Tag Archive | "synthetic biology"

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Synthetic Biology Creates Smallest Bacteria

Posted on 12 April 2016 by Jerry

Craig Venter, a longtime leader in synthetic biology if not a founder, has continued to pursue creation of a life form with the smallest number of genes that can act as a living envelop for a created synthetic organism. Venter’s team has now announced a bacterial cell that Venter calls the “most simple of all organisms.”   It only has 473 genes.

An article published on March 24, 2016 by Science magazine describes the new organism as a “Tour de force” in a quote of George Church, a synthetic biologist at Harvard University. Also known as Syn 3.0, the living bacterium has been cut down to the bare essential genes to sustain life. It has the least known or smallest genome of a living organism to date.

The problem with this new development is that it can be described as creating more questions than it answers. In trying to eliminate genes that did not keep this most basic bacterium alive, the synthetic biologist team found 149 of the 473 genes whose purpose was unknown. These genes remained a mystery because no one on the team could identify what functions these particular genes had.

The March 25, 2016 issue of Science magazine has an article entitled Design and synthesis of a minimal bacterial genome, which was written by Venter’s own team. This article said in conclusion, “The minimal cell concept appears simple at first glance but becomes more complex upon close inspection. In addition to essential and nonessential genes, there are many quasi-essential genes, which are not absolutely critical for viability but are nevertheless required for robust growth….Unexpectedly, it also contains 149 genes with unknown biological functions, suggesting the presence of undiscovered functions that are essential for life.”

This represents a continuation of a trend that was last highlighted in an article in this blog entitled, “Troubling Progress for Synthetic Biology” see www.iamaguardian.com/category/protect/synthetic-biology/page/2/ . This May 2012 article shows that the same teams are making progress on their respective objectives. It also shows that this research team is taking the easiest path to a conclusion and the simplicity of their approach to research, simplicity that allows for 149 unknown genes. These bacteria represent the next chapter of the J. Craig Venter team. These bacteria grow and thrive in a laboratory environment.

We continue to call for regulation of Venter’s team’s experimental efforts. It is clear they are taking a very ‘ham-handed’ approach to finding the secret of life. What else will they fail to know about the microbes they create? What will they care? What will stop them from taking a shortcut to wealth when they find a path to an IPO or a new product rather than take the appropriate steps to be safety conscious? This again highlights that this area has no government regulator or regulatory regime to look over their shoulder and insure their efforts are in the public interest.

The announcements themselves seem to respond to funders thirst for progress, which must be threatening to not give them any more money. These numbers do not assuage the concerns of the public.

Would you announce proudly the fact that you have whittled down bacterial genes to 473 when you continue to not know what 149 or over 30% of these genes do? Why would you make sweeping public announcements about this accomplishment? We need regulation and oversight of this area now. We must slow these teams and their zeal to reach the next plateau in living out their founder’s dreams of great wealth and renown.

Use the following links to access more information or read the source documents used to prepare this article.

http://news.yahoo.com/stripped-down-synthetic-organism-sheds-light-nature-life-204848392–finance.html

http://www.sciencemag.org/news/2016/03/synthetic-microbe-lives-less-500-genes

http://www.sciencemag.org/news/2003/11/designer-genomes-pronto

http://www.bbc.com/news/science-environment-35895138

http://sciencemag.org/content/351/6280/aad6253

http://sciencemag.org/content/351/6280/1380

http://science.sciencemag.org/content/351/6280/aad6253.full

 

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Disagree (and Agree) With Stephen Hawking

Posted on 26 January 2016 by Jerry

Dr. Stephen Hawking, professor and research director at Cambridge University’s Department of Applied Mathematics and Theoretical Physics, has expressed his belief that technology will be our undoing and will bring new ways for things to go wrong and end humanity’s future existence. Hawking said at a teleconference in Hong Kong, “Life on Earth is at the ever-increasing risk of being wiped out by a disaster such as sudden global warming, nuclear war, a genetically engineered virus or other dangers we have not yet thought of.” He made substantially the same statements in response to questions when recording the BBC’s annual Reith Lectures on January 7, 2016.

