Science Friday - The End of Everything, Bright Fluorescence, Gene Editing a Squid. August 7, 2020, Part 2

Episode Date: August 7, 2020

When it comes to the eventual end of our universe, cosmologists have a few classic theories: the Big Crunch, where the universe reverses its expansion and contracts again, setting the stars themselves on fire in the process. Or the Big Rip, where the universe expands forever—but in a fundamentally unstable way that tears matter itself apart. Or it might be heat death, in which matter and energy become equally distributed in a cold, eventless soup. These theories have continued to evolve as we gain new understandings from particle accelerators and astronomical observations. As our understanding of fundamental physics advances, new ideas about the ending are joining the list. Take vacuum decay, a theory that’s been around since the 1970s, but which gained new support when CERN confirmed detection of the Higgs Boson particle. The nice thing about vacuum decay, writes cosmologist Katie Mack in her new book, The End of Everything: (Astrophysically Speaking), is that it could happen at any time, and would be almost instantaneous—painless, efficient. Mack joins Ira to talk about the diversity of universe-ending theories, and how cosmologists like her think about the big questions, like where the universe started, how it might end, and what happens after it does.  Over the years, researchers have created thousands of chemical dyes that fluoresce in every color of the rainbow—but there’s a catch. Most of those dyes fluoresce most brightly when they’re in a dilute liquid solution. Now, researchers say they’ve created what they call a “plug-and-play” approach to locking those dyes into a solid form, without dimming their light.   The new strategy uses a colorless, donut-shaped molecule called a cyanostar. When combined with fluorescent dye, cyanostar molecules insulate the dye molecules from each other, and allow them to pack closely together in an orderly checkerboard—resulting in brightly-fluorescing solid materials.  Amar Flood, a professor of chemistry at Indiana University, says the new materials can be around thirty times brighter than other materials on a per-volume basis, and the approach works for any number of off-the-shelf dyes—no tweaking required. Flood joins SciFri’s Charles Bergquist to discuss the work and possible applications for the new technology. Scientists at Woods Hole Marine Biological Laboratory recently thrilled the genetics world by announcing they’ve successfully knocked out a gene in squid for the first time.  “I’m like a kid in a candy store with how much opportunity there is now,” says Karen Crawford, one of the researchers and a biology professor at St. Mary’s College of Maryland. Crawford explains this modification has huge implications for the study of genetics: Squids’ big brains mean this work could hold the key to breakthroughs in research for human genetic diseases, like Huntington’s disease and cystic fibrosis. Joining Ira to talk about the news are Crawford and her co-lead on the research, Josh Rosenthal, a senior scientist at the Marine Biological Laboratory in Woods Hole, Massachusetts.  Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

This is Science Friday. I'm Iroflato. A bit later in the hour, scientists have created the first genetically altered squid. We'll talk about why that's a big deal. But first, one day, the universe is going to end. Not just the Earth, not even just our galaxy, all of it. Every star, every nebula, nothing we have ever done will remain. My next guest is someone who has spent a lot of her time thinking about the end. More specifically, half. How will that ending happen? There are, it turns out, a lot of possibilities for the end of something as infinitely large and massively energetic as our universe. Try the big crunch or the big rip. How about heat death or my favorite vacuum decay? But which will it be? Will it be fast or slow?

How soon could it happen? Would we get a new Big Bang at the end of it all? And a new universe of stars and planets? The jury is still out, but telescopes and particles? colliders are giving us clues to what may come. And here to help us wrap our head around the finite nature of our infinity is Dr. Katie Mack, who tackles our universal demise in her new book, The End of Everything. Dr. Mack is a cosmologist and assistant professor of physics at North Carolina State University in Raleigh. Welcome, Dr. Mack. Hello, thanks. Thanks for having me. So tell me, I've got to say this.

This is an awfully cheerful book about the end of the universe. Is that how you feel? I think I'm just excited about big things happening in the universe, and I guess I have some professional remove from the idea of everything really ending, although there are some points in the book where I do sort of wrestle with that idea that, you know, we will have no legacy in the cosmos ultimately, and that is a scary idea. But it's fun to think about these big, powerful, destructive forces. Does that bother you that we're not going to have any legacy? I mean, do you think about that as a scientist? I do think about it sometimes. And sometimes I think, you know, that's fine. We're just doing our thing. And someday that'll be over and that's how it should be. And other days, it's a little bit unsettling.

