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Precision Gene Editing

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."

128 comments

  1. day pass? by master0ne · · Score: 0, Offtopic

    is it just me pr did slashdot add a "daypass" if you watch a commercial to see unreleased stories yet instead of subscribing?

    --
    Noone writes jokes in base 13!
    1. Re:day pass? by Anonymous Coward · · Score: 0

      Jeeze, did everyone get one of these? I thought I was special, kind of defeats the point if EVERYONE can see the article first doesn't it? That being said it's actually kind of cool, I never saw the point of subscribing, but I think I am now. $5 1000 articles, not too shabby.

    2. Re:day pass? by jericho4.0 · · Score: 0, Flamebait

      Give it up, Taco.

      --
      "A language that doesn't affect the way you think about programming, is not worth knowing" - Alan Perlis
    3. Re:day pass? by master0ne · · Score: 1

      yeah i would have thought about it if this whole thread didnt get bashed with an offtopic stick, kinda makes me feel like we wernt supposed to discuss it here, i dont see how that was offtopic when it pertained to that article?

      --
      Noone writes jokes in base 13!
  2. Precision genetic engineering? by bobscealy · · Score: 4, Interesting

    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?

    1. Re:Precision genetic engineering? by myc · · Score: 1

      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.

      --
      NO CARRIER
    2. Re:Precision genetic engineering? by nmb3000 · · Score: 1

      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.

      --
      "What do you despise? By this are you truly known." --Princess Irulan, Manual of Muad'Dib
      /)
  3. Clarification by caryw · · Score: 2, Interesting

    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

    1. Re:Clarification by Taladar · · Score: 1

      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.

    2. Re:Clarification by Anonymous Coward · · Score: 0

      yeah, or it can be attached into modified viruses and spread to a localized area of the body, the virus infects the bad cells like it would normaly, only it spreads fixed DNA insted of its own harmful whatevers.

    3. Re:Clarification by crypto55 · · Score: 1

      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...

      --
      Due to financial difficulties, the light at the end of the tunnel has been turned off.
    4. Re:Clarification by mpthompson · · Score: 1

      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.

    5. Re:Clarification by Anonymous Coward · · Score: 0

      This works because you don't have to correct the mutation in ALL the cells in the body. The only cells that need to be fixed are the stem cells that will go on to produce the immune system. Pull out some marrow, isolate cells, fix, and then stick them back in.

    6. Re:Clarification by saytan · · Score: 2, Informative

      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. By doing this, you get around the problems caused by random retroviral insertion. The key breakthrough in the new technology was the ability to make proteins that can cleave highly specific sequences. Researchers at Sangamo can custom make a protein to bind at only one place in a genome of 3 billion base pairs.

      Both of these techniques work by taking out some stem cells from your body, transforming them, and placing them back in with your normal stem cells. This means that the DNA sequence of your germ cells, the cells that pass down your DNA to your children, is not changed.

    7. Re:Clarification by Fadeproof69 · · Score: 3, Informative

      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 cells, so that future specialized cells will all have the fix incorporated.

      To make this change heritable, you need to fix the mutation in the sperm or egg which is eventually used to create an embryo. Otherwise, the mutation will be passed on.

      From what the article says, there's only an 18% transformation efficiency so of all of the cells treated (this would never be the entire human body, just the cells collected), only 18% will be fixed.

      We are a long way off from doing the 100% effective gene therapy you see on Star Trek.

    8. Re:Clarification by YU+Nicks+NE+Way · · Score: 1

      Unfortunately, no. The pole cells (the gamete progenitors) stop dividing at the blastocyst stage, which is reached at about the time of conception in humans.

    9. Re:Clarification by jericho4.0 · · Score: 1
      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.

      --
      "A language that doesn't affect the way you think about programming, is not worth knowing" - Alan Perlis
    10. Re:Clarification by k98sven · · Score: 1

      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. And you don't really want to try to change the DNA of every cell in the body, because you don't have to, you only need to change the DNA in some of the relevant cells. Mucking about with other cells (such as your sperm cells) would increase the risks.

      If you read the article, what they're planning to do is take blood from the body, treat it, and reinject it.

      (Although I think that sounds a bit strange; The disease is caused by faulty T-cells, which are in the blood. Shouldn't they be fixing the bone marrow cells, which create the T-cells? That's what these other treatments do. But this isn't my field.)

    11. Re:Clarification by lukesl · · Score: 1

      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.

  4. Re:I don't care what they say.. by grasshoppa · · Score: 1

    I would say that's a bit paraniod, and possibly based on some educational time spent watching the sci-fi channel.

    Science is full of ethical questions, bio-sciences especially. What we can do we will do ( as a race ), that's a proven fact. It's better to do what we will do in the open, in front of many eyes, instead of being done in a third world country for some wacked out group intent on bringing their own version of reality to pass.

    --
    Mod me down with all of your hatred and your journey towards the dark side will be complete!
  5. Re:I don't care what they say.. by thanasakis · · Score: 4, Insightful

    If sick people can get cured by something like this, we can't afford not to exploit it.

    Let's just not forget that there is not such thing as evil knowledge. The way we use it makes good or evil.

  6. mmmyep by Anonymous Coward · · Score: 0

    With adblock on it was just a matter of clicking a couple times, didn't see the ad. Now I see what I'm missing by not subscribing (hint: nothing).

    1. Re:mmmyep by master0ne · · Score: 1

      i didnt see the ad either just noticed it said sompthing about a comercial >:)

      --
      Noone writes jokes in base 13!
  7. Re:I don't care what they say.. by flawedgeek · · Score: 0

    Sure, we could cause a ton of long-term problems. Keep in mind, though, that this sort of treatment is completely voluntary, and any doctor who doesn't go through the potential risks probably shouldn't be a doctor anyway. That, and the potential for fixing several of those nasty skeletons in the closet known as the human genome is motivation for quite a few, despite the risks.

