Wednesday, September 27, 2023

Answer: What is dietary fiber?

 It seems obvious...  

.. but as I said, I suddenly realized that I didn't really understand what "fiber in my diet" really meant.  

This happens all the time. There's a kind of skill of recognizing that something isn't lining up--of knowing that you don't quite know what something really is. 

As you might have noticed, a lot of these posts start with "I didn't know..."  

In this particular case, I thought I knew was "dietary fiber" was.  Isn't fiber just the indigestible part of your food--you know, the little threads, husks, hulls, and tiny fragments that just pass straight through without much digestion seeming to take place?  

But as I noticed when I let my cereal sit for too long in the milk, things that say they have fiber in them (like my whole grain cereal) often don't look like there's anything fibrous within.  There's nothing like the kernels of corn or bits of apple skin that (as far as I can tell) are untouched by my digestive juices.  How could there be any "fiber" there?    

So... what is fiber really?  It's obviously not just undigested bits of food.  

Can you help me understand what's going on here?  Today's Challenges are: 

1. So what, really, is dietary fiber?  Is it something more than indigestible bits like wheat bran, corn kernels, and rice husks?  

I wanted to start with the basics.  First query: 
     [ define fiber ] 

This starts to untangle part of my confusion. I was thinking of dietary fiber as a kind of textile-like fiber.  That is, my mental model of "fiber in food" was based on what I thought of as a fiber that I might see in clothing or the husk of a seed.  This is very much along the lines of that word you see at the bottom of the definition, "roughage."  

But reading carefully, I learned that "fiber" (or "fibre") is also a "dietary material containing substances such as cellulose, lignin, and pectin that are resistant to the action of digestive enzymes." 

And THAT is a surprise. It means that the fiber in my diet can be pretty non-fibrous.  

Just a few weeks ago I had way too many plums on the tree at my house, so I spent a few happy hours making jelly and jam.  One of the steps in the process is to put pectin into the mix.  But when I do that, I can see that the pectin dissolves into a clear liquid... there aren't any obvious fibers that look like roughage.  

I was curious about lignin and cellulose, so I looked up those terms as well.  Are they fibrous in the way I'd expected? 

Answer: NO!  If you look at images of lignin, cellulose, or pectin, it's pretty clear that all of those come in powdered form--and if you look for [ liquid cellulose ] or [ liquid pectin ] it's pretty obvious that those don't have any roughage in them. 

So dietary fiber must mean something other than the roughage you get from (say) celery.  

My next query was for: 

     [ fiber in food ] 

and I quickly learned that fiber is, indeed, not just the rough indigestible bits, but is actually all the long-chain molecules that make up those indigestible bits!  

As the Wikipedia entry on dietary fiber tells us "Dietary fiber consists of non-starch polysaccharides and other plant components such as cellulose, resistant starch, resistant dextrins, inulin, lignins, chitins (in fungi), pectins, beta-glucans, and oligosaccharides."  

Okay.  I now know that "dietary fiber" is really all of those complex (long-chain) molecules in the food I eat.  So, "high fiber foods" have a lot of those chemicals AND roughage. 

But wait... there's more!  

I also learned by reading some of the links from the SERP that there are two kinds of dietary fiber!  There's "soluble" and "insoluble," that is, fiber that dissolves, and fiber that doesn't.  

     [ soluble insoluble fiber ] 

The first result is to the Medline page about dietary fiber, which includes this: 

"There are 2 different types of fiber -- soluble and insoluble. Both are important for health, digestion, and preventing diseases.

Soluble fiber attracts water and turns to gel during digestion. This slows digestion. Soluble fiber is found in oat bran, barley, nuts, seeds, beans, lentils, peas, and some fruits and vegetables. It is also found in psyllium, a common fiber supplement. Some types of soluble fiber may help lower risk of heart disease.

Insoluble fiber is found in foods such as wheat bran, vegetables, and whole grains. It adds bulk to the stool and appears to help food pass more quickly through the stomach and intestines." 

Ah ha!  So there really are two kinds of fibers in our food.  The soluble kind and the insoluble kind.  

Insoluble fiber:  This type of fiber does not get dissolved in the body and is also known as “roughage”, helping to clear out the intestinal tract. Since it's not broken down in the body, insoluble fiber has effectively zero calories. This is why a high fiber diet is recommended for weight loss as insoluble fiber will fill you up and pass through your body unchanged. 

Soluble fiber: By contrast, this kind of fiber is a bit more complex than the other. Unlike insoluble fiber, soluble fiber dissolves making a gel like substance, which is incredibly handy for slip/sliding your gut contents along.  

2. What is the current recommendation for dietary fiber in my diet?  Is 5 grams of fiber in a serving a lot?  Or is it a little?  

