| Topic: |
Religions > Atheism |
| User: |
"johac" |
| Date: |
25 Jan 2008 02:02:01 AM |
| Object: |
Scientists Create First Synthetic Bacterial Genome |
Getting closer to the first to the first totally synthesized cell in the
lab. No gods involved.
---
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically
Defined Structure Synthesized In The Lab
ScienceDaily (Jan. 24, 2008) ‹ A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA structure
by synthesizing and assembling the 582,970 base pair genome of a
bacterium, Mycoplasma genitalium JCVI-1.0. This work, published online
today in the journal Science by Dan Gibson, Ph.D., et al, is the second
of three key steps toward the team¹s goal of creating a fully synthetic
organism. In the next step, which is ongoing at the JCVI, the team will
attempt to create a living bacterial cell based entirely on the
synthetically made genome.
The team achieved this technical feat by chemically making DNA fragments
in the lab and developing new methods for the assembly and reproduction
of the DNA segments. After several years of work perfecting chemical
assembly, the team found they could use homologous recombination (a
process that cells use to repair damage to their chromosomes) in the
yeast Saccharomyces cerevisiae to rapidly build the entire bacterial
chromosome from large subassemblies.
³This extraordinary accomplishment is a technological marvel that was
only made possible because of the unique and accomplished JCVI team,²
said J. Craig Venter, Ph.D., President and Founder of JCVI. ³Ham Smith,
Clyde Hutchison, Dan Gibson, Gwyn Benders, and the others on this team
dedicated the last several years to designing and perfecting new methods
and techniques that we believe will become widely used to advance the
field of synthetic genomics.²
The building blocks of DNA‹adenine (A), guanine (G), cytosine (C) and
thiamine (T) are not easy chemicals to artificially synthesize into
chromosomes. As the strands of DNA get longer they get increasingly
brittle, making them more difficult to work with. Prior to today¹s
publication the largest synthesized DNA contained only 32,000 base
pairs. Thus, building a synthetic version of the genome of the bacteria
M. genitalium genome that has more than 580,000 base pairs presented a
formidable challenge. However, the JCVI team has expertise in many
technical areas and a keen biological understanding of several species
of mycoplasmas.
³When we started this work several years ago, we knew it was going to be
difficult because we were treading into unknown territory,² said
Hamilton Smith, M.D., senior author on the publication. ³Through
dedicated teamwork we have shown that building large genomes is now
feasible and scalable so that important applications such as biofuels
can be developed.²
Methods for Creating the Synthetic M. genitalium
The process to synthesize and assemble the synthetic version of the M.
genitalium chromosome began first by resequencing the native M.
genitalium genome to ensure that the team was starting with an error
free sequence. After obtaining this correct version of the native
genome, the team specially designed fragments of chemically synthesized
DNA to build 101 ³cassettes² of 5,000 to 7,000 base pairs of genetic
code. As a measure to differentiate the synthetic genome versus the
native genome, the team created ³watermarks² in the synthetic genome.
These are short inserted or substituted sequences that encode
information not typically found in nature. Other changes the team made
to the synthetic genome included disrupting a gene to block infectivity.
To obtain the cassettes the JCVI team worked primarily with the DNA
synthesis company Blue Heron Technology, as well as DNA 2.0 and GENEART.
From here, the team devised a five stage assembly process where the
cassettes were joined together in subassemblies to make larger and
larger pieces that would eventually be combined to build the whole
synthetic M. genitalium genome. In the first step, sets of four
cassettes were joined to create 25 subassemblies, each about 24,000 base
pairs (24kb). These 24kb fragments were cloned into the bacterium
Escherichia coli to produce sufficient DNA for the next steps, and for
DNA sequence validation.
The next step involved combining three 24kb fragments together to create
8 assembled blocks, each about 72,000 base pairs. These 1/8th fragments
of the whole genome were again cloned into E. coli for DNA production
and DNA sequencing. Step three involved combining two 1/8th fragments
together to produce large fragments approximately 144,000 base pairs or
1/4th of the whole genome.
At this stage the team could not obtain half genome clones in E. coli,
so the team experimented with yeast and found that it tolerated the
large foreign DNA molecules well, and that they were able to assemble
the fragments together by homologous recombination. This process was
used to assemble the last cassettes, from 1/4 genome fragments to the
final genome of more than 580,000 base pairs. The final chromosome was
again sequenced in order to validate the complete accurate chemical
structure.
The synthetic M. genitalium has a molecular weight of 360,110
kilodaltons (kDa). Printed in 10 point font, the letters of the M.
genitalium JCVI-1.0 genome span 147 pages.
³This is an exciting advance for our team and the field. However, we
continue to work toward the ultimate goal of inserting the synthetic
chromosome into a cell and booting it up to create the first synthetic
organism,² said Dan Gibson, lead author.
The research to create the synthetic M. genitalium JCVI-1.0 was funded
by Synthetic Genomics, Inc.
Background/Key Milestones in JCVI¹s Synthetic Genomics Research
The work described by Gibson et al. has its genesis in research by Dr.
Venter and colleagues in the mid-1990s after sequencing M. genitalium
and beginning work on the minimal genome project. This area of research,
trying to understand the minimal genetic components necessary to sustain
life, began with M. genitalium because it is a bacterium with the
smallest genome that we know of that can be grown in pure culture. That
work was published in the journal Science in 1995.
In 2003 Drs. Venter, Smith and Hutchison made the first significant
strides in the development of a synthetic genome by their work in
assembling the 5,386 base pair bacteriophage É„X174 (phi X). They did so
using short, single strands of synthetically produced, commercially
available DNA (known as oligonucleotides) and using an adaptation of
polymerase chain reaction (PCR), known as polymerase cycle assembly
(PCA), to build the phi X genome. The team produced the synthetic phi X
in just 14 days.
In June 2007 another major advance was achieved when JCVI researchers
led by Carole Lartigue, Ph.D., announced the results of work on genome
transplantation methods allowing them to transform one type of bacteria
into another type dictated by the transplanted chromosome. The work was
published in the journal Science, and outlined the methods and
techniques used to change one bacterial species, Mycoplasma capricolum,
into another, Mycoplasma mycoides Large Colony (LC), by replacing one
organism¹s genome with the other one¹s genome.
Genome transplantation was the first essential enabling step in the
field of synthetic genomics as it is a key mechanism by which chemically
synthesized chromosomes can be activated into viable living cells.
Today¹s announcement of the successful synthesis of the M. genitalium
genome is the second step leading to the next experiments to transplant
a fully synthetic bacterial chromosome into a living organism and ³boot
up² the cell.
Ethical Considerations
Since the beginning of the quest to understand and build a synthetic
genome, Dr. Venter and his team have been concerned with the societal
issues surrounding the work. In 1995 while the team was doing the
research on the minimal genome, the work underwent significant ethical
review by a panel of experts at the University of Pennsylvania (Cho et
al, Science December 1999:Vol. 286. no. 5447, pp. 2087 2090). The
bioethical group's independent deliberations, published at the same time
as the scientific minimal genome research, resulted in a unanimous
decision that there were no strong ethical reasons why the work should
not continue as long as the scientists involved continued to engage
public discussion.