    --
    My other Sig is .40 caliber.
  8. Re:I don't care what they say.. by Angry+Toad · · Score: 2

    Errr...only if you affect the germ cells (sperm&eggs). Otherwise no altered trait can be passed along.

  9. I'm Safe.. by ackthpt · · Score: 4, Funny
    I've got PGGP - Pretty Good Gene Protection

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

    --

    A feeling of having made the same mistake before: Deja Foobar
    1. Re:I'm Safe.. by Anonymous Coward · · Score: 0

      Watch out, when you die grave robbers might unencrypt you.

    2. Re:I'm Safe.. by Anonymous Coward · · Score: 0

      I've got PGGP - Pretty Good Gene Protection

      Celibacy only prevents genes from being carried to the next generation.

    3. Re:I'm Safe.. by nmb3000 · · Score: 1

      What? No recursion? How about:

      PGGP Generated Gene Protection.

      --
      "What do you despise? By this are you truly known." --Princess Irulan, Manual of Muad'Dib
      /)
  10. Re:I don't care what they say.. by EdwinBoyd · · Score: 2, Insightful

    While I see where you are coming from, this process is no different than surgery on a fundamental level. Similar to removing a tumour or cist, it is a proceedure that if done properly can vastly improve the quality of life for the patient. According to the article after the 'cut' is made the body repairs the strand itself, so no insertion of new genes are required.

  11. "It is the business of the future to be dangerous; by StefanJ · · Score: 4, Interesting

    "and it is among the benefits of science that it equips the future for its duties."

    -- Alfred North Whitehead, 1927

  12. I only agree partially... by bennomatic · · Score: 4, Insightful
    There are indeed dangers, but we've been doing this sort of thing for thousands of years; breeding of animals and plants is an old, old practice.

    I know people who are geneticists, and who work in a lab where they are able to essentially make a mouse to order. You want one that grooms obsessively, here you go! Want one that glows in the dark? You got it. Just because they do it through genetic manipulation rather than breeding doesn't make it any more evil than other means.

    What it does do is accelerate our ability to learn about life. Should we take things in measured steps? Absolutely! We should also have been more careful about asbestos, lead based paint, DDT, agent orange and more. But should we ignore these amazing advances? Absolutely not!

    --
    The CB App. What's your 20?
    1. Re:I only agree partially... by RealAlaskan · · Score: 1
      ... we've been doing this sort of thing for thousands of years; breeding of animals and plants is an old, old practice.

      ... a lab where they are able to essentially make a mouse to order. You want one that grooms obsessively, here you go! Want one that glows in the dark?

      I think there's a slight difference between selective breeding (which determine which of the genes already present in the species get expressed) and introducing new genes which were never before found in that species.

      I see nothing wrong with these new techniques, just as I see nothing wrong with nuclear fusion, but I think your supporting argument is needlessly weak.

    2. Re:I only agree partially... by bennomatic · · Score: 1
      Yeah, I got that "my argument could be better" feeling in the pit of my stomache as I was writing, but I figured enough people would know what I meant. I'd thank you for the constructive criticism, but it was mostly just criticism.

      So, thanks for the criticism :-)

      --
      The CB App. What's your 20?
    3. Re:I only agree partially... by Lord_Dweomer · · Score: 1
      Thank you for your insightful post. I'd like to add to this that even if WE don't do the research, SOMEONE will because it is too profitable an idea to let slip. Better we do it and have control over it than others who might not be so peacefully minded.

      Remember, never underestimate Greed.

      --
      Buy Steampunk Clothing Online!
  13. That never stopped anybody... by nebaz · · Score: 3, Interesting

    Before the first atom bomb was detonated, there were some scientists that thought that the nuclear reaction would spread and ignite the entire atmosphere. Despite their reservations, the tests were done anyway. Screwing up has never been a risk people considered worthy enough to stop a scientific experiment.

    --
    Rhymes that keep their secrets will unfold behind the clouds.There upon the rainbow is the answer to a neverending story
    1. Re:That never stopped anybody... by John+Seminal · · Score: 1
      Before the first atom bomb was detonated, there were some scientists that thought that the nuclear reaction would spread and ignite the entire atmosphere. Despite their reservations, the tests were done anyway. Screwing up has never been a risk people considered worthy enough to stop a scientific experiment.

      Yeah, that made me feel good about the USA. President Truman was told, we are doing the math, and we are 35% done, and so far we have not found a spike in the graph which indicates the nuclear explosion will continue until all mass is gone.

      But then again, maybe Truman had alien data not available to the scientific community.

      --

      Rosco: "If brains were gunpowder, Enos couldn't blow his nose."

    2. Re:That never stopped anybody... by Solder+Fumes · · Score: 1

      And the reason we went ahead and tested nukes? It was because those "scientists" could not come up with any better theories than crackpot ravings. They were ignored because their argument had no merit. If we held back everytime someone mentions eternal doom, we'd have never struck a flint into some tinder.

    3. Re:That never stopped anybody... by Anonymous Coward · · Score: 1, Interesting

      According to Bill Bryson's book (A Brief History of Everything, if I remember the title correctly), every young incoming physicist on the Manhattan project was assigned the problem of proving that the atmosphere wouldn't catch fire or that some new form of matter that would alter the earth would not be created...

      Jack.

    4. Re:That never stopped anybody... by mpthompson · · Score: 1

      Well, that all good and fine, but I for one am just glad we don't live on planet Psychlo where a nuclear bomb causes their entire atmosphere to catch on fire -- at least in the movie.