He said that he believes our only hope is to spread out in space and colonize other worlds. He believes that it will take at least 100 years to establish a colony on another world in our solar system and the next 1000 years to spread to other solar systems. Our objective must be to establish self-sustaining colonies that are independent of our home planet Earth. This is because he believes we will kill ourselves on planet Earth and we need to be self-sustaining elsewhere for humanity to survive.

While we agree on the threats, we must be a pessimist about the space options and an optimist that human beings on this planet are taking the steps necessary for us to survive. We must support space colonization because of the knowledge we gain about surviving in hostile environments. We cannot believe we can colonize other solar systems. We cannot believe that colonies can support more than a few thousand humans, certainly not any real fraction of the seven plus billion population of the world.

Dr. Hawking has reliance on the science fictional development of a technology that allows our speed to approach that of light. The author sees no practical approach that permits us to significantly increase our speed.  This Hawking suggestion represents his ‘hail Mary’ pass about the future.

In our book, Beyond Animal, Ego and Time, it is shown it would take 18,000 years at 150,000 miles per hour, our current rate of maximum speed, to reach the nearest star. Even if you triple or quadruple this speed the time to reach the star dwarfs our ability to maintain life in outer space by a large margin. The book is explicit about our practical isolation in the universe (see Chapter 4 about travel to Alpha Centuri C).

Those readers who have the book Beyond Animal, Ego and Time or follow the blog www.iamaguardian.com know that the writer has warned about these hazards specifically with the exception of artificial intelligence. The author has warned about climate change, nuclear weapons and genetic engineering/synthetic biology. While we have also warned about the ozone depletion of the planet’s atmosphere, we have recently written blog articles about asteroids and meteors hitting the earth. On these threats there is agreement.

Although the writer wishes it were not so, he is not the fatalist that Dr. Hawking is proving to be. The outcomes we fear, while all legitimate, must be solved soon by us before our worst fears come to pass. There is certainly no option to wait for a century to solve these problems. The climate change outcome is dependent upon what humanity does in the next decade.

All of these problems should be dwelt with in the next few decades. We must have faith there is a solution to each of these hazards that has been spelled out in the blog articles over the last four years or so.

The only one we have not dealt with is the meteor strike on our planet and this too can be solved. We can interrupt the trajectory of a meteor or asteroid that we know is coming toward us. So far we are making too little an effort to identify these objects and are making no effort to learn how to modify trajectories. We just need to get going.

We must stay the course on each of the threats we face. None of them involve quick or easy fixes. We cannot give up as Dr. Hawking suggests. We can be fatalistic but not in his way. We must believe human beings will confront each threat and solve the underlying problems. We should believe in ourselves to triumph over problems we have created or we can foresee.

Use the following links to access additional information or the source documents used to support this article.

http://www.nbcnews.com/id/13293390/ns/technology_and_science-space/t/hawking-says-humans-must-go-space/#.Vp6tixHSalU

http://www.heraldsun.com.au/news/breaking-news/scientific-progress-a-disaster-hawking/news-story/deadb3343090a1e679c6795cee076d32

http://www.huffingtonpost.com/2015/04/28/stephen-hawking-humanity-1000-years_n_7160870.html

http://www.dailymail.co.uk/sciencetech/article-3406751/Hawking-Threats-human-survival-likely-new-science.html

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Is Synthetic Biology Now Safe?

Posted on 06 December 2015 by Jerry

A couple of years ago a team led by George Church at Harvard Medical School, which included Farren Isaacs now a synthetic biologist at Yale University, made a strain of Escherichia coli that abandoned an old instruction to terminate protein synthesis and had a new instruction to make a synthetic amino acid within its proteins. It required this new strain of E-coli to look for the new amino acid or die as too reliant on the synthetic amino acid.

Now two teams independently have produced other genetically modified bacteria that are dependent upon amino acids that are not naturally occurring in the environment. Both bacteria will die if not nourished by the synthetic amino acids that of course only occur in a laboratory. This offers a protection should either bacteria escape the laboratory environment.

