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Biotech Science

Precision Gene Editing 128

Posted by Zonk
from the i'd-like-some-gills-please dept.
mpthompson writes "NewScientist.com is reporting that scientists at Sangamo Biosciences have developed a method of editing DNA mutations with unprecedented precision without weaving in potentially harmful foreign genetic material. Different combinations of amino acids are designed to latch on and cut the DNA at exactly the place where the mutated gene lies. This triggers the body's natural repair process which corrects the gene where the DNA was cut. The technique will be used to target diseases caused by single-gene mutations such as combined immune deficiency (X-SCID) - or bubble boy disease - and sickle cell anaemia."
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Precision Gene Editing

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  • by bobscealy (830639) on Friday April 08, 2005 @07:41PM (#12182255)
    The article only mentions cutting the DNA and then "allowing the body's natural repair processes" to do the rest - it seems that this technique could also be useful in inserting genes at precise locations in DNA instead of letting viruses and bacteria insert genetic material wherever they please? I am no genetic engineer, can anyone comment?
    • I have a feeling that this has to do with homologous recombination, where damage to a certain gene causes the chromosomes to auto-repair themselves by copying the target gene from the "good" chromosome. At least that's my take on why they would mention damaging the DNA to repair it.
      • by Anonymous Coward
        Yes, it does have to do with homologous recombination. Creating a double strand break in the chromosomal DNA induces various DNA repair pathways including homologous recombination. The break can be healed by "copying" information off of the non-broken chromosome as you suggest.

        If, however, you introduce a piece of "foriegn DNA" into the system at the same time that you make the chromosomal break, and that foreign DNA has homology to the DNA sequence flanking the chromosomal break, then the forien DNA can b
        • In fact that's exactly what the article says: "This triggers the body's natural repair process, called homologous recombination, which corrects the gene where the DNA was cut, The researchers provided the cells with a copy of the correct gene as a template."
    • you are completely correct. I fact, depending on how easy it is to design and make the custom zinc finger enzyme, I see this technology having far more use in research and engineering than in medicine. Many human diseases are recessive, which means both copies of a gene are defective, in which case getting a "normal" DNA template from which to repair from into a patient's cells is still a problem.
    • This triggers the body's natural repair process which corrects the gene where the DNA was cut.

      No way. Anyone knows anything knows this will really result in a crazy mutation. Maybe they could play with the part of my genome that doesn't let me create fireballs in the palm of my hand and the body will "fix" it so I can?

      Flying would be cool too.
    • Hello Greg Bear, are you reading this? We need a trilogy. Maybe Darwin's TV. For /.ers -> for reference read Darwin's Radio and Darwin's Children. Much fun and profit in them there genes.
  • Clarification (Score:3, Interesting)

    by caryw (131578) <[carywiedemann] [at] [gmail.com]> on Friday April 08, 2005 @07:42PM (#12182260) Homepage
    So this treatment actually alters the genetic code of a human? So any genetic disease would not get passed down to future generations? How is something like this administered? Our DNA is found in every cell of our body.
    --
    Fairfax Underground: Fairfax County message board and public records [fairfaxunderground.com]
    • Theoretically (without knowing anything about DNA,...) you could administer it in an early fetal state where the number of cells is still low. This wouldn't help the parent but could rid the child of the gene.
    • Maybe the scientists could create a virus that enacts the process at the cellular level to allow the change to take place throughout the body...
    • The article states that "In the latest work, the gene was corrected in 18% of the cells treated, enough to finally make the method therapeutically viable." This would seem to actually alter the recipient cells' genetic code, but it is not completely effective over all the cells. Perhaps with time the technique will grow to the 80%, 90% or perhaps even 100% effective.
    • Re:Clarification (Score:2, Informative)

      by saytan (170239)
      While I haven't read the article, I have heard a presentation on this from one of the researchers involved.

      The old technology involves the use of a retrovirus containing the correct copy of the X chromosome gene involved. This copy inserts itself (nearly randomly) into the DNA. The problem with this was that you couldn't control the point of insertion, causing a whole new set of diseases.