  14. Re:Is X-SCID a DiVx format? by Tackhead · · Score: 3, Funny
    > NewScientist.com is reporting [ ...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."
    >
    > Just wondering.

    Funny you should ask. I just got this video from Paul Simon.

    It's a turn-around jump shot
    It's everybody jump start
    It's every moderator throws a hero up the crackpipe
    Singin' filk is magical and magical is pain, think of the boy in the plastic bubble
    I'm a Slashbot with a baboon brain

    (And I believe)
    These are the days of lasers on a shark's head,
    Lasers on a shark's head somewhere,
    Staccato signals of constant information,
    A loose affilliation of megabytes
    And gigabytes and baby...

    These are the days of miracle and wonder,
    This is a long-distance boast,
    The way the duplicate posts appear in slo-mo,
    The way we go for first post.

    The way we look to a Netcraft BSD troll,
    That's dying like a server at NewSci,
    These are the days of miracle and wonder
    And don't cry baby, don't cry...

  15. Homologous Recombination by Seoulstriker · · Score: 2, Interesting

    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.

    --
    I am defenseless. Use your button. Mod me down with all of your hatred.
    1. Re:Homologous Recombination by Anonymous Coward · · Score: 1, Informative

      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 by recombined into the chromosome at the break point. Thus, one can insert any gene into a specific place on any chromosome (in theory).

  16. Precise Gene Editing = Hex Editor by Proudrooster · · Score: 4, Interesting

    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 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.

    1. Re:Precise Gene Editing = Hex Editor by Anonymous Coward · · Score: 3, Funny
      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.
    2. Re:Precise Gene Editing = Hex Editor by harvardian · · Score: 2, Informative

      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 anemia, the DNA sequence GAG is replaced by GTG. This causes a glutamine amino acid to be incorporated into the Hemoglobin beta chain instead of a valine (this can be predicted since we know the entire triplicate-to-amino acid dictionary). Partly because glutamine is a charged amino acid and valine isn't, this causes Hemoglobin with this mutated beta chain to clump together when deoxygenated -- hence the sickle cell phenotype.

      So in this case it isn't true that we're hacking binary code. We're hacking a DNA code that we know enough about to fix simple point mutations like the one found in sickle cell anemia. As for other, more complicated, diseases, we are indeed still poking in the dark. But that doesn't mean progress isn't being made...

    3. Re:Precise Gene Editing = Hex Editor by SCVirus · · Score: 1

      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!

    4. Re:Precise Gene Editing = Hex Editor by k98sven · · Score: 1

      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 in a healthy person. They know what it looks like in a person with the disease. They know that without this protein, the T-cell will die. They know that without T-cells the immune system won't work.

      They don't know every last detail of the mechanism. But in this case; do they need to?

      They know that replacing these faulty cells will cure the disease. This can be done through a bone-marrow transplant from a healthy person. (Donors for which are very hard to come by)

      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.

      Yes you're being overcautious, I think. You're missing the point that this disease already has been cured through other methods. You're missing that they know what the effects of changing this are. You're missing the point that these patients have a terrible quality of life and a very short life-expectancy. The alternative is literally letting them die.

      You're missing the fact that they already are very cautious. They're not talking about using gene therapy to cure the common cold here. Gene therapy has so far only been used in cases like this, for very deadly diseases which we understand relatively well.

    5. Re:Precise Gene Editing = Hex Editor by Donny+Smith · · Score: 1

      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 not reliable, but look at the WAR3Z community - it's thriving and they're doing exactly the same thing - patching binaries based on trial and error. If individuals want to try out new things without harming others, let them give it a shot.

      "Self-protection alone can justify either the states tampering with the liberty of the individual or any personal interference with another's freedom."
      http://www.uark.edu/depts/comminfo/free speech/jsmi ll.html
      (Crappy /. code screws up URLs. Can't that be fixed?)

    6. Re:Precise Gene Editing = Hex Editor by John+Newman · · Score: 1

      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" gene therapy, where you can remove the cells from the body, them put them back in - mostly disorders of blood. So hurrah for them, and good news for the fairly limited set of patients this might help. Otherwise, for single-gene disorders, there's no paradigm shift here - we've been trying to do gene therapy for a while, and we know exactly *what* to do, just not *how* best to do it.

      For more complex problems, ones that cannot be traced to known mutation in a single gene, this will not be used in the clinics any time soon. It's value is for the researchers. Biologists who work on model organisms like yeast and mice have, for years now, been able to do precision "knock-ins/knock-outs" - that is, very precisely deleteing a particular gene, or replacing it with a peculiarly defective version that will help you figure out the function of the gene. This is an incredibly powerful technique for working out the biology of a complex system, and it's one that has been essentially inaccessible to human biologists.

      These guys have promised that they can target any arbitrary gene with their cutsomized proteins. If so, and if they can do it for a reasonable price, it will be a major boon for human biologists, giving them access to the same powerful genetic techniques that yeast and mouse biologists have found so useful. But all this work will happen in cultured cell lines, not in people. No one's going to start randomly "hacking" the germ-line quite yet.

    7. Re:Precise Gene Editing = Hex Editor by lukesl · · Score: 1

      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 really is that simple. In theory, this could be true for a lot of diseases, but we only know the details for a few simple cases, which include SCID, sickle-cell anemia, and a couple other diseases that are really outliers. "Just because we can do something, doesn't mean we should."

      I understand your point, but try telling that to a patient with one of these diseases. In any case, this research is probably going to be be more powerful as a research tool than as a therapeutic tool.

