
Crispr now cuts and splices whole chromosomes - pseudolus
https://www.sciencemag.org/news/2019/08/forget-single-genes-crispr-now-cuts-and-splices-whole-chromosomes
======
aaavl2821
It seems like there has been more hype around synthetic biology in the tech
press the last year or so, but it still feels like this field is being slept
on a bit. AGI gets a lot of press but is at best decades out, however one
could argue that the potential (for good and bad) of synbio is close to as
large, but the tech is much more real. In many cases it already exists -- we
can modify human embryos, the first human study of CRISPR in the US kicked off
a few weeks ago -- and in others it doesn't seem too far out

I'm a non scientist and have been excited to learn more about this field, but
to find out the most exciting stuff you need to read scientific papers. The
details are the coolest parts IMO. A bit of self promo here, but I recently
wrote a blog post summarizing a Stanford synbio paper in layman's terms [0].

[0] [https://www.baybridgebio.com/blog/synbio-laymans-
terms.html](https://www.baybridgebio.com/blog/synbio-laymans-terms.html)

~~~
dhash
(Full disclosure, i run a YC startup selling to synbio + think that it's
undervalued)

The field really doesn't do blog posts, it's a shame.

For some interesting stuff in synbio that's approachable to your prototypical
HNer, check out [1], a Verilog-to-DNA compiler that works with small logic
circuits. [2] (Not really synbio) but using reed solomon codes to better do
High-Throughput Screening. [3] PACE, a way to ask evolution to implement a
particle filter for us. [4] A remapping of the base pair 3-tuple to amino acid
that maximizes edit distance, filling in the gaps with STOP codons - stopping
something from evolving, and [5] some cool people working on wholly synthetic
cells.

[1] Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V.,
Strychalski, E. A., … Voigt, C. A. (2016). Genetic circuit design automation.
Science, 352(6281).
[https://doi.org/10.1126/science.aac7341](https://doi.org/10.1126/science.aac7341)

[2] Erlich, Y., Gilbert, A., Ngo, H., Rudra, A., Thierry-Mieg, N., Wootters,
M., … Zuk, O. (2015). Biological screens from linear codes: theory and tools.
BioRxiv, I(1), 35352.

[3] Dickinson, B. C., Leconte, A. M., Allen, B., Esvelt, K. M., & Liu, D. R.
(2013). Experimental interrogation of the path dependence and stochasticity of
protein evolution using phage-assisted continuous evolution. Proceedings of
the National Academy of Sciences, 110(22), 9007–9012.
[https://doi.org/10.1073/pnas.1220670110](https://doi.org/10.1073/pnas.1220670110)

Esvelt, K. M., Carlson, J. C., & Liu, D. R. (2011). A system for the
continuous directed evolution of biomolecules. Nature, 472(7344), 499–503.
[https://doi.org/10.1038/nature09929](https://doi.org/10.1038/nature09929)

[4]
[https://www.biorxiv.org/content/10.1101/695569v2](https://www.biorxiv.org/content/10.1101/695569v2)

[5] [http://buildacell.io/](http://buildacell.io/)

~~~
The_rationalist
Well if you have time to waste (or to invest) I've made an analysis of how to
cure ageing.

I have some unanswered questions about what is feasible in DNA editing, maybe
your knowledge could enlighten me? [https://github.com/LifeIsStrange/An-
algorithm-for-curing-age...](https://github.com/LifeIsStrange/An-algorithm-
for-curing-ageing/blob/master/README.md)

I would like an answer for e.g: [https://github.com/LifeIsStrange/An-
algorithm-for-curing-age...](https://github.com/LifeIsStrange/An-algorithm-
for-curing-ageing/issues/4)

------
gradys
People who work in or near genetic engineering:

CRISPR seems to solve the problem of editing DNA to contain arbitrary human-
designed data. Are there major caveats or limitations to this that people
outside the field don't recognize? e.g. is delivery to the right cells a major
obstacle?

If editing is solved, it seems like the major remaining problem is designing
the right data to insert. I'd imagine this is a much vaster problem than
editing. What are the major subproblems there? What does the frontier look
like?

