The Weirdness of CRISPR
alliance.nautil.us
alliance.nautil.us
The CRISPR system here was discovered in a single-celled organism that likes brine water - a tool it used to intercept hijackers. The 'standard' Cas9 that is being used extensively in the rest of the CRIPSR stories comes from the bacteria that causes strep throat. Studies are now mining the genomes of organisms found in 'mud pits' and 'pond scum' to find all sorts of smaller, faster, more efficient variants of Cas9. And that's just for the single purpose of editing a genome.
The capabilities of proteins found (off the top of my head) in jellyfish, in sulfur springs, in colored algae, in electric eels, in little pond creatures, in HIV, in waterbears, etc. are all depositing huge amounts of technology into our collective knowledgebank. We have been given a store of 'alien' technologies to sift through that are applicable in every condition to be found on Earth, literally. The cures to many of our ills will not be engineered from scratch, but rather will be adapted from existing technologies found in extant organisms literally scattered across the globe. This is how 'basic science' works. A magnanimous scientist is curious how a little cell can survive in really salty water, and owing to his curiosity we discover a nanotechnology that can edit an organism's genome. We humans are smart - but not yet that smart.
(some of those protein technologies we like to talk about here on HN: https://serotiny.bio/notes/proteins/ )
As we know well from experience and might expect, just understand is nearly necessary for a huge fraction of fantastic progress and often sufficient or nearly so. The track record is the best of any allocation of resources.
Or toss some rocks into the camp fire and in the morning find some clump at the bottom. Then, try to UNDERSTAND that? That clump is different; what the heck is it? This was the first time saw this; what caused it? Can do that again?
Okay, just used the carbon in the fire to remove the oxygen from copper oxide and leave some copper metal. Start of exploitation of metals for humans ....
Flashbacks to that "Can a protein originally found in jellyfish improve your memory? Our scientists say yes!" commercial I've heard a million times without even setting out to watch TV. I was skeptical at the time, but I guess this means such a thing is at least in the realm of theoretically possible.
Edit: turns out that specific thing was still illegitimate anyway.
http://www.nbcnews.com/health/health-care/jellyfish-memory-s...
If in a sci-fi novel an alien handed a character their 'magic rock' (iPhone) and they smelted it for its gold content rather than reverse-engineered it's wireless charging, communication, and computation capabilities you would scream at the character for being horribly short-sighted. Such a waste of sophisticated technology laid right in front of them for such little temporary gain.
check out the HHGG books
Even endowment for the arts can produce significant impact on how we think and use technology.
* http://www.mpegla.com/main/pid/CRISPR/default.aspx
* http://www.mpegla.com/Lists/MPEG%20LA%20News%20List/Attachme...
...you are not. What is this insanity?
"We are the world’s leading packager of patent pools for standards and other technology platforms used in consumer electronics, as well as chemical, eCommerce, education, energy, environment, healthcare and biotechnology, manufacturing and materials, transportation and wireless technology. We developed the pool market space. (view link) Our business model supports a large number of patent users – creating reasonable access and profitable opportunities for all parties."
How is that not a valuable service?
They have no biomedical or biochemical expertise. They have no hand whatsoever in discovering or understanding any science at all. It now appears as though they would like to try to get another group of mega-companies in a room to cross license their patents on Cas9 variants - there are as many (natural) variants as there are bacteria out there, and there are a combinatorially large number of synthetic variants on top of those. The Berkeley/MIT faceoff you've likely heard about in the news is over a very broad patent on using Cas9 therapeutically, but the space of natural Cas9 variants is actually broader still than even that patent could cover.
We as a country need to have a conversation about patents and how the policies that work for computer code may not be the same policies that work for small molecules, which may not be the same processes that work for genetically encoded materials. Each of those technologies are all extreme in terms of the cost of R&D, verifiability, producibility, reproducibilty, and longevity. It is difficult to shoehorn each of these technologies into the same patent framework.