    8. Re:Precise Gene Editing = Hex Editor by Anonymous Coward · · Score: 0

      Great, now the gene splicers have the equivalent of a hex editor, but still have no clue what they are editing.

      Actually, this isn't anything close to a hex-editor. It's more akin to having a program that will zero in on a known defective block of memory and corrupt it further. It is then hoped that the regular system will recognize the corruption and fetch a correct copy from backup.

      (The zinc finger nucleases recognize a specific bad sequence and cut the DNA there. This trashes the gene at that location. They then hope that the cell's natural repair process will repair the DNA damage, with a fix in the faulty sequence.)

    9. Re:Precise Gene Editing = Hex Editor by CupBeEmpty · · Score: 1

      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 system is changing how it normally runs. That has been the dogma in cellular biology and genetics for a long time. To find out how systems work scientist make mutations. Stop the function of processes and find out why they stopped, whats necessary and whats important.

  17. Wow. Birth Defects No More by Anonymous Coward · · Score: 0

    This means the son of the goatse.cx man will not be posing on the Internets.

  18. Re:I don't care what they say.. by iostream_dot_h · · Score: 2, Insightful

    "short term good"? This has the potential to eradicate several crippling diseases and increase the quality of life of an innumerable number of people. You're going to have to give a better reason against gene therapy than "you're acting as god." You're personal religious opinions are not welcome in a diverse global arena, which is (or ought to be) tailored toward the pursuit of the greater good. You only serve to alienate those of us who may not subscribe to the notion that scientific progress runs counter to moral norms (a concept whose ontological coherence is debatable).

    On a related note, this kind of attitude is precisely why scientific progress often stagnates. Irrational fear hinders societal good. Messing up a few times, as cold and calculating as this might sound, may be necessary in order to develop effective medicines and therapies and pinpoint options that do not work. The individuals who sign up for clinical trials are aware of the risks, and those who do should be applauded for their selfless contribution to the good of humanity.

    Regardless of your personal beliefs, gene therapy is one of the most promising developments in medicine. It has the potential to revolutionize our perceptions of the human body.

  19. Re:I don't care what they say.. by Prophetic_Truth · · Score: 1, Informative

    I would say that's a bit paraniod, and possibly based on some educational time spent watching the sci-fi channel.

    PFFFT!!! GIVE ME A BREAK! You want the truth!?

    I predict the following Prophecy:

    Years from now we will have enhanced ourselves to the point where our skulls grow large and our eyes turn black. We no longer need to speak with our tounges, rather our minds. We no longer use sex as a means to reproduce. We have geneticly engineered ourselves to do things even I, Prophetic Truth, can not invision. BUT THERE'S A FLAW! A horrible flaw which can not be fixed by our future selves. A flaw of such consiquence that it will wipe out our species.

    The solution?

    Time travel, anal probes, and sperm collection.

    The Prophecy has already been fulfilled

    --
    time is a perception of a being's consciousness
    time is your 6th sense, the wierd ones are 7+
  20. Re:I don't care what they say.. by Rei · · Score: 1

    While the gp was really just being flamebait, there is a significant element of danger in genetic engineering.

    Example: biobricks are really advancing, and you can already get custom genes made for a price that anyone can afford. Lets say that biobricks advance to the point where it's relatively trivial to make a gene that produces proteins that create Sarin, for example (or perhaps a different nerve agent with a longer life). You insert the gene into a common strain of phytoplankton found all over the globe, along with another gene to help give it a competitive advantage against its wild relatives. You then release it into the ocean (preferably in multiple points to speed up the process), and wait. The discovery of the source of the gas would likely be too late; almost everything with a nervous system would end up dead as the wind carries the gas across continents. A bioengineered apocalypse, in short, produced by someone with a bit of bioengineering knowledge and a couple thousand dollars investment.

    --
    sed "s/SJW.*$/... never mind. I was about to say something stupid, and also, I'm a troglodyte./Ig"
  21. Re:Is X-SCID a DiVx format? by Anonymous Coward · · Score: 0

    Just stay away from the brown X-SCID man.

  22. Re:I don't care what they say.. by ciroknight · · Score: 3, Insightful

    Forgive me for not believing in your esoteric views of this "God" character nobody has any proof of, but I feel genetic manipulation is going to be one of the few things that allow us (the human race) to continue existing.

    As time goes on, we defeat simple diseases such as the bubonic plague, then upgrade to tougher ones like smallpox. We're now at the point where the only communicable diseases that are seriously fatal are biologically engineered bacteria, and viruses. On top of that, we've still got Cancer to worry about, which is kicking our asses.

    While it may be cheaper to produce drugs for everyone alive and distribute them to everyone, no company in their right minds would do this. But if we could figure out genetically how to teach our immune systems to deal with cancer, and certain foreign invaders, we could save millions simply by changing our children's genes.

    I think the biggest paranoia attributed to genetic engineering is the fear of change; just because we know how something works now, and we assume that it'll continue working the same way into the future, we give up the notion that we can change things for the better or for the worse. Yes, we are foulable creatures, but at the same time, we now know how to clean up our mistakes. It's far past time we take our fates into our own hands. Why use medicines that can screw up other things in our bodies when we can simply prevent the problem from occuring naturally?

    --
    "Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
  23. Mutations... by John+Seminal · · Score: 3, Insightful
    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?

    --

    Rosco: "If brains were gunpowder, Enos couldn't blow his nose."

    1. Re:Mutations... by Fadeproof69 · · Score: 1
      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?

    2. Re:Mutations... by Joe+Tie. · · Score: 1

      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 for. In any case, just like some groups today won't accept blood transfusions I'm sure there'll be humans who won't take advantage of new genetics based medical technology. If in some sci-fi channel crazy situation we wind up taking ourselves out, fine, the amish, jehovahs witnesses and the like can just keep on going as they did before.

