Thursday, February 09, 2012

Synthetic life

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Synthetic_lifeHas man finally crossed the line of playing God?

Does the announcement of the successful synthetic creation of a living cell represent “the quintessential Pandora’s box moment - like the splitting of the atom or the cloning of Dolly the sheep,” a turning point in the history of our species and our planet in our fight against climate by 'growing' cleaner biofuels  and feeding the globe’s ever expanding population? Or does it represent the point at which man finally crosses the line of playing God?

News broke last week in a paper published in Science, that controversial scientist and entrepreneur Dr J. Craig Venter and his team at the JC Venter Institute (JCVI) in Rocville, Maryland, USA has succeeded in the creation of a cell controlled by a synthetic genome. In a convergence of biotechnology and computer science, “a code generated within a digital computer is now self-replicating as the genome of a line of living cells. From the point of view of biology, a code generated by a living organism has been translated into a digital representation for replication, editing, and transmission to other cells," according to science historian, George Dyson.

The article in Science suggests that  synthetic biology could help clean up the environment, save humanity from climate change, and address the food crisis.

While the computer-generated DNA was inserted into the microplasma of an “emptied” living bacterial cell, it cannot be said that there was the de novo “creation of life". A new line of cells was generated. This is new life that is self-propagating i.e. "the cells with only the synthetic genome are self-replicating and capable of logarithmic growth."

In the words of Venter himself, at a news conference introducing the paper, it represents "the first self-replicating species we've had on the planet whose parent is a computer."

Physicist Freeman Dyson, commenting on the paper, said that "the sequencing and synthesising (of) DNA give us all the tools we need to create new forms of life".

He added, "But it remains to be seen how it will serve in practice. I feel sure of only one conclusion. The ability to design and create new forms of life marks a turning point in the history of our species and our planet.”

The magnitude of the ethical, moral, security and religious implications of the development was (perhaps not deliberately) implied by  Venter when he said "this is a philosophical advance as much as a technical advance." This suggests that the "synthetic cell" raises new questions about the nature of life.

This is "a defining moment in the history of biology and biotechnology," said Mark Bedau, a philosopher at Reed College in Portland, Oregon, and editor of Artificial Life.

The Canadian-based ETC Group, which has been monitoring developments in synthetic biology for the past five years and has pioneered civil society activism around the field, said in its reaction: "This is the quintessential Pandora’s box moment - like the splitting of the atom or the cloning of Dolly the sheep. We will all have to deal with the fallout from this alarming experiment."

The Group said that this will “stir a firestorm of controversy over the ethics of building artificial life and the implications of the largely unknown field of synthetic biology.”

It added that instead of being a one-stop shop for all our societal woes, “It is much more likely to cause a whole new set of problems that governments and society are ill-prepared to address."

ETC further claims that "synthetic biology is a high-risk, profit-driven field, building organisms out of parts that are still poorly understood. We know that lab-created life forms can escape, become biological weapons, and that their use threatens existing natural biodiversity.

"Most worrying of all, Craig Venter is handing this powerful technology to the world’s most irresponsible and environmentally damaging industry by partnering with the likes of BP and Exxon to hasten the commercialisation of synthetic life forms."

In 2006, ETC Group joined with other organisations to demand the formal, open and inclusive oversight of synthetic biology and has since called for a global halt on research pending the development of global regulations. The Group reiterated that call at a scientific meeting of the United Nations Convention on Biological Diversity (CBD) in Nairobi, attended by more than 100 governments.
ETC said in a statement that “the lack of global rules governing the field also concerns many governments, illustrated by the biodiversity talks in Nairobi."

Mundita Lim of the Philippines delegation to the CBD expressed her country’s concerns "about the serious potential impacts of synthetic biology on biodiversity... we believe that there should be no field release of synthetic life, cell or genome into the environment until thorough scientific assessments have been conducted in a transparent, open and participatory process involving all parties, indigenous and local communities that will all be potentially affected by these synthetic life forms with unknown consequences on biodiversity, the environment and livelihoods.