Dan Mandell, leader of the Harvard Medical School team (with George Church) is quoted in a January 22, 2015 article in Nature magazine as saying, “Our strains, to the extent that we can test them, won’t escape.” The article goes on to state, “The microbes also do not swap their engineered DNA with natural counterparts because they no longer speak life’s shared biochemical language.”

The article continued that the Mandell (and Church) team at Harvard started with protein structures “and added elements to help integrate and accommodate the artificial amino acids.” To the contrary, the Isaacs team from Yale began with genomic sequencing looking for sites in the proteins where microbes could use synthetic amino acids with no detrimental effect on the microbe.

“Establishing safety and security from the get-go will really enable broad and open use of engineered organisms,” stated Farren Isaacs, a Yale synthetic biologist. Farren Isaacs who led the second study was quoted from the same Nature magazine article.

In the original article from Yale that appeared online on Nature.com on January 21, 2015 the report says, “Here we describe the construction of a series of genomically recoded organisms (GROs) whose growth is restricted by the expression of multiple essential genes that depend on exogenously supplied synthetic amino acids (sAAs).” Farren Isaacs believes in this containment so much that he and Alexis J. Rovner applied for a provisional patent at the US Patent and Trademark Office. A “Corrigendum: Recoded organisms engineered to depend on synthetic amino acids” was filed in conjunction with this report. This filing also identifies Isaacs as a founder of enEvolv, Inc.

Isaacs was also quoted by BBC News on January 21, 2015 as saying “What we’re seeing here is an important proof of concept that re-coding genomes and engineering dependence on synthetic amino acids is technically feasible and in not just E coli but other micro-organisms and multicellular organisms such as plants.”

It would appear it is now possible to develop synthetically modified organisms that would be safer than today’s synthetic organisms. They are dependent on a continuous supply of synthetic amino acids for continued sustenance in all environments. Whether these developments are actually used by other researchers and companies in their products remains to be seen. It is safe to say we should applaud this research as a breakthrough that has the safety of the populous and its environments in mind.

We must increase and continue regulatory oversight over this synthetic biology area. We need caution from the government, private entrepreneurs and venture capitalists concerning synthetic biology experiments. But we should feel heartened that progress is being made and scientists are looking for ways to contain the resulting synthetic organisms.

Use the following links to obtain additional information or access the source articles used for this report.

http://www.nature.com/news/gm-microbes-created-that-can-t-escape-the-lab-1.16758?WT.ec_id=NATURE-20150122

http://www.nature.com/nature/journal/v518/n7537/full/nature14095.html

http://www.nature.com/nature/journal/v518/n7537/full/nature14121.html

http://www.nature.com/nature/journal/v527/n7577/full/nature15537.html

http://www.bbc.com/news/science-environment-30915785

http://www.sciencedaily.com/releases/2015/01/150121135617.htm

http://phys.org/news/2015-01-synthetic-amino-acid-enables-safe.html

http://news.yale.edu/2015/01/21/synthetic-amino-acid-enables-safe-new-biotechnology-solutions-global-problems

 

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“CRISPR”, Breakthrough or Trouble?

Posted on 16 August 2015 by Jerry

No, the new CRISPR is not a better way to hold fresh produce in refrigerators.  Instead it is a new gene-editing tool that has been described as “Jaw dropping” by Craig Mello of the University of Massachusetts Medical School who shared the 2006 Nobel Prize for medicine.  A June 3, 2015 article in Nature Magazine goes on to say it will “allow researchers to quickly change the DNA of nearly any organism – including humans.  CRISPR is turning everything on its head.”

It allows researchers to alter the DNA of almost all organisms. This is undoubtedly good because it dramatically accelerates experimentation.  It should lead to many medical breakthroughs.  But are there risks?

To some extent CRISPR is a breakthrough that threatens all of us.  It revolutionizes an area that has no direct government regulation.   Researchers can now mix and match the genetic code of any set of disparate animals and do it cheaply.  Unfortunately, it only takes one mistake to create a new organism that we struggle to control.