      --
      Everything will be taken away from you.
    3. Re:Mutations... by Frumious+Wombat · · 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 simply kills you more slowly). Two copies, and you have sickle-cell anemia, and die early. The benefit of the gene outweighs the risk only as long as you don't have effective treatments for malaria. If you have good control of malaria, then it's better that you don't have that gene at all, as the net effect is deleterious.

      We can't be sure of all of the ramifications, so we should make backups of anything we delete (CVS for your genes, so to speak), but in the end if we can short-circuit the process of better adapting ourselves to our environment, then we should do it.

      A thousand years ago, genes that helped you resist smallpox and survive poorly fed winters were essential. Now, genes that coded for better DNA repair and reduced fat synthesis/uptake would be a better adaptation. We can wait for them to arise naturally (teenagers start keeling over from hardening of the arteries due to our first-world diet before they can reproduce), or we can engineer them, and introduce them into volunteers.

      --
      the more accurate the calculations became, the more the concepts tended to vanish into thin air. R. S. Mulliken
    4. Re:Mutations... by John+Seminal · · Score: 1
      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 kills you more slowly). Two copies, and you have sickle-cell anemia, and die early. The benefit of the gene outweighs the risk only as long as you don't have effective treatments for malaria. If you have good control of malaria, then it's better that you don't have that gene at all, as the net effect is deleterious.

      We can't be sure of all of the ramifications, so we should make backups of anything we delete (CVS for your genes, so to speak), but in the end if we can short-circuit the process of better adapting ourselves to our environment, then we should do it.

      A thousand years ago, genes that helped you resist smallpox and survive poorly fed winters were essential. Now, genes that coded for better DNA repair and reduced fat synthesis/uptake would be a better adaptation. We can wait for them to arise naturally (teenagers start keeling over from hardening of the arteries due to our first-world diet before they can reproduce), or we can engineer them, and introduce them into volunteers.

      That is a good post. My point was, sometimes people think about the immediate and not the long term ramifications beyond our generation and the next. Not that our cave living ancestors probably gave much thought about us. But since we know nature works, I would say lets not mess with a good thing. Not for a few extra years of life, in our 80's or 90's, when we'll probably not be able to enjoy it. 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.

      It is like a game of chess, but the rules change. And we think we have a chance to change a rule to our benifit. But can even our best see the end game? Or are we just making a good guess, forseeing the next 4 or 5 or 6 moves?

      --

      Rosco: "If brains were gunpowder, Enos couldn't blow his nose."

    5. Re:Mutations... by BewireNomali · · Score: 2, Interesting

      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 net.

      the reason this is interesting is that we can see maybe a number of generations down the line... se how current trends in gene distribution occurred and possibly predict future trends.

      --
      un burrito me trampeó.
    6. Re:Mutations... by BewireNomali · · Score: 1

      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.

      --
      un burrito me trampeó.
    7. Re:Mutations... by Anonymous Coward · · Score: 0

      >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?

      Your logic is flawed.
      We could just so easily cure the cancer right now, and when the super environmental change comes along, change the genes again.
      Simple.

    8. Re:Mutations... by CharlesEGrant · · Score: 1
      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 interaction of those random mutations with differential reproductive success. It isn't laying up clever mutations for a rainy day.

      I'm sure DNA therapy will have long term unforseen consequences, but then so did the invention of antibiotics. I don't understand your basis for distinguishing between the two. I suppose you could have a religious belief that mutations are sent by god, but then so is Y. pestis.
  24. More detail, less ZFN by shift.red.avni · · Score: 1

    http://www.biologynews.net/archives/2005/04/05/res earchers_pioneer_new_gene_therapy_technique_using_ natural_repair_process.html

  25. In the case of specific genetic diseases by MichaelPenne · · Score: 2, Informative

    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 mediates transduction of the c signal. Mutation of its gene also causes SCID."

    http://en.wikipedia.org/wiki/Severe_combined_immun odeficiency

    1. Re:In the case of specific genetic diseases by Proudrooster · · Score: 2, Interesting

      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 of Molecular and Cell Biology at University of California, Berkeley. From his article "Crisis position". [EL]


      So does this mean that until we understand the environmental interactions between, you won't fully understand how the organism will express its genes. This is similar to programming, since a program may run differently based on the environment in which it is run.

    2. Re:In the case of specific genetic diseases by CTachyon · · Score: 1

      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.

      --
      Range Voting: preference intensity matters
  26. Re:I don't care what they say.. by John+Seminal · · Score: 1
    Science is full of ethical questions, bio-sciences especially. What we can do we will do ( as a race ), that's a proven fact. It's better to do what we will do in the open, in front of many eyes, instead of being done in a third world country for some wacked out group intent on bringing their own version of reality to pass.

    Just lable the experiments as labratories making weapons of mass destruction. LOL. Bomb. Invade. Elect pro-western government. Move on to next country.

    But seriously. With genetic engineering, do you think that a third world country will work on curing cancer when they can work on building roads or opening hospitals?

    The true threat is some western scientists move shop to a third world country. But we can track them down and arrest them for violating international law. Plus, the possibility of being punished in the third world country, and not the USA should be a huge detterant. We don't even need a fair trial.

    --

    Rosco: "If brains were gunpowder, Enos couldn't blow his nose."

  27. Re:I don't care what they say.. by Anonymous Coward · · Score: 0

    You exist in a dimension of space and time and you think its all coincidence..The universe has no purpose, its just here.

  28. Not specific enough for safety (yet) by G4from128k · · Score: 3, Informative

    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).