"Today’s announcement will give new urgency to the debate on synthetic biology and provides a dramatic example of the need for rigorous oversight over new technologies before their environmental or commercial release is permitted.”

There are also those who are expressing the fear that the new technology could be used to develop new biological weapons.

From Rome, it is reported that Catholic religious leaders have expressed fears that scientists are "playing God".

"It is human nature which gives its dignity to the human genome, not the inverse. The nightmare to be fought is the manipulation of life," said Bishop Domenico Mogavero, head of the legal affairs commission for the Italian Episcopal Conference, in an interview with La Stampa daily.

In South Africa, Professor Henk Huismans of the University of Pretoria’s Department of Genetics, according to a report in Die Burger, warned that people should not allow their imagination to run away with them. “New life has not suddenly been created. Life was only successfully copied.”

The start of the new synthetic cell is not a test tube, but a living cell from which the original DNA has been removed and replaced with synthetic DNA, which was copied from another cell. It has, however, important implications because “cells could be generated which were designed for the performance of specific functions," said Prof. Huismans.

“With synthetic cells, you can design cells which are functionally completely differently directed as the cells you now find in nature.”

There are ethical implications, but these are not necessarily more fundamental as when people for the first time started with the manipulation of cells, he added.

Comments (5)
  • Professor Pranab Kumar BHattac  - Synthetic DNA and artificial cell – what are the e
    Authors
    o*Professor Pranab Kumar Bhattacharya MD(cal) FIC path(Ind), Additional Professor Dept of pathology
    oRupak Bhattacharya Bsc(cal)MSc(JU), Ritwik Bhattacharya B****(cal), Somayak Bhattacharya MBA 7/51 Purbapalli,Sodepur, Kol-110, Miss Upasana Bhattacharya – daughter of Prof PK Bhattacharya Dr. Avisnata Das MBBs(cal) Dalia Mukherjee BA(hons) cal Miss Oindrila Mukherjee, Mrs Chandrani Dutta BSC(Zoology)* Dr Hriday Das MD(cal) DTM&H(cal) *Dr Tarun Biswas MBBS(cal) Dept of Pathology
    *Institute of Post Graduate Medical Education Research 244a AJC Bose Road kol-20 West Bengal, India
    Artificial life is a field of study and an associated art form which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. There are three main kinds of artificial life named for their approaches: soft from software; hard , from hardware; and wet, from biochemistry molecules. Artificial life imitates traditional biology by trying to recreate biological phenomena. Artificial life has had a controversial history. John Maynard Smith[11] criticized certain artificial life work in 1994 as "fact-free science". However, the recent publication of artificial life articles in widely read world’s top impact factor and coveted science journals such as Science and Nature is evident that artificial life techniques are becoming more accepted in the mainstream-as synthetic biology, at least as a method of studying Darwin’s Chemical evolution. Synthetic and self replicating DNA or RNA is part of such an artificial life and tool for studying evolution of life in earth. Evolving such an artificial DNA in laboratory was thus for long years before attempt of research since Watson and Crick Double Helix. The artificial DNA-like molecule directed the synthesis of copies of itself and then copies of the copies, mimicking the natural process of evolution as it was first outlined by Charles Darwin. A nucleotide is a building block of DNA, or a "letter" in the genetic alphabet used to write the "book" describing our genetic inheritance. The first Synthetic Virus was done in 2002 in stony brook university New york by a team of scientist led by Eckarde wimmr (Science, 9 August 2002, p. 1016) Benner and Michael Sismour- two Graduate astudent of university of California in 2004 first made a synthetic DNA of 12 nucleotides of a virus but it could not however copied itself. In 2010, The first synthetic and self replicating DNA /cell as a bacterium has been claimed by Professor Dr C J Venter of J. Craig Venter Institute (JCVI) in Rockville, Maryland, and San Diego, California, [ He was best known for his work with the Human Genome Project] is successful and same is published in journal the science [1]. The cell is claimed totally derived from a synthetic chromosome [They bought it from a company more than 1000 -1080-base sequences that covered the whole M. mycoides genome], made with four bottles of chemicals on a chemical synthesizer, starting with information and using genetic code created by a super computer. The Venter’s team [20 members team] synthesized the largest piece of DNA so far — a million units in length — and in making it accurate enough to substitute for the cell’s own DNA at cost of $40 million research. Venter's team said they worked with a synthetic version of the DNA from a small bacterium called Mycoplasma mycoides which was transplanted into another bacterium called Mycoplasma capricolum, which had most of its insides DNA removed. The new microbe came to life and began replicating in the lab dish. Specifically, the team showed that the artificially created DNA-like molecule containing six gene-building nucleotides - instead of the four found in natural DNA - could support the molecular "photocopying" operation known as polymerase chain reaction. The genome Dr. Venter synthesized is copied from a natural bacterium that infects goats. 