A quick search for: 

     [ dietary fiber recommendations ] 

generated a lot of hits.  Interestingly, when you compare the top 5 reputable sources, you see this: 

Mayo Clinic – Women:  21 to 25 grams / day; men: 30 to 38 grams / day
UCSF – everyone: 25 to 30 grams / day from food, not supplements 
NIH -everyone:  25-29 grams / day (more than 30 grams would be better) 
Harvard – people < 50 years, 25 grams for women and 38 grams for men. 
                For people > 49, Women and men should have 21 and 30 daily grams

Oddly, none of the sources break down the amount of fiber by soluble vs. insoluble.  But it's clear that "fiber from food" solves a lot of the soluble/insoluble question by providing both in roughly equal quantities.  

Basically, if you can dissolve the food in water, it's got soluble fiber.  If it doesn't dissolve, it's insoluble fiber.  You need both.  

Bottom line: Women need slightly less fiber than men, but everyone needs roughly 30 grams / day.  

If you look up various foods (after doing a query like [ data set food fiber amount ]), you'll probably end up on the USDA's list of foods with the amount of fiber listed for each.  In that list you'll see a lot of high fiber foods that you probably won't eat in large amounts (who eats 100 grams of cinnamon?), but you'll be able to look up your favorite foods and estimate the amount of fiber you're getting.  

US folks: Note that the table is given in "amount of fiber in 100 grams of food."   So you'll have a vivid image--100 grams is around 3.5 ounces, or to make it visually memorable, small cans of cat food are 3.5 ounces (100 grams). 

And you'll see that my favorite cereal has 10 grams of fiber in 100 grams of cereal.  But take note--most people I know don't eat 100 grams of cereal in a serving at breakfast.  My bowl of morning cereal usually has 36 grams of cereal, which means I'm getting 4 grams of fiber in each bowl. 
Apple with 2.8 grams of fiber

That's okay, I guess, but an average apple has 2.8 grams of fiber, and a regular serving of plain old oatmeal has 4 grams of fiber and 6 grams of protein.  (And it's about half the cost per serving.)  

SearchResearch Lessons 

1. Search out the things you don't understand, even sometimes fairly obvious things.  This was just one of those little things that struck me while reading: I couldn't actually define dietary fiber.  I make it a practice to question what I'm reading at a very basic level.  This is deeply important when you're reading something that's complicated or has an intricate back story.  Do you really understand all of the parts and pieces that are involved?  

Being a skilled searcher is, in large part, having enough background knowledge to know when something you just read (or heard) doesn't fit in with the other things you've read.  In this case, it was a small observation about my breakfast cereal.  For you, it might be something else.  Follow up those small questions--they could be deeply important.  

2. Look for multiple sources.  As I did with searching for multiple sources of fiber recommendations, it's easy to find them.  Be aware of differences between measurements! 

Keep Searching!  

Wednesday, September 20, 2023

SearchResearch Challenge (9/20/23): What IS dietary fiber?

 I realized I don't know what "fiber" really is!  

I was at a farmer's market buying a few veggies for the week ahead, and while standing in line I was browsing my news feed, and came across an article about the amount of dietary fiber in different foods.  I was impressed to read that my favorite breakfast cereal, a "high fiber" food, delivered a "whopping" 3.57 grams of fiber in each serving.  

Years of SRS have taught me to be very wary of anything I read, especially when it's surrounded by such superlative adjectives. 

So I found myself wondering my SearchResearch type of questions:  "Is that a lot of fiber?"  And "so how much fiber should I be getting?"  

When I got home I did a little searching around and found that... I really don't understand what fiber is! 

In particular, I thought that fiber was the indigestible part of your food--you know, the little threads, husks, hulls, and tiny fragments that just pass straight through without much digestion seeming to take place. 

But when I let my cereal sit for too long in the milk, I know it turns into a pure paste.  There's nothing like the kernels of corn or bits of apple skin that (as far as I can tell) are untouched by my digestive juices.  How could there be any "fiber" in that glop?  

Later, I saw a bottled drink for sale in my grocery store that promised a solid 6 grams of fiber in a single drink.  So far as I could tell, the drink looked pretty much like some kind of exotic juice--not the pulpy slurry I would have expected.  

Can you help me understand what's going on here?  Today's Challenges are: 

1. So what, really, is dietary fiber?  Is it something more than indigestible bits like wheat bran, corn kernels, and rice husks?  

2. What is the current recommendation for dietary fiber in my diet?  Is 5 grams of fiber in a serving a lot?  Or is it a little?  

These don't look like difficult questions--BUT--when I did my research, I found the story much more interesting and complicated than I'd originally thought.  

Among other things, I've started looking at the listed amount of fiber in a food product with a huge grain of salt.  (Which will then upset my sodium intake, but so be it.)  