    --
    Two wrongs don't make a right, but three lefts do.
    1. Re:Not specific enough for safety (yet) by Anonymous Coward · · Score: 0

      Don't have the specific details, but zinc fingers are modular to the point that you can build them to recognize sites in increments of 3. Most of the engineered proteins I know of use an 18 base pair site which is long enough to be unique in almost any organism's DNA.

    2. Re:Not specific enough for safety (yet) by Anonymous Coward · · Score: 1, Informative

      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.

    3. Re:Not specific enough for safety (yet) by Anonymous Coward · · Score: 1, Informative

      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 repaired using the sister chromosome as template. Therefor it does not introduce the gene in unexpected places. Easy.

    4. Re:Not specific enough for safety (yet) by Anonymous Coward · · Score: 0

      Nonsense. You BLAST the seqence to make sure it's unique. We sequenced the human genome for a reason.
      There's no need for probabalistic arguments about likelihood of a sequence coming up when you've got the whole thing.

  29. Re:I don't care what they say.. by Anonymous Coward · · Score: 0

    I'm allowed to think whatever I want, and as there is no proof in any general direction, I simply don't think about it. Besides, if "God" didn't want us to manipulate our genes, it would stop us.

  30. with a PhD in Genetic engineering by cinnamon+colbert · · Score: 4, Informative

    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,

    1. Re:with a PhD in Genetic engineering by Anonymous Coward · · Score: 3, Interesting

      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 spread out over the cells they are treating.

      If I had a disease of the blood requiring gene therapy, I'd rather have this treatment than gene therapy using an adenoviral vector - that method is just asking for trouble with near random genomic insertion.

      It's a clever idea - hope to see it developed further :)

  31. When does the emacs module come out? by Jeff+DeMaagd · · Score: 1

    Really, emacs is a whole lot of stuff that just happens to have text editing functionality along with it, so why not genes?

  32. having RTFA, by cinnamon+colbert · · Score: 0

    I note that the process involves removing blood from the body, running the process on cells purified from teh blood, and then reinjecting the cells back intothe patient.

    I believe, but am not an expert in this field, that the simple process of removing cells from the body is in and of itself, highly mutagenic.

    There is *no way* the cells could be checked before reinjection.

    In any event, it is an interesting piece of science, but a LONG way from clinical practice - stay tuned for the update in 2020.

    1. Re:having RTFA, by saytan · · Score: 1

      The process of removing cells from the body isn't mutagenic. You are correct, however, in the assumption that it isn't ready for clinical practice quite yet, but it should be within a few years. At the moment, this only looks useful for single-gene traits caused by simple mutations (i.e. small deletions/insertions or single nucleotide polymorphisms, as opposed to major chromosomal rearrangements).

    2. Re:having RTFA, by Anonymous Coward · · Score: 0

      Are you sure removing cells is not mutagenic ? How would you verify this ? In mice, you could setup, say, in inactive GFP, or use a positive selection like an inactive G408 antibiotic maker, or HPRT or whatever, and inject balbc with akr cells, or whatever actually would work with out MHC rejection, and count how often it gets turned on, but you can't measure things in vivo in humans very well.

    3. Re:having RTFA, by lockholm · · Score: 2, Informative
      Actually, the simple process of removing blood from the body is not mutagenic - for example, think of blood transfusions, where blood is not only removed from the body, but frozen and stored.

      Also, the large percentage of blood consisting of the red blood cells and platelets don't actually have any DNA in them to be mutated - these cells don't have nuclei.

      Finally, in bone marrow transplants, one method of collecting the marrow cells to transplant is to hook the donor up to a machine through which their blood flows. In the machine, the stem cells (the cells that divide to produce all the elements of blood, including red blood cells and immune cells) are separated out, and these are the cells that are then transferred as the marrow transplant. You can find out more about this process here. The objective with this treatment is to cure the cancer - so if simply removing the cells from the body causes cancer, it would be a very counter-productive treatment.

  33. Corrected link to More detail, less ZFN by WillAffleckUW · · Score: 1

    I think you meant the biology news link to the same research

    Your original has some extra characters and can't be used.

    --
    -- Tigger warning: This post may contain tiggers! --
  34. Good luck getting medical industry to fund this by Locke2005 · · Score: 2, Insightful

    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!"

    --
    I've abandoned my search for truth; now I'm just looking for some useful delusions.
  35. Re:I don't care what they say.. by Rei · · Score: 1

    Bubonic plague isn't "defeated"... FYI.

    --
    sed "s/SJW.*$/... never mind. I was about to say something stupid, and also, I'm a troglodyte./Ig"
  36. What if we get hit by an asteroid by MichaelPenne · · Score: 1

    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).

  37. Re:I don't care what they say.. by Anonymous Coward · · Score: 0

    Maybe something you don't understand is that diseases, cancerous cells and the like are an evolution of life themselves. Something such as a cure for cancer is not only hypocritical in the sense that it is essentially killing a form of life, the fact is that it is an expression of natural population control.

    Being stuck in a master-slave mentality of good and bad makes it remarkably simple for points of view like yours to seem reasonable when in fact they are intrinsically hypocritical. Just because something hurts or kills doesn't make it bad and just because something feels good or prolongs life doesn't make it good.

  38. The biggest danger of bubble boy disease... by isny · · Score: 1

    [obscure Seinfeld reference] The Mooks.

    1. Re:The biggest danger of bubble boy disease... by slazar · · Score: 1

      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.

      GEORGE: MOOPS,

      DONALD: MOORS!

  39. Sounds like Strohman is talking about by MichaelPenne · · Score: 1

    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.

  40. When are we going to see the treatments by Anonymous Coward · · Score: 0

    I am getting real tired seeing all this great research, only to realize that treatments are the same tired treatments at the beginning of the century.