I mean, I'm not fully comfortable with the idea that I'm going to die. And I'm certainly not comfortable with the idea that the whole universe is going to die. But it seems like that's the way of things. Give us a short tour of what could possibly go wrong to end our universe. Well, there are several possibilities based on different ways that we look at the data and how we extrapolate. what's happening now in the universe into the future. So in the book, I talk about The Big Crunch, which is this idea that the expansion of the universe that's currently happening now could reverse

and everything could kind of come crashing back together. That's probably not how it's going to happen, but that's an idea that's been kicked around for decades as one of the possibilities. Let me stop you there and tell us why that's probably, use a scientist, know or feel it's probably not going to happen that way. Well, when we look at the expansion of the universe, One of the things that we can observe about it now is that the expansion of the universe is speeding up.

That means that the distant galaxies that are moving away from us are moving away from us faster and faster all the time. And that suggests that there's something in the cosmos that's accelerating the expansion of the universe. We don't know what that is. We call it dark energy. But in the presence of dark energy, it's hard to imagine that accelerated expansion stopping and turning around and everything coming back. Now, we don't know for sure because we don't understand dark energy. But based on what we do know about it, it looks like it's probably something that's just going to keep going the way it's going, and the universe will continue to expand forever. Okay, let's go to option door number two. Well, that's the heat death.

This is what we think is probably the most likely based on how we see the universe evolving now. Again, this is just the universe keeps expanding forever. And the end result of that is that everything gets more and more isolated. So galaxies get farther apart from each other. everything gets more and more sort of contained in its own little space. It's harder for things to interact with each other over these increasing distances. And so over time, the universe just gets more and more diffuse, darker, colder. There are no new stars forming after a while and particles decay and everything kind of fades and decays away. And ultimately, you're left with basically just

the waste heat of the cosmos. Okay, let's go to option number three. Well, this is a dramatic one. This is called the big rip. And this is based on the idea that maybe dark energy is not what we currently think it is. So our best guess about dark energy right now is that it's something called a cosmological constant. Basically, just a property of the cosmos that space time has this sort of expansion built into it. And so if you have some space, it'll have a tendency to expand. We think that that's probably what the dark energy is. We're not entirely certain. If it's something else, if it's something that isn't just a property of space, but some kind of field in the universe that changes over time, it could be something that gets more

powerful over time. And if that's true, then it could actually, instead of just moving galaxies away from each other, it could start pulling galaxies apart and pulling stars away from planets, then pulling apart planets and stars themselves, and eventually ripping apart atoms and sort of tearing space itself asunder. Very interesting. I love to talking about dark energy, dark matter. I mean, we talk about we don't know what 96% of the universe is made out of, right? Dark energy and dark matter. So then how can we make predictions about anything if we don't know what most of the universe is made at? Well, we don't know what it is, but we know a lot about how it acts. For dark energy, it's whatever it is, it's something that's

making the universe expand faster. And we can see the expansion of the universe. We can see how galaxies are moving apart from each other. And because we can see into the past in the universe. By looking at very distant things, we're looking at things as they were billions of years ago, we can see how that expansion has changed over time. And so we can deduce what dark energy is doing to our universe from those observations. We can survey galaxies all over the universe and see how they're moving and how they're relating to each other. With dark matter, dark matter is a very difference phenomenon. Dark matter is some kind of invisible matter. So it's something that has gravity, it has mass, but we can't see it. And it seems.

to be the stuff that's holding galaxies together. It's sort of this extra gravity where there are clumps of this invisible matter and galaxies and clusters of galaxies and so on are embedded in these clumps of this invisible dark matter. Now, we don't know what dark matter is made of, but we can map it out. We can figure out what it's doing and where it is by how it affects the regular matter, the stars and the galaxies that we do see in the universe. So we might see stars at the edges of galaxies moving around faster than we would expect, and we can say, oh, that must mean there's extra gravity holding them in. We know a lot about where it is and how it acts. We just don't know what it's made of. Now, we have an option number four that we, is sort of a relatively newcomer,

is it not? Yeah, yeah. So my personal favorite cosmic apocalypse is called vacuum decay. It's sort of been around since maybe the 70s or 80s, but it's gained a lot of prominence recently because as we've learned more about particle physics and as we've done things like Discover the Higgs boson, which is this particle associated with the Higgs field, a kind of energy field that pervades all of space, it's allowed us to understand our model of particle physics a little better. And what we've found is that it looks like maybe particle physics or maybe the physics that governs the universe isn't quite as stable as we thought. What we're predicting now is that the way that physics works in our universe is not really the only option.