Dr. Venter and the team at JCVI continue to work with bioethicists,
outside policy groups, legislative members and staff, and the public to
encourage discussion and understanding about the societal implications
of their work and the field of synthetic genomics generally. As such,
the JCVI¹s policy team, along with the Center for Strategic &
International Studies (CSIS), and the Massachusetts Institute of
Technology (MIT), were funded by a grant from the Alfred P. Sloan
Foundation for a 20-month study that explored the risks and benefits of
this emerging technology, as well as possible safeguards to prevent
abuse, including bioterrorism. After several workshops and public
sessions the group published a report in October 2007 outlining options
for the field and its researchers.
---
http://www.sciencedaily.com/releases/2008/01/080124175924.htm
--
John #1782
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| User: "Apostate" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
25 Jan 2008 12:00:51 PM |
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On Fri, 25 Jan 2008 00:02:01 -0800, johac <jhachmann@remove.sbcglobal.net> wrote:
Getting closer to the first to the first totally synthesized cell in the
lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically
Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their goal posts,
becoming a lot more detailed in what scientists will 'never succeed in doing'.
--
Apostate a.a. #1931
..sig currently undergoing maintenance
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.
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| User: "johac" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
26 Jan 2008 01:25:12 AM |
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In article <io8kp3hf9csjd1jr4dsecakr1ugdabkf9f@4ax.com>,
Apostate <godless.*****@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac <jhachmann@remove.sbcglobal.net>
wrote:
Getting closer to the first to the first totally synthesized cell in the
lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically
Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their goal
posts,
becoming a lot more detailed in what scientists will 'never succeed in
doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA could
not be synthesized in the lab, or was that some other troll?
--
John #1782
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| User: "Apostate" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
26 Jan 2008 02:45:52 PM |
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On Fri, 25 Jan 2008 23:25:12 -0800, johac <jhachmann@remove.sbcglobal.net> wrote:
In article <io8kp3hf9csjd1jr4dsecakr1ugdabkf9f@4ax.com>,
Apostate <godless.*****@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac <jhachmann@remove.sbcglobal.net>
wrote:
Getting closer to the first to the first totally synthesized cell in the
lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically
Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their goal
posts,
becoming a lot more detailed in what scientists will 'never succeed in
doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA could
not be synthesized in the lab, or was that some other troll?
Don't remember, but I seem to recall his being among the ones whose defiant trump card was that
scientists will never succeed in 'creating life'.
--
Apostate a.a. #1931
..sig currently undergoing maintenance
want a free or premium posting account with Teranews?
https://secure.usenetbilling.com/newbilling/manageaccount.cgi?referredby=1089312943&action=Create+New+Account&vendor=teranews
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Posted via a free Usenet account from http://www.teranews.com
.
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| User: "Agent Smith" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
26 Jan 2008 08:13:29 PM |
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Apostate <godless.*****@yeehaw.org.invalid> wrote in
news:7t6np3p527kmvns19ap0ul7qcds2ulec1q@4ax.com:
On Fri, 25 Jan 2008 23:25:12 -0800, johac
<jhachmann@remove.sbcglobal.net> wrote:
In article <io8kp3hf9csjd1jr4dsecakr1ugdabkf9f@4ax.com>,
Apostate <godless.*****@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac
<jhachmann@remove.sbcglobal.net> wrote:
Getting closer to the first to the first totally synthesized cell
in the lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest
Chemically Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their
goal posts,
becoming a lot more detailed in what scientists will 'never succeed
in doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA
could not be synthesized in the lab, or was that some other troll?
Don't remember, but I seem to recall his being among the ones whose
defiant trump card was that scientists will never succeed in 'creating
life'.
Assuming that he's a Christian nutjob, I'm guessing that he's taken a
kernel of scientific truth and distorted it beyond recognizability.
What he probably meant was that scientists will never unravel the
sequence of events that took place in the Earth's primordial
"biota" that led to the creation of a functioning cell from an
undifferentiated bath of pre-biotic chemicals.
That problem is turning out to be an extremely difficult one for
scientists to unravel, and I figure that there's a pretty good chance
that, if I live to 85, which would be the year 2045, I still won't ever
see it solved.
AFAIK, that problem is turning out to be about as difficult as making
nuclear fusion work, or unraveling the origin of consciousness from the
neurology of the human brain. There are still a number of very
difficult, unsolved scientific problems. IMO, the notorious Millennium
Problems are extraordinarily simpler than the problem of figuring out
how the origin of life happened.
It may even be the hardest problem that there is. :p
.
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| User: "Apostate" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
26 Jan 2008 09:28:14 PM |
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On Sun, 27 Jan 2008 02:13:29 GMT, Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
Apostate <godless.*****@yeehaw.org.invalid> wrote in
news:7t6np3p527kmvns19ap0ul7qcds2ulec1q@4ax.com:
On Fri, 25 Jan 2008 23:25:12 -0800, johac
<jhachmann@remove.sbcglobal.net> wrote:
In article <io8kp3hf9csjd1jr4dsecakr1ugdabkf9f@4ax.com>,
Apostate <godless.*****@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac
<jhachmann@remove.sbcglobal.net> wrote:
Getting closer to the first to the first totally synthesized cell
in the lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest
Chemically Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their
goal posts,
becoming a lot more detailed in what scientists will 'never succeed
in doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA
could not be synthesized in the lab, or was that some other troll?
Don't remember, but I seem to recall his being among the ones whose
defiant trump card was that scientists will never succeed in 'creating
life'.
Assuming that he's a Christian nutjob, I'm guessing that he's taken a
kernel of scientific truth and distorted it beyond recognizability.
What he probably meant was that scientists will never unravel the
sequence of events that took place in the Earth's primordial
"biota" that led to the creation of a functioning cell from an >undifferentiated bath of pre-biotic chemicals.
That problem is turning out to be an extremely difficult one for
scientists to unravel, and I figure that there's a pretty good chance
that, if I live to 85, which would be the year 2045, I still won't ever
see it solved.
AFAIK, that problem is turning out to be about as difficult as making
nuclear fusion work, or unraveling the origin of consciousness from the
neurology of the human brain. There are still a number of very
difficult, unsolved scientific problems. IMO, the notorious Millennium
Problems are extraordinarily simpler than the problem of figuring out
how the origin of life happened.
It may even be the hardest problem that there is. :p
D00d! You're not seeing the same fundie nutjobs I am. I don't remember one subtle
enough to 'mean' what you've suggested. More like, he wasn't aware (and being fair, may
be that the last time I heard the one I mentioned toss that gauntlet down may have preceded
the event) of the total synthesis from stock bottle constituents of an infective polio virus,
and couldn't fathom the recent synthesis and in vivo assembly of a bacterial genome. He's
rash enough to suppose he can live out a lifetime, sure not to see/hear of a lab's "creating"
a live bug, or any of his tauntees witnessing the same.