What IS the story with fiber?   It seems there's more here than meets the eye, the tooth, and the entire alimentary canal.  

Can you find out? 

Let us know what you discovered, and what you did to find out about it.  

Keep Searching!  

Friday, September 15, 2023

Answer: A mysterious octopus? And the woman who understood.

  An octopus has eight arms... 

Gloomy octopus. P/C John Turnbull.

... and, even though it's a mollusk, it doesn't have a shell.  They do have a hard beak, but there's no shell in the ordinary sense of a mollusk.    

As I've mentioned before, there are exceptions to just about every generalization (even this one). A friend mentioned an octopus that DOES have a shell.  How can we find out about this?   Is that true?  Here are the Challenge questions for the week:  

1. Is my friend right?  Is there an octopus that has a shell?  Really? 

Let's start with the obvious: 

     [ octopus has shell ] 

and we quickly learn that it's complicated...  The short answer is "yes..but..."    

It's not hard to find that there are actually two octopus creatures (that is, they have 8-legs, in the Order of Octopoda).  One is the Cirrina sub-order of Octopoda--they have a small, internal shell and two fins on their head, and NO ink sack.  Here's a deep-water Cirrinothauma, often called the "Dumbo Octopus" for its resemblance to the Disney character.  

This dumbo octopus (Cirrothauma murrayi) is often called the blind octopod due to the lack of a lens and reduced retina in its eyes. Its eyes can really only detect light and cannot form images P/C NOAA

Then there's the other one--the Argonaut (Argonauta argo), a fabulous creature that also creates a very thin, papery shell that it uses to move up and down in the water column... but only the females do so. They are not attached to the body of the female.  But, oddly, they make the shell by extruding it from their body and then holding onto it for the rest of their lives.  

So the shell is of the Argonaut, but not part of the Argonaut.  They make shells for use as egg-cases.   By searching for [ argonaut shell ] I was able to find this lovely image of just the shell.  

Argonauta argonaut eggcase / shell. P/C James St. John (Flickr) CC by attribution 2.0

For our purposes, if the Argonaut creates it, we'll call it her shell.  This is what one looks like in the wild: 

The white shell is on the left, with the octopus eye and
tentacles sticking out on the right.

But then there's the more delicate issue of whether or not an Argonaut is an octopus or not.  It behaves a lot like a regular nautilus (it's got that nautilus-looking shell that it hangs onto), but the Argonauta argo is a genuine octopus that just seems like a nautiloid.  By comparison, a regular nautilus (e.g., Nautilus belauensis) has a very different body plan.  In this image you can see the outside and the inside of an "ordinary" nautilus shell.  

Exterior and interior of a nautilus shell showing the chambered interior construction

As we've talked about before, these distinctions are important when you're doing your online research.  

Early illustrations of the Argonauta. P/C Wikimedia. Original from Natural History: Mollusca (1854), p. 22 - "Paper nautilus" [Argonauta]

For a wonderful paper about the Argonauta (in particular, with great details about its shell), I highly recommend the paper Recognising variability in the shells of argonauts (Cephalopoda: Argonautidae): the key to resolving the taxonomy of the family Memoirs of Museum Victoria 77: 63–104 (2018).  

2. As I read more, I learned a couple of fascinating details about the life of this particular octopus.  Can you find two really unexpected things about this animal? 

There are many remarkable things to notice about the Argonauta argo, but perhaps the two most remarkable things I picked up just by reading. 

A. The Argonauta argo controls its buoyancy by scooping air into its shell while on the surface. With this little bubble of air, it can hover easily in the water column.  By contrast, other octopuses linger at the bottom of the sea.  They can swim around, but they prefer to hide out on the bottom.  The Argonauta defies this with its mid-water behaviors.    

B. The little octopus can repair its shell!  The shell is large, but has thin walls with just one chamber (not like the chambered nautiluses above).  The material of the shell is high in magnesium, but is primarily a kind of calcium carbonate. The biggest surprise to me was learning that if the shell of the paper nautilus is damaged, a female can repair it or can completely rebuild it as needed. 

C. Males have a modified sex arm called the hectocotylus.  When mating, the hectocotylus detaches from the male and is left inside the body of the female.  Sometimes, mature female Argonauts are often found with multiple male hectocotyli (each from a different male) wrapped around the gills inside their mantle cavities. When this was first observed by naturalist Georges Cuvier, it was thought that the hectocotyli were actually a kind of worm.  Seems like a strange mistake to make, but the hectocotyli are small and, lets face it, kind of worm-like.  If you see several of them wiggling around inside of a female Argonaut's mantle cavity, you too might think they were worms.  

I could go on... but I'll let discover more about these strange and wonderful creatures on your own. 

