A scientist is poised to create
the world's first man-made species, a synthetic
microbe that could lead to an endless supply of
biofuelCraig Venter, an American who cracked the
human genome in 2000, has applied for a patent
at more than 100 national offices to make a bacterium
from laboratory-made DNA.It is part of an effort
to create designer bugs to manufacture hydrogen
and biofuels, as well as absorb carbon dioxide
and other harmful greenhouse gasses. DNA contains
the instructions to make the proteins that build
and run and organism.The J Craig Venter Institute
in Rockville, Maryland, is applying for worldwide
patents on what it refers to as "Mycoplasma laboratorium
"based on DNA assembled by scientists. Venter
said: "it is only an application on methods".
As for whether the world's first synthetic bug
was thriving in a test tube in Rockville, all
he would say was: "We are getting close".The Venter
Institute's US Patent application Claims exclusive
ownership of a set of essential genes and a synthetic
"free-living organisms that can grow that replicate"
that is made using those genes.To create the synthetic
organism his team is making snippets of DNA, known
as oligonucleotides or "oligos", of up to 100
letters of DNA.The Candian ETC Group, which tracks
developments in biotechnology, believes that this
development in synthetic biology is more significant
than the cloning of Dolly the sheep a decade ago.On
Wednesday, and ETC spokes man, Jim Thomas, called
on the world's patent offices to reject the applications.
He said: "These monopoly claims signal the start
of high stakes commercial race to synthesise and
privatise synthetic life forms. Will Venter's
company become the 'Microbesoft' of synthetic
biology?"A colleague, Pat Mooney, said: "For the
first time, God has competition, Venter and his
colleagues have breached a societal boundary,
and the public hasn't even had a chance to debate
the far-reaching social, ethical and environmental
implications of synthetic life.
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One
of the most exciting developments in biology in
the past 100 years has been the transformation
of bacterial systematics from a largely subjective
area of study with little relevance to the rest
of science into a rigorous and objective discipline
that now provides a phylogenetic framework that
supports research in all other areas of microbiology.
The history of bacterial systematics can be divided
into four distinct phases: the phase of "early
description" between 1872 and 1900; a phase between
1900 and 1955 in which bacterial physiology and
ecology were first explored and described; the
era from 1955 until 1980, when many new approaches
were developed; and the modern era, from 1980
until today, in which modern DNA technique were
incorporated into the species description. Today,
the prevailing opinion among microbiologist appears
to be shifting away from demarcating bacterial
species using arbitrary and artificial definitions
and towards a description of species as ecologically
or genetically meaningful entities with a shared
phylogenetic heritage.
In 1872, Ferdinand Cohn demonstrated
that bacteria could be divided into genera and
species using the paradigm proposed for plants
and animals by the father of modern taxonomy,
Carl Linnaeus. During this early phase of microbial
taxonomy, the field was largely dominated by
the concerns of medical microbiology; most of
the pathogenic bacteria known today were described
before the end of the 19th century. At the time,
the pattern of properties used to identify new
species of bacteria included pathogenic potential,
a chemical reaction, requirements for growth,
and morphology, all of which are still in use
today. Bringing order to the bacterial world
proved difficult, however. Only two decades
after the first bacterial species was described,
K.B.Lehmann and R.Newmann denounced the state
of bacterial taxonomy as "haphazard and non-scientific".
At the end of 19th century,
bacterial physiology began to have an impact
on taxonomy, but systematics still employed
a typically "botanical" technique for naming
new species; the classified bacteria according
to the morphology first, and then used physiology
to discriminate among the more closely aligned
organisms- a mode of classification that did
not began to change until the 1950s . Also during
this time, in 1923, the Society of American
Bacteriologists (which later became the American
Society for microbiology) presented a report
on the characterization and classification of
bacterial types that became the basis for Bergey's
Manual, a text that remain the primary reference
in bacterial taxonomy even today.
By 1955, the field had adopted
a pragmatic, arbitrary, and artificial definition
for bacterial species: "the type culture together
with such other cultures or strains of bacteria
that are accepted by bacteriologist as sufficiently
closely related". Although this definition was
widely accepted, the meaning of "sufficiently
closely related" could not be articulated as
there was no effective way to determine relatedness
at that time.
Between 1955 and the 1980s,
bacterial taxonomists developed many new techniques
for parsing the bacterial world. Chemotaxonomy,
in which the chemical structures of cell constituents
are used to different bacteria into relatedness
groups, was integrated into species description.
In 1961, McCarthy and Bolton presented a means
of comparing genetic material through DNA-DNA
hybridization, a method bacterial systematists
rely on to this day to draw distinctions between
closely related species. Numerical phenotypic
analysis also emerged during this time, followed
by the more sophisticated protein sequence analysis.
In 1965, Zuckerkandl and
Pauling evaluated the fitness of various types
of biological molecules for deriving the phylogeny
of organisms. They concluded that the most appropriate
molecules are the "semantide, "the molecules
that carry genetic information and change slowly
over time. In the 1970s, Carl Woese complied
a database of partial rRNA gene sequence and
used sequence comparison to derive a tree of
life that put the Bacteria and Eukaryotes on
distinctly different branches and uncovered
the existence of a third Kingdom, the Archaea.
This work explained the techniques used in protein
sequence comparison that were developed in the
preceding years. Methodological advances that
enabled the cultivation of anaerobes also facilitated
progress in developing the tree of life and
in adding novel branches to the bacterial and
archaeal trees. The combination of molecular,
chemotaxonomic, physiological, and other cellular
trait analyses also led to new insights into
the relatedness among prokaryotic species and
revolutionized microbial systematic. (The terms
"prokaryotic and "prokaryote denote organisms
that lack a nucleus. i.e., the Bacteria and
Archeae). Although the term is not useful for
biological classification, as it denotes the
lack of a feature, it is commonly used to designate
microscopic organisms that are neither eukaryotes
(possessing a nucleus) nor viruses.
By the 1980s, the list of
bacterial names had reached 40,000, a number
that many systematic agreed was out of proportion
with the sum of bacterial diversity described
to date. In 1980, a group of invested microbiologist
hewed the list of 40,000 down to trim 2,500
names designated as "validly published species".
In the following years, nucleic
acid analysis, including 16SrRNA sequence analysis,
protein-encoding gene sequence analysis, and
gene profiling methods, influenced bacterial
taxonomy. As new methods were developed, many
were integrated into the requirements for defining
new species. Today, fewer than 600 new species
of bacteria are described every year, in part
because of the onerous amount of testing required
to ensure a bacteria can be discerned from neighboring
species of the same genus.
In 2000, Hagstrom et
al. reported their comparison of 16SrRNA
sequence similarities with DNA-DNA reassociation
values. They asserted that 97% 16SrRNA sequence
identify or lower between two bacteria was sufficiently
dissimilar to characterize those bacteria as
different species. Later this value was increased
to 99% sequence identify in light of new data.
In summary, molecular analyses
have enabled bacterial taxonomists to decode
the phylogeny of the bacterial world and the
distinctions between different types of bacteria
are being drawn with a finer and finer brush.
However, there is still no consensus in the
microbiology community about what exactly constitutes
a bacterial species, what tests (and results)
are required to identify a bacterium as a unique
species, or how to classify those bacteria that
cannot be cultivated in the lab.
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