--
Apostate a.a. #1931
..sig currently undergoing maintenance
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| User: "johac" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
27 Jan 2008 01:15:33 AM |
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In article <7t6np3p527kmvns19ap0ul7qcds2ulec1q@4ax.com>,
Apostate <godless.*****@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 23:25:12 -0800, johac <jhachmann@remove.sbcglobal.net>
wrote:
In article <io8kp3hf9csjd1jr4dsecakr1ugdabkf9f@4ax.com>,
Apostate <godless.*****@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac <jhachmann@remove.sbcglobal.net>
wrote:
Getting closer to the first to the first totally synthesized cell in the
lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically
Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their goal
posts,
becoming a lot more detailed in what scientists will 'never succeed in
doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA could
not be synthesized in the lab, or was that some other troll?
Don't remember, but I seem to recall his being among the ones whose defiant
trump card was that
scientists will never succeed in 'creating life'.
Depends what one calls life. We have synthesized viruses. Cellular life
is the next step and these guys are getting very close.
Time for our friends to move the goal posts again.
--
John #1782
.
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| User: "Budikka666" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
27 Jan 2008 08:07:51 AM |
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On Jan 27, 1:15 am, johac <jhachm...@remove.sbcglobal.net> wrote:
In article <7t6np3p527kmvns19ap0ul7qcds2ule...@4ax.com>,
Apostate <godless.bast...@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 23:25:12 -0800, johac <jhachm...@remove.sbcglobal.net>
wrote:
In article <io8kp3hf9csjd1jr4dsecakr1ugdabk...@4ax.com>,
Apostate <godless.bast...@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac <jhachm...@remove.sbcglobal.net>
wrote:
Getting closer to the first to the first totally synthesized cell in the
lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically
Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their goal
posts,
becoming a lot more detailed in what scientists will 'never succeed in
doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA could
not be synthesized in the lab, or was that some other troll?
Don't remember, but I seem to recall his being among the ones whose defiant
trump card was that
scientists will never succeed in 'creating life'.
Depends what one calls life. We have synthesized viruses. Cellular life
is the next step and these guys are getting very close.
Time for our friends to move the goal posts again.
--
John #1782
No one can define life! LoL!
I just began reading "Genesis" by Robert Hazen. He begins chapter two
by referring to a "recent origin-of-life text" without identifying
what it was. He remarks that it had an appendix with definitions of
life from 48 different authorities and not one of them matched any
other one!
They ranged from Maynard Smith's "any population of entities which has
the properties of multiplication, heredity and variation" to someone
unidentified who said, "life is a flow of energy, matter, and
information".
It seems to me that Maynard Smith was further off base than the second
quote is. I mean, are we to say that someone who lived and died
without having any children was never alive?!
He does speak of populations rather than individuals, though, so I'm
not really being fair to him, but what if there were some alien life
somewhere that simply lived on and on, but which never varied or
procreated? Would that population not be alive?
That's probably an extreme. Perhaps there is or can be no life like
that. But in this era of exobiology, I think we have to start looking
at how we would determine what was alive on another planet rather than
on our own.
Budikka
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| User: "johac" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
28 Jan 2008 12:50:41 AM |
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In article
<fcce1bbc-5ec8-41d9-95c7-8a6e0dac39c4@e4g2000hsg.googlegroups.com>,
Budikka666 <budikka1@netscape.net> wrote:
On Jan 27, 1:15 am, johac <jhachm...@remove.sbcglobal.net> wrote:
In article <7t6np3p527kmvns19ap0ul7qcds2ule...@4ax.com>,
Apostate <godless.bast...@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 23:25:12 -0800, johac
<jhachm...@remove.sbcglobal.net>
wrote:
In article <io8kp3hf9csjd1jr4dsecakr1ugdabk...@4ax.com>,
Apostate <godless.bast...@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac
<jhachm...@remove.sbcglobal.net>
wrote:
Getting closer to the first to the first totally synthesized cell in
the
lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest
Chemically
Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their
goal
posts,
becoming a lot more detailed in what scientists will 'never succeed in
doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA could
not be synthesized in the lab, or was that some other troll?
Don't remember, but I seem to recall his being among the ones whose
defiant
trump card was that
scientists will never succeed in 'creating life'.
Depends what one calls life. We have synthesized viruses. Cellular life
is the next step and these guys are getting very close.
Time for our friends to move the goal posts again.
--
John #1782
No one can define life! LoL!
I just began reading "Genesis" by Robert Hazen. He begins chapter two
by referring to a "recent origin-of-life text" without identifying
what it was. He remarks that it had an appendix with definitions of
life from 48 different authorities and not one of them matched any
other one!
Good book!
They ranged from Maynard Smith's "any population of entities which has
the properties of multiplication, heredity and variation" to someone
unidentified who said, "life is a flow of energy, matter, and
information".
It seems to me that Maynard Smith was further off base than the second
quote is. I mean, are we to say that someone who lived and died
without having any children was never alive?!
He does speak of populations rather than individuals, though, so I'm
not really being fair to him, but what if there were some alien life
somewhere that simply lived on and on, but which never varied or
procreated? Would that population not be alive?
That's probably an extreme. Perhaps there is or can be no life like
that. But in this era of exobiology, I think we have to start looking
at how we would determine what was alive on another planet rather than
on our own.
I know that is a problem. Something as obvious as life, we all know what
it is, right? But how do we define it. It's not so simple.
Budikka
--
John #1782
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| User: "Budikka666" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
27 Jan 2008 07:50:01 AM |
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On Jan 26, 2:45 pm, Apostate <godless.bast...@yeehaw.org.invalid>
wrote:
On Fri, 25 Jan 2008 23:25:12 -0800, johac <jhachm...@remove.sbcglobal.net> wrote:
In article <io8kp3hf9csjd1jr4dsecakr1ugdabk...@4ax.com>,
Apostate <godless.bast...@yeehaw.org.invalid> wrote:
On Fri, 25 Jan 2008 00:02:01 -0800, johac <jhachm...@remove.sbcglobal.net>
wrote:
Getting closer to the first to the first totally synthesized cell in the
lab. No gods involved.
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically
Defined Structure Synthesized In The Lab
Watch for people like Cudchewer (Codebreaker) to begin moving their goal
posts,
becoming a lot more detailed in what scientists will 'never succeed in
doing'.
Oh, I'm sure they will. Was he the doofus who was arguing that DNA could
not be synthesized in the lab, or was that some other troll?
Don't remember, but I seem to recall his being among the ones whose defiant trump card was that
scientists will never succeed in 'creating life'.
But he and his ilk are talking about creating it from the basic
chemistry, not from synthesizing chunks of known DNA and poking it
into a cell membrane.