      The new technology involves repairing the endogenous gene sequence rather than inserting a good copy at another locus
    • Re:Clarification (Score:3, Informative)

      by Fadeproof69 (874100)

      In order to answer your question, i'm going to have to give a little background...

      contrary to popular belief, 99.99% of the body's cells don't keep dividing. The somatic cells of the body are replenished by stem cells and progenitor cells which act as the main copy from which all the "backup" cells are made. These cells specialize into skin cells, blood cells, and possibly nerve cells. The only way to have a permanent effect with this treatment would be to fix the mutation in the stem cells/progenitor ce

      • It's true that to make the change heritable, you will need to put it in the embryo. However, for lots of blood-related diseases (i.e. sickle-cell anemia), all you have to do is replace the right cell populations in the bone marrow, so in theory you can irradiate the person and repopulation them from that 18%. And that would be 100% effective.
    • For many diseases, you wouldn't need to get every cell in the body, only a propotion of the cells of a specific organ, like a bunch of bone marrow cells, for example.

      The method used can vary by treatment, but in many cases, a virus is used.

    • So this treatment actually alters the genetic code of a human?

      Yes it changes the genetic code. But it's not a treatment yet. It's a method which could be developed in a treatment. There's quite some difference between changing the DNA of a cell in a test-tube and doing it in someone's body. (In medical terms: in vitro versus in vivo)

      So any genetic disease would not get passed down to future generations? How is something like this administered? Our DNA is found in every cell of our body.

      Well, exactly.
  • I'm Safe.. (Score:4, Funny)

    by ackthpt (218170) * on Friday April 08, 2005 @07:45PM (#12182279) Homepage Journal
    I've got PGGP - Pretty Good Gene Protection

    they say diarrhea is hereditary, it runs in the jeans...

  • by Proudrooster (580120) on Friday April 08, 2005 @07:52PM (#12182338) Homepage
    Great, now the gene splicers have the equivalent of a hex editor, but still have no clue what they are editing. It's like hacking binary code out of one program and inserting into another program and somehow getting it to work.

    Until we have a better handle on Gene Expression [wikipedia.org] and how to actually interpret the genetic code we should proceed cautiously.

    To quote Dr. J. Craig Venter, Time's Scientist of the year (2000).

    "We know far less than one per cent of what will be known about biology, human physiology, and medicine.
    My view of biology is 'We dont know shit.' "


    If any am being overcautious or am ill-informed please feel free to correct me. I try to live by the motto, "Just because we can do something, doesn't mean we should." This applies to System Administration as much as it does to gene-hacking.
    • like the 'bubble boy' defect mentioned in the article, we often know the specific bit of code that causes the problem.

      "IL-7 signalling pathway

      Most cases of SCID are derived from mutations in the c chain in the receptors for interleukins IL-2, IL-4, IL-7, IL-9 and IL-15. These interleukins and their receptors form part of the IL-7 signalling pathway.

      The IL-2 receptor (IL-2R) gene is located on the X chromosome and mutation of this gene causes X-linked SCID.

      Janus kinase-3 (JAK3) is an enzyme that mediate
      • In certain isolated cases this has found to be true, but Dr. Richard Strohman, from UC Berkley wrote this.

        "Genes exist in networks, interactive networks which have a logic of their own. The [gene] technology point of view does not deal with these networks. It simply addresses genes in isolation. But genes do not exist in isolation. And the fact that the [biotech] industry folks don't deal with these networks is what makes their science incomplete and dangerous."
        Dr. Richard Strohman, Professor Emeritus
        • germ line changes.

          If a person has a terminal disease, somatic changes may or may not help, but they aren't likely to cause more damage than the disease.

          And by the time they have a terminal (or even chronic) disease, you can get a pretty good idea how "the organism will express it's genes".

          Treating disease in somatic cells is a much different issue from creating new lines of plants/animals/humans via changing germ line cells--at least in organisms that reproduce sexually.
        • There isn't really much in the way of danger when replacing a known bad gene with a known good gene. We'll only need a solid understanding of gene interaction once we start creating deliberate mutations and writing new genes from scratch, and we'll have to understand protein folding before we can even reach that step. We have a long way to go.