3. Who was the woman who first did serious research on this octopus?  What essential piece of research gear did she invent?  

Since the argonaut octopus is such a wonderful animal, I was curious about who did the first research on the topic.  My query was: 

     [ first researcher argonaut octopus ] 

Note that I added the term "octopus" in order to get better, more focused results. But once I did that, the results were great.  

Who was Jeanne Villepreux-Power

Jeanne Villepreux-Power  P/C Wikimedia

She has a remarkable story.  Orphaned at 11, began working as a seamstress in Paris, married an English merchant and moved to Sicily where she began an intensive study of geology, archaeology, and natural history.  While walking on the beaches near Messina she came across the washed-up shell of the Argonauta and started studying them.  In the process, she invented glass-sided aquariums for research purposes, devising clever ways to work with the difficult Argonauts.  

Just as importantly, she published her work as a member of the Zoological Society of London.  Unfortunately, much of her work was lost in a shipwreck.  

But she was the first to show that the Argonaut can create its shell.  At the time, some thought that they stole the shells from other mollusks.  But Villepreux-Power showed that the paper nautilus actually secretes its own shell material. The ability to generate the shell also lets the creature add onto its shell to make it ever larger, and then repair the shell if it breaks (or if a malicious scientist comes along and breaks off a bit).  

SearchResearch Lessons 

1. You may find more than you bargained for!  When I started this research, I thought there was only one such octopus. I was very surprised to learn of the Cirrina sub-order of Octopoda.  I then found myself in a rathole making sure the results I was finding were about the Argonauta argo, and not the "classic" nautilus.  Be careful when you find a lot of results--be sure the thing you're reading is actually about the target of your search.  

2. Reading matters.  One thing I notice about young searchers is a remarkable ability to NOT read the articles they find. Reading in detail (or syntopical reading) is a real skill that you should practice.  That's how you find the most remarkable observations.  (Such as learning about hectocotyli that look like worms...)  

Keep searching.  



Wednesday, September 6, 2023

SearchResearch Challenge (9/6/23): A mysterious octopus? And the woman who understood.

 I thought I knew what an octopus was... 

Gloomy octopus. P/C John Turnbull.

... they're the ultimate shape-shifter with an amazing ability to solve puzzles, slip through tiny holes, and possessed of a fascinating kind of intelligence.  I've watched them for hours while scuba diving, and I have to admit--they're probably my favorite undersea animal.  (Full disclosure: they're SO interesting that I can't eat them any longer--it would be like eating a very smart pet house cat.)  

But my understanding of them was as a shell-less mollusk.  Their bodies are as close to fluid as you can imagine--they flow rather than walk.  Even so, as they move across the ocean floor, they seem to move as an ensemble, rather than just as a single animal.  That's NOT what I think of as an octopus.  This video of a mimic octopus moving around, shifting shapes and colors--that's an octopus. 

But when I was talking with a scuba-diving friend, they mentioned that there's a kind of octopus that actually DOES have a shell.  This claim, naturally, leads to today's Challenges--one about the surprising octopus, and the woman who did the first serious research on this remarkable beast.  

1. Is my friend right?  Is there an octopus that has a shell?  Really? 

2. As I read more, I learned a couple of fascinating details about the life of this particular octopus.  Can you find two really unexpected things about this animal? 

3. Who was the woman who first did serious research on this octopus?  What essential piece of research gear did she invent?  

I love Challenges like this.  It's not hard to find the answer, but once you know, it's hard to stop from reading more about this particular octopus and about the researcher who understood more than anyone else.  Trust me, there are many more than 2 "fascinating details" about this very surprising octopus.  

Let us know what you've found by leaving a comment here.  Enjoy the SearchResearch!  

Keep searching. 

Wednesday, August 30, 2023

Answer: What's that in the belly of the Redondasaurus?

 It's not everyday you see a phytosaur... 

... yet, there it was in the Carnegie Museum of Natural History. Big, with an impressive set of teeth, and looking for all the world like a massive crocodile. 

This is Redondasaurus bermani. 

But what really shocked me was what looks just like ribs in its belly.  Is that a thing?  Why have I never noticed this before?    

Here's a close-up shot: 

See what I mean?  There is the backbone above, with a lot of ribs hanging off the vertebrae.  You can easily see the massive leg bones and feet. 

Here's a redrawing I made of the photo, emphasizing the "belly ribs." 

Note how they seem to be kind of U-shaped, with long, pointed arms wrapping up as if to encase the abdomen.  Note too how the ribs hanging down from above are squared-off at the ends.  The two different kinds of ribs look very, very different.  These belly ribs are mostly free-floating except for the one at the left, which attaches to a kind of sternum that runs up to the phytosaur equivalent of a collar bone.  

I don't know that I've seen that on any other animal.  Or have I just not been paying attention?  