    NONE OF THIS RESEARCH has changed people lives.

    Stop with the fairy tales. People have not and will not get any new cures to any existing health issues.

  41. Re:I don't care what they say.. by jericho4.0 · · Score: 1
    Devil's Advocate; There must be a point at which it no longer makes sense to spend resources and risk opening Pandora's Box just to save sick people. People die.

    GE is the technological revolution to shame them all, and will have massive impact on our society.

    That said, I'm all for it, and will be first in line for gills.

    --
    "A language that doesn't affect the way you think about programming, is not worth knowing" - Alan Perlis
  42. Re:I don't care what they say.. by gr3g · · Score: 1

    because viruses never alter DNA

    --
    "It has always been this way and it won't change, god bless the fucked up USA" The Briefs
  43. Thats why have brains by elucido · · Score: 1

    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.

  44. Yeah by elucido · · Score: 1

    Thats why we don't depend on that industry. Buy your drugs in India, take a vacation and come back with your genes fixed.

  45. Re:I don't care what they say.. by iostream_dot_h · · Score: 1

    "Just because something hurts or kills doesn't make it bad and just because something feels good or prolongs life doesn't make it good."

    If you don't believe that human life is intrinsically valuable, and if you don't think that our cognizance and rationality are unique characteristics, then there is something fundamentally flawed about your point of view. Human life is uniquely valuable and we ought to make efforts to improve it. READ: It is not okay to acquiesce supinely while individuals needlessly die, especially when techniques are available to prevent such a thing from happening. Prolonging and improving human life is good. Ending it prematurely is bad. Simple? Sure. Deontologically sound? Definitely.

  46. Precise Gene Editing = Patch Files by cookie_cutter · · Score: 2, Informative
    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 the hell gene does; we just know to a high degree of certainty that a particular error causes a particular phenotype.

    This new technology, if it lives up to the hype it's given here, could mean we can fix these kinds of diseases.

    1. Re:Precise Gene Editing = Patch Files by Proudrooster · · Score: 1

      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" 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 thought we would have a DNA construction kit by now, where you could hook it up to your computer and make custom organism with a limit on genome complexity e.g. (Banana Tomato Plant) or custom pets e.g. (Pet dog with tiger stripes). I believed we would have a complete understanding of DNA by Y2K, but then again I also believed that in the future we would have flying cars and computers would be able to program themselves with voice commands from the end users making programmers obsolete. Now I am wondering if we will figure it all out before my life is over.

  47. Isn't that how Umbrella does it? by Anonymous Coward · · Score: 0

    Yikes!!!!

  48. Re:I don't care what they say.. by Frumious+Wombat · · Score: 1

    Actually, we have a whole number of 'seriously fatal', excessively natural, diseases left. AIDS, Flu, Ebola, Malaria, and TB come to mind, plus the various drug-resistant streps, West Nile.

    Genetic manipulation might allow us to finally treat diseases by some method other than mining other organisms for specialized toxins, then hoping the disease (which reproduces on the seconds to minutes time scale) doesn't become resistant too quickly.

    --
    the more accurate the calculations became, the more the concepts tended to vanish into thin air. R. S. Mulliken
  49. Re:I don't care what they say.. by ianbean · · Score: 1

    I don't understand your arguement that cancer is a form of life. It is simply your own cells that have become defective. Curing yourself of cancer is like having your appendix removed (except that it's harder to achieve). It's not a form of life. Your immune system actively does this every day.

    Cancer isn't an evolution of life either - life has spent billions of years evolving to a point where it is really good at preventing cancer. A car with smashed-in bumpers and its engine stuck on isn't a new type of car, it's just a damaged one.

    Sure, cancer does contribute to population control, but if you're worried about that then maybe you should be campaigning against soap and fresh drinking water. Those make more of a difference than cancer treatments ever will.

  50. Re:I don't care what they say.. by Anonymous Coward · · Score: 0
    No, I think all 20 billion years' worth of time and countless light years of space were created by a magical bearded guy just so you and I can exist on a little planet and persecute the people that don't believe in fairy tales.

    Yeah, THAT makes sense.

  51. Re:I don't care what they say.. by mlyle · · Score: 1

    ...the only communicable diseases that are seriously fatal are biologically engineered bacteria, and viruses.

    As opposed to what, just-kidding-fatal? :)

  52. Gattaca!! by tyman · · Score: 1

    My children can finally be bred as Valids!!!

  53. Re:I don't care what they say.. by BewireNomali · · Score: 1

    guess it's a matter of perspective.

    aren't cancer cells defective in that they are effectively immortal? They divide endlessly, choking off pertinent cells in an organ or system? to that end, they are a form of life... just an entropic form. thus the defect in cancerous cells is the greed with which they use resources and disrupt essential functionality.

    i'd go as far to say that understanding and being able to control some of the processes in cancerous cells will lead us to significantly increase our life spans.

    going of on a tangent: are cancers cells prone to the same replication errors that normal cells are prone to over a long enough time span?

    --
    un burrito me trampeó.
  54. Re:I don't care what they say.. by deimtee · · Score: 1

    The way to look at cancer is not as a thing that is invading the body, but as a colony of things. They grow, divide, evolve and die. That is why it is generally fatal. The first chemo treatments will often kill >90% of cancer, but what survives is the cells that have mutated to be resistant. So the doctors prescribe a different chemo. Once again the susceptible cells die, but the colony goes on.
    There are basically only three ways you can permanently beat cancer:
    1/ Sometimes you can cut it out - and get it all.
    2/ Sometimes you can beat it down to the point where the immune system can beat it.
    3/ Sometimes the cancerous mutation involves a weakness that makes a treatment 100% lethal to the cancer.
    But those are rare, mostly you are buying time not a cure.
    Back to the tangent, yes they are susceptible to replication errors, but in a colony those provide diversity for evolution to select from. That is one of the things that make cancer so nasty.