Besides the mechanics of editing and designing the sequences to insert, what
other major problems stand in the way of sci-fi level genetic engineering?

~~~
aaavl2821
I'm not a scientist but have friends who do research in this field and I've
worked at startups in this field.

Delivery is a major obstacle. DNA, RNA and proteins don't typically get into
cells on their own. Typically you use vectors, often viruses or lipid
nanoparticles, to get DNA into cells, but these vectors have their own
challenges. One of which is that they aren't typically very specific to
particular cell types. It can also be tough to get vectors to the right
tissue. So most early gene therapy efforts focus on blood disease, liver
disease and eye disease because it is easier to deliver to those areas. CNS
has also become a popular target because a particular viral vector, AAV9,
tends to get into neurons pretty well

But viral vectors are commonly "immunogenic", ie the immune system learns to
reject them as foreign after one dose. These are viruses after all, and the
body is designed to reject them. Some people have pre-existing antibodies to
many popular vectors. And often you can only dose a viral vector once, so if
you don't dose it right, or if the effect isn't permanent, you don't get
another shot

I can't speak to some of the other more technical problems, but one limitation
is that you are limited as to how large your DNA payload can be. But it seems
this paper is a big step towards removing that barrier. Which I believe is why
this paper is such a big deal (others more knowledgable should correct me)

Also CRISPR works best to cut DNA as of now (which renders a gene non-
functional), but it is a bit harder to insert DNA reliably from what I
understand. Again, a scientist in this field would much better understand the
state of the art than I do, but this is my understanding

Another major unknown is the degree to which gene editing tech causes off-
target edits. If your DNA editing tool accidentally snips a gene that protects
you from getting cancer, it can lead to cancer. I'm not close enough to the
science to know what current thinking is on this risk or how to best mitigate
it, but it is very real. More primitive gene therapies did in fact cause
cancer in patients (often children)

In many ways sci-fi level genetic engineering is possible. We just don't do it
because we don't know the risks, and the risks are huge. We can already
genetically modify human embryos, and our toolkit for doing so grows every
day. Editing human embryos is a very scary proposition.

EDIT: I will also add that if you are interested in learning about this field,
try reading / struggling through a couple scientific papers, really trying to
understand every detail. Ideally with the help of a scientist friend. It is
time consuming and daunting to get through all of the jargon, but the papers
lay out the design, engineering and testing process in some detail. Often they
provide the derivation of the mathematical models used and the specific DNA
sequences used. You can begin to appreciate how amazing this work is when you
get into these details

~~~
cauthon
This is a good summary, and I can follow up on a couple points. (I don’t have
direct experience with Crispr data, but I’m currently a PhD student in a
computational genomics program, and have 4 years of experience in a lab that
does crispr experiments in addition to my projects.)

Related to both the idea of inserting DNA and off target effects - the issue
is that scientists can engineer a cut, but then rely on the cell’s repair
mechanisms to “stitch” the cut DNA back together. These mechanisms are
inherently stochastic and error prone and are how many somatic mutations, such
as those in cancer cells, arise. So for off target effects, even if you make
the cut at the right place, you can still end up with new unintended SNPs and
indels nearby. And for inserting new DNA, it’s not a guarantee. You can
provide the template that you want to incorporate, but it might get missed, or
get copied in more than once or in the wrong orientation.

~~~
subroutine
IMO the biggest concern is not whether CRISPR-Cas9, and DNA ligase, will do
their job reliably (given appropriate guide RNA, and methodology)... the
biggest concern to me is that we don't know what _else_ the target SNP tends
to do, aside from whatever we've found from GWAS.

Here's an example...

APOE e4 is associated with Alzheimer's disease risk. People in Guatemala have
a high prevalence of this allele. Some researchers from the US might decide
it's a good idea to fly down to Guatemala and launch a CRISPR clinical trial
to 'protect' newborn Guatemalans from this increased risk of Alzheimer's. So
they do; come back to the US, have a toast to longevity for these children. It
has recently come to light however, that APOE e4 confers protection against
Malaria parasites. Not a big deal if you live in Norway - huge deal if you
live in Guatemala. Suddenly, the risk of developing an age related dementia
doesn't seem all that pertinent.

So, my 2 cents is that, if we're really going to start CRISPRing babies, we'd
better be doing our due diligence, and for now limit to diseases that
significantly and immediately impair wellbeing.

------
khaki54
Can this remove extra chromosomes and be used to reverse or mitigate Down
Syndrome?

~~~
echelon
Once you have a multicellular animal, it's far too late. You have to do the
gene editing before cell division occurs. You can't ensure delivery or uniform
uptake otherwise. And beyond this, delivery itself is incredibly hard. You
can't get eukaryotic cells to uptake genes.