Here are last week's two Challenges for you: 

1. What do you call that thing in the chest and belly of the Redondasaurus bermani?  

For something that I'd never seen before, I was pleased with my first query: 

     [ ribs in dinosaur belly ] 

Yes, I know that technically the Redondasaurus isn't a dinosaur (it's a phytosaur), but for the purposes of searching, I figured that the term "dinosaur" would be used on the page, if only to explain that it's not a dinosaur.

This query worked remarkably well, and told me about a word I'd never read before: gastralia, the "belly bones" of dinosaurs, such as the T. rex.  

Naturally I checked.  Just because a therapod like T. rex (that lived during the Cretaceous period, about 70 to 65 million years ago), there's no guarantee that a phytosaur (that lived during the Triassic some 252-201 million years ago) would have the same skeletal feature. There's a decent change that something might have evolved differently over the distance of 180 million years. 

A quick search for: 

     [ gastralia phytosaur ] 

leads to all kinds of interesting results, including this book chapter (from Vertebrate Evolution) with lovely illustrations of Redondasaurus and its gastralia. 

Bottom line: these additional bones are called gastralia, and were (as Regular Reader remmij pointed out), pretty clearly used as part of their breathing apparatus.

 Remmij used the search [Dinosaur gastralia and their function in respiration] and found Some video that might be helpful for understanding gastralia's role in breathing.

2. Do other animals have this thing now, or was it just an Age of the Dinosaurs skeletal feature?  

What about modern animals with gastralia?

The Wikipedia article about gastralia tells us that "Gastralia (singular gastralium) are dermal bones found in the ventral body wall of modern crocodilians and tuatara, and many prehistoric tetrapods." That's a complicated way of saying that there's a basket of bones in the belly of the beasts... or at least of some crocodilians (alligators and crocodiles) and tuatara (a kind of lizard from New Zealand).  

But to remember the past, as we've seen already, gastralia are also part of other classic dinosaurs such as T-rex.  

As you know, there's a T-rex skeleton on the Googleplex campus in Mountain View, California.  (Discussed before in SRS.)  Here's Stan, the Google T-rex with flamingos... 

But note that Stan seems to be missing his gastralia!  Here's a better image to show the missing bones. I see ribs, but no gastralia.   

When I did an image search for [ t-rex skeletons ] I found this somewhat variable set of results: 

As you can see, about half of the reconstructed skeletons (including the one of Stan from the Black Hills) are missing their gastralia.  

A quick search for [ missing gastralia ] led me to this article from the Field Museum (Chicago) about how they recently revamped their T-rex display of Sue.  (It's worth clicking on that link--it's a really nice article about how they changed their minds about Sue's abdominal bones.) 

When fossil hunters first uncovered SUE, they found a set of rib-like bones that clearly belonged to the dinosaur, but no one was really sure where they fit in with the rest of the skeleton.

Now we know that the gastralia sit below the ribs and along the belly. Most likely, they helped T. rex breathe by pushing air in and out of the lungs (we humans have a diaphragm for this purpose). SUE’s gastral basket is the most complete among over 30 known T. rex specimens. It includes 26 of approximately 60 total gastral bones. We don't know exactly how many bones make up the gastralia since most—but not all—segments consist of two pieces. And there isn't yet a complete T. rex gastralia for us to check out and confirm how many segments do have two pieces.

So our understanding the appearance of a T-rex has changed over time. Now, if you see a T-rex without a gastralia, you know that someone has left out part of the skeleton! 

SearchResearch Lessons

This wasn't a difficult search--my very first search was pretty obvious [ribs in dinosaur belly], but it worked just fine, and I learned a very specific term--gastralia--that was useful in digging more deeply into the subject. 

It was great fun to learn that so many dinosaurs skeletons that we see in museums (and on the silver screen) are actually missing a major part of their anatomy.  But by doing quick visual comparisons, we came to learn how to see dino skeletons as part of a full ensemble.  

As a reminder of the value of checking Wikipedia articles in other languages, Regular Reader Ramón points out that in the Spanish language Wikipedia article on gastralia it tells us about the origin of the term: 

"Dinosaur gastralia were first described by Eudes-Deslongchamps in 1838 in Poekilopleuron bucklandii , but without having recognized them as dermal bones. Therefore, Osborn's description of the gastralia of a Tyrannosaurus rex from 1906 is often cited as the first description."

Even though T-rex gastralia were among the first described (over 100 years ago), they're STILL left off of many T-rex skeletons.  

Keep searching! 

Wednesday, August 23, 2023

SearchResearch Challenge (8/23/23): What's that in the belly of the Redondasaurus?

 I looked at the Phytosaur in real shock... 

