A CRISPR first produces squid as clear as glass | Hacker News Reader

A CRISPR first produces squid as clear as glass

nature.com

150 pointsapsec11263 comments

For anyone coming to the comments before reading the article: the squid is already clear, they just removed some spots of pigment.

Thank you! I don't like admitting to this behavior, but I can't trust a headline (any headline).

The reason this is a significant achievement is that the DNA of living cells in the organism were "edited" to remove the pigmentation, thereby effectively changing the phenotype of an adult squid.

They edited embryos:

we determined whether a TDO-selective inhibitor (680C91) impeded pigmentation in developing embryos. The development of D. pealeii has been divided into 30 stages and eye pigmentation appears at ∼stage 25, while chromatophore pigmentation starts at stage 26 [21]. We added 680C91 to developing embryos at stage 20

While you're right they edited the embryos the sentence you quoted is describing a drug (680C91) that they bath-applied to inhibit the TDO enzyme (as a positive control), rather than the CRISPR strategy they used, in which they injected the Cas9 and sgRNA into the embryo.

Oops, I should have quoted this part, from the summary:

Knocking out TDO in squid embryos efficiently eliminated pigmentation. By precisely timing CRISPR-Cas9 delivery during early development, the degree of pigmentation could be finely controlled.

And the advantage here is that it's the start of development of a genetic-modification toolkit (similar to that we already have for fruit flies and c elegans and zebrafish) for using them as animal models. Much more complex of a brain than any of the other animal models we usually use.

Isn't this a bit of a slippery slope? The better a model of a human brain you experiment on, the closer you approach the ethics of performing the same experiment on human embryos, infants, children, and adults (as they age). I think this is already pretty close to the case for mice, but when you start doing it to cephalopods, primates, and dolphins/orcas, you're really skirting the line.

I wonder if there'll ever be a time where if we aren't comfortable with doing something to human embryos (or other stages) in experiments, we also won't be comfortable doing it to the animals closest to us on the intelligence and awareness totem pole, and eventually perhaps any sentient animals at all (so nearly all of them besides jellyfish, sponges, anemomes, and some other ocean dwellers). This day feels inevitable to me, but I don't know whether it's 20 years or 200 years away.

We're still chopping up likely-sentient animals and eating them, so it's probably a ways off..

I believe I read this in the book Grandfather by Tom Brown [1] (could have been somewhere else). The author was taught by an Apache elder about survival, etc.

Part of that was learning how to track and hunt.

The first time he killed a deer, he was required to sneak up on the deer and kill it with a knife. That way he would know the gravity of what he was doing.

He wrote that he cried for a good while afterwards.

I think that is a perspective more people should take with eating meat. To know you are taking the life of a living, breathing thing to sustain your own life.

I think it used to be a much more common view, but it's hard to view a chicken nugget or a hamburger as an animal that lost its life to continue yours.

[1] https://www.goodreads.com/book/show/434013.Grandfather

There's also the problem that for most people in developed countries, you don't actually need to take a conscious life to sustain your life. It's a luxury, like wearing fur.

Indeed. But many experiments are more cruel to sentient beings than, say, getting shot by a hunter. I'd much prefer to be summarily executed than to end up in Mengele's lab. Both are wrong, but one is worse.

Wait until you read about pig intelligence levels. And unfortunately, it seems I still love ham and bacon :-(

Still impressive, but definitely not as complicated as taking an opaque squid and making it clear.

They missed a spot! Sorry, couldn't help myself.

The paper Highly Efficient Knockout of a Squid Pigmentation Gene [1]

> two key advances have made it possible to develop techniques for the genetic manipulation of squid. The first is the CRISPR-Cas9 system for targeted gene disruption, a largely species-agnostic method. The second is the sequencing of genomes for several cephalopod species.

The point is not a clear squid lacking chromatophores, a rather discomforting thought, but creating a new animal model with knockout genes.

[1] https://www.cell.com/current-biology/fulltext/S0960-9822(20)...

When can we use CRISPR to address the mutation with the L-gulono-γ-lactone oxidase gene (GLO; EC number 1.1.3.8) which controls the synthesize l-ascorbic acid (vitamin C) in humans?

Is it possible with CRISPR? Can it be introduced in a person and have it reverse the mutation?

