8 ms·
Five big mysteries about CRISPR’s origins
- neom 10y agoPeripherally related book recommendation: https://www.amazon.com/Vital-Question-Evolution-Origins-Complex/dp/0393088812 https://www.amazon.com/Vital-Question-Evolution-Origins-Comp... Someone here on HN recommended it to me and it was an awesome read (that I doubt I understood).
- joekrill 10y agoI really loved this book -- it's definitely highly recommended by many folks (I think know Bill Gates was a big fan). But I don't recall it containing much -- if anything at all -- about CRISPR?
- neom 10y agoIt doesn't directly. However, in reading the article I was able to think about what I learned about prokaryotes, archaea, and generally just feel like having read that book I enjoyed the article a lot more, if that makes sense? :)
- joekrill 10y agoAh got it -- I thought maybe I missed something in there! Was a great book, for sure.
- joshbaptiste 10y agoI listened to the audio book and must state that it's very involved and not really for the layman like me. I got lost on the eukaryotes explanation which lost me for much of the other topics.
- rqebmm 10y agoI've found audiobooks (and podcasts) to be great for lighter reading, but I tend to drift in and out. That's not a great system for something more scaffolded like a textbook where you have to thoroughly understand each part in order to build the next piece on top
- neom 10y agoAs someone who is severely dyslexic: basically the only way I can consume large amounts of written content in an acceptable amount of time is audio book. Thankfully- I'm pretty sure listening to an audio book for me is the same level of comprehensible intake as a non-dyslexic via written word. :)
- alextheparrot 10y agoIn line with this, I'd also like to recommend 'The Gene'[0]. The author has informed me of new things (Even though I studied biochemistry during college) and also focused a lot on the ethical discussions relating to genetic modification. It also directly discusses CRISPR as it is quite new. I'd recommend all of Mukherjee's other books as well (Mainly Emperor of all Maladies). [0]https://www.amazon.com/dp/1476733503 https://www.amazon.com/dp/1476733503
- fossuser 10y agoI'd second this recommendation - currently reading it right now and it has the nice combination of being really interesting and really easy to read. Mukherjee's style is really clear and enjoyable.
- Splendor 10y agoIIRC it was on Bill Gates' book list last year.
- s_dev 10y agoI found this Kurzgesagt video a useful intro to CRISPR: https://www.youtube.com/watch?v=jAhjPd4uNFY https://www.youtube.com/watch?v=jAhjPd4uNFY
- problems 10y agoRadiolab also did a very good job with it: http://www.radiolab.org/story/antibodies-part-1-crispr/ http://www.radiolab.org/story/antibodies-part-1-crispr/
- Wonnk13 10y agoFresh Air on NPR yesterday did an hour where they discussed gene editing and the such. Incredibly fascinating! I was recently diagnosed with colon cancer (i'm doing great) and I'm totally rediscovering genomics. Having not given any thought to this stuff since AP Bio in highschool so many advances have been made!! I'm especially curious how machine learning will play into all of this (the broader genomics community). So much more interesting than the "cyber" stuff I work on now :)
- palamoun 10y agoI listened to this program on NPR yesterday too and was very intrigued. For everyone else, the guest on Fresh Air was Michael Specter, who recently wrote an article in the New Yorker about CRISPR. Here's a link: http://www.newyorker.com/magazine/2017/01/02/rewriting-the-code-of-life http://www.newyorker.com/magazine/2017/01/02/rewriting-the-c... (Glad you're doing well by the way)
- benrapscallion 10y agoMachine learning was heavily used in the most recent version ("Ruleset 2") of the genomewide CRISPR library design. https://blog.benchling.com/rule-set-2-the-science-behind-the-metric/ https://blog.benchling.com/rule-set-2-the-science-behind-the... http://www.nature.com/nbt/journal/v34/n2/full/nbt.3437.html http://www.nature.com/nbt/journal/v34/n2/full/nbt.3437.html
- epberry 10y ago> often only about one bacterium in 10 million will gain a spacer that lets it defend itself. Incredible... The scale and probabilities involved in these processes are mind blowing. In general I liked this article because it posed a few open ended research questions and explained why they were relevant. As someone who barely knows the difference between a bacteria and a virus I felt it was pretty understandable.