That's very kind. They also historically have done everything they can to keep the pool alive by evergreening it, and allowing companies to evergreen it. They also have done pretty much everything they aren't supposed to since the original BRL the DOJ sent (https://www.justice.gov/atr/response-trustees-columbia-unive...)
People keep saying this about whole host of issues, and it makes me wonder if that's ever happened about anything. Have Americans ever "had a conversation" about any issue and decided anything collectively like that?
MPEG LA, LLC is a firm based in Denver, Colorado that licenses patent pools covering essential patents required[1][2] for use of the MPEG-2,[3] MPEG-4 Visual (Part 2), IEEE 1394, VC-1, ATSC, MVC, MPEG-2 Systems, AVC/H.264 and HEVC standards.
MPEG LA is not affiliated with MPEG, the Moving Picture Experts Group.
Doesn't that mean MPEG LA is affiliated with MPEG?
MPEG LA, however, would like you to believe that, seeing as LA is (or at least, was) an abbreviation of Licensing Authority -- something they clearly aren't.
Right now I'm killing time until my residency starts and I've been reading recent journal articles relating to each of these.
One of the weirder journal articles I read was about this one group taking fibroblasts from XX and XO (Turner's syndrome) females and XY cells from a male and de-differntiating them into induced pluripotent stem cells. They then re-differentiated the cells into germ cells. Sure, that's not controversial just yet, but then they decided to put the XX female germ cells into a teste. The female germ cells (XX and XO) and the male XY cells all differentiated into cells that could succesfully undergo meiosis. And these cells, could terminally become sperm. That means an XX skin cell could be induced to become a sperm and possibly fertilize an egg from another woman. Of course all offspring would be XX female. This process totally bypasses males.
Anyways, very interesting to me, maybe it will be to others. Here's the journal article.
http://www.nature.com/articles/srep06432
I know this article I'm posting under is about CRISPR, but I feel like new/controversial biology research could be posted here too. Hopefully anyone reading gets the same feeling of discovery/wonder/incredulity that I had when reading about it.
It's not exactly anyone's first choice place to publish.
Crispr/Cas9 is not as robust as people make it out to be, but it's promising. (I do some work with crispr/cas9)
Please expand on this. I feel like CRISPR is being overhyped, and would love to hear form someone educated on the subject as to what its possible limitations are, or at least some of the known challenges ahead.
The protein is special for two different reasons: 1) it is able to locate DNA sequences with very high precision 2) and the sequence it locates can be swapped out as easily as changing the sequence of the RNA it grabs ahold of (trivial to do, can be done in a day, and can cost >$1 per target sequence to swap). Note, it is not special because it can cut DNA - there are lots of proteins that do that, and there are lots of better ways to change or alter DNA once you get to a particular sequence - but Cas9 was originally a self-defense mechanism, so it's evolutionary function in strep throat bacteria was to kill invaders by dicing up their DNA (at particular sequences that strep throat doesn't have).
Cas9 is powerful because it could be used to direct any function at a particular DNA sequence, where the sequence can be altered in the lab quickly and cheaply. As it is a protein encoded by a particular sequence, you can fuse it to other proteins with other functions to build a more powerful machine. (see [1] if you want to play with those sequences yourself.) As an experimental tool it will likely become a foundational tool used all throughout molecular biology - and for that alone is is worth it's fame. Thermophilic polymerase used in PCR is another such tool. As are restriction enzymes. As is GFP. That's the scientist's perspective.
However, Cas9 also previews the capability of directly and arbitrarily editing of a genome - a holy grail of biomedical sciences. Though unengineered Cas9 it's not great at editing a genome (we're not entirely sure why what it does even works) - but some 2-10% of the time it can actually edit a genome with fidelity. And that's good enough for many experiments (though not good enough for therapies). It has off-target cuts, and when it cuts it slices all the way through the double stranded DNA, and if it isn't properly stitched back together you have a broken chromosome. And getting payload DNA to the site that Cas9 cut is still really tricky. It's also a multi-part system (it needs it's little RNA as well as the protein itself), and so it's hard to deliver directly as a therapeutic. So the wild-type Cas9 is likely limited in its direct therapeutic relevance in terms of pure genome editing. But it will be used extensively for its ability to 1) further research quickly and cheaply, 2) prototype what genomic changes would do if they were successful (when you only need 10% efficacy to conduct a study), and 3) act as an engineering platform upon which other functions can be placed, and its own wild-type limitations can be overcome.