CRISPR stands for clustered regularly interspaced short palindromic repeats.  CRISPR uses a part of a bacteria’s immune system.  A bacteria keeps copies of the dangerous viruses that prey on it so it can recognize and defend against those viruses should they try to infect it again.  This ability has been borrowed from the bacteria so genetic engineers can take a normal sequence of DNA and define it as the target that is to be cut out – the Cas9 enzyme cuts the DNA.

Its process involves a set of enzymes called Cas or CRISPR-associated proteins, which allow the bacteria to precisely cut out a section of DNA and cut it up as it would an invading virus.  The best-known enzyme, of a number of Cas enzymes, is called Cas9.  It is from the Streptococcus pyogenes or the bacteria that causes strep throat.   It forms the CRISPR/Cas9 system that is most often used.

This tool and new technique dramatically simplifies the ability to edit genomes or genetic chromosomes and has been “likened to editing the individual letters on any chosen page of an encyclopedia without creating any spelling mistakes.”

Professor Mello continued by saying “It’s one of things that you have to see to believe.  I read scientific papers like everyone else but when I saw it working in my own lab, my jaw dropped.  A total novice in my lab got it to work.  The CRISPR technique dramatically ‘lowers the threshold’ for carrying out ‘germ line’ gene therapy on human IVF embryos,” Professor Mello added.

A June 2015 article in Nature magazine quotes James Haber, a molecular biologist at Brandeis University in Waltham, Massachusetts, as saying “That (CRISPR) effectively democratized the technology so that everyone is using it,” says Dr. Haber.  “It’s a huge revolution.”

The article offers another summary of the CRISPR technique,  “It relies on an enzyme called Cas9 that uses a guide RNA molecule to home in on its target DNA, and edits the DNA to disrupt genes or insert desired sequences.  Researchers often need to order only the RNA fragment; the other components can be bought off the shelf.  Total cost: as little as $30.”

An added benefit is the technique takes far fewer cycles than the earlier technology to make a genetic change in a species.  An article on gizmodo.com that ran 5/6/2015 states, “Researchers inject the CRISPR/Cas9 sequences into mouse embryos.  The system edits both copies of a gene at the same time, and you get the mouse in one generation.  With CRISPR/Cas9, you can also alter, say five genes at once, whereas you would have to had to go that same laborious, multi-generational process five times before.”

An article in the June 8, 2015 issue of Nature states about Jennifer Doudna, a CRISPR pioneer at UC Berkeley, that “Her worries began at a meeting in 2014 when she saw a postdoc present work in which a virus was engineered to carry the CRISPR components into mice.  The mice breathed in the virus, allowing the CRISPR system to engineer mutations and create a model for human lung cancer4.”

The article continued “Doudna got a chill; a minor mistake in the design of the guide RNA could result in a CRISPR that worked in human lungs as well.  ‘It seemed incredibly scary that you might have students who were working with such a thing.  It’s important for people to appreciate what this technology can do.’ ”

A June 25, 2015 bloomberg.com article stated, “CRISPR could encourage editing of all kinds of genomes that, if unsupervised, may present unanticipated risks,” says Arthur Caplan, head of medical ethics at New York University School of Medicine.  “The technique could be used to try to amplify genes thought to boost intelligence in adults.”  Use on animals and insects could also lead to ecological havoc, Caplan says.  “You could have a disaster on your hands, and you don’t have to touch a human to do it,” he said.

As documented in a previous article, see “We Need Worldwide Regulation of Synthetic Biology” http://iamaguardian.com/1680/we-need-worldwide-regulation-of-synthetic-biology/, regulation of Synthetic Biology and Genetic Engineering is split amongst five different federal government departments.  Depending on the development, the organizations that have partial responsibilities are the Environmental Protection Agency (EPA), the Department of Agriculture (USDA), the Food and Drug Administration (FDA), the Commerce Department and the Department of Health and Human Services (HHS).

There needs to be absolute regulatory responsibility for genetic engineering and synthetic biology.  When we have small researchers and venture funded startup companies articulating opportunities and experimenting with alterations to life’s genetic codes with only self-regulation or murky departmental responsibility, we must call a halt.  There should not be the freedom to take all of these risks in the name of profit.