Because there, in the dinosaur hall of the Carnegie Museum of Natural History in central Pittsburgh, was what looked to be a massive crocodile.  

This is Redondasaurus bermani. It was huge and utterly evil looking, clearly a watery death machine that was 6.4 m (21 feet) long, and lived in the rivers and swamps of Triassic North America some 252-201 million years ago.


I've seen lots of assembled skeletons before.  It was big and carnivorous, but as I stood in front of the skeleton, I noticed something that I don't think I'd seen before.  

See that collection of what look like ribs in its belly?  

Here's a close-up shot: 

See what I mean?  There is the backbone above, with a lot of ribs hanging off the vertebrae.  You can easily see the massive leg bones and feet. 

But there, hanging below the backbone and ribs is something else--a kind of basket of upward pointing ribs that seems attached to the sternum.  

I don't know that I've seen that on any other animal.  Or have I just not been paying attention?  

Naturally, this led me on a merry SRS quest, which condensed into these two Challenges for you: 

1. What do you call that thing in the chest and belly of the Redondosaurus bermani?  

2. Do other animals have this thing now, or was it just an Age of the Dinosaurs skeletal feature?  

I've found the answer now after a bit of quick searching on my phone while standing in front of the beast.  I have to say, I was pretty surprised by the answer to Challenge 2.  

Another surprise was learning that the Redondosaurus is actually NOT related to any living crocodiles or alligators?  It was, as they say, a "Late Triassic clade of crocodylian-like predators."  That is, there were other kinds of Redondosaurus (collectively called the Phytosaurs) that filled the ecological niche that crocs and alligators fill in todays swamps.  They had short legs, wide, heavy bodies with rows of armored scales, long tails, and long toothy snouts. The only obvious difference between crocodiles and phytosaurs is that crocodiles have their nostrils at the ends of their snouts, and phytosaurs had them on raised hump in front of their eyes. Despite the strong similarities between phytosaurs and crocodiles, the two groups are not closely related.

Let us know what answers you found to this week's Challenge.  Of course, tell us HOW you found them.  We all want to learn from your search strategy.  

Hope you find this as interesting and entertaining as I did.  

Keep searching! 

Friday, August 18, 2023

Answer: Animal? Plant? How do you know?

Mixotrophs for the win...  

Elysia chlorotica, a sea slug that incorporates chloroplasts into its body.
P/C Patrick J. Krug, Creative Commons CC BY-NC 3.0 license, via Wikimedia Commons

Remember the Elysia cholorotica (the big green slug above, aka "Emerald green sea slug")?   

It's technically a mixotroph, but it's pretty big (up to 60 mm in length, but typically between 20 mm to 30 mm).  As you know, they feed on algae, extracting chloroplasts and then merging them into its body, making it able to both eat food AND use sunlight to photosynthesize for energy.  

We also know about other slugs (also called nudibranchs) that will steal the nematocysts of cnidarians (such as sea anemones, hydroids, jellyfish, corals, siphonophores, etc.). The slugs use them for defense, with the nematocysts stinging anything that tries to eat the nudibranch.  The nematocysts are stored in protruding cerata (those spine-looking things) on their backs.  And at the tip of each branch of the cerata, the nematocysts are stored in a small sac, the cnidosac

Here's a spectacular photo of an aeolid nudibranch taken by SRS friend Randall Spangler.  

The cerata on the back of this Aeolidia papillosa end with cnidosacs.  Like Elysia, they incorporate dinoflagellates that provides some photosynthesis capability.  P/C Randall Spangler. 

But the term mixotroph usually refers to really small critters--plankton--that are microscopic--much smaller than slugs. The size table from the Wikipedia article about plankton gives this as the breakdown for different kinds of small plankton.  

We're primarily interested in the smallish single-celled plankton--and only those that are carnivorous... if that means anything at the single-cell level.  

This led to a couple of questions about the microscopic mixotrophic plankton. To wit,   

1. Do mixotrophic plankton ONLY steal chloroplasts, or are their other kinds of organelles that they rip out of the prey?  If so, what else gets stolen? 

Started my search with a "fill in the blank" style search: 

      [ mixotrophs “steal the *”] 

And find this article on mixotrophs in Science Daily

“Traditionally mixotrophs are considered as curiosities or irrelevant. ... for the first time, [they have] mapped the presence of these "body-snatching" mixotrophs which shows that they are present in oceans all over the world.

These "body-snatchers" come in two forms. One type steal the photosynthetic factories from their prey during digestion and use these chloroplasts to make food as do plants. Other mixotrophs enslave whole photosynthetic prey communities within their body, drifting in the oceans like microscopic green houses. Marine researchers have been mislabelling 50% of these organisms as "animals" when they are actually eating and photosynthesizing within the one cell. The good body-snatchers support fisheries, while the bad ones can be highly toxic.” 