    • by Anonymous Coward
      Great, now the gene splicers have the equivalent of a hex editor, but still have no clue what they are editing.
      Oh great, I can just imagine:

      Razor 1911 brings you the penis extension hack.
      Sequence cracked by: PhARAOh

      GREETZ to MadKillas, Beowulf, Syxus, Toast, Trilithium.
    • Great, now the gene splicers have the equivalent of a hex editor, but still have no clue what they are editing. It's like hacking binary code out of one program and inserting into another program and somehow getting it to work.

      This isn't entirely true. We can figure out where a gene starts in DNA, and we know how to read the DNA into a protein. We know that from the start point, DNA is broken up into 3's such that each set of three DNA bases code for one amino acid. To use the case of sickle cell anemi
    • Your right in that this doesn't give us the ability to do really novel gene manipulation.

      But it does give us the ability to create the equivalent of patch files for bad/defective genes when a good/functional version of the gene is available.

      There are many genetic diseases where the mistake in the DNA is well characterized, and it is very clear exactly what difference between the normal version of the gene and the defective version causes the disease, even if we don't have a full understanding of what th

      • Good Thread! I've learned a lot. To summarize, we could say that "everything we need to know about gene replacement therapy we have learned from Sesame street." when we learned the "One of these things is not like the other" [tripod.com] song :)

        I just really bugs that I can look at hex and turn it back into op codes and get a general idea of what the code does, but we can't do the same with DNA. Maybe one day someone will be able to read DNA gene sequences like the morning newspaper.

        Back in High School, I thoug
    • Uhuh... its not like experimentation has to start on humans... mice, small animals and blac... uh anyway, point being big step to super soldiers programmed to commit genocide!
    • Great, now the gene splicers have the equivalent of a hex editor, but still have no clue what they are editing.

      They've had that for a long time. This is just a new one. Don't exaggerate the importance.

      It's like hacking binary code out of one program and inserting into another program and somehow getting it to work.

      A bit. But not quite as random as that. In this case, they know what the gene in question codes for a certain protein which acts as a receptor on T-cells. They know what the gene looks like
    • I just wanted to make this comment about hex editing (I thought to say that's like editing binary files with the vi editor) but I don't agree they shouldn't do it.

      First, there are millions of ill people desperate for anything remotely promising. The alternative is suffering and death. Can it get any worse for them?

      Secondly, initially they could perform this "patching" only on folks who agree to be sterilized (in order to limit impact on individual people until the technique is safe).

      Thirdly, yes, it's no
    • This isn't going to be used all willy-nilly in clinical trials. For genetic diseases caused by known single-gene defects, this is simply a safer form of gene therapy. Gene therapy trials have been underway for years now, and the major drawback has been the danger of random integration - that is, inserting your corrected gene at a random point in the genome, quite possibly in the middle of a cancer-causing gene. This technique virtually eliminates that risk. However, it's useful only for so-called "ex vivo"
    • If any am being overcautious or am ill-informed please feel free to correct me.

      You are being overcautious and ill-informed. The thing is, Craig Venter is right, we know less than 1%. However, it's more like we know quite a bit about certain things, and those things are less than %1 of everything. For example, the genetics of sickle-cell anemia are basically 100% understood, and they have been for quite a while. Replacing the "bad" gene with the "good" gene will have a 100% predictable effect. It re
    • As someone entering the field of genetics and cellular biology I have to agree that we definitely have a lot more to learn that we have learned to date.

      However, to say "Just because we can do something, doesn't mean we should," is probably not true in this case.

      Researchers can already make specific point changes to DNA, this just seems like it will speed things up and do it more cleanly. This is what is going to help us learn more about gene expression. Because often the best way to learn about a sy
  • Mutations... (Score:4, Insightful)

    by John Seminal (698722) on Friday April 08, 2005 @07:57PM (#12182385) Journal
    That is how nature changes people, that is how humans evolved to what we are today. I dunno how smart it is messing with mother nature. So far, mother nature has been able to keep things going well for thousands and thousands of years. But for some human to say, I am not happy living to 80 years old, I want to live to 90 years old, that is a risky proposition considering they are not using standard medicine, but messing with DNA. Maybe what would have happened naturally now won't.

    I think there is a natural equilibrium between nature and gene mutations. When the hand of man starts changing one side of the equation, can the consequences on the otherside be foreseen? For example, who is to say that some form of cancer today won't mutate to something 1,000 years from now that will save humanity from some enviormental change?