And the Higgs field, which is this energy field, it can have different properties and it can change. And so there's a possibility that somewhere in the universe, there will be a quantum event that changes the Higgs field in that point in some single spot in the universe. And that would create a bubble of a different kind of space where physics works differently inside that space. And that bubble would expand outward at about the speed of light and just destroy everything. thing in the universe. And it would be an unpredictable event. We wouldn't know when or where it would happen, but it would be a totally inescapable bubble of doom. Now, there are reasons that we're not convinced that that's definitely going to happen, because first of all, it depends on the idea that we really understand all of particle physics, and we're not quite that arrogant. We know

that there are pieces missing to our puzzle, and so it may be that something will come up that it'll prove that vacuum decay can't happen. But the current equations kind of point that way, which is a very interesting consequence of the calculations people have been doing recently. If there's a bubble that bubbles up inside our universe, could there be a bubble that bubbles up outside our universe too and have another universe? Well, you know, outside of our observable universe, the region of space that we can actually see with telescopes and so on, we have no idea what's going on out there. There could be vacuum decay happening there. There could be new universes popping up out of the larger space we're embedded in, there could have been many

universes being created around the same time as ours or popping out of some larger space. There's a lot that could happen beyond the realm of our observable universe, which is this volume about 46 billion light years across, that we can actually get any information from. So what we visibly can see is not what might be out there. There might be a lot of other stuff out there that is beyond a horizon. Yeah, yeah. And our horizon is defined by how far away something can be where the light from that thing can have reached us by now in the age of the universe. So if there was a galaxy 46 billion light years away and the light left that galaxy at the moment of the creation of the universe, it would only just be reaching us now. So that defines the distance we can see because anything farther away from that, there just hasn't been enough time for the light to reach us. It turns out that because the the universe is expanding faster and faster, we're actually never going to be able to see things that are beyond that point because they're being carried away from us faster than light can travel

by the expansion of the universe. So there's this real hard edge to what we can see. There's a lot of interesting mysteries around what might be beyond our horizon. Now, I know as a theorist, you're not just inventing these ideas out of thin air. And you've mentioned that there's data guiding everything in those theories. And my question is, where does the data come from? That's most useful. important to you? Well, there are a lot of different things we can study. We can look at how galaxies are moving through the cosmos. During the expansion of the universe, we can see galaxies moving apart. We can look at very distant galaxies and see how they're different from galaxies that are nearby, and that tells us something about how the cosmos has been changing over time. And we can look at

actually the background light from the Big Bang itself. One of the most important pieces of data we have about the early universe, about the evolution of the universe, comes from the fact that we can see the afterglow of the Big Bang. So if we look at a galaxy that's five billion light years away, we're looking back billions and billions of spears, if we look farther away than that, if we look as far out as we can see, we can see the universe as it was at the very beginning,

because it took 13.8 billion years for the light to get to us from that point, we can see it as it was in the very, very early stages of the cosmos. And what we see when we look as far as we can see is, we see this glowing light, this light from a universe that is so young, it's just finishing up the big bang, and it's still in that primordial fire stage. So the early universe was hot and dense and sort of roiling with plasma, and we can see that because we can look so far away that we're looking so far back in time that we see that hot, early young universe. And that light has in it patterns of little blips of higher density here and lower density over there. And it tells us,

what the sort of seeds of the structure of the universe looked like and how the universe went from being this kind of fiery, roiling plasma state to this big, cool cosmos with galaxies and clusters of galaxies and so on in it. We're going to take a break. And when we come back, more cosmology and deep thoughts with Dr. Katie Matt, cosmologist and author of The End of Everything. This is Science Friday. I'm Ira Plato. If you just joined us, we're talking this hour about the End of the Universe with my guest, Dr. Katie Mack, author of the new book, The End of Everything. You know, I like the way you write in your book because you write just like a regular person, so to speak, in language that we can understand. And you write that there's a point you're

describing the heat death of the universe and you put it in all caps, but it gets even stranger, right? And you go on to say the universe is freaking weird. You're a cosmologist. How do you think the universe is weird if you understand it so well? I mean, I'm a cosmologist, but I'm also a person who lives a day-to-day life, and I get used to things making sense in my normal existence. And when you start to study these concepts in cosmology and these really deep time things that particle physics and quantum mechanics, it really is very different and it really is very weird. And sometimes you have to step back and say, you know, this is strange. This is not our usual experience. And you have to kind of take notice of that and just give yourself a chance to experience the oddness and the wonder of how weird physics really gets.