Fascinating.  Clearly, some mixotrophs steal the chloroplasts and incorporate them into their own bodies.  That's not too much of a surprise.  Unlike the Elysia, it's happening at the microscopic level, but it's the same idea.  Steal a chlorplast and live a microscopic life of luxury.  

In addition, some single cell mixotrophs ingest the whole prey organism and keep them intact, but within their body.  Plankton using this "swallow them whole" strategy are called endosymbiotic specialist nonconstitutive mixotrophs.  (You can use that phrase at your next party as you devour your very tasty living oyster.) 

Example: Noctiluca scintillans eats Pedinomonas notilucae, harboring them like a little garden of plants to generate important nutrients. 

But in my reading, I seem to remember some mixotrophs that ingested more than just the chloroplasts. 

On a lark, I turned to both Bard and ChatGPT for their opinions, asking both 

     [ do some mixotrophs steal organelles
       other than chloroplasts? ] 

Bing's version of ChatGPT told me that: 

"Yes, some mixotrophs can steal organelles other than chloroplasts. According to a Wikipedia article on mixotrophs, there are two types of eukaryotic mixotrophs: those with their own chloroplasts, and those with endosymbionts—and those that acquire them through kleptoplasty or through symbiotic associations with prey or enslavement of their organelles." 

That's fine, but it's basically what we already knew.  

Bard told me that: 

"Yes, some mixotrophs steal organelles other than chloroplasts. For example, the green hydra (Hydra viridissima) is a freshwater polyp that can steal chloroplasts from the algae it consumes. The chloroplasts are incorporated into the hydra's cells and allow it to photosynthesize. The hydra can also steal other organelles from algae, such as mitochondria and nuclei.

Another example of a mixotroph that steals organelles is the coral Pocillopora damicornis. This coral can steal chloroplasts from the algae that live in its tissues. The chloroplasts provide the coral with energy, which it uses to grow and reproduce.

The ability to steal organelles is a rare adaptation, but it is found in a variety of organisms. This ability allows these organisms to get the best of both worlds: they can photosynthesize and produce their own food, but they can also consume other organisms for nutrients.

Here are some other examples of mixotrophs that steal organelles:

The dinoflagellate Gonyaulax tamarensis can steal mitochondria from other dinoflagellates.

The ciliate Paramecium bursaria can steal chloroplasts from the green algae Euglena gracilis.

The fungus Pythium insidiosum can steal mitochondria from the plant cells it infects."

Again, we knew most of this.  But Bard also told me that some mixotrophs also steal mitochondria.  And that's a different organelle than the chloroplasts.  Interesting.  Are there others beyond mitochondria?  

So I changed my prompt to be: 

     [ do mixotrophic plankton only steal chloroplasts or are there other organelles that get ripped out of their prey?  If so, what else gets stolen? ] 

Bing/ChatGPT told me that: 

According to an article in Scientific American, Mesodinium is a mixotroph that sucks photosynthesizing organs from another organism called Dinophysis. Mesodinium takes in the organelles responsible for photosynthesis whole. Within minutes the pale Mesodinium starts to turn darker red as it fills its body with the stolen parts—chloroplasts and nucleosomes—which remain intact and functional. Mesodinium is not able to take in and use carbon dioxide as true photosynthesizers are, so it relies on its victims’ chloroplasts to accomplish that task

Bing also gave me a link to the Scientific American article with the information.  Nice job. 

The same prompt to Bard told me basically the same information, but without the details and certainly with the link to a useful article.  It did, however, mention that some mixotrophs also steal vacuoles.  

That doesn't make a lot of sense, so I checked it by reading a few papers on mixotrophs with vacuoles, and found that the mixotrophs often ingest their prey into THEIR vacuoles, not that they ingest the vacuole from the prey.  That's an important distinction that Bard got just slightly wrong. The vacuoles are where the stolen organisms are kept in the klepto-organism!    

Curious about the role of nucleosome theft in Mesodinium, I did a search for: 

     [ mesodinium mixotrophy nucleosomes ] 

and found a number of articles about how Mesodinium DOES in fact steal nucleosomes.  But why?  

In their Nature (2007) paper "Retention of transcriptionally active cryptophyte nuclei", Johnson, et al. show that the nucleosomes are "transcriptionally active,"  (that is, they're busy working within the body of the mixotroph) making substances that the chloroplasts that were also stolen just happen to need.  

Isn't that handy?  The mixotroph steals the chloroplasts AND the nucleosomes that also contain the instructions for the care and feeding of the chloroplasts.  

Alas, the nuclei only seem to last for about a month in the body of mixotroph, so they need keep eating in order to keep things running.  

So we've figured out that mixotrophs not only steal chloroplasts, but also mitochondria and nucleosomes.  