    --
    I'm guessing that wasn't on their radar screen...
  55. Re:I don't care what they say.. by Pecisk · · Score: 1

    See, I guess mostly fear from change are not because changes are bad. Changes are usually good - those who doesn't kill us, make us stronger, and we learn a bunch of new stuff even if things don't work out as we hoped for.

    Problem is in inrationality, emotionality hidden by... rationality. If everything is done in colobrative way (like open source), I would believe that process. And such change in state of mind of the human is started - but it comes slowly. People don't trust each other, people don't trust other nation, people better hang on on the stupid believes which leads them nowhere than risk with trusting to others.

    Because if someone fails them, they hearts are broken, they don't want to trust anyone. They better off with single-minded, narrow-wided point of view, because it allows them to live peacefully.

    For example, someone says coorporations are out here for money. NOT exactly. I guess they are out there for satisfy their greed to money and power. Why? Because companies are usually headed by someone for whom money and power is everything in his life. Must be a very misguided soul, if you ask me. And that is what I FEAR most. I fear human being who claims to have reasonable interests, yet, it he is laying to himself to make himself happy.

    Went a little offtopic, but nevermind...

    --
    user@ubuntubox:~$ stfu This server is going down for shutdown NOW!
  56. It's Darwin's Radio by GomezAdams · · Score: 1

    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.

    --
    Too lazy to create a sig...
  57. Re:I don't care what they say.. by Lord_Dweomer · · Score: 1
    "On top of that, we've still got Cancer to worry about, which is kicking our asses."

    Um....I don't mean to be a jerk, because cancer is a horrible horrible thing, but how is it kicking our asses? True, we haven't found a cure for all of it, but we can sure as hell get rid of a lot of it. And don't forget that our races birth rate still far surpasses our death rate. Now, the bubonic plague, that wiped out 2/3 of Europe, that is significant.

    --
    Buy Steampunk Clothing Online!
  58. mod parent up ! by free2 · · Score: 2

    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."

  59. Myotonic Muscular Dystrophy cure by RhettLivingston · · Score: 2, Informative

    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.

    1. Re:Myotonic Muscular Dystrophy cure by toddreichert · · Score: 1

      If this is rhett livingston who I worked with in the late 90's at a certain aerospace company located in the midwest, let me know, thanks todd. PS I was being purposefully vague just in case you did not want details posted.

  60. I \cannot agree with the common modded-up thesis by awfar · · Score: 1

    Selective breeding in the past did not create the equivalent of a "critical mass". One or two relatively minor mutations across may be tens or hundreds of specimens, then later, more interbreedings to select the characteristics. All the while, nature and time being the moderator allowing the weak, damaged, or DANGEROUS to fail or be isolated in the necessarily small group. Instead, a hurried implementation of mass genetic change could conceivably create a critical mass, such as planting a gene corn throughout the world, and though maybe technically inferior over a long time, but strong enough to survive in the ecosystem and disrupt native species, even though the erosive nature of time and nature would eventually win by selection.

    Does ten small, hairless dogs have a chance to propagate in the wilderness?

    Does a million? A big difference.

    I simply cannot agree that old style breeding == new style en-masse genetic manipulation.

  61. the article by bikerguy99 · · Score: 3, Informative

    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

  62. Different types of DNA repair by bradbury · · Score: 1
    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 cut the defective DNA to initiate the homologous recombination process. If you had bothered to read the abstract you would understand that they are also providing an "an extrachromosomal DNA donor" (I would suspect on a plasmid) as the source for the corrected DNA sequence.

    So this process *need not* be error prone. Of course they are obviously looking at a number of cells after the fact to determine the fraction of cells in which the process was successful. If one did this with stem cells (which seems to be where they are going) and put them back into the body then one would indeed be able to correct SCID or sickle cell anemia. Diseases that are present in adults in specific cell types such as cystic fibrosis or muscular dystrophy are going to be a bit trickier.

  63. Re:I don't care what they say.. by amchugh · · Score: 1

    Speaking as a type-I diabetic, it would be nice to be cured, but not at the expense of becoming the carrier for some god awful flu mutation that kills 100 million people. When you can't even quantify the risk, it's usually a good idea to pour more research into what you are doing.

  64. Re:I don't care what they say.. by ciroknight · · Score: 1

    Yeah we can treat it, but at what cost? I know more people who have cancer than I'd like to have known; practically all have either died of the cancer being non-responsive to chemo, or die because the chemo reduced their immune response so severely that an ordinary sinus infection or the flu killed them.

    Once again, Slashdot obscures the meaning of "Our". If you look at deathrates of the United States, Cancer is up at the top of the list, next to heart disease. Heart disease can be dealt with by simply eating better, no need to fix our genes there, but cancer, we can simply give people a highly toxic drug cocktail, and tell them goodluck.

    --
    "Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
  65. Precision Gene Editing by intragamgal · · Score: 1

    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 by dioxin and radiation and any number of chemicals eg PCB's etc. in the environment. So how is this technique going to change the face of being human? And to those who have made fun of the illness, I suggest that you fully investigate the illness and the suffering it causes thousands of people every day. There are {at current tally} at least 85 variations of Primary Immune Deficiency - X-linked SCID being only one of them. The technique mentioned will only cure one variation anyway. Not the other 84. Still it is worth pursuing as more knowlege is another link in the chain eliminated. Check out; http://www.jmfworld.com/ http://www.pia.org.uk/