This nicely outlines how it is
possible for molecular complexity to arise in an evolutionary environment. Read it slowly as it is important. The whole process turns out to be easy and
inevitable. It allows a range of altered
proteins to be on standby should they be needed. It also informs us that life is hugely over
engineered with an excess of viable options should they prove useful.
It is also the molecular
underpinning for evolutionary intelligence itself. It is clear that cells themselves are able to
respond to a changing environment by making decisions that change its nature
and is most dramatically expressed with slime molds that imitate flowers.
The carry on into higher forms of
life is vastly more difficult, but the same driver is at work. The organism recognizes an attractive
ecological niche and then proceeds to swiftly adapt its offspring to that
niche. It already has the capacity to
make appropriate changes at the cellular level and appropriate changes ensue in
the offspring that enhance the ability to exploit that new niche.
The controversy over whether the
direction is affected by subconscious decisions of the organism or is simply
caused by superior survival will remain, however, recall the improved options
need to be presented before they are encouraged and exploited. There I return
to the unusual knee callus on a camel that the creature is born with.
Random mutation is nonsense there
and it has always been nonsense except in the framework just described in this
article. This article actual eliminates
the random problem and provides a palette of choice to the organism to respond
to a changing environment.
Evolution of complexity recreated using 'molecular time travel'
by Staff Writers
File image: V-ATPase proton pump. One of the pump's major components is
a ring that transports hydrogen ions across membranes. In most species, the
ring is made up of a total of six copies of two different proteins, but in
fungi a third type of protein has been incorporated into the complex. To
understand how the ring increased in complexity, Thornton
Much of what living cells do is carried out by "molecular
machines" - physical complexes of specialized proteins working together to
carry out some biological function. How the minute steps of evolution
produced these constructions has long puzzled scientists, and provided a
favorite target for creationists.
In a study published early online in Nature, a team of scientists from
the University of Chicago and the University of Oregon demonstrate how just
a few small, high-probability mutations increased the complexity of a molecular
machine more than 800 million years ago.
By biochemically resurrecting ancient genes and testing their functions
in modern organisms, the researchers showed that a new component was
incorporated into the machine due to selective losses of function rather than
the sudden appearance of new capabilities.
"Our strategy was to use 'molecular time travel' to reconstruct
and experimentally characterize all the proteins in this molecular machine just
before and after it increased in complexity," said the study's senior
author Joe Thornton, PhD, professor of human genetics and evolution and ecology
at the University of Chicago, professor of biology at the University of Oregon,
and an Early Career Scientist of the Howard Hughes Medical Institute.
"By reconstructing the machine's components as they existed in the
deep past," Thornton
The study - a collaboration of Thornton's molecular evolution
laboratory with the biochemistry research group of the UO's Tom Stevens,
professor of chemistry and member of the Institute of Molecular Biology -
focused on a molecular complex called the V-ATPase proton pump, which helps
maintain the proper acidity of compartments within the cell.
One of the pump's major components is a ring that transports hydrogen
ions across membranes. In most species, the ring is made up of a total of
six copies of two different proteins, but in fungi a third type of protein has
been incorporated into the complex.
To understand how the ring increased in complexity, Thornton
To do this, the researchers used a large cluster of computers to
analyze the gene sequences of 139 modern-day ring proteins, tracing evolution
backwards through time along the Tree of Life to identify the most likely
ancestral sequences. They then used biochemical methods to synthesize those
ancient genes and express them in modern yeast cells.
The group found that the third component of the ring in Fungi
originated when a gene coding for one of the subunits of the older two-protein
ring was duplicated, and the daughter genes then diverged on their own
evolutionary paths.
The pre-duplication ancestor turned out to be more versatile than
either of its descendants: expressing the ancestral gene rescued modern yeast
that otherwise failed to grow because either or both of the descendant ring
protein genes had been deleted.
In contrast, each resurrected gene from after the duplication could
only compensate for the loss of a single ring protein gene.
The researchers concluded that the functions of the ancestral protein
were partitioned among the duplicate copies, and the increase in complexity was
due to complementary loss of ancestral functions rather than gaining new ones.
By cleverly engineering a set of ancestral proteins fused to each other
in specific orientations, the group showed that the duplicated proteins lost
their capacity to interact with some of the other ring proteins.
Whereas the pre-duplication ancestor could occupy five of the six
possible positions within the ring, each duplicate gene lost the capacity to
fill some of the slots occupied by the other, so both became obligate
components for the complex to assemble and function.
"It's counterintuitive but simple: complexity increased because
protein functions were lost, not gained," Thornton
The research team's last goal was to identify the specific genetic
mutations that caused the post-duplication descendants to functionally
degenerate.
By reintroducing historical mutations that occurred after the
duplication into the ancestral protein, they found that it took only a
single mutation from each of the two lineages to destroy the same specific
functions and trigger the requirement for a three-protein ring.
"The mechanisms for this increase in complexity are incredibly
simple, common occurrences," Thornton
"Gene duplications happen frequently in cells, and it's easy for
errors in copying to DNA to knock out a protein's ability to interact with
certain partners. It's not as if evolution needed to happen upon some special
combination of 100 mutations that created some complicated new function."
Thornton proposes that the accumulation of simple, degenerative changes
over long periods of times could have created many of the complex molecular
machines present in organisms today.
Such a mechanism argues against the intelligent design concept of
"irreducible complexity," the claim that molecular machines are too
complicated to have formed stepwise through evolution.
"I expect that when more studies like this are done, a similar
dynamic will be observed for the evolution of many molecular complexes," Thornton
"These really aren't like precision-engineered machines at
all," he added. "They're groups of molecules that happen to stick to
each other, cobbled together during evolution by tinkering, degradation, and
good luck, and preserved because they helped our ancestors to survive."
The paper, "Evolution of increased complexity in a molecular
machine," appears in the January 18, 2012, issue of Nature [doi:
10.1038/nature10724]. The work was a collaboration of Thornton 's
molecular evolution lab with the research group of Tom Stevens, a yeast
geneticist at the University
of Oregon University of Oregon
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