580,000 DNA units in length, of a small bacterium, Mycoplasma genitalium. His goal however was to make cells that might take carbon dioxide out of the atmosphere and produce methaneose .”
    Replacing the genome of any bacterial cell with one from another species by transplanting a whole genome as naked DNA is however a long known method as gene cloning[3] / and or gene transfer mechanism called genome transplant. Gene cloning will result a new species[2] De novo synthesis of a self replicating bacterial or human DNA is here an increasingly valuable resource for a broad research and future application. Synthesis of Gene /DNA is also not new but an old concept. Synthesis of gene length (1-3Kb) DNA is however very common[5]. The Process of Synthetic DNA construction involves the assembly of Overlapping Oligonucleotides into contiguous fragments of dsDNA using PCR based and or ligation based methods[4 ,5] or by Pair wise Selection assembly(PSA) methods for large scale long length ...
  • Professor Pranab Kumar Bhattac  - Synthetic DNA and artificial cell – what are the e
    continued from last post-
    long length automated synthetic DNA production more then 91Kb DNA[6], where A target assembly sequence is broken down into sub-fragments that are synthesized with flanking tags .At PSA level 0, sub-fragments are inserted into one of two PSA vectors where tags activate two, divergently oriented selectable markers . Level 0 sub-fragment pairs are excised so that only one activation tag is retained for each sub-fragment. Subsequent pair ligation occurs in a second PSA vector where tags activate a second set of selectable markers , producing a PSA level 1 product. This hierarchical process is repeated, switching between two vectors with different selectable markers, until the full-length product is assembled[6].
    Recently, recombination-based methods were also used range of applications to construct a 134-kb fragment in Bacillus subtilis and 583- Kb fragment of Saccharomyces cerevisiae Synthetic DNA (7,8 ). While synthesis of gene-length DNA (1–3 kb) is common, the ability to quickly and cost-effectively assemble longer-length DNA (>10 kb) remained of course a challenge. 256 orthologous genes shared by the Gram-negative Haemophilus influenzae and the Gram-positive bacterial life Mycoplasma genitalium genomes are a close approximation of a minimal gene set . The Mollicutes, generically known as the mycoplasmas, are the best experimental platform for experimentally defining a minimal gene set. Mycoplasmas are obligate parasites that live in relatively unchanging niches requiring little adaptive capability. M. genitalium, a human urogenital pathogen, is the extreme manifestation of this genomic parsimony, having only 482 protein-coding genes and the smallest genome, at 580 kb, of any known free-living organism capable of being grown in axenic culture[9] Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. To construct synthetic DNA of Mycoplasma genetelium it is always very essential to identify and delete all the putative non essential gene, isolation and characterization of trasposon mutants and mixture of mutant genes but preservation and non-disruptions of DNA recombination & six DNA repair gene like recA,recU, DNA hellicase genel ike ruvA, ruvB DNA Glycosylase gene muteM which excises oxidized purine from DNA and DNA damage inducible gene[10]
    In 1995, a team led by the trio Venter, Smith and Hutchison sequenced the 600,000-base chromosome of bacterium Mycoplasma genitalium, the smallest genome of a free-living organism. The microbe has about 500 genes, and researchers found they could delete 100 individual genes without ill effect (Science, 14 February 2003, p. 1006) In 2007, Venter, Smith, Hutchison, and colleagues finally demonstrated that they could transplant natural chromosomes from one microbial species to another (Science, 3 August 2007, p. 632). By 2008, they showed that they could make an artificial chromosome that matched M. genitalium's but also contained "watermark" DNA sequences that would enable them to tell the synthetic genome from the natural one (Science, 29 February 2008, p. 1215) The first Synthetic Virus was done in 2002 in stony brook university New York by a team of scientist led by Eckarde wimmr (Science, 9 August 2002, p. 1016)