The problem is that even if scientists did put a bunch of chemicals
into a test tube and coax the contents into forming a living cell, the
fundie argument is going to be that it was "designed" and "created" by
an intelligence and doesn't "prove evolution" (even though evolution
has nothing to do with abiogeneseis!).
This is remarkable science though. As we learn to create more and
more living things, we're going to learn a lot more about what is and
isn't required in the genome. That in itself will be worth the work.
Budikka
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| User: "Agent Smith" |
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| Title: Re: Scientists Create First Synthetic Bacterial Genome |
26 Jan 2008 08:04:50 PM |
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johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA structure
by synthesizing and assembling the 582,970 base pair genome of a
bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M. genitalium
and beginning work on the minimal genome project. This area of
research, trying to understand the minimal genetic components
necessary to sustain life, began with M. genitalium because it is a
bacterium with the smallest genome that we know of that can be grown
in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name suggests that
it's one of the ones that causes human genital yeast infections. Those
microbes have the unique property that they can change species, from
yeast to bacteria and back again. That is possible because it is a
simpler life form than the traditional prokaryotic bacteria, and is
therefore less reliably differentiated from its sister phylum.
Please note that the article does not state the range of base pair
numbers that occurs throughout the bacterial kingdom, nor does it
specify the mean or median values of that range, nor the number of base
pairs in E. Coli, the most studied bacteria.
Not that this isn't an incredible breakthrough, but I believe that the
task of assembling the first, man-made species of bacteria has yet to be
performed. I would predict that Ventner's next step would be to scale
this process up to a more "useful" species.
As a measure to differentiate the synthetic genome versus the
native genome, the team created üwatermarksý in the synthetic genome.
These are short inserted or substituted sequences that encode
information not typically found in nature.
Since there are four available bases (A, G, T & C) each base pair codes
for two 'bits' of binary data. Thus it would be possible to encode
ASCII data into these watermarks, if desired. Text such as "Copyright
J. Craig Ventner Research Inst." could conceivably be inserted.
.
|
|
|
| User: "Agent Smith" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
29 Jan 2008 06:50:16 PM |
|
|
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote in
news:Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
As a measure to differentiate the synthetic genome versus the
native genome, the team created "watermarks" in the synthetic genome.
These are short inserted or substituted sequences that encode
information not typically found in nature.
Since there are four available bases (A, G, T & C) each base pair
codes for two 'bits' of binary data. Thus it would be possible to
encode ASCII data into these watermarks, if desired. Text such as
"Copyright J. Craig Ventner Research Inst." could conceivably be
inserted.
Please note my comment above anticipated this NY Times article. Once
again, I have successfully predicted the future. I'm so vain I probably
think this song is about me. ;)
http://snipurl.com/1yjwo
Synthetic Genome: Signed, Sealed, Decoded
By ANDREW POLLACK
Published: January 29, 2008
You were expecting poetry, perhaps? The secret messages hidden in J.
Craig Venter’s synthetic bacterial genome have now been revealed. They
are Dr. Venter’s name, and that of his research institute and co-
workers.
Dr. Venter announced last week in the journal Science that his team had
become the first to synthesize the complete DNA of a bacterium. He
revealed that the genome had five “watermarks,” sequences of genetic
code that would spell words using the letters for the amino acids that
would be produced by the DNA.
Wired Science reported Monday that it had ferreted out the messages,
with help from government scientists. One watermark said
“VenterInstitvte,” using the unusual spelling because there is no amino
acid represented by the letter “u.”
The other messages were CraigVenter, HamSmith, GlassandClyde and
CindiandClyde for his co-authors Hamilton O. Smith, Clyde A. Hutchison
III, John I. Glass and Cynthia Andrews-Pfannkoch. A Venter spokeswoman
confirmed them.
In 2003, scientists from Icon Genetics, a German biotechnology company,
engineered the plant Arabidopsis thaliana to contain a line from
Virgil’s “Georgics,” with the meaning “Neither can every soil bear every
fruit.”
.
|
|
|
| User: "johac" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
30 Jan 2008 12:50:38 AM |
|
|
In article <Xns9A34C9CE1155Fagentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote in
news:Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
As a measure to differentiate the synthetic genome versus the
native genome, the team created "watermarks" in the synthetic genome.
These are short inserted or substituted sequences that encode
information not typically found in nature.
Since there are four available bases (A, G, T & C) each base pair
codes for two 'bits' of binary data. Thus it would be possible to
encode ASCII data into these watermarks, if desired. Text such as
"Copyright J. Craig Ventner Research Inst." could conceivably be
inserted.
Please note my comment above anticipated this NY Times article. Once
again, I have successfully predicted the future. I'm so vain I probably
think this song is about me. ;)
http://snipurl.com/1yjwo
Synthetic Genome: Signed, Sealed, Decoded
By ANDREW POLLACK
Published: January 29, 2008
You were expecting poetry, perhaps? The secret messages hidden in J.
Craig Venter’s synthetic bacterial genome have now been revealed. They
are Dr. Venter’s name, and that of his research institute and co-
workers.
Dr. Venter announced last week in the journal Science that his team had
become the first to synthesize the complete DNA of a bacterium. He
revealed that the genome had five “watermarks,” sequences of genetic
code that would spell words using the letters for the amino acids that
would be produced by the DNA.
Wired Science reported Monday that it had ferreted out the messages,
with help from government scientists. One watermark said
“VenterInstitvte,” using the unusual spelling because there is no amino
acid represented by the letter “u.”
The other messages were CraigVenter, HamSmith, GlassandClyde and
CindiandClyde for his co-authors Hamilton O. Smith, Clyde A. Hutchison
III, John I. Glass and Cynthia Andrews-Pfannkoch. A Venter spokeswoman
confirmed them.
In 2003, scientists from Icon Genetics, a German biotechnology company,
engineered the plant Arabidopsis thaliana to contain a line from
Virgil’s “Georgics,” with the meaning “Neither can every soil bear every
fruit.”
Yeah I saw that too! Clever. In the last lab where I worked, we
developed a new peptide synthesizer. To test it, we designed a series of
peptides which using the one letter aa code spelled out our names, the
company name, and several slightly 'naughty' words.
Some have suggested the use of synthetic DNA sequences which could be
attached to various objects to be used as 'barcodes' to detect
unauthorized copying, for instance.
--
John #1782
.
|
|
|
| User: "Agent Smith" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
30 Jan 2008 07:14:32 PM |
|
|
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-61019C.22503829012008@news.giganews.com:
In article <Xns9A34C9CE1155Fagentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote in
news:Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
As a measure to differentiate the synthetic genome versus the
native genome, the team created "watermarks" in the synthetic
genome. These are short inserted or substituted sequences that
encode information not typically found in nature.
Since there are four available bases (A, G, T & C) each base pair
codes for two 'bits' of binary data. Thus it would be possible to
encode ASCII data into these watermarks, if desired. Text such as
"Copyright J. Craig Ventner Research Inst." could conceivably be
inserted.