We should be writing letters to the editor and letters to our elected representatives to tell them of our expectations.  We need to speak out against self-regulation and murky, conflicting regulations by multiple government departments.  We need to lobby for new legislation and a single department to assume regulatory oversight.

Use the following links to gain additional information or access the original documents used in this article.

http://www.nature.com/news/crispr-the-disruptor-1.17673

http://www.independent.co.uk/news/science/exclusive-jawdropping-breakthrough-hailed-as-landmark-in-fight-against-hereditary-diseases-as-crispr-technique-heralds-genetic-revolution-8925295.html

http://gizmodo.com/everything-you-need-to-know-about-crispr-the-new-tool-1702114381 (scroll down)

http://www.bloomberg.com/news/articles/2015-06-25//the-promise-and-peril-of-crispr

http://www.nature.com/news/crispr-science-can-t-solve-it-1.17806

http://www.nature.com/news/crispr-move-beyond-differences-1.17805

http://www.iamaguardian.com/1680/we-need-worldwide-regulation-of-synthetically-biology/

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We Need Worldwide Regulation of Synthetic Biology

Posted on 11 March 2015 by Jerry

Following the thought of the creation of new nucleotides, the x-y pair (see Synthetic Biology Advances With No Oversight, 7/15/14), synthetic biologists at Yale and a separate group at Harvard have constructed genetically altered organisms that require special synthetic amino acids to live.  Synthetic biologists reason this makes the synthetic organisms safer since they would die if released into the environment that lacks the amino acid.

This breakthrough would eventually allow synthetic organisms to be raised in laboratories for use in experimentation.  According to an article in the January 22, 2015 volume of Nature entitled Safety boost for GM organisms “The microbes also do not swap their engineered DNA with natural counterparts because they no longer speak life’s shared biochemical language.”  The article continued with a quote from a Yale synthetic biologist, Farren Isaacs who said, “Establishing safety and security from the get-go will really enable broad and open use of engineered organisms.”

While this does provide another layer of security to the development of synthetic organisms, it still begs the question of when there will be proper regulation of synthetic biology.  This is not to say there is no regulation today, for there is.  It is as if we have a bedspread that has been pulled in many different directions as we try to cover a synthetic biology spot by expanding existing coverage of a wide array of bureaucratic organizations each of which are designed to respond to other priorities.

This is like stating that in an environment where everyone is responsible, no one is.  The closest anyone comes to directly regulating this area is the National Institute of Health (NIH).  The law requires that any entity that receives money for research from the NIH must adhere to its guidelines that cover synthetic biology.  Everyone else is free to follow the guidelines or not, or worry about another governmental agency with a regulatory role that can be extended to synthetic biology.

The Environmental Protection Agency (EPA), the United States Department of Agriculture (USDA), the Food and Drug Administration (FDA), the Commerce Department and the Department of Health and Human Services (HHS) all have overlapping responsibility for Synthetic Biology.  It is doubtful that any of them has been given any additional budget to extend their regulation to include synthetic biology.  Let us reiterate that when all are responsible, no one is responsible.

There is a thorough description of the patchwork quilt of regulation of synthetic biology which can be found by accessing “synberc.org/safety-and-security-resources” and selecting the “The Regulation of Synthetic Biology: A Guide to U.S. & European Regulations, Rules & Guidelines.”

Synthetic biologists are working to solve humanity’s problems.  Today they are largely self-regulated.  This must change.  There must be regulation but it should be one regime that is worldwide (maybe from the U.N.) and assures that humans will not unleash a foreign organism into the world’s environment.

Use the following sites to gain additional information or access the original documents that were used to generate this article.

http://www.iamaguardian.com/category/protect/synthetic-biology/

http://www.nature.com/nature/journal/v518/n7537/full/nature14095.html

http://www.nature.com/nature/journal/v518/n7537/full/nature14121.html

Access “synberc.org/safety-and-security-resources” and select the “The Regulation of Synthetic Biology: A Guide to U.S. & European Regulations, Rules & Guidelines.”

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554958/

 

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