It's better to screen beforehand.

~~~
mbreese
> You can't ensure delivery or uniform uptake otherwise

That's all true (and I agree), but that's a practical/technical issue. That
may be solvable, but even in that case, that's not the whole story. There are
also developmental biology issues at play once you have a full organism (or
even an embryo that is just a few cell divisions in). The way our bodies
operate as adults is just as much a function of how our cells developed and
grew as it is a product of genetics. There are a lot of processes that happen
only at very specific timepoints in development. And once you're past those
points, editing the genes required won't have any phenotypic effect.

We can alter genetics with CRISPR. We can't alter morphology in the same way.
For example, in certain eye diseases, you can have a loss of a gene that is
involved in how the retina processes light. But, the same gene is also
involved in how the optic nerve is formed (or migrates) in the brain. You
could use gene editing approaches to knock in a good copy of the gene, which
might help the retina absorb light, but the nerves have already formed and are
already in place. That isn't going to change.

And none of that actually addresses the ethics involved in changing the
genetics of a person, which is non-trivial to say the least.

------
craftinator
Does CRISPR still leave cells with a mess of disconnected strands after the
fact? Read about this being an issue a couple years ago, but haven't seen any
follow-up since then.

------
glofish
There are two schools of thought:

1\. DNA is the hardware

2\. DNA is the software

CRISPR gets a lot of press because it seems to give biologists exactly what
they've always wanted - a tool to mess with the DNA - to alter the hardware,
i.e. move around transistors

Biologists love CRISPR because they are hardware people - that's how they were
trained, that's how they think, and there are millions of them all thinking
the same thing, yearning for the same.

Then there are the others who think DNA is software, the genes themselves are
"merely" the CPU. For them, the hype around CRISPR is a distraction, and it
only sets back scientific progress as it keeps channeling the focus and
attention to the mere physical act of cutting pasting DNA as if that would
ever explain anything.

In a nutshell, genes are probably not that important, it is the repetitive and
seemingly senseless elements in between then that regulate the individual
pieces. For an analogy think about how you can run radically different
software of the same hardware.

See: "A 21st century view of evolution: genome system architecture, repetitive
DNA, and natural genetic engineering"

[http://shapiro.bsd.uchicago.edu/Shapiro.2005.Gene.pdf](http://shapiro.bsd.uchicago.edu/Shapiro.2005.Gene.pdf)

~~~
JMTQp8lwXL
> genes are probably not that important

Genes encode for proteins, which seem pretty crucial to biological functions
of the cell.

~~~
refurb
Yes, but genes in and of themselves explain very little in terms of the
overall functioning of a cell. The process that determines if and when a gene
gets expressed is probably as important as the gene itself.

~~~
COGlory
Genes determine expression though.

~~~
refurb
Sometimes, but there is a lot outside the specific gene that has an impact.

~~~
COGlory
Yes, other genes. Transcription factors. Methylation. DNA accessibility. All
determined by proteins which are in-turn determined by genes. Genes determine
expression.

~~~
refurb
What about all that DNA that never gets transcripted?

~~~
COGlory
To do anything, requires interaction with a protein, which in turn is
expressed by a gene.

------
wonderwonder
I look forward to the Red Rising.

In all seriousness though this is pretty amazing. Especially in light of how
fast this technology appears to be progressing. Seems like we are rapidly
approaching being able to utilize biological factories at a small scale.

~~~
orcasauce
The rising happens later, first we need a god-emperor to rise up and topple
the Empire of the Rising Sun... Oh dear.

------
plants
As someone who is super interested in genetic engineering, are there any
survey papers/online courses/intro textbooks that someone could recommend as
an intro to either modern gene editing or using probabilistic techniques to
determine gene encodings? I always feel more confident taking recommendations
from people than I do scouring the internet for random resources...

------
0000011111
This is cool! Let's not forget that over time genes variate on their own. Both
human-modified genes continue to mutate along with side organic genes.

For folks looking to learn more about Genes in general I recommend the book
below.

The Gene: An Intimate History

[https://g.co/kgs/EPDUmk](https://g.co/kgs/EPDUmk)

------
gwern
Fulltext:
[https://www.gwern.net/docs/genetics/editing/2019-wang.pdf](https://www.gwern.net/docs/genetics/editing/2019-wang.pdf)

------
loeg
It would be nice to one day be able to edit out heritable genetic diseases,
e.g., known deleterious BRCA mutations, in humans.

------
improof
All the predictions for the end of Mankind; AI, global warming, asteroids,
etc. Wait till they weaponize this. ie Twelve Monkeys. Pick a racial trait of
your enemy, find its genetic expression and splice in whatever you want there
in its stead. Perhaps just cut the chromosome there and leave the ends
dangling. What are the odds this is being worked on already? Our science
fiction overtakes us!

~~~
new299
CRISPR gives us an editing mechanism. But you still need to deliver it to
hosts. Perhaps via some kind of viral vector:

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356701/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356701/)

But... it's not clear to me that this will work. You'd have all kinds of
issues with the viral population mutating. I'd guess the virus would in most
cases not kill the host before their natural defenses kick it. Not really
spreading in the population etc.