- woliveirajr 10y ago> "There are typically 40 million bacterial cells in a gram of soil" [1] That would mean 4 in each gram of soil, if Wikipedia is correct. Bacteria scale is so disproportional to what we deal in daily basis that I'm pretty sure we know almost 0.01% of all existing species, families or any other kind of grouping them you like. [1] https://en.wikipedia.org/wiki/Bacteria https://en.wikipedia.org/wiki/Bacteria
- edge17 10y agoThese types of probabilities are all over the place though. Even in chips with a billion transistors or more we have to design redundancy because manufacturing at that scale isn't perfect. Imagine there's a 1 in 10 million chance of some sort of manufacturing defect on some modern processor; you're pretty much guaranteed 100 defects.
- problems 10y agoThe amount of knowledge we lack with regards to species still surprises me. We can do pretty well with plants and animals, but we don't even have good genetic analysis on types of mushrooms that grow on the surface, picking up any field guide often results in "this looks quite like it, but the ones from this part of the world make people sick and we don't actually know if they're related".
- toufka 10y agoWe really don't have a good grasp even on the variety of plants and animals. We do know a lot about the foundations of each organism's genetics, but we're just now peeking into their variation. And that is precisely why you see biotech starting to get interesting and useful above and beyond basic discovery. When we start looking not just for 'how life works', but for 'how does it glow', 'how does it climb', 'how does it live so long', we start getting pretty cool answers. But we're JUST starting. Much of what know comes from a short list of organisms (that can grown in lab conditions). There is a 'model organism' [1] for the simplest organism (that can grown in lab) for each step up the ladder of biological complexity (towards humans). - bacteria : E coli - eukaryote : yeast - multi-cellular : nematode - plant : arabidopsis - nervous system : fruit fly - spinal cord : zebrafish - mammal : mouse - primate : monkey There are definitely others (sorry for leaving out your favorite model...), but in general, we know a lot about these model organisms. And that covers a wide gamut, but still we know very little specifics about everything in between. Further, because we've been so focused on (funding) human health, we know a lot about how humans work. But what we've missed is all the ancillary tech that could be used to support human health, or human society/technology/industry at large. CRISPR proteins (and its similar tech) which will end up revolutionizing our biological tehcnology come from non-human-like, and otherwise unfundable hobby research. PCR/GFP all came from looking at weird things and saying, "that's cool, how does that work?" not "I want to cure cancer". It's hard to get funding to study how various bacteria battle each other in the soil when you cannot know how it might affect human health... [1] https://en.wikipedia.org/wiki/Model_organism https://en.wikipedia.org/wiki/Model_organism
- sk1zzyk1d 10y agoI found the quote below from Surviving the 21st Century by Julian Cribb similar to many attitudes I've encountered on the other end of the interest spectrum. The warnings are worth heeding, yet how can we ignore such tech, just as we pursue nanotechnology that has similar dangers, when such scientific pursuits may be what allows the human race to persist long after the Earth ceases to be habitable. "All biowarfare laboratories - and indeed, many ordinary biotech labs – thus represent an ongoing existential threat to humanity whose safety, like that of nuclear materials, cannot ever be guaranteed. "This was highlighted in early 2016 when James Clapper, U.S. director of national intelligence, issued a warning that even gene editing (such as by the technology known as CRISPR) should be added to the list of weapons of mass destruction, adding that it 'increases the risk of the creation of potentially harmful biological agents or products'. (Regalado 2016). Other scientists warned that genetically modified lifeforms could be used to target specific groups of humans carrying certain genes, or if released in agricultural ‘designer crops’ might result in uncontrollable plagues. They cautioned that gene editing technology is far cheaper and easier to access than nuclear or chemical weapons." - Surviving the 21st Century, Julian Cribb, Chapter 8 "The Urbanite (Homo urbanus)"
- kneel 10y agoJames Clapper's job is to worry about everything, of course he would say that. The common flu is a lot more dangerous than CRISPR/cas9. The CRISPR/cas9 system has potential for existential threat in the same way that AI does (not anytime soon.) This is what happens when you develop a new set of tools.