Fixing this mutation might have the biggest impact on global human health, in humans the GLO mutation only impact the synthesis of vitamin C, unlike in other animals like primates, bats, guinea pigs and fish the mutation can't be reversed because it impacts other systems.

Is there a specific disease you're targeting, or are you trying to give general humans abilities they don't already have? The latter is not being considered at this point.

It's both. No human has the ability to synthesize vitamin C in their own bodies, leading to scurvy, unless you supplement vitamin C in your diet. Most people eat enough vitamin C to not lead to scurvy. There is a disease that would be eliminated, but it's preventable by watching out what you eat. Also, usually it takes more than just the synthesis of the enzyme. It also needs to be regulated, which requires the systems that regulate it to be around as well (and work correctly). Neither producing too much of the enzyme, nor too little is a good outcome.

So yeah, I think it's better to focus on other diseases first, that are more serious and where a human carrier of the healthy variant of the gene already walks among us, here on earth.

I don't think this makes sense since the risk of attempting to add a phenotype greatly outweighs the low cost of just taking vitamin C.

Even just producing the right amount of enzyme is a first-order approximation to what actually has to be done to add a phenotype without side effects.

> No human has the ability to synthesize vitamin C in their own bodies, leading to scurvy, unless you supplement vitamin C in your diet. This is a disease that would be eliminated

We could fall in the opposite situation easily, excess of vitamin C (from our body plus the same amount as before in the diet), leading to a scenery of nausea, vomit, headache and diarrhea, maybe permanent.

Ira Flatow interviews two of the scientists on a Science Friday podcast:

https://www.sciencefriday.com/segments/squid-gene-editing/

This is a great 17 minute high-level overview of the science. The breakthrough is the tool/technique used to access the embryo without physically damaging the egg. The glass-like embryo is a unique characteristic of this species, not the knockout gene. This work is a proof of concept; this species does not (yet) reproduce in captivity. Both scientists demonstrate a deep love for cephalopods and for science. They also discuss the ethics surrounding cephalopod research.

As a learner, is it possible to self learn more about Gene Editing and these things, and can these things can be learned in a hacker way without going through a formal academic route ?

In my country (France) the use of CRISPR is highly regulated (its basically regulated as biological weapon material).

You could learn about it from articles and textbooks but are very unlikely to be able to play with it.

As much as I appreciate the desire for governments to stem the tide, what you're saying is likely very difficult--if not impossible--for a government to effectively stop. Of course, people who don't want to break the law will comply but those who don't care will have no trouble doing as they please. Gene editing is quite simple now, and with only a few purchased parts one can edit whatever they please. Maybe you're thinking of editing human embryos?

Is editing human embryos harder? Or how is it less difficult for a government to stop?

It has already been done - and the scientist is in jail:

https://en.wikipedia.org/wiki/He_Jiankui_affair

> is it possible to self learn more about Gene Editing

You could (1) read a basic textbook in genetics (or look at online courses in genetics and molecular biology), (2) read a textbook in genetic engineering, and then (3) read a book in CRISPR. Maybe there could also be some shorter path than reading 3 books.

Youtube is fantastic for this. What you'll find out is that once you understand how DNA works (codons map to amino acids), and that amino acids fold into specific 4D shapes that trap molecule A and mush it into molecule B to make molecule C, the rest kind of falls into place.

4D shapes as in changing over time?

Yes, exactly. It's really quite fascinating--everything just vibrates, like a lot, all the time. The vibrations of some bits have frequencies that resonate with the frequency of other bits. And when they sync up, they change their frequency and then no longer resonate with each other. The whole universe is basically a giant musical instrument and chemical reactions are just wavelettes resonating with other things.

Haha, as a Biochemistry PhD student, this is almost exactly how I will often break down biology to a layperson: DNA corresponds to proteins that are essentially just shapes bumping into other shapes, sometimes making new shapes and sometimes destroying them in the process.

Of course, provided 4 billion years of evolution, this has yielded staggering complexities, but at the heart of it is just globs.

"Given enough time, Hydrogen starts to wonder where it came from, and where its going."

I cannot recommend the YouTube Channel "The Thought Emporium" highly enough, for this topic or many others. Self taught tinkerer/chemist/biohacker, his latest videos are primarily about gene editing.