Well, how do people react to you when you say that you don't know something? I mean, you speak to the public a lot. Can they accept scientists saying, I just don't know. It's freaking weird. So what I try and do is I try to emphasize what we do know or what we have good evidence for versus what we're still trying to figure out. you know, science is always a process of trying to get better and better approximations to what's really happening out there in the universe. We come up with theories, we come up with models of how things fit together, how everything works, and then we try and test those theories. We test those

models and we try and get a better and better approximation. We are developing tools to understand and describe our universe. But we don't know for sure every time we develop a new tool, every time we do, come up with a new theory if that's the ultimate answer or not. And we don't fool ourselves by saying we're definitely describing true reality. We're just trying to get an idea of how we can think about this, how we can model this, how we can find useful ways to describe it. And so I try and say, like, sure, there are things we don't know. There are things we're figuring out. But we do have very good, useful theories that predict a lot of the data that match what we see. And we can use those and we can understand our universe better by further developing those and further testing and

verifying what we know. When do you give up on a theory that you can't collect enough data for? You know, I'm thinking of string theory. It's entering middle age now or any other theory that you want to describe the universe. When do you just say, well, we can't test it out. We have to go to something else. I think that it's very hard to fully set something aside and say, I'm not going to think about that. there are areas of physics where it's very, very hard to get data because you would need to

take a particle collider and do collisions at energies we can't possibly reach or we'd have to take data right at the edge of a black hole and we can't get there. There are all sorts of things like that where we're trying to understand something about the universe that really only shows up in places we can't really test easily. But what we can do is we can come up with models that are consistent that mathematically fit together well in all the places we can test, and we can see what those consequences are for other areas where we can't test it. We're always trying to find new creative ways to look at the data where maybe we wouldn't need to build that solar system size collider. Maybe we could look very carefully at the data we have and test the theory that way. So I don't think we're at the point where we give up trying to describe things.

But it is important, I think, to always keep in mind that if you come up with a new model, you need to be able to compare that to other models and do some kind of testing that tells you, at least if it fits the data a little bit better than another model or not. So it's always about taking what we have and saying, is this a better fit than this other idea we have? If so, we'll maybe move toward that one. if not, then we'll stick with what we have and try and come up with something new. So I haven't given up on understanding these things, but I do think that ultimately what we want

is a picture of the universe that is useful and that tells us something new. Albert Einstein was asked many times whether the human mind has the ability to actually comprehend the universe. And he once said the most incomprehensible thing about the universe is that it's comprehensible. You know, I think I think that I'm constantly fascinated by how. much we can know. We can see the big bang, right? We can see the background light from the time when the universe was still on fire. We can see the parts of the universe that from our perspective still are on fire. We can study that and we can see the little variations in the temperature

of that primordial fire and use that information and put that into simulations and come out with a whole universe full of galaxies in our numerical simulations. You know, we can watch the expansion to the universe, we can calculate to very high precision how much matter and energy and dark matter and dark energy and all that stuff is in the cosmos. It's astonishing how much we know and how well we know it, whether or not we'll ever get to the point of, you know, ultimate truth of, you know, exactly how the whole cosmos is put together. You know, we're working on that. But it is fascinating how much we do know. I'd like to get one more listener in. Harriet in Hawaii, who asks, what if the end of the cosmos is just,

the end of the story we've been telling ourselves about the cosmos. How do we know the universe isn't capable of many Big Bangs? Well, it's very possible that there could be cycles in the universe where the universe goes through an ending and then a new beginning of a different kind of phase of the universe. You know, you can have, you can even have regions of the universe that are beyond our observable universe or beyond our horizon where the universe is, is being. beginning again or a new universe is kind of popping out over there somewhere. You can have regions of space where the universe continues even after ours is over. So it's very possible that there are larger spaces and that there are more things before and after the timeline of our

observable universe. When I talk in my book about the end of the universe, what I'm really talking about is the process by which everything, all structure inside our observable universe is ultimately destroyed. And we're pretty sure that's going to happen. But what happens beyond that or before that or after that, we don't know. Well, it's not like quite ending on a sad note because we know how it's going to end. But it's all part of great stuff in your book, Dr. Mack. Thank you very much for taking time to be with us today. Thank you. It's always fun to talk about ultimate destruction. Dr. Katie Mack, assistant professor of physics at North Carolina State University in Raleigh, an author of the new book, The End of Everything.

I highly recommend it. It's a great read, and you can see an excerpt of it on our website, Science Friday.com slash the end. When you hear the word fluorescent, you might think of day glow colors you see in something like a psychedelic rock poster under black light, right? The colors can seem literally to glow from within. Over the years, researchers have created thousands of chemical dyes, that fluoresce in every color of the rainbow. And now a new approach to working with those dyes

can produce some of the brightest fluorescent materials yet. Science Fridays Charles Berkowitz has more. In the Minerals Gallery of the Smithsonian's National Museum of Natural History, there's a case of samples collected from the Sterling Hill Mine in New Jersey. Under regular light, they don't look like much there, gray rocks. But when the black light clicks on, they glow bright, neon, orange, green, and blue until the black light clicks off again and they're plain gray rocks. The minerals in that display are able to fluoresce. They're absorbing the ultraviolet radiation