Please note my comment above anticipated this NY Times article. Once
again, I have successfully predicted the future. I'm so vain I
probably think this song is about me. ;)
http://snipurl.com/1yjwo
Synthetic Genome: Signed, Sealed, Decoded
By ANDREW POLLACK
Published: January 29, 2008
You were expecting poetry, perhaps? The secret messages hidden in J.
Craig Venter’s synthetic bacterial genome have now been revealed.
They are Dr. Venter’s name, and that of his research institute and
co- workers.
Dr. Venter announced last week in the journal Science that his team
had become the first to synthesize the complete DNA of a bacterium.
He revealed that the genome had five “watermarks,” sequences of
genetic code that would spell words using the letters for the amino
acids that would be produced by the DNA.
Wired Science reported Monday that it had ferreted out the messages,
with help from government scientists. One watermark said
“VenterInstitvte,” using the unusual spelling because there is no
amino acid represented by the letter “u.”
The other messages were CraigVenter, HamSmith, GlassandClyde and
CindiandClyde for his co-authors Hamilton O. Smith, Clyde A.
Hutchison III, John I. Glass and Cynthia Andrews-Pfannkoch. A Venter
spokeswoman confirmed them.
In 2003, scientists from Icon Genetics, a German biotechnology
company, engineered the plant Arabidopsis thaliana to contain a line
from Virgil’s “Georgics,” with the meaning “Neither can every soil
bear every fruit.”
Yeah I saw that too! Clever. In the last lab where I worked, we
developed a new peptide synthesizer. To test it, we designed a series
of peptides which using the one letter aa code spelled out our names,
the company name, and several slightly 'naughty' words.
Some have suggested the use of synthetic DNA sequences which could be
attached to various objects to be used as 'barcodes' to detect
unauthorized copying, for instance.
That should turn out to be a little more secure than proposed techniques
for preventing copying of digital music files.
.
|
|
|
| User: "johac" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
30 Jan 2008 11:55:40 PM |
|
|
In article <Xns9A35CDEC766A0agentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-61019C.22503829012008@news.giganews.com:
In article <Xns9A34C9CE1155Fagentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote in
news:Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
As a measure to differentiate the synthetic genome versus the
native genome, the team created "watermarks" in the synthetic
genome. These are short inserted or substituted sequences that
encode information not typically found in nature.
Since there are four available bases (A, G, T & C) each base pair
codes for two 'bits' of binary data. Thus it would be possible to
encode ASCII data into these watermarks, if desired. Text such as
"Copyright J. Craig Ventner Research Inst." could conceivably be
inserted.
Please note my comment above anticipated this NY Times article. Once
again, I have successfully predicted the future. I'm so vain I
probably think this song is about me. ;)
http://snipurl.com/1yjwo
Synthetic Genome: Signed, Sealed, Decoded
By ANDREW POLLACK
Published: January 29, 2008
You were expecting poetry, perhaps? The secret messages hidden in J.
Craig Venter’s synthetic bacterial genome have now been revealed.
They are Dr. Venter’s name, and that of his research institute and
co- workers.
Dr. Venter announced last week in the journal Science that his team
had become the first to synthesize the complete DNA of a bacterium.
He revealed that the genome had five “watermarks,” sequences of
genetic code that would spell words using the letters for the amino
acids that would be produced by the DNA.
Wired Science reported Monday that it had ferreted out the messages,
with help from government scientists. One watermark said
“VenterInstitvte,” using the unusual spelling because there is no
amino acid represented by the letter “u.”
The other messages were CraigVenter, HamSmith, GlassandClyde and
CindiandClyde for his co-authors Hamilton O. Smith, Clyde A.
Hutchison III, John I. Glass and Cynthia Andrews-Pfannkoch. A Venter
spokeswoman confirmed them.
In 2003, scientists from Icon Genetics, a German biotechnology
company, engineered the plant Arabidopsis thaliana to contain a line
from Virgil’s “Georgics,” with the meaning “Neither can every soil
bear every fruit.”
Yeah I saw that too! Clever. In the last lab where I worked, we
developed a new peptide synthesizer. To test it, we designed a series
of peptides which using the one letter aa code spelled out our names,
the company name, and several slightly 'naughty' words.
Some have suggested the use of synthetic DNA sequences which could be
attached to various objects to be used as 'barcodes' to detect
unauthorized copying, for instance.
That should turn out to be a little more secure than proposed techniques
for preventing copying of digital music files.
Indeed.
--
John #1782
.
|
|
|
|
|
|
|
| User: "johac" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
27 Jan 2008 01:13:11 AM |
|
|
In article <Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA structure
by synthesizing and assembling the 582,970 base pair genome of a
bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M. genitalium
and beginning work on the minimal genome project. This area of
research, trying to understand the minimal genetic components
necessary to sustain life, began with M. genitalium because it is a
bacterium with the smallest genome that we know of that can be grown
in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name suggests that
it's one of the ones that causes human genital yeast infections. Those
microbes have the unique property that they can change species, from
yeast to bacteria and back again. That is possible because it is a
simpler life form than the traditional prokaryotic bacteria, and is
therefore less reliably differentiated from its sister phylum.
They used a yeast to assemble the M. genitalium genome. The goal, as I
understood it, is to eventually put it back into M. genitalium which is
a bacterium.
Please note that the article does not state the range of base pair
numbers that occurs throughout the bacterial kingdom, nor does it
specify the mean or median values of that range, nor the number of base
pairs in E. Coli, the most studied bacteria.
M. genitalium is a very primitive bacterium compare to E. coli. That is
why it is the subject of this study. Ventner also wants to see what are
the minimum genetic requirements for life.
Not that this isn't an incredible breakthrough, but I believe that the
task of assembling the first, man-made species of bacteria has yet to be
performed. I would predict that Ventner's next step would be to scale
this process up to a more "useful" species.
As a measure to differentiate the synthetic genome versus the
native genome, the team created üwatermarksý in the synthetic genome.
These are short inserted or substituted sequences that encode
information not typically found in nature.
Since there are four available bases (A, G, T & C) each base pair codes
for two 'bits' of binary data. Thus it would be possible to encode
ASCII data into these watermarks, if desired. Text such as "Copyright
J. Craig Ventner Research Inst." could conceivably be inserted.
Yes. The idea of using DNA for barcoding has been around for some time:
http://www.medicalnewstoday.com/articles/26061.php
--
John #1782
.
|
|
|
| User: "Agent Smith" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
27 Jan 2008 06:20:52 AM |
|
|
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article <Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA
structure by synthesizing and assembling the 582,970 base pair
genome of a bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome project. This
area of research, trying to understand the minimal genetic
components necessary to sustain life, began with M. genitalium
because it is a bacterium with the smallest genome that we know of
that can be grown in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name suggests
that it's one of the ones that causes human genital yeast infections.