    Picture-: The Mycoplasma Genetalium’s Genome. Taken from the journal the Science

    The synthetic genome created by Venter's team is almost identical to that of a natural bacterium. It was achieved at great expense; an estimated $40 million, and effort, 20 people working for more than a decade. Dr. Venter took a first step toward this goal three years ago, showing that the natural DNA from one bacterium could be inserted into another and that it would take over the host cell’s operation. He said that before copying the DNA, he excised 14 genes likely to be pathogenic, so the new bacterium, even if it escaped, would be unlikely to cause goats harm.
    Dr. Venter calls the result a “synthetic cell” and is presenting the research as a landmark achievement that will open the way to creating useful microbes from scratch to make products like biofuels. At a press conference Thursday, Dr. Venter described the converted cell as “the first self-replicating species we’ve had on the planet Though the scientists claim for creation of artificial living cell “He has not created life, only mimicked it,” what we want to say








    There remains much about the ethical issues to be solved

    1] Consequence of progress in the new field of synthetic biology is an emerging view of cells as assemblages of parts that can be put together to produce an organism with a desired phenotype

    2].Over the long term, the approach will be used to synthesize increasingly novel designed genomes, and may...
  • Professor Pranab Kumar Bhattac
    Continued from post-2

    2].Over the long term, the approach will be used to synthesize increasingly novel designed genomes, and may be a tool for bioterrorism and we need protections from military or terrorist misuse and abuse,"

    3]. Will the newer synthetic biology help human mankind by detecting where is the defect lies the human genome that give rise cancer or in formulation of new drug or vaccine?

    4]. is it a step towards ... creation of living beings or artificial life with capacities and natures that could never have naturally evolved."

    5]. In Future Can some one will design for Human clone?




    References
    1] Elizabeth Pennisi Synthetic Genome Brings New Life to Bacterium News of the Week Genomics: Science 21 May 2010:Vol. 328. no. 5981, pp. 958 – 959 DOI: 10.1126/science.328.5981.958

    2] R. L. Warren, J. D. Freeman, R. C. Levesque, D. E. Smailus, S. Flibotte, and R. A. Holt Transcriptions of foreign DNA in Escherichia coli Genome Res. 18, 1798-1805. 2008

    3] G. A. Benders, V. N. Noskov, E. A. Denisova, C. Lartigue, D . G. Gibson, N. Assad-Garcia, R. Y. Chuang, W. Carrera, M. Moodie, M. A. Algire, et a Cloning whole bacterial genomes in yeast. Nucleic Acids Res. 38, 2558-2569 2010

    4] Tian,J., Gong,H., Sheng,N., Zhou,X., Gulari,E., Gao,X. andChurch,G. (2004) Accurate multiplex gene synthesis fromprogrammable DNA microchips. Nature, 432, 1050–1054.

    5] Mandecki,W. and Bolling,T.J. (1988) FokI method of genesynthesis. Gene, 68, 101–107.