    • in 500 years, and between then and now millions of people suffer painful deaths to avoid changing something that might be helpful in the case of your hypothetical event?

      Anyway, there is the whole somatic vs. germ line thing, if genetic engineering is limited to somatic cells, changes won't be passed on to children (unless we start reproducing via mitosis).
    • Maybe we've evolved to a point where it's our destiny to control our future evolution?

      If a form of cancer today will mutate into something that will save humanity in 1000 years, wouldn't it make sense to use our newfound knowledge and technology to keep people with these cancers alive longer so that they can pass these mutations on and allow them to mutate into something more interesting?

      • Re:Mutations... (Score:2, Interesting)

        by BewireNomali (618969)
        i think u bring up an interesting point. digital gene modeling.

        programs similar to automata programs that currently run with simple sets of rules. each data set is a discrete genome. recombine over generations, tag all genomes that have disease preconditions and allow them to "evolve" that way.

        it's interesting, because computing is ridiculously cheap and so is data storage. This can even be run as a distributed project. people volunteer their genomes anonymously and the entire simulation is run across the
    • our brains allow us to control nature, not just exist in it. We can do whatever want, but we should be responsible when it comes to genetics because it puts our entire species at risk. If a person wants to design their genes let them, but there must be some rules and standards.
    • I dunno how smart it is messing with mother nature. Maybe what would have happened naturally now won't.

      I know to some extent this is just complaining about syntax, but humans aren't magic. Anything we do is natural, and a part of our nature. We're no more violating some natural order by tinkering with our genes than the plant mentioned here a while back is by automatically changing its genes as a result of stress. If it works out well, great, it'll be selected for and in fact add to what can be selected f
      • it's really interesting, because we started playing with fire way before we were ready, and we're still haven't perfected it yet... as judged by the ubiquitious fire stations. some of us are gonna get burned. we still have to play though.
    • Re:Mutations... (Score:2, Insightful)

      If you read Barbara McClintock's work and modern genetics, you'll see there are three events to worry about; mutations, exchanges with external organisms (virus, etc) and cross-overs. (genes exchanged during replication). Some people working with GA's have found that you don't need mutations at all, as cross-over events will give you all the variability you could want.

      To answer your question, think of sickle-cell anemia. One copy of the gene, and you're resistant to malaria (but not immune, i.e. it sim
      • If you read Barbara McClintock's work and modern genetics, you'll see there are three events to worry about; mutations, exchanges with external organisms (virus, etc) and cross-overs. (genes exchanged during replication). Some people working with GA's have found that you don't need mutations at all, as cross-over events will give you all the variability you could want.

        To answer your question, think of sickle-cell anemia. One copy of the gene, and you're resistant to malaria (but not immune, i.e. it simply

        • I am for medicine advances, all for research, but when it comes to changing DNA, I see a red flag. I think that even our brightest people are not able to consider all the potential ramifications.

          This attititude puzzles me. It seems to ascribe some sort of benevolent intelligence to nature, and makes DNA into a message from the Platonic realms, letting us know "HOW THINGS ARE MEANT TO BE". But nature is not benevolent, mutations are a random process, and our DNA is just a large molecule forged by interacti

  • http://www.biologynews.net/archives/2005/04/05/res earchers_pioneer_new_gene_therapy_technique_using_ natural_repair_process.html
  • by G4from128k (686170) on Friday April 08, 2005 @08:09PM (#12182477)
    TFA noted that the zinc fingers cue in on two sets of 6 base pairs to find the site that needs correction. Assuming randomness in the base-pair sequences, this 12 base-pair key will bind with approximately 1 out of every 16.8 million (actually 1 out of every 8.4 million due to complementarity of the base pairs). Given that the human genome has about 3.2 billion base pairs, this means that the modifier will match in 381 positions more or less.

    Thus, this method will fix the error in one place and introduce an error in 380 other locations. The key needs more than 16 base pairs to be statistically assured of homing in on a unique mutation (depending on the statistics of DNA, it may need more or less).
    • by Anonymous Coward
      Upon careful reading of the paper, it seems from Fig. 1a, the Introduction, and the Materials and Methods, that two zinc fingers, each recognizing 12 bp are required for editing to work. The boolean sum of the recognition sequences of the two zinc fingers -- 24 bp in total -- is unique in the human genome.
    • by Anonymous Coward
      The point is that it induces a break which will be repaired by homologous recombination, which is error free. This is in contrast to non homologous end joining which is also a common repair pathway, but introduces errors.