Those microbes have the unique property that they can change
species, from yeast to bacteria and back again. That is possible
because it is a simpler life form than the traditional prokaryotic
bacteria, and is therefore less reliably differentiated from its
sister phylum.
They used a yeast to assemble the M. genitalium genome. The goal, as I
understood it, is to eventually put it back into M. genitalium which
is a bacterium.
Please note that the article does not state the range of base pair
numbers that occurs throughout the bacterial kingdom, nor does it
specify the mean or median values of that range, nor the number of
base pairs in E. Coli, the most studied bacteria.
M. genitalium is a very primitive bacterium compare to E. coli.
Mycoplasma are yeasts. Myco = yeast.
That
is why it is the subject of this study. Ventner also wants to see what
are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for whatever
industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which is almost
10x larger than Ventner's mycoplasma. Also, please note another mistake
in the article was its refernces to the "chromosome" in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of base pairs,
neither can yeasts.
.
|
|
|
| User: "johac" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
28 Jan 2008 12:46:18 AM |
|
|
In article <Xns9A324AC545CB3agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article <Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA
structure by synthesizing and assembling the 582,970 base pair
genome of a bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome project. This
area of research, trying to understand the minimal genetic
components necessary to sustain life, began with M. genitalium
because it is a bacterium with the smallest genome that we know of
that can be grown in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name suggests
that it's one of the ones that causes human genital yeast infections.
Those microbes have the unique property that they can change
species, from yeast to bacteria and back again. That is possible
because it is a simpler life form than the traditional prokaryotic
bacteria, and is therefore less reliably differentiated from its
sister phylum.
They used a yeast to assemble the M. genitalium genome. The goal, as I
understood it, is to eventually put it back into M. genitalium which
is a bacterium.
Please note that the article does not state the range of base pair
numbers that occurs throughout the bacterial kingdom, nor does it
specify the mean or median values of that range, nor the number of
base pairs in E. Coli, the most studied bacteria.
M. genitalium is a very primitive bacterium compare to E. coli.
Mycoplasma are yeasts. Myco = yeast.
Sorry, it's a bacterium:
http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gmg
(Note "Kingdom")
from:
http://en.wikipedia.org/wiki/Mycoplasma_genitalium
That
is why it is the subject of this study. Ventner also wants to see what
are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for whatever
industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which is almost
10x larger than Ventner's mycoplasma. Also, please note another mistake
in the article was its refernces to the "chromosome" in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of base pairs,
neither can yeasts.
I would recommend that you read the full article when published. If you
have a subscription to Science you can read it here:
http://www.sciencemag.org/cgi/content/abstract/1151721
If not it should be out soon and available in your library.
--
John #1782
.
|
|
|
| User: "Agent Smith" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
30 Jan 2008 10:40:59 AM |
|
|
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-D98541.22461827012008@news.giganews.com:
In article <Xns9A324AC545CB3agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article <Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA
structure by synthesizing and assembling the 582,970 base pair
genome of a bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome project.
This area of research, trying to understand the minimal genetic
components necessary to sustain life, began with M. genitalium
because it is a bacterium with the smallest genome that we know
of that can be grown in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name
suggests that it's one of the ones that causes human genital yeast
infections.
Those microbes have the unique property that they can change
species, from yeast to bacteria and back again. That is possible
because it is a simpler life form than the traditional prokaryotic
bacteria, and is therefore less reliably differentiated from its
sister phylum.
They used a yeast to assemble the M. genitalium genome. The goal,
as I understood it, is to eventually put it back into M. genitalium
which is a bacterium.
Please note that the article does not state the range of base pair
numbers that occurs throughout the bacterial kingdom, nor does it
specify the mean or median values of that range, nor the number of
base pairs in E. Coli, the most studied bacteria.
M. genitalium is a very primitive bacterium compare to E. coli.
Mycoplasma are yeasts. Myco = yeast.
Sorry, it's a bacterium:
http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gmg
(Note "Kingdom")
from:
http://en.wikipedia.org/wiki/Mycoplasma_genitalium
That
is why it is the subject of this study. Ventner also wants to see
what are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for whatever
industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which is
almost 10x larger than Ventner's mycoplasma. Also, please note
another mistake in the article was its refernces to the "chromosome"
in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of base
pairs, neither can yeasts.
I would recommend that you read the full article when published. If
you have a subscription to Science you can read it here:
http://www.sciencemag.org/cgi/content/abstract/1151721
If not it should be out soon and available in your library.
When the article is printed, why don't you post it here, for physicists
like me, who don't buy the magazine, because it's all biology and
medicine?
.
|
|
|
| User: "johac" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
31 Jan 2008 12:01:25 AM |
|
|
In article <Xns9A3576DB15FF1agentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-D98541.22461827012008@news.giganews.com:
In article <Xns9A324AC545CB3agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article <Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA
structure by synthesizing and assembling the 582,970 base pair
genome of a bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome project.
This area of research, trying to understand the minimal genetic
components necessary to sustain life, began with M. genitalium
because it is a bacterium with the smallest genome that we know
of that can be grown in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name
suggests that it's one of the ones that causes human genital yeast
infections.
Those microbes have the unique property that they can change
species, from yeast to bacteria and back again. That is possible
because it is a simpler life form than the traditional prokaryotic
bacteria, and is therefore less reliably differentiated from its
sister phylum.
They used a yeast to assemble the M. genitalium genome. The goal,
as I understood it, is to eventually put it back into M. genitalium
which is a bacterium.
Please note that the article does not state the range of base pair
numbers that occurs throughout the bacterial kingdom, nor does it
specify the mean or median values of that range, nor the number of
base pairs in E. Coli, the most studied bacteria.
M. genitalium is a very primitive bacterium compare to E. coli.
Mycoplasma are yeasts. Myco = yeast.
Sorry, it's a bacterium:
http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gmg
(Note "Kingdom")
from:
http://en.wikipedia.org/wiki/Mycoplasma_genitalium
That
is why it is the subject of this study. Ventner also wants to see
what are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for whatever
industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which is
almost 10x larger than Ventner's mycoplasma. Also, please note
another mistake in the article was its refernces to the "chromosome"
in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of base
pairs, neither can yeasts.
I would recommend that you read the full article when published. If
you have a subscription to Science you can read it here:
http://www.sciencemag.org/cgi/content/abstract/1151721
If not it should be out soon and available in your library.
When the article is printed, why don't you post it here, for physicists
like me, who don't buy the magazine, because it's all biology and
medicine?
Science has many physics articles too. I didn't post it because it is by
subscription only. I don't think it is fair to those who subscribe to
the journal. You can purchase the article on line for $10, if you wish.
It should be eventually available in libraries.