    6] *, William J. Blake Brad A. Chapman, Anuradha Zindal, Michael E. Lee, Shaun M. Lippow and Brian M. Baynes , Pair wise selection assembly for sequence-independent construction of long-length DNA Nucleic Acids Research, 2010, Vol. 38, No. 8P 2594–2602 Published online 1 March 2010 doi:10.1093/nar/gkq123

    7] Gibson,D.G., Young,L., Chuang,R.Y., Venter,J.C.,Hutchison,C.A. III and Smith,H.O. (2009) Enzymatic assembly ofDNA molecules up to several hundred kilo bases. Nat. Methods, 6, 343–345,2009.

    8] Gibson,D.G., Benders,G.A., Andrews-Pfannkoch,C.,Denisova,E.A., Baden-Tillson,H., Zaveri,J., Stockwell,T.B., Brownley,A., Thomas,D.W., Algire,M.A. et al Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome., Science 319, 1215–1220.2008

    9] Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A.,Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. 1995) Science 270, 397–403.1995

    10 John I. Glass, Nacyra Assad-Garcia, Nina Alperovich, Shibu Yooseph, Matthew R. Lewis, Mahir Maruf,Clyde A. Hutchison III, Hamilton O. Smith*, and J. Craig Venter Essential genes of a minimal bacterium, proceeding Nat Academy Science USA PNAS _ January 10, 2006 _ vol. 103 ,425-30 ***.pnas.org_cgi_doi_10.1073_pnas.0510013103

    11] Horgan, J. 1995. From Complexity to Perplexity. Scientific American. p107



    Copy Right- Copy Right of the article belongs to Professor Pranab kumar Bhattacharya as per IPR Copy Right Rules. Please don’t try to Infringe it by any means




  • Dov Henis  - They do not understand what they did
    Synthetic Biology?
    Proof Of Something Else, Not Synthetic Cell.
    So What Else is New?
    DNA Genomes Are Cells' RNA's Functional Organs


    I admit having read only the first four paras. Made me feel so empathically embarrassed. Could'nt read further...

    A. From "Genome from a bottle"
    Synthetic DNA makes cells switch species
    *****//***.sciencenews.org/index/generic/activity/view/id/59438/title/ Genome_from_a_bottle_

    - An unprecedented wholesale genome swap. Stitched and transferred the entire M. mycoides
    bacteria genome into emptied-from-genome M. capricolum cell. This genome switch caused the M. capricolum cell to switch species. The newly converted cell was nearly identical to the natural M. mycoides.

    - "Proof of concept experiment, take the sequence out of a computer, build it and boot it up to make a synthetic cell”.


    B. From "03.2010 Updated Life Manifest"

    The RNA genes are life's prime strata organisms. They evolved their DNA-images as their organ, their continuously updated operational worklogs primal Earth's organisms libraries, and genomed them, i.e. nucleusized them, and celled them with their other organ, the outer cell membrane.

    It is the RNA genes and their DNA replicas, life's prime strata organisms, that evolve, and the evolution of genomes, the 2nd stratum of life, and of the 3rd life stratum cellular organisms, is an interenhancing consequence of their genes' evolution.


    Dov Henis
    (Comments From The 22nd Century)
    03.2010 Updated Life Manifest
    *****//***.the-scientist****/community/posts/list/54.page#5065
    Cosmic Evolution Simplified
    *****//***.the-scientist****/community/posts/list/240/122.page#4427
    EOTOE.Embarrassingly obvious expanding horizons beyond Darwin And Einstein.
    *****//***.molecularfossils****/2010/05/formal-test-of-theory-of-unive rsal.html
  • john noble  - God is not phased
    I believe God is secure in his role and has gifted man to search out his mysteries. It is His gift in us to discover what He has created for man. Keep searching, discovering and He will reveal Himself to all of us through the work of the sciences...

    Much love

    John N
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