You can take an at-home course from the-odin.com. Their kits are useful and their youtube videos are too (though they can be a bit slow).

I don't mean to sound pointed, as these links may seem, but honestly just reading the wikis for genetic engineering and genome editing is a viable way to learn more in my opinion. Just make sure to remain in the general sections and click the hyperlinks of unfamiliar topics, and venture into the weeds of the topics once you begin to feel comfortable with the jargon. https://en.wikipedia.org/wiki/Genome_editing https://en.wikipedia.org/wiki/Genetic_engineering

Are its eyes messed up in the photo or is that normal?

They removed the dots in the eyes as well.

So it’s blind? Reminds me of the Invisible Man plot hole where the guy gets turned invisible and thus his retinas also become transparent and therefore he shouldn’t be able to see anything.

Not necessarily. The animals in the photo aren't the same animals. This is the normal aspect of a squid larvae.

The eyes seem normal to me. In any case squids belong to the exclusive club of animals that can have different types of eyes (different size or shape) at the same time.

Yeah it really looks like the eye pigments are not the same.

They aren't, and the article notes as much.

From the article: The protein encoded by TDO helps to add pigment to the animal’s eyes and chromatophores

So we're getting closer to RayFish Footwear https://www.rayfish.com/ - https://www.youtube.com/watch?v=gVk_Vw1C7cs

IIRC it's a big deal because this is the first crack at cephalopod DNA - I don't recall where I read this. Anyone has a source?

It's in the first sentence of the article: "...the first use of CRISPR in cephalopods, a class of marine invertebrates."

Could this have been done on an adult squid??

I assume not. I am pretty confidnet the whole purpose is for the cells to never grow.

It works by editing cell information. If you let original cells divide there will be more unedited cells. So the eariler in the development you apply modification the more prononuced the effect. I think I read somewhere that they could alter amount of pigmentation by timing application of treatment. So that would fit.

It doesnt work by killing existing cells. Maybe it could work if old cells died and new ones would be edited, so they could gradually replace original ones but I guess its pretty hard to deliver gene editor to so many cells.

Cells divide really slowly so if you could edit most cells in one day then only a negligible amount of new cells would be unedited.

* I guess its pretty hard to deliver gene editor to so many cells* this is the breakthrough waiting CRISPR and impossible to find a great up to date scientific resource on the technical issues and on the path towards progress.

Remove the 4 year lifespan then things will get interesting

Read Sheena 5 by Stephen Baxter, great short story.

I feel creeped out/put off about this. These are intelligent beings, apparently limited only by their short lifespan. They communicate by modulating the pigments into patterns. Now that has been taken away. Imagine toasting some genes in a human embryo to the effect of lock in syndrome. Crispy!

edit: I think this is a case for PETA to look into.

That's octopodes; squid are much less intelligent.

They're moving on next to much smaller (and hence even less intelligent) hummingbird bobtail squid.

My starting assumption is that octopus, cuttlefish, and squid have similar intelligence levels. If chromatophore manipulation is correlated to cephalopod intelligence then bobtail squid are small but smart.

My own anecdotal evidence is that juvenile cephalopods exhibit adult-level intelligence which is a good reminder not to project mammalian behavior assumptions on cephalopods.

The big squids are probably much more intelligent than octopus.

Octopuses are solitary. Squids are social and top predators able to travel very long distances and live in a wider range of habitats. They can make light and use light and color patterns to display complex behaviour or lure preys

Is also well known that squids are able to communicate two opposite messages to different colleagues at the same time.

Cephalopods are amazing animals but I would be careful about anthropomorphizing their behavior. If they are communicating via chromatophores, then this type of animal model will be key to understanding how this kind of signalling works.

Cruelty implies stress or pain; albino social animals might be a better analogy than lock in syndrome.

Probably mute(ness) would be most fitting.

Feels wrong to me, any way.

What would PETA look into? They have no authority, and a huge bias wrt moral judgements.

If shortening the lifespan of a squid is inhumane, then what is catching and eating squid by the tonne?

There is a third squid in there, on the top right.

It is actually clear as glass! Wow

Please do this to great White Sharks.

invisible, glass-like sharks? no thanks.

Though at least if you got a limb bitten off, you could see in which shark it resides.

Reply on news.ycombinator.com