It's powerful. It's not perfect, there's lots more engineering to do with/to it. It's not going to get to the holy grail of genome editing all on its own, but it's a very solid platform to start building off of, as well as simply being a solid tool that will become a workhorse of further synthetic biology.
Can you expand on the part I italicized, preferably also linking to some journal articles?
Here is CRISPR breaking DNA and creating the insult: https://www.ncbi.nlm.nih.gov/pubmed/27866150
Some recent work on understanding how those double-stranded breaks actually repair themselves: https://www.ncbi.nlm.nih.gov/pubmed/27924007
Some basic research in Yeast: https://www.ncbi.nlm.nih.gov/pubmed/27915381
Double-stranded break repair in breast cancer: https://www.ncbi.nlm.nih.gov/pubmed/28053956
Have you considered that mechanism (NHEJ) is not even necessary to explain the rise in proportion of mutant cells after the CRISPR-Cas9 treatment? Because while it may happen to some extent, I do not think that is the simplest explanation for what I have seen reported.
I've been thinking this for awhile now, but never bothered to really write it up and keep track... you can check the discussion here (there are some other posts about CRISPR-Cas9 strewn about that thread as well): https://news.ycombinator.com/item?id=14014098
I have really only read papers other people bring up in conversations online or that get media coverage I come across on this topic. But every single paper I looked into has reported results that fit my explanation just as well as , or even better than, the NHEJ one, and this has been a couple years now...
As mentioned, I only looked quickly, but I do not think any will be helpful on the point I am bringing up. Let me know if I missed it.
It also says: "Yeasts, like other eucaryotes, exhibit cell cycle arrest in response to DNA damage (17)."
If it was just 2-10 percent, everyone would still be using Agro.
And creating perfect humans and cloning them in artificial wombs sounds beyond the scope of science at this point. The paper I posted could lead to offspring now (viable or perhaps so epigenetically modified they are doomed -although a germ cell undergoes some demodification in the ovary's environment).
It wasn't supposed to be an alternative future for humans (such as perfect humans), although I could see a total female society having less anti-social personality disorders and less violent crime.
Have bodies that are engineered to live forever, but accidents abound. Should anything happen to you, they'll re-clone you and restore the last brain backup.
Like the cylons did in Battlestar Galactica.
Imagine living for 10s of thousands of years and the only way to truly die is for your genetic material to be disposed of and the backups wiped.
If tech like that were available. I'd happily sign up. Travel the stars and explore the unknown!
Would it be possible to introduce a genetic template from a viral disease into an embryo to produce a human essentially immune to that virus?
The crux of the debate is that mammals have the interferon system to respond to viruses, so why would they have kept around a system like CRISPR?
So its a balance between error correction and error introduction. In Bacteria its worth it, in humans not so much, especially as we have a bunch of other subtler more complex ways of handling viruses before they get all the way to the nucleus https://en.wikipedia.org/wiki/RNA_interference Bacteria dont have this luxury as their DNA lacks this extra barrier. The biggest difference is simply cells dont matter in a human and can just kill themselves if all else fails.
The rest of the "innate" immune system has similar proteins involved nearly everywhere e.g. https://en.wikipedia.org/wiki/Toll-like_receptor These are the components involved in cell surface recognition of sugars. But much more similar between all animals than animals and bacteria.
Answer to your second question is yes you could add a CRISPR construct with templates for known disease and add artificial immunity. However, finessing this so that CRISPR doesnt cause lots of damage from randomly cutting your DNA throught your life leading to a higher risk of systemic cancers... is a big hurdle.