--
John #1782
.
|
|
|
| User: "Agent Smith" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
31 Jan 2008 09:04:08 AM |
|
|
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-F2D223.22012530012008@news.giganews.com:
In article <Xns9A3576DB15FF1agentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-D98541.22461827012008@news.giganews.com:
In article <Xns9A324AC545CB3agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article
<Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA
structure by synthesizing and assembling the 582,970 base
pair genome of a bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome project.
This area of research, trying to understand the minimal
genetic components necessary to sustain life, began with M.
genitalium because it is a bacterium with the smallest genome
that we know of that can be grown in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name
suggests that it's one of the ones that causes human genital
yeast infections.
Those microbes have the unique property that they can change
species, from yeast to bacteria and back again. That is
possible because it is a simpler life form than the traditional
prokaryotic bacteria, and is therefore less reliably
differentiated from its sister phylum.
They used a yeast to assemble the M. genitalium genome. The
goal, as I understood it, is to eventually put it back into M.
genitalium which is a bacterium.
Please note that the article does not state the range of base
pair numbers that occurs throughout the bacterial kingdom, nor
does it specify the mean or median values of that range, nor
the number of base pairs in E. Coli, the most studied bacteria.
M. genitalium is a very primitive bacterium compare to E. coli.
Mycoplasma are yeasts. Myco = yeast.
Sorry, it's a bacterium:
http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gmg
(Note "Kingdom")
from:
http://en.wikipedia.org/wiki/Mycoplasma_genitalium
That
is why it is the subject of this study. Ventner also wants to
see what are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for whatever
industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which is
almost 10x larger than Ventner's mycoplasma. Also, please note
another mistake in the article was its refernces to the
"chromosome" in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of base
pairs, neither can yeasts.
I would recommend that you read the full article when published. If
you have a subscription to Science you can read it here:
http://www.sciencemag.org/cgi/content/abstract/1151721
If not it should be out soon and available in your library.
When the article is printed, why don't you post it here, for
physicists like me, who don't buy the magazine, because it's all
biology and medicine?
Science has many physics articles too.
None that ever caught my eye, and I was a member for a year or two. In
fact, it's a reasearch journal, and the only reason I can imagine buying
would be to have the privilege of putting it onto my resume.
I didn't post it because it is by subscription only.
Information wants to be free.
I don't think it is fair to those who subscribe to
the journal. You can purchase the article on line for $10, if you
wish.
I'm not coughing up $10 for something that will almost certainly still
be boring and unintelligible.
It should be eventually available in libraries.
Arthritis limits my mobility.
.
|
|
|
| User: "johac" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
01 Feb 2008 12:44:33 AM |
|
|
In article <Xns9A36667055708agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-F2D223.22012530012008@news.giganews.com:
In article <Xns9A3576DB15FF1agentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-D98541.22461827012008@news.giganews.com:
In article <Xns9A324AC545CB3agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article
<Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made DNA
structure by synthesizing and assembling the 582,970 base
pair genome of a bacterium, Mycoplasma genitalium JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome project.
This area of research, trying to understand the minimal
genetic components necessary to sustain life, began with M.
genitalium because it is a bacterium with the smallest genome
that we know of that can be grown in pure culture.
This isn't strictly a bacteria, but a yeast, and it's name
suggests that it's one of the ones that causes human genital
yeast infections.
Those microbes have the unique property that they can change
species, from yeast to bacteria and back again. That is
possible because it is a simpler life form than the traditional
prokaryotic bacteria, and is therefore less reliably
differentiated from its sister phylum.
They used a yeast to assemble the M. genitalium genome. The
goal, as I understood it, is to eventually put it back into M.
genitalium which is a bacterium.
Please note that the article does not state the range of base
pair numbers that occurs throughout the bacterial kingdom, nor
does it specify the mean or median values of that range, nor
the number of base pairs in E. Coli, the most studied bacteria.
M. genitalium is a very primitive bacterium compare to E. coli.
Mycoplasma are yeasts. Myco = yeast.
Sorry, it's a bacterium:
http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gmg
(Note "Kingdom")
from:
http://en.wikipedia.org/wiki/Mycoplasma_genitalium
That
is why it is the subject of this study. Ventner also wants to
see what are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for whatever
industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which is
almost 10x larger than Ventner's mycoplasma. Also, please note
another mistake in the article was its refernces to the
"chromosome" in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of base
pairs, neither can yeasts.
I would recommend that you read the full article when published. If
you have a subscription to Science you can read it here:
http://www.sciencemag.org/cgi/content/abstract/1151721
If not it should be out soon and available in your library.
When the article is printed, why don't you post it here, for
physicists like me, who don't buy the magazine, because it's all
biology and medicine?
Science has many physics articles too.
None that ever caught my eye, and I was a member for a year or two. In
fact, it's a reasearch journal, and the only reason I can imagine buying
would be to have the privilege of putting it onto my resume.
It is an interesting journal. I've been a member of AAAS for over 40
years and I still read it. There are many interesting articles,
sometimes on politics and policy if not science.
I didn't post it because it is by subscription only.
Information wants to be free.
The other consideration is that the article is 13 pages long, which is a
little long for a usenet post. Lot's of graphics too.
I don't think it is fair to those who subscribe to
the journal. You can purchase the article on line for $10, if you
wish.
I'm not coughing up $10 for something that will almost certainly still
be boring and unintelligible.
It should be eventually available in libraries.
Arthritis limits my mobility.
Sorry to hear that.
--
John #1782
.
|
|
|
| User: "Agent Smith" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
01 Feb 2008 05:09:06 PM |
|
|
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-1FFC67.22443331012008@news.giganews.com:
In article <Xns9A36667055708agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-F2D223.22012530012008@news.giganews.com:
In article <Xns9A3576DB15FF1agentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-D98541.22461827012008@news.giganews.com:
In article
<Xns9A324AC545CB3agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article
<Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made
DNA structure by synthesizing and assembling the 582,970
base pair genome of a bacterium, Mycoplasma genitalium
JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome
project. This area of research, trying to understand the
minimal genetic components necessary to sustain life,
began with M. genitalium because it is a bacterium with
the smallest genome that we know of that can be grown in
pure culture.
This isn't strictly a bacteria, but a yeast, and it's name
suggests that it's one of the ones that causes human genital
yeast infections.
Those microbes have the unique property that they can
change
species, from yeast to bacteria and back again. That is
possible because it is a simpler life form than the
traditional prokaryotic bacteria, and is therefore less
reliably differentiated from its sister phylum.
They used a yeast to assemble the M. genitalium genome. The
goal, as I understood it, is to eventually put it back into
M. genitalium which is a bacterium.
Please note that the article does not state the range of
base pair numbers that occurs throughout the bacterial
kingdom, nor does it specify the mean or median values of
that range, nor the number of base pairs in E. Coli, the
most studied bacteria.
M. genitalium is a very primitive bacterium compare to E.
coli.
Mycoplasma are yeasts. Myco = yeast.