      Homologous recombination needs a template which is usually a sister chromosome, however, in this case the template should be engineered with the non-mutated gene. Breaks other places in the genome will not be repaired by the engineered template since it is no homologous, it will be repaire
  • by cinnamon colbert (732724) on Friday April 08, 2005 @08:10PM (#12182492) Journal
    I have not read the article, but repair processes can be "error prone". That is, the mechanisms cells use to repair DNA often involve high error rates.

    The human genome is 3e9 BP long (roughly..not counting indels, the unsequenced centromeres, etc etc)

    So the chemical process of identifying the one single mutated basepair has to have a chemical specificity of >>1e9, because there are >>1e6 cells that are exsposed. That is, lets say you feed the reagent to a person. Millions of cells, each with 1e9 bp, are expsosed. Say the process has an error rate of 1e10 - many, many cells will have incorrect repairs done
    This is just like error rates in, say, reading data from a harddrive: the larger the file, the lower the error rte has to be

    What /.ers may not appreciate is that typically, it is VERY, repeat VERY hard to get chemcial reaction specificity of anywhere close to 1e9 for reactions invovling DNA.

    I will rtfa,
    • by Anonymous Coward
      Yeah, but you have to ask yourself whether the elevated rate of DNA repair is significant compared to the constant repair going on due to standard ROS/RNS/other radical attacks.

      And their current results of the 18% corrected rate, as they point out, is therapeutically effective.

      Plus, their recognition system using zinc fingers may have a higher recognition rate for the targeted sequence, and the corrections are applied to only a small area of DNA - so the overall error rate of DNA replication/repair is spr
    • You may have a PhD in Genetic Engineering but you seem to know little about DNA repair. There are at least 5 different types of DNA repair. Some of these are error prone some are not. The type being used by the Sangamo group is "homologous recombination" which tends to *not* be error prone unless the DNA being copied contains an error. This does from time to time occur and can result in cancer. When this happens it is known as "gene conversion".

      In this case, the Zinc Finger Nuclease is simply used to

  • Really, emacs is a whole lot of stuff that just happens to have text editing functionality along with it, so why not genes?
  • by Locke2005 (849178) on Friday April 08, 2005 @08:18PM (#12182550)
    Pharmacorp executive: "Let's see now, we can sell them a one-time treatment that cures them for the rest of their lives, OR we can charge them $1000/month for drugs to maintain their current status for the rest of their lives... well, obviously we'll choose the method that is best for the patient's well being, our profits be damned! I mean, it's not like we have a board of directors that will sack us if our revenues don't increase every quarter!"
    • by elucido (870205)
      Thats why we don't depend on that industry. Buy your drugs in India, take a vacation and come back with your genes fixed.
  • [obscure Seinfeld reference] The Mooks.
    • DONALD: Ok, history. This is for the game. How ya doin' over there? Not too good!

      GEORGE: All right BB. Let's just play... Who invaded Spain in the 8th century?

      DONALD: That's a joke. The moors.

      GEORGE: Oh, Noooo, I'm so sorry. It's the MOOPS. The correct answer is, The MOOPS.

      DONALD: Moops? Let me see that. That's not Moops you jerk, it's Moors. It's a misprint.

      GEORGE: I'm sorry the card says MOOPS.

      DONALD: It doesn't matter. It's the MOORS. There's no MOOPS.

      GEORGE: It's MOOPS.

      DONALD: MOORS.