of the black light and shifting it into a different part of the spectrum that humans can see. Chemists have been able to duplicate some of those effects using chemicals called dyes, but it's harder than you might think. Most of those fluorescent dyes shine best when they're in a dilute liquid solution. They don't work as well in solid form, and that can make them hard to work with. Now researchers say they've created a way to lock those dyes into a solid without dimming their light. Joining me now to talk about it is Amar Flood, a professor of chemistry at Indiana University in Bloomington, and co-author of an article on the research published this week in the journal Chem. Welcome to Science Friday, Dr. Flood. It's fantastic to be here. What's happening

when something fluoresces. Why do some things glow and others don't? Great question. The dyes that we work with, they absorb light. That's what we readily see. That's the colored dye stuff, that colored clothes. But when a dye can fluoresce, it holds onto that light momentarily as energy and then re-releases it as light. So molecules that fluoresce have the property of being very efficient, at returning the energy it absorbed back as light. And just to be clear, this is different from the chemical glow of a firefly or those glow sticks that you play with. That's correct.

That's a chemiluminouscence for a chemical or in fireflies, biochemical, event is converted into light. For the fluorescent materials that we work with, you have to energize them with UV light. and that's how they pick up that energy and then re-radiate it. People talk a lot about fluorescent highlighters or fluorescent safety clothing. How many of those things are actually fluorescent technically? I did a couple of experiments myself with a range of highlighter pens and put them down a piece of paper.

I looked at them under UV light and it turns out that half of them are fluorescent and the other half are not. So they will have this property of popping off the page, but maybe half of them are fluorescent. Why is it hard to make something solid fluorescent? You mentioned the minerals at the beginning and are inspiring because they get us to think, hey, look, if we could uncover the rules that govern the fluorescence in that material, maybe I could make a new material that uses those same rules. but I could be in charge of the color. I could be in charge of, you know, the lifetime over which it fluoresces. It turns out we've learned the rules often, but it's hard to make new materials that enlist those rules. There are two pieces of the puzzle here.

When you try and make them into solids by growing a crystal, you know, they don't often behave like we would like them to behave. They don't form a nice, say, checkerboard arrangement. So that's a very difficult area of science that could at any point thwart your efforts to take or transfer a fluorescent dye into a fluorescent solid. So that's getting the packing of the molecules just right. The reason why that matters is because generally if you just let the fluorescent molecules in our case pack. however they want willy-nilly, they typically come intimately close to each other. And this is where I sort of liken it to small children in a classroom. They're great as individuals, but you get them together and they start fidgeting and interfering

with each other and they stop behaving as a unique person and take on a life of their own. And when you do this with fluorescent molecules, when you put them together, they stop fluorescing. The other thing that they do is they change color. You might have your fluorescent compound and you look at it in the dilute solution you mentioned at the beginning and they appear red. And then when you make them into a solid, you're expecting a red solid and you get a green product out the other end. So can you control the way the molecules pack together? And if they do pack together, can you stop the molecules from interfering with their intrinsic fluorescent properties? And that's really the essence of what we have done in the materials that we are

sharing with the world at the moment. So in essence, it's a way to insulate the dye molecules from each other as they pack closer together into this orderly checkerboard lattice. Absolutely. You know, it's COVID-19. The word socially distance has popped up. In this particular case, that's pretty much what's happening. You're listening to Science Friday from WNYC Studios. Once it's in that stable checkerboard lattice, what can you do with it? Is it, you put it in paints, plastics? What's the end goal here? So we are exploring what those end goals are at the base level. They need to be used. in potential technologies where brightness really matters. There's medical diagnostics where perhaps you might make faster and more efficient detection of early disease.

There are medical lasers where you might want to be able to change the color out of your laser more easily. And in different types of solar energy technologies, where you might like to capture different areas of the solar spectrum, but related to the solar energy area are also advanced materials that scientists and engineers are looking at that haven't yet made it to prime time. One of particular is a phenomenon called up conversion. And in essence, what you do is you put in two low energy photons of light that come from the sun, and normally

but too low in energy you can't really drive an electrical circuit and so they are often they just hit the earth surface and they're not used. So the dream for up conversion is hey look if we can

capture two of those low energy photons, double them together and create a higher energy state inside material can we pull that higher energy out to drive analytical circuit?

And the underlying a phenomenon of that works really well in solution, works really well in dilute solution. But the moment you put those dyes into the solid, they have the problems that we discussed earlier. They stop working. So people in the community have been asking us, hey, look, can we take that solution-based phenomenon of up conversion and transfer it into the solid state using our materials? We have some pictures of some of your sample materials on our website at ScienceFriiday.com, and these beautifully glowing, twisted structures, how much brighter are your things than once you get it into that solid form than a traditional material?

