecular factors that create mutations at statistically regular

> The concentration of free radicals
> in the cell, for instance, is partly a matter of what kinds of foods are
> eaten. At least that's my understanding.

Some evidence suggests that this true, but there is no unambigious
experimental demonstration of this concept, nor is there any unambiguously
clear link between free radicals and mutations.

> Fresh fruits and vegetables are
> supposed to fight cancer.

Again, while there is some tantalizing evidence to support this, there is no
definitive demonstration that this claim is true.

> Cancer is caused by somatic mutations.

Some are; some are caused by viruses that insert oncogenes into the cellular

> Ergo, diet can significantly affect mutation rate.

Assuming the mutations are caused by free radicals. Assuming there is a
direct correlation between the amount of free radicals and the rate at which
the mutations occur. Assuming that beta-carotein or some other active
ingredient in vegetables reduces the amount of of free radicals in a whole
organism. Those are three pretty big assumptions. And even if it were true,
it would only apply to a few mutations, none of which are linked to known
molecular clocks.

> And why are replication errors considered the "normal" way mutation occurs?

Again, I admit that was a poor choice of words; see my above comments for

> How do you determine whether a mutation was caused by a replication error
> or a mutagen?

Most mutagenic agents cause very specific effects, so if you see that effect
you can usually identify the mutagenic agent or class of agents that did it.
In other cases, you can try to induce a specific mutation by using mutagenic
agents. If no agent can produce the specific mutation, it's a good bet that
it's produced by replication errors. In still other cases the specific
replication error has been identified. On top of that, mutations caused by
mutagenic agents are far more variable than the mutations involved with
molecular clocks are known to be. I don't know all the details, but I am
confident that if mutagenesis was a significant part of molecular clocks we
would have strong evidence of that by now.

> Also, in Drosophila 50-85% of the mutations are caused by transposon
> insertions [1], which I assume occur at other times than during cell
> division.

According to Barry Polisky ("Plasmids and Transposons" in David Freifelder
and George Malacinski, eds., _Essentials of Molecular Biology_, Second
Edition, Jones and Bartlett, Boston, 1993, pg. 256-7): "**Transposition
occurs preferentially immediately after DNA replication of the element
itself**" [emphasis in original]. This sounds like it occurs during or just
after that part of interphase just before mitosis. Maybe Steve Clark can
fill us in on the details.

> (Of course transposons preferentially target non-coding DNA,
> so you might not want to count them in a discussion of the mutation rate
> of genes.)

Even if that were not true, the rate of transposition (in bacteria) is
partially determined by the amount of transposase enzyme present (which is
variable) and partially determined by the fact that it must occur after
replication but before methylation (a time interval which is largely
constant), so it would not be constant enough to serve as the basis for a
good molecular clock. The regulation of transposition frequency in
eukaryotes is not well understood, but appears to be similar in some aspects.

> [1] "Cytosine methylation and the ecology of intragenomic parasites", by
> Jeffrey Yoder et al, Trends in Genetics, Aug 1997, vol 13, no. 8. They
> also say that the fraction of mutations due to transposons varies wildly
> with the species; in humans, it's only 1 in 500.

Kevin L. O'Brien