      GE

  • My children can finally be bred as Valids!!!
  • by RhettLivingston (544140) on Saturday April 09, 2005 @09:49AM (#12186792)
    If they were to concentrate this work on Myotonic Muscular Dystrophy, they could likely achieve a success very quickly. It is caused by an unstable CTG sequence of DNA that expands in length when replicated. The progression of the disease is characterized by the number of expansions. Since it is an unstable sequence and of little use, simply cutting it out of all DNA should "cure" the disease. I put the "cure" in quotes because reversing the damage is likely not possible, but it could at least eliminate it from future generations and stop the progression.
  • the article (Score:3, Informative)

    by bikerguy99 (650704) on Saturday April 09, 2005 @10:32AM (#12186996)
    Highly efficient endogenous human gene correction using designed zinc-finger nucleases

    FYODOR D. URNOV1, JEFFREY C. MILLER1, YA-LI LEE1, CHRISTIAN M. BEAUSEJOUR1, JEREMY M. ROCK1, SHELDON AUGUSTUS1, ANDREW C. JAMIESON1, MATTHEW H. PORTEUS2, PHILIP D. GREGORY1 & MICHAEL C. HOLMES1

    1 Sangamo BioSciences, Inc. Pt. Richmond Tech Center 501, Canal Blvd, Suite A100 Richmond, California 94804, USA
    2 Department of Pediatrics and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA

    Correspondence should be addressed to M.C.H. (mholmes@sangamo.com) or M.H.P. (matthew.porteus@UTSouthwestern.edu); requests for materials should be addressed to M.C.H.

    Permanent modification of the human genome in vivo is impractical owing to the low frequency of homologous recombination in human cells, a fact that hampers biomedical research and progress towards safe and effective gene therapy. Here we report a general solution using two fundamental biological processes: DNA recognition by C2H2 zinc-finger proteins and homology-directed repair of DNA double-strand breaks. Zinc-finger proteins engineered to recognize a unique chromosomal site can be fused to a nuclease domain, and a double-strand break induced by the resulting zinc-finger nuclease can create specific sequence alterations by stimulating homologous recombination between the chromosome and an extrachromosomal DNA donor. We show that zinc-finger nucleases designed against an X-linked severe combined immune deficiency (SCID) mutation in the IL2Rbold italic gamma gene yielded more than 18% gene-modified human cells without selection. Remarkably, about 7% of the cells acquired the desired genetic modification on both X chromosomes, with cell genotype accurately reflected at the messenger RNA and protein levels. We observe comparably high frequencies in human T cells, raising the possibility of strategies based on zinc-finger nucleases for the treatment of disease.

    Most human monogenic disorders remain difficult to treat because therapeutic transgenes do not undergo homologous recombination (HR) into the mutated locus1, 2, and gene addition by virus-driven random integration remains a challenge owing to transgene silencing, improper activity or misintegration3, 4. Furthermore, targeted alteration of DNA sequence in vivo--in principle, a powerful basic research technique for studying genome function--in mammals requires sophisticated targeting vectors and drug-based selection1, 2, which limits the use of this approach5-7.

    The C2H2 zinc-finger, originally discovered in Xenopus8, is the most common DNA binding motif in all metazoa9. Each finger recognizes 3-4 base pairs of DNA via a single alpha-helix10, 11, and several fingers can be linked in tandem to recognize a broad spectrum of DNA sequences with high specificity12-14. Engineered zinc-finger protein (ZFP)-based DNA binding domains with novel specificities have been extensively applied in vivo to target various effector domains12, 15. Work from the Chandrasegaran laboratory has shown that a ZFP can be coupled to the nonspecific DNA cleavage domain of the Type IIS restriction enzyme, FokI, to produce a zinc-finger nuclease (ZFN)16, which then cuts the DNA sequence determined by the ZFP16, 17. An important specificity mechanism derives from the requirement that two ZFNs bind the same locus, in a precise orientation and spacing relative to each other, to create a double-strand break (DSB; Fig. 1a)17. One mechanism by which eukaryotic cells heal DSBs is homology-directed repair (Fig. 1b)18-20, which transfers information missing at the break from a homologous DNA molecule (Fig. 1b). Work from the Jasin laboratory21, followed by that of others22, 23, demonstrated that the endonuclease I-SceI can potentiate HR into loci previously engineered to contain its own recognition site, and the Carroll24, 25 and Baltimore26 laboratories have shown that a ZFN-invoked DSB increases the rate of HR in model systems.

    Figure
  • To have a technique that could possily cure people and then not use it for "religious" or for whatever fear is to my mind immoral - we may as well be living in the dark ages. Obviously the technique needs work still, and there are always risks with any medical procedure. Provided the patient knows fully those risks and agrees I don't see a problem, particuarly when no harm to anyone else is being done. The technique isn't introducing any alien material into a human. AND in any case we are already mutated b

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