Those images are of our materials put into polymers. And in terms of brightness, it turns out that when you try and put fluorescent dyes in into polymers, it has the same problem as you increase the amount of the fluorescent dye you put into the polymers. They stop working. They stop fluorescing and it's of no use to you. So what our materials allows us to do is to push right through that limit and to have bright fluorescence where you simply couldn't have a polymer material fluoresce at all. So that's one metric in those sort of polymer materials that we've got images of. Another metric comes with those medical diagnostics.

The brightnesses are 30 times greater than in existing medical diagnostic particles that go by the name of CABium saline. Interesting. Well, thank you very much for taking time to talk with me, today. Thanks. It's been really nice chatting with you too, Charles. Dr. Amar Flood is a professor of chemistry at Indiana University in Bloomington. For Science Friday, I'm Charles Burgquist. We need to take a break, but when we come back, Gene editing a squid. Stay with us.

This is Science Friday. I'm Iroflato. Out east on the southwest corner of Cape Cod is the town of Woods Hole. The water in this area is flush with marine life. So it's the perfect home for the Marine Biological Laboratory and International Center for Research. And it's here that big news in genetics world has come out. For the first time, scientists have successfully knocked out a gene in squid. This has huge implications for the study of genetics. Here to talk to us about the research are two of these scientists involved. Josh Rosenthal, senior scientist at the Marine Biological Lab in Woods Hole,

and Karen Crawford, Professor of Biology at St. Mary's College of Maryland. She is a visiting research fellow at the laboratory. Welcome both of you to Science Friday. Thank you. It's great to be here. Thank you very much for having us. Josh, I want to start with the why. Why was there this quest to knock out a gene and a squid? I think this goes back to really a big initiative we have at the NBL, which recognizes that, you know, life started in the ocean. And more biodiversity exists in the ocean. than anywhere else, but we really don't have the tools to study it. There are a lot of creatures that have all sorts of interesting biological programs that we'd like to get at. And really,

in order to get at those things in these days, you need what we call genetic tractability. That's the ability to manipulate genes and see the outcomes. So one of the groups of organisms that were very interested in are cephalopods because of their biological novelties. We want to use genetically tractable organisms to answer some of the fundamental problem and questions about marine organisms. And Karen, what gene did you target here? I understand it was a pigmentation gene. Why did you choose that? We chose the tryptophan 2-3 dioxygenase gene, which I'm just going to call TDO, because it's the very first enzyme step in making a set of pigments called omacromes. So just think of pigment cells. And we chose that enzyme because we not do that. We not

just that enzyme, then the pigments could not form, and the embryo would be a direct readout that we had been successful. So we could actually visualize control embryos with their beautiful chromatophores coming up, their pigment cells, and we could visualize our injected embryos and actually see them appear as partial or maybe even complete albino embryos lacking pigment. And so it's a way for us to get a readout directly from one embryo that the project is working. Yeah, you can certainly tell in cephalopods because they're so talented in changing the pigmentation of the skin themselves. You can certainly tell when it's when it's been changed. And I'm looking at the photos of this squid we're talking about it. It looks like you made them clear as

glass. Is that right, Karen? The pigments are missing, but the clear as glass quality is actually something that's unique to that embryo, which also is a great feature for studying it as it's developing from the fertilized egg until the little squidlet that you're looking at, the embryo is completely clear so you can actually watch everything happen as it's happening in the living embryo. How difficult was it in knocking out this gene?

Well, the most important part about knocking out the gene was actually getting into the embryo without damaging it. So when I think about the two elements that came into play, one is to be able to create fertilized embryos and culture them. We'd done that. The second advancement was more recent, and that was the injections. So the embryo is surrounded and protected by a clear, tough rubbery layer called the Correon.

It needs this layer to develop normally. If you remove it, the embryo doesn't develop. And if you make a large hole in it, the embryo extrudes out like toothpaste. So I want you to think of a pair of very fine tweezers, a little thicker at the end, than an eyelash. Then I want you to bend those very tips of the tweezers about 30 degrees so that they criss-cross. And that creates a very tiny scissor that can cut holes in the rubbery layer of the embryo smaller than the diameter of a single red blood cell.

That's pretty tiny. But the holes are big enough to allow my injection needle through, yet small enough to hold the embryo inside and even heal up. And so I set the stage, I do my injections, and the embryo does the work. and my job is to just watch the show. Well, but how much practice does this take? I mean, it takes a lot.