Sorry, it's a bacterium:
http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gmg
(Note "Kingdom")
from:
http://en.wikipedia.org/wiki/Mycoplasma_genitalium
That
is why it is the subject of this study. Ventner also wants to
see what are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for
whatever industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which
is almost 10x larger than Ventner's mycoplasma. Also, please
note another mistake in the article was its refernces to the
"chromosome" in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of
base pairs, neither can yeasts.
I would recommend that you read the full article when published.
If you have a subscription to Science you can read it here:
http://www.sciencemag.org/cgi/content/abstract/1151721
If not it should be out soon and available in your library.
When the article is printed, why don't you post it here, for
physicists like me, who don't buy the magazine, because it's all
biology and medicine?
Science has many physics articles too.
None that ever caught my eye, and I was a member for a year or two.
In fact, it's a reasearch journal, and the only reason I can imagine
buying would be to have the privilege of putting it onto my resume.
It is an interesting journal. I've been a member of AAAS for over 40
years and I still read it. There are many interesting articles,
sometimes on politics and policy if not science.
When I was a member, I always managed to find one or two news stories
worth reading every month, but nothing that could justify the $100 a
year, especially since I was a poor grad student at the time. Of
course, having the AAAS on your resume looks really good, but still not
$100 a year good, and that went out the window when I was invited into
the NY State Academy of Science, anyhow. My goal is to get into the
national academy before I die, but they're so prestigious that they'll
probably want $500 a year. Anyhow, it almost certainly won't matter,
because I have like a snowball's chance in Dante's Inferno of pulling
that off. ;(
I didn't post it because it is by subscription only.
Information wants to be free.
The other consideration is that the article is 13 pages long, which is
a little long for a usenet post. Lot's of graphics too.
Depending on whether it's pdf or html, I guess that you could always
post it to a binary group, but you've already made it clear that you're
not into that, and if I needed it that badly, I'd find a way to get to
the library, anyhow.
I guess the impediment to making articles like this public is the
question, if you're going to risk your neck, by taking a chance on
getting your subscription cancelled, what's in it for you, to make it
worth that risk? That would rather presume a group of "black hat
scientists" who would each hack a pay journal that they own, and post
the article to the internet.
Except for computer science, where hacking has always been a badge of
honor, I don't think that sort of risky behavior would be typical of
people who go into science. However, there is a new business model
making its advent, giving away for free what was previously extremely
expensive. Here are some practitioners (http://www.iop.org/EJ/) who
participate in that business model.
Personally, I think that's the way it think it should be done, and it
will open the door to amateurs getting real science done, rather than
just playing at it. Of course it raises the question of how they'll
stay in business, so it remains to be seen whether this business model
will survive. But it certainly goes a *long* way to building customer
loyalty, which is something some formerly big businesses, notably ebay
and microsoft, seem to have never understood is infinitely more precious
than money. :p
I don't think it is fair to those who subscribe to
the journal. You can purchase the article on line for $10, if you
wish.
I'm not coughing up $10 for something that will almost certainly
still be boring and unintelligible.
It should be eventually available in libraries.
Arthritis limits my mobility.
Sorry to hear that.
Someday I hope to find a nice person willing to mail me photocopies, or
email me scans, but again, this article is nothing that I specifically
need for my research work. I have a backlog of articles in mathematical
physics, and I should be able to pay copying and mailing fees with
paypal, but of course, there's the problem of never knowing whether you
need something until you've seen it. Copying articles from
bibliographies can very quickly produce thick stacks of paper. :p
.
|
|
|
| User: "johac" |
|
| Title: Re: Scientists Create First Synthetic Bacterial Genome |
02 Feb 2008 02:23:16 AM |
|
|
In article <Xns9A37B8AAE1E28agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-1FFC67.22443331012008@news.giganews.com:
In article <Xns9A36667055708agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-F2D223.22012530012008@news.giganews.com:
In article <Xns9A3576DB15FF1agentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-D98541.22461827012008@news.giganews.com:
In article
<Xns9A324AC545CB3agentsmithtwoblockso@207.115.33.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-5012A2.23131126012008@news.giganews.com:
In article
<Xns9A31D676F3ECDagentsmithtwoblockso@207.115.17.102>,
Agent Smith <agent-smith@two-blocks-on-your-left.com> wrote:
johac <jhachmann@remove.sbcglobal.net> wrote in
news:jhachmann-DD8FDB.00020125012008@news.giganews.com:
A team of 17 researchers at the J. Craig
Venter Institute (JCVI) has created the largest man-made
DNA structure by synthesizing and assembling the 582,970
base pair genome of a bacterium, Mycoplasma genitalium
JCVI-1.0.
[snip]
Venter and colleagues in the mid-1990s after sequencing M.
genitalium and beginning work on the minimal genome
project. This area of research, trying to understand the
minimal genetic components necessary to sustain life,
began with M. genitalium because it is a bacterium with
the smallest genome that we know of that can be grown in
pure culture.
This isn't strictly a bacteria, but a yeast, and it's name
suggests that it's one of the ones that causes human genital
yeast infections.
Those microbes have the unique property that they can
change
species, from yeast to bacteria and back again. That is
possible because it is a simpler life form than the
traditional prokaryotic bacteria, and is therefore less
reliably differentiated from its sister phylum.
They used a yeast to assemble the M. genitalium genome. The
goal, as I understood it, is to eventually put it back into
M. genitalium which is a bacterium.
Please note that the article does not state the range of
base pair numbers that occurs throughout the bacterial
kingdom, nor does it specify the mean or median values of
that range, nor the number of base pairs in E. Coli, the
most studied bacteria.
M. genitalium is a very primitive bacterium compare to E.
coli.
Mycoplasma are yeasts. Myco = yeast.
Sorry, it's a bacterium:
http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gmg
(Note "Kingdom")
from:
http://en.wikipedia.org/wiki/Mycoplasma_genitalium
That
is why it is the subject of this study. Ventner also wants to
see what are the minimum genetic requirements for life.
Of course he does. Nobody is saying it in print, but this is a
milestone on the way to assembling *real* bacteria, for
whatever industrial or medical purpose scientists can invent.
I looked up e.coli, and it has four million base pairs, which
is almost 10x larger than Ventner's mycoplasma. Also, please
note another mistake in the article was its refernces to the
"chromosome" in m. genitalium.
Bacteria don't have chromosomes, and with 1/10 the number of
base pairs, neither can yeasts.
I would recommend that you read the full article when published.
If you have a subscription to Science you can read it here:
http://www.sciencemag.org/cgi/content/abstract/1151721
If not it should be out soon and available in your library.
When the article is printed, why don't you post it here, for
physicists like me, who don't buy the magazine, because it's all
biology and medicine?
Science has many physics articles too.
None that ever caught my eye, and I was a member for a year or two.
In fact, it's a reasearch journal, and the only reason I can imagine
buying would be to have the privilege of putting it onto my resume.
It is an interesting journal. I've been a member of AAAS for over 40
years and I still read it. There are many i | | | | | | | | | | |