The dual presence of mitochondria and functional chloroplasts within these mixotrophic cells that have been stolen from another species of plankton suggests a high degree of biochemical similarity.  I didn't expect that degree of interoperability.  This is likely the key to their functional presence and essential endosymbiotic activity for over 2.5 billion years.

Totally amazing.  

2. How long has the concept of mixotrophic plankton been around?  Is it possible that this is relatively new understanding of planktonic ecology?  

The obvious approach here is to check out Google Ngrams for a brief history of the use of the terms that start with "mixotroph-."  

Here's that chart: 

It looks like the first uses of "mixotrophic" starts in 1900, but then really picks up in the 1970-2000, falls a bit, then really takes off around 2010.  

Of course, this is only from the Books corpus, so to get a better sense of the use of the word in the scientific literature, I turn to and filter by date, here I'm filtering for papers published up to 1940. 

Note that there are about 34 results pre-1940.  

But ALSO note that several of those (results 3, 4, 5) are all actually from the 2000s.  (I checked: they actually are from the 2000s and are not pre-1940. Metadata problems.)  

Luckily, those date errors don't change the overall story.  Mixotroph-* came into common usage around 1950, with the other forms of the word (mixotrophy, mixotrophic) really becoming common after 1990.  Since I had completed my graduate training by 1984, it's very likely I never heard the word before running across it in that Scientific American article.  In the grand sweep of scientific history, it's a relatively recent word.  

SearchResearch Lessons 

1. Remember the fill-in-the-blank search method.  (That is, the * search.)  It can come in handy when you're looking for possible completions.  

2. LLMs can be handy tools for finding concepts and terms to further your own searching.  In all of the LLM examples here, there were problems with the text they generated.  HOWEVER, they also gave me some great ideas about what to search for next.  Be sure to check out their claims--don't just accept what an LLM tells you at face value.  (Example: Bard was deeply confused about the role of vacuoles in mixotrophy.)  

3. Bing shows citations for claims made--that's a really nice feature.  I sure wish that Bard would do the same.  (Oddly enough, for a few short weeks, Bard included citations.  It has since stopped doing that.  Don't know why, but I can guess that it was hallucinating too many references. Pity.)  

P.S.  A couple of people pointed out that they're not biologists and found reading the papers about this fairly esoteric topic to be heavy going.  One nice feature of the LLMs is that they are pretty decent at summarization.  Here's one such summary of an abstract from the  Johnson paper of above.  Here's the prompt, and Bard's nice summary... 

Dan:  I need a simplified summary of this article.  Can you give this to me at a 9th grade level? It is well documented that organelles can be retained and used by predatory organisms, but in most cases such sequestrations are limited to plastids of algal prey. Furthermore, sequestrations of prey organelles are typically highly ephemeral as a result of the inability of the organelle to remain functional in the absence of numerous nuclear-encoded genes involved in its regulation, division and function. The marine photosynthetic ciliate Myrionecta rubra (Lohmann 1908) Jankowski 1976 (the same as Mesodinium rubrum) is known to possess organelles of cryptophyte origin, which has led to debate concerning their status as permanent symbiotic or temporary sequestered fixtures. Recently, M. rubra has been shown to steal plastids (that is, chloroplasts) from the cryptomonad, Geminigera cryophila, and prey nuclei were observed to accumulate after feeding. Here we show that cryptophyte nuclei in M. rubra are retained for up to 30 days, are transcriptionally active and service plastids derived from multiple cryptophyte cells. Expression of a cryptophyte nuclear-encoded gene involved in plastid function declined in M. rubra as the sequestered nuclei disappeared from the population. Cytokinesis, plastid performance and their replication are dependent on recurrent stealing of cryptophyte nuclei. Karyoklepty (from Greek karydi, kernel; kleftis, thief) represents a previously unknown evolutionary strategy for acquiring biochemical potential.


Sure, here is a simplified summary of the article at a 9th grade level:

* Some organisms can steal organelles from other organisms and use them for their own benefit. This is called organelle sequestration.

* In most cases, organelle sequestration is short-lived because the organelles can't function without the genes from the organism that they were stolen from.

* The marine organism Myrionecta rubra can steal plastids (chloroplasts) from the cryptomonad Geminigera cryophila.

* M. rubra can keep the cryptophyte nuclei for up to 30 days. These nuclei are still active and help to keep the plastids functioning.

* Without the cryptophyte nuclei, the plastids in M. rubra stop working. This means that M. rubra needs to keep stealing nuclei from cryptomonads in order to stay alive.

* This is a new way for organisms to get the nutrients they need. It's called karyoklepty, which means "nucleus theft."

I hope this summary is helpful! Let me know if you have any other questions.

That was nice, Bard.  

For you humans... Keep searching!