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But we do want to use this time here at the top of the episode to let you know that there is some brand new Journey to the Microcosmos products available at We’ve got a new tardigrade shirt either in white or in blue and from now until the end of August, we’ll be taking pre-orders for them, and whichever color sells the most will continue to live on in our store, while the other will go away forever.

So, if you want to get your color of choice, head on over to the link in the description between now and the end of August to pre-order your tardigrade shirt. Nostoc are a genus of cyanobacteria known for gathering their thin, thread-like bodies into gelatinous colonies, forming what look like, basically, a weird noodle soup. Of course you might not want your bowl of noodle soup to be bright green like this, and that is fair.

But outside the world of imagined meals, the color of cyanobacteria like nostoc are an indicator of their life-sustaining ability, turning their chlorophyll into a vivid display as they reflect green wavelengths into our vision. Then, with a flick of a switch, we can change the light on our sample from white light to ultraviolet light. And everything changes.

Our soup of filaments is now a bright, bright red, like we just doused our noodles in hot sauce. To be clear, there were no filters involved in changing the color of the chlorophyll molecule. And we did not add any kind of chemical to make the nostoc glow red.

The nostoc is making that light. All we did was flip a switch, and electrons did the rest. What the nostoc are doing here is fluorescing.

And as you will see today, they are not the only organisms who can do this. Throughout this video, we’re going to be showing you different organisms, first under white light, and then under one of the more narrow bands of light that are part of our new fluorescence microscopy toolkit. Fluorescence is what it looks like when light makes electrons jump around in their orbitals.

Inside an organism there are many, many chemicals, and inside those chemicals are atoms and bonds and electrons arranged in a way that makes life possible. Now depending on the structure of those atoms and bonds, sometimes certain wavelengths of light will excite the electrons, sending them jumping up to a higher energy state. But those electrons will very quickly fall back down to their original state.

And when they do that, those electrons release photons. And that light is what we’re seeing here, the emission light--bright against a dark backdrop, while a filter blocks the original excitation from obscuring the sight of our organism fluorescing. When a chemical is able to produce fluorescence, it’s called a fluorophore.

And for our nostoc and other photosynthetic organisms, we know that the fluorophore glowing red under UV light is chlorophyll. But we know this only because we know enough about the cyanobacteria’s biology and chlorophyll’s fluorescence to narrow down the source. For other organisms, the source of the fluorescence is a mystery to us, though with the right combination of tools and experiments, we might be able to narrow down the source4.

When we see this fluorescence, we know something exciting is happening in our organism, we just don’t know exactly where it’s coming from. The only clue we have is the color orange. And since there are all sorts of possible fluorophores in the world, we don’t even know if there’s even just one molecule making this light.

We might be watching several fluorophores at work here, their excited electrons lighting up the organism in unison. Now fluorescence is when organisms take in light and then reemit it a different wavelength. But some organisms can make their own light.

And perhaps the most famous glowing residents of the microcosmos are the dinoflagellates, whose bioluminescent light you can sometimes see across the surface of waves. That light is not from fluorescence. It is the result of a molecule called luciferin, which emits light when it’s oxidized by the luciferin enzyme.

This is a chemical process rather than a physical one. The effect is similar to fluorescence: a glimmer of incandescent light coming from within a microscopic body. But the cause is entirely different.

Dinoflagellates are bioluminescent, their light is the result of chemicals reacting with one another. Chlorophyll and other fluorophores, however, don’t require another chemical to light up. They just need the right wavelength of light to hit them.

They then use that light to make light. But while bioluminescence and fluorescence are different phenomena, biology loves to muddy the boundaries between the categories we assign to things, and there are moments where these two seemingly distinct phenomena are in fact linked together. Off the west coast of North America, there’s a bioluminescent jellyfish called Aequorea Victoria, which shines blue when calcium activates a molecule called aequorin.

But the light from that reaction is able to provide energy to another protein, a protein that fluoresces green when hit by that light and it gives the jellyfish a somewhat more verdant hue. When scientists found this protein, they gave it the very literal name of Green Fluorescent Protein, or GFP. But there’s nothing wrong with a name that cuts right to the chase like that, especially when you’re naming what has since become one of the most famous fluorescent proteins.

The beauty of fluorescent proteins like GFP goes beyond just the colors they show us under the microscope. They have allowed scientists new ways to illuminate organisms from the inside, to introduce fluorescent proteins through stains or genetic engineering into an organism like a fluorescent molecular marker. And from there, the fluorescence helps us map out the events inside a cell that might otherwise be invisible, like the dynamics of gene expression or the course of a cell’s fate.

Often, when you see those stunning images of cells awash in a rainbow haze, you’re looking at the careful work of decades of science, of the lessons we’ve learned from nature about how to see it in a new way. And as we apply these lessons, it’s important for us to make sure we give the organism’s their due for the fluorescence made of their own structures--like the red glow of the Nostoc’s chlorophyll, which we call autofluorescence. But it’s not simply a matter of giving credit.

In one form, autofluorescence illuminates, providing us with another way to see the molecules of an organism at work. The autofluorescence of chlorophyll can, for example, tell us more about the health of a plant. Yet in another form, autofluorescence obscures.

If we introduce our own fluorescent markers into a cell, only to find that the cell’s own molecules produce a light similar to our markers’, the colors become very difficult to interpret. And so the usefulness of autofluorescence ultimately becomes decided by its context. For the scientist, it is a consideration as experiments are planned and interpreted.

For the organism, it is simply a reaction in its own body: a light made into new light, a color made into new color. And for us, it is a glimmer of something new, made by old friends. Thank you for coming on this journey with us as we explore the unseen world that surrounds us.

We recently celebrated a couple of milestones here on this channel. Our two year anniversary as a channel was back on June 24th, and our one hundredth episode was uploaded on July 12th. So, to celebrate, and also just because we had a lot of fun hanging out the last time we did this, we’re going to have another livestream here on the channel this Wednesday, July 28th.

So, if you have any questions you’d like us to answer during that stream you can leave them in the comments below, or in the chat during the stream. We hope to see you there! Like we mentioned at the beginning of this episode, we also have some brand new Tardigrade shirts that are available for pre-order at

So, visit the link in the description if you want to make sure you get your color of choice. And while you’re there you can also check out some of our other products like these paramecium socks and even our Journey to the Microcosmos coloring book. The folks you’re seeing right now on the screen, they are our Patreon patrons.

If you, watching right now, are one of those people, allow me to say thank you on behalf of this entire Microcosmos team and also on behalf of the people who are able to get this content because you have helped support us. If you would like to join these folks in being a patron of Journey to the Microcosmos, you can go to If you want to see more from our Master of Microscopes James Weiss, you can check out Jam & Germs on Instagram or on TikTok.

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