It takes a lot. And for years, I had created holes in corions in different ways, making tiny, tiny little round holes with my forceps. And a colleague of mine told me that they were beautiful, but impossible for anybody else to make. So we fashioned these scissors, and now I'm in the process of teaching others how to use them, and they're being successful.

So it's not as impossible as it sounds, but it does take some sharing and some training up. Josh, you mentioned this a bit earlier in an answer to my question, and because when we think of genetic research, we usually think of lab rats and fruit flies. Does this breakthrough mean that squid could be added to that list of lab animals that you test things on? Well, we're moving in the right direction. You know, probably starting in about the 80s, 90% of biology was full. focused on those animals you're talking about, things like the fruit fly and lab mouse, et cetera. And there's been unbelievable progress in those systems. The things you can do really

wow me every day. However, we're starting to move towards closing that gap. And really, I think we got to credit this revolution with CRISPR Kass 9 genome editing with that because it's kind of species agnostic. If you can culture a species in the lab and have access to the embryos, you have a good chance of being able to do gene knockouts, and we took advantage of that. So we're at the first steps. We can do a gene knockout now in this species, but there's a long way to go for what we really want to accomplish. Well, is there something special with this gene editing technique and this specific gene that we're talking about that could be beneficial for other animals or for humans? This gene that we're talking about right now was really just a

proof of principle for us. But cephalopods, some of their novelties, I think, hold tremendous promise for a lot of things that can really change, you know, the human condition. I am happy to talk about some of their novelties, but, you know, things that you're not going to find in a fruit fly or a lab mouse, there's just all this biological diversity, and cephalopods really embody that. We're happy to talk about that because we have a whole cephalopod week. We love cephalopods. And we understand how diverse the talents that they have. Yeah, I realize that I'm preaching to the converted with you. Yeah, so, you know, the cool thing about cephalopods is that they've developed over a completely different evolutionary trajectory.

So in life, you have two groups that have achieved really incredible behavioral sophistication. And those are animals along the vertebrate lineage and cephalopods. So if you study things along the vertebrate lineage, let's say you're interested in behavioral sophistication and in a fish or a bird or a monkey or any mammal, you're going to be studying a lot of similar innovations because they've been derived along the similar pathway. However, cephalopods have done this independently. I'll give you a couple examples. Like, they have these enormous brains. The brain of an adult octopus, for instance, is about six times bigger than that of a mouse. And for an invertebrate, this is tremendous.

And so there are some big differences. It's organized in a completely different manner. For instance, in vertebrate brains, in our brains, it's very centralized. So if you think something or you want to control your hand or you smell something, that's all being processed in your brain up in your head. Over half of all cephalopod neurons are peripheral. They're outside of that central brain. And that means they've figured out ways to do things differently, to control their lives, to control their movements and their sensory in a fundamentally different way. And we don't know how it works. So being able to access the genes now, basically we can have a way in to start studying these processes. Karen, are you as excited about cephalopods as Josh is? Oh, my goodness. I'm very excited about cephalopods. I first was drawn to them because of their beauty. but also many important qualities.

The embryo that I work on, they're actually very tiny. They're 1.6 by 1 millimeter in size, smaller than the head of a pin. Cephalopods are related to mollusks, snails, clams, and oysters. And even though their eggs are tiny, some species have larger eggs. They contain a lot of yolk and divide differently than all the other members of the Spiralian group, which they belong to. interestingly about squid and octopus and cuttlefish is the first cell division, unlike in us, but it divides the squid embryo into a right and left side.

So we can take advantage of this quality and inject one cell at the two-cell stage. We can inhibit our knock out a gene, we can add a gene or knock in a gene, and do this on only one side of the embryo. As a result, as it develops, we can see in comparison to the unison. injected side, what the gene does. We can actually begin to answer a question in one embryo, what does this gene do? We're at a place now where it's not, are there interesting questions to ask? It's more what interesting questions can we ask first because there's so many. Would it be fair to say then, Karen, that you have created by knocking out a gene,

you've created a new species of squid? No, it's not a new species. And then, This particular organism, the Atlantic longfin squid, it doesn't culture in aquaculture in the laboratory. So this life cycle has not been closed. So we are not getting animals to breed in the laboratory and creating another generation. What we have done, though, is we've modified a squid to allow us to know that we can manipulate its DNA and ask important questions and analyze that result. And this opens the field to questions about neurogenesis, developmental biology, basic self-functions, possibly even relating to neurodegenerative diseases, Alzheimer's, and Parkinson's. There are many, many scientists studying the neural pathways in encephal pods that will be excited by this method

and want to then bring their own questions to the early embryo to get an answer and bring them closer to what we understand. Are there any questions, Josh, about how ethical it is to study the squid and cephalopods? Yeah, I mean, absolutely. This is, as most people probably don't know, that cephalopod use is regulated in Europe and Canada presently. This is a recent change, but it isn't in the United States. However, at the NBL, this is something we take really seriously. And actually, we've come up with a comprehensive set of guidelines for the ethical and humane use of cephalopods in research. And so anyone who comes to the NBL has to follow these guidelines and they're constantly evolving. The important point here, I think, is that we want to make sure that these guidelines are based in science.