- ahazred8ta 10y ago> James Clapper's job is to worry about everything "And Ye Shall Know the Truth and the Truth Shall Make You Free" is inscribed in the lobby of the CIA, but informally they say "the truth will just make you nervous". :(
- obstinate 10y agoFeel the same. Would be much more worried if we had figured out how to fix cancerous cells with CRISPR already.
- adventured 10y agoI'm rather obsessed with CRISPR these days. I'm considering leaving traditional tech and self-funding a new CRISPR company. The accessibility - in most every regard - of CRISPR has entirely changed the game in gene editing. It's only going to accelerate and there is so much land to discover, pick a direction and go. Cas9, Cpf1, CasX, CasY, it's all so exciting compared to most of the things I see in tech these days (except for AI and VR).
- nyolfen 10y agodo you have any suggested reading (for a layperson)?
- takinola 10y agoCan someone ELI5 how gene editing works? I understand that CRISPR can target specific genes to make changes but how does that work in practice? Suppose we identified the gene for Huntington's disease and wanted to design a therapy to snip it out and put a benign replacement in its place. Given the human body contains trillions of cells, each carrying the complete set of genes, which cells would be targeted by the therapy? If the CRISPR therapy targeted only cells in a certain organ or region, does this mean the person would have different sets of genes in different parts of their body? What does this mean for any children born post-treatment? Do they inherit the new genes or are they stuck with the old crappy version?
- yellow_viper 10y agoCRISPR is a newly adopted technology that allows the bacteria in the cell to fight against the Viruses that affects the Human cells. It also allows making some specific changes in the DNA of the Human Being and some other organisms. Clustered Regularly Interspaced Short Palindromic Repeat is the acronym for CRISPR. It is an RNA gene-guided editing platform, which is helping to break a double-stranded DNA at a specific location within the genome by making use of a Protein Coat (Cas9) and a synthetic RNA guide. In the simple life forms like bacteria and another organism, a simple sequence of CRISPR acts as a crucial component of the Immune System for protecting the organisms health. Viruses are the small infectious agents that invade the bacteria in the cells and attack the bacteria. If viral infection threatens this invaded bacteria, then the CRISPR immune system can attack and destroy the genome of the invading virus. The genome of the virus contains the genetic material for its replication. By destroying the genome, the CRISPR immune system protects the bacteria from viral infections. Source:http://www.whitedust.net/what-is-crispr-and-how-can-it-edit-your-dna/ http://www.whitedust.net/what-is-crispr-and-how-can-it-edit-... you can learn more about it and watch the video about CRISPR/Cas9's mechanism and function.
- tstactplsignore 10y ago>Given the human body contains trillions of cells, each carrying the complete set of genes, which cells would be targeted by the therapy? Depends on the disease being treated. Obviously it would be extremely infeasible to edit all cells of all types in an adult human with existing technology. >If the CRISPR therapy targeted only cells in a certain organ or region, does this mean the person would have different sets of genes in different parts of their body? Yes that's correct and would be the case in any proposed adult humam crispr treatment. >What does this mean for any children born post-treatment? Do they inherit the new genes or are they stuck with the old crappy version? Only if the therapy edited the germline cells (sperm and egg), which would probably be unintentional.
- dankohn1 10y agoI love this quote from the article: "Viruses outnumber prokaryotes by ten to one and are said to kill half of the world's bacteria every two days."
- hyperpallium 10y ago> when viruses infiltrate a bacterial ecosystem, often only about one bacterium in 10 million will gain a spacer that lets it defend itself. Sounds like, when under mortal threat, grab some DNA. Even if it mostly causes cellular suicide by grabbing its own DNA, if just one bacterium acquires immunity, the group as a whole benefits. Of course, group selection doesn't seem to work... but maybe the very high probability of death means this low probability last-ditch attempt is worth it for the individual - which then passes on the CRISPA machinery and the specific immunity to its "progeny"... which then have a nicely cleared out environment all to themselves... like eucalyptus after a bushfire. Desparate times call for desparate measures; and high risk/high reward.