And the issue is there hasn't been that much science done. So, for instance, if you're going to make, if you want to use an anesthetic, you have to make sure it actually works in a cephalopod. So we're actively working in these areas as well. I'm Ira Flato. This is Science Friday from WNIC Studios. In case you're just joining us, we're talking with Dr. Josh Rosenthal and Dr. Karen Crawford, both working at the Marine Biological Laboratory in Woods Hole, I'm talking about gene modification of cephalopods, and in this case, a squid. So what is so special about cephalopods that you have these special limitations on them?

They're behavioral sophistication. You know, in the U.S., we have this division between invertebrates and vertebrates that if you work on invertebrate like a fruit fly, you aren't regulated. If you work on a vertebrate like a fish, you are regulated. And generally, that is along a very vertebrate-centric access, thinking that the vertebrates are the behaviorally sophisticated groups and invertebrates aren't. But cephalopods are this one example of behavioral sophistication in invertebrates. And that's why we're taking it so seriously. Speaking of sophistication, I understand that you were part of a team that made another squid discovery recently, that they can edit their own RNA in an unexpected way. What is that all about?

Yeah, you know, this is one of the really cool things about cephalopod. Some of their biological novelties you can just see, like their ability to camouflage, which is incredible. Some of them are more hidden. And so what we stumbled across is that they're able to edit their genetic information on the fly. And I think a good analogy is, you know, your genome contains all the genes that that encode all the information you need during your lifetime. And at any one moment, you only need a little bit of that information, a subset. I liken it to your genome as like a library, and at any one moment you might only want to take out a couple books.

However, let's say you take out a book today because you want to bake a loaf of bread, and you go and you start making that bread, and the instructions say, okay, let it rise for four hours, but your kitchen is very hot. And you see after two hours, it's already risen enough. Wouldn't you like to be able to modify those instructions? Well, Squid have figured out a way to do this in a massive level where they recode or change genetic information on the fly as it goes through these RNA molecules. And this has, I think, tremendous applications. It's very interesting from a biological perspective.

And it has tremendous applications in biomedical realms as well. because if you can tap this ability to edit genetic information, it's one of the most powerful ways to intervene for therapeutics. Karen, is that where you think this is very important also, using it eventually in genetic therapeutics for people? The first steps for me, I'm a developmental biologist, which means I study how you go from being an egg to being you with all the parts in the right place.

And so for me, there are so many fundamental questions and classic questions that initially some with cephalopods were started at the NBL with other scientists that have taken us to a place. So there's so many basic fundamental biology questions, neuroscience questions that I want to answer, but I cannot believe that some of the answers that we get from those questions won't lead to a better understanding of our own nervous system, cell function, cell cell communication, and in the end, therapeutics. Because cephalopods do become senescent and they have changes and we can study that in relation to how our own nervous system changes. So I'm going to start more in the classic embryology side of

things, but I believe very quickly we'll, through collaboration, have applications that will help with human health. Well, as I said, we love cephalopods on Science Friday and devote a lot of time to it, and I'm glad we could add some more cool knowledge about what you guys know about cephalopause. I want to thank both of you for taking time with us today. Josh Rosenthal, senior scientist at the Marine Biological Lab in Woods Hole,

Karen Crawford, Professor of Biology at St. Mary's College of Maryland and a visiting research fellow at Woods Hole Laboratory in Massachusetts. Thank you both for taking time to be with us today. Good luck in your work. Thank you so much. It's been a pleasure. Thank you very much for having us. And if you

missed any part of this program or you'd like to hear it again. Subscribe to our podcasts or ask your smart speakers to play Science Friday. Every day now is Science Friday. Okay, here's our Science Friday Vox Pop Ask for this week. Have you had to navigate pregnancy or childbirth during this pandemic? We want you to tell us about it. So tell us about what hurdles you had to go through to safely have a baby or take care of your newborn. That's on the Science Friday Voxpop app wherever you get your apps. You can also say hi to us on social media, Facebook, Twitter, Instagram, or email us the classic way, SciFri at ScienceFriety.com. Send us feedback and tell us what you like us to cover. We really do want to hear from you. Have a great weekend. We'll see you

next week